[{"oa":1,"issue":"1","language":[{"iso":"eng"}],"date_published":"2021-01-01T00:00:00Z","publisher":"De Gruyter","doi":"10.1515/forum-2020-0074","article_type":"original","external_id":{"arxiv":["2003.09593"],"isi":["000604750900008"]},"page":"147-165","year":"2021","quality_controlled":"1","arxiv":1,"month":"01","scopus_import":"1","_id":"8742","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"T. D. Browning and R. Heath-Brown, “The geometric sieve for quadrics,” <i>Forum Mathematicum</i>, vol. 33, no. 1. De Gruyter, pp. 147–165, 2021.","apa":"Browning, T. D., &#38; Heath-Brown, R. (2021). The geometric sieve for quadrics. <i>Forum Mathematicum</i>. De Gruyter. <a href=\"https://doi.org/10.1515/forum-2020-0074\">https://doi.org/10.1515/forum-2020-0074</a>","ama":"Browning TD, Heath-Brown R. The geometric sieve for quadrics. <i>Forum Mathematicum</i>. 2021;33(1):147-165. doi:<a href=\"https://doi.org/10.1515/forum-2020-0074\">10.1515/forum-2020-0074</a>","chicago":"Browning, Timothy D, and Roger Heath-Brown. “The Geometric Sieve for Quadrics.” <i>Forum Mathematicum</i>. De Gruyter, 2021. <a href=\"https://doi.org/10.1515/forum-2020-0074\">https://doi.org/10.1515/forum-2020-0074</a>.","mla":"Browning, Timothy D., and Roger Heath-Brown. “The Geometric Sieve for Quadrics.” <i>Forum Mathematicum</i>, vol. 33, no. 1, De Gruyter, 2021, pp. 147–65, doi:<a href=\"https://doi.org/10.1515/forum-2020-0074\">10.1515/forum-2020-0074</a>.","ista":"Browning TD, Heath-Brown R. 2021. The geometric sieve for quadrics. Forum Mathematicum. 33(1), 147–165.","short":"T.D. Browning, R. Heath-Brown, Forum Mathematicum 33 (2021) 147–165."},"publication_status":"published","volume":33,"type":"journal_article","status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.09593"}],"date_created":"2020-11-08T23:01:25Z","article_processing_charge":"No","publication_identifier":{"eissn":["1435-5337"],"issn":["0933-7741"]},"publication":"Forum Mathematicum","title":"The geometric sieve for quadrics","day":"01","isi":1,"project":[{"call_identifier":"FWF","grant_number":"P32428","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","name":"New frontiers of the Manin conjecture"}],"department":[{"_id":"TiBr"}],"author":[{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","last_name":"Browning","full_name":"Browning, Timothy D"},{"first_name":"Roger","last_name":"Heath-Brown","full_name":"Heath-Brown, Roger"}],"date_updated":"2025-04-15T07:39:01Z","intvolume":"        33","oa_version":"Preprint","abstract":[{"text":"We develop a version of Ekedahl’s geometric sieve for integral quadratic forms of rank at least five. As one ranges over the zeros of such quadratic forms, we use the sieve to compute the density of coprime values of polynomials, and furthermore, to address a question about local solubility in families of varieties parameterised by the zeros.","lang":"eng"}]},{"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"related_material":{"link":[{"url":"https://doi.org/10.1111/evo.14225","relation":"erratum"}]},"publication":"Evolution","acknowledgement":"This work was financed by the Spanish Agencia Estatal de Investigación (CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P), awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the Cabildo of Tenerife. The authors wish to thank the following for field work and sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar. We also thank V. García‐Olivares for assistance with laboratory and bioinformatic work.","date_created":"2020-11-08T23:01:26Z","main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/10261/223937"}],"status":"public","article_processing_charge":"No","author":[{"first_name":"Antonia","full_name":"Salces-Castellano, Antonia","last_name":"Salces-Castellano"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"first_name":"Paula","last_name":"Arribas","full_name":"Arribas, Paula"},{"last_name":"Patino","full_name":"Patino, Jairo","first_name":"Jairo"},{"full_name":"Karger, Dirk N. ","last_name":"Karger","first_name":"Dirk N. "},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"},{"first_name":"Brent C.","last_name":"Emerson","full_name":"Emerson, Brent C."}],"abstract":[{"lang":"eng","text":"Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change."}],"oa_version":"Submitted Version","date_updated":"2023-08-04T11:09:49Z","intvolume":"        75","day":"01","title":"Long-term cloud forest response to climate warming revealed by insect speciation history","department":[{"_id":"NiBa"}],"isi":1,"page":"231-244","external_id":{"pmid":["33078844"],"isi":["000583190600001"]},"quality_controlled":"1","year":"2021","date_published":"2021-02-01T00:00:00Z","publisher":"Wiley","language":[{"iso":"eng"}],"doi":"10.1111/evo.14111","issue":"2","oa":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","volume":75,"publication_status":"published","citation":{"ista":"Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 75(2), 231–244.","mla":"Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” <i>Evolution</i>, vol. 75, no. 2, Wiley, 2021, pp. 231–44, doi:<a href=\"https://doi.org/10.1111/evo.14111\">10.1111/evo.14111</a>.","chicago":"Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino, Dirk N.  Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” <i>Evolution</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/evo.14111\">https://doi.org/10.1111/evo.14111</a>.","short":"A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger, R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244.","ieee":"A. Salces-Castellano <i>et al.</i>, “Long-term cloud forest response to climate warming revealed by insect speciation history,” <i>Evolution</i>, vol. 75, no. 2. Wiley, pp. 231–244, 2021.","ama":"Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest response to climate warming revealed by insect speciation history. <i>Evolution</i>. 2021;75(2):231-244. doi:<a href=\"https://doi.org/10.1111/evo.14111\">10.1111/evo.14111</a>","apa":"Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D. N., Butlin, R., &#38; Emerson, B. C. (2021). Long-term cloud forest response to climate warming revealed by insect speciation history. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14111\">https://doi.org/10.1111/evo.14111</a>"},"pmid":1,"month":"02","scopus_import":"1","_id":"8743"},{"publication":"Nature Reviews Neuroscience","publication_identifier":{"issn":["1471-003X"],"eissn":["1471-0048"]},"article_processing_charge":"No","file_date_updated":"2021-02-04T10:34:22Z","status":"public","date_created":"2020-11-15T23:01:18Z","abstract":[{"lang":"eng","text":"Traditional scientific conferences and seminar events have been hugely disrupted by the COVID-19 pandemic, paving the way for virtual forms of scientific communication to take hold and be put to the test."}],"date_updated":"2025-07-10T12:01:24Z","intvolume":"        22","oa_version":"Published Version","author":[{"full_name":"Bozelos, Panagiotis","last_name":"Bozelos","first_name":"Panagiotis","id":"52e9c652-2982-11eb-81d4-b43d94c63700"},{"orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","last_name":"Vogels"}],"department":[{"_id":"TiVo"}],"has_accepted_license":"1","isi":1,"day":"01","ddc":["570"],"title":"Talking science, online","year":"2021","quality_controlled":"1","page":"1-2","external_id":{"pmid":["33173190"],"isi":["000588256300001"]},"article_type":"letter_note","issue":"1","doi":"10.1038/s41583-020-00408-6","publisher":"Springer Nature","language":[{"iso":"eng"}],"date_published":"2021-01-01T00:00:00Z","oa":1,"file":[{"relation":"main_file","creator":"dernst","success":1,"date_created":"2021-02-04T10:34:22Z","content_type":"application/pdf","date_updated":"2021-02-04T10:34:22Z","file_size":683634,"file_id":"9088","file_name":"2021_NatureNeuroScience_Bozelos.pdf","access_level":"open_access","checksum":"7985d7dff94c086e35b94a911d78d9ad"}],"volume":22,"type":"journal_article","citation":{"ista":"Bozelos P, Vogels TP. 2021. Talking science, online. Nature Reviews Neuroscience. 22(1), 1–2.","mla":"Bozelos, Panagiotis, and Tim P. Vogels. “Talking Science, Online.” <i>Nature Reviews Neuroscience</i>, vol. 22, no. 1, Springer Nature, 2021, pp. 1–2, doi:<a href=\"https://doi.org/10.1038/s41583-020-00408-6\">10.1038/s41583-020-00408-6</a>.","chicago":"Bozelos, Panagiotis, and Tim P Vogels. “Talking Science, Online.” <i>Nature Reviews Neuroscience</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41583-020-00408-6\">https://doi.org/10.1038/s41583-020-00408-6</a>.","short":"P. Bozelos, T.P. Vogels, Nature Reviews Neuroscience 22 (2021) 1–2.","apa":"Bozelos, P., &#38; Vogels, T. P. (2021). Talking science, online. <i>Nature Reviews Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41583-020-00408-6\">https://doi.org/10.1038/s41583-020-00408-6</a>","ama":"Bozelos P, Vogels TP. Talking science, online. <i>Nature Reviews Neuroscience</i>. 2021;22(1):1-2. doi:<a href=\"https://doi.org/10.1038/s41583-020-00408-6\">10.1038/s41583-020-00408-6</a>","ieee":"P. Bozelos and T. P. Vogels, “Talking science, online,” <i>Nature Reviews Neuroscience</i>, vol. 22, no. 1. Springer Nature, pp. 1–2, 2021."},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8757","scopus_import":"1","month":"01","pmid":1},{"article_processing_charge":"No","acknowledgement":"We would like to thank Peter Trapa for useful discussions, and Dragan Milicic and Arun Ram for valuable feedback on the structure of the paper. The first author acknowledges the support of the European Unions Horizon 2020 research and innovation programme under the Marie Skodowska-Curie Grant Agreement No. 754411. The second author is\r\nsupported by the National Science Foundation Award No. 1803059.","main_file_link":[{"url":"https://arxiv.org/abs/1910.08286","open_access":"1"}],"date_created":"2020-11-19T10:17:40Z","status":"public","publication":"Proceedings of the American Mathematical Society","publication_identifier":{"issn":["0002-9939"],"eissn":["1088-6826"]},"ec_funded":1,"department":[{"_id":"HeEd"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"day":"01","title":"Contravariant forms on Whittaker modules","abstract":[{"text":"Let g be a complex semisimple Lie algebra. We give a classification of contravariant forms on the nondegenerate Whittaker g-modules Y(χ,η) introduced by Kostant. We prove that the set of all contravariant forms on Y(χ,η) forms a vector space whose dimension is given by the cardinality of the Weyl group of g. We also describe a procedure for parabolically inducing contravariant forms. As a corollary, we deduce the existence of the Shapovalov form on a Verma module, and provide a formula for the dimension of the space of contravariant forms on the degenerate Whittaker modules M(χ,η) introduced by McDowell.","lang":"eng"}],"oa_version":"Preprint","date_updated":"2025-04-14T07:43:50Z","intvolume":"       149","author":[{"last_name":"Brown","full_name":"Brown, Adam","id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam"},{"full_name":"Romanov, Anna","last_name":"Romanov","first_name":"Anna"}],"keyword":["Applied Mathematics","General Mathematics"],"article_type":"original","publisher":"American Mathematical Society","date_published":"2021-01-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1090/proc/15205","issue":"1","oa":1,"quality_controlled":"1","year":"2021","page":"37-52","external_id":{"arxiv":["1910.08286"],"isi":["000600416300004"]},"_id":"8773","month":"01","scopus_import":"1","arxiv":1,"volume":149,"type":"journal_article","publication_status":"published","citation":{"ama":"Brown A, Romanov A. Contravariant forms on Whittaker modules. <i>Proceedings of the American Mathematical Society</i>. 2021;149(1):37-52. doi:<a href=\"https://doi.org/10.1090/proc/15205\">10.1090/proc/15205</a>","apa":"Brown, A., &#38; Romanov, A. (2021). Contravariant forms on Whittaker modules. <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/proc/15205\">https://doi.org/10.1090/proc/15205</a>","ieee":"A. Brown and A. Romanov, “Contravariant forms on Whittaker modules,” <i>Proceedings of the American Mathematical Society</i>, vol. 149, no. 1. American Mathematical Society, pp. 37–52, 2021.","chicago":"Brown, Adam, and Anna Romanov. “Contravariant Forms on Whittaker Modules.” <i>Proceedings of the American Mathematical Society</i>. American Mathematical Society, 2021. <a href=\"https://doi.org/10.1090/proc/15205\">https://doi.org/10.1090/proc/15205</a>.","ista":"Brown A, Romanov A. 2021. Contravariant forms on Whittaker modules. Proceedings of the American Mathematical Society. 149(1), 37–52.","mla":"Brown, Adam, and Anna Romanov. “Contravariant Forms on Whittaker Modules.” <i>Proceedings of the American Mathematical Society</i>, vol. 149, no. 1, American Mathematical Society, 2021, pp. 37–52, doi:<a href=\"https://doi.org/10.1090/proc/15205\">10.1090/proc/15205</a>.","short":"A. Brown, A. Romanov, Proceedings of the American Mathematical Society 149 (2021) 37–52."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.02618"}],"date_created":"2020-11-22T23:01:26Z","acknowledgement":"G. Schimperna has been partially supported by GNAMPA (Gruppo Nazionale per l'Analisi Matematica, la Probabilità e le loro Applicazioni) of INdAM (Istituto Nazionale di Alta Matematica).","article_processing_charge":"No","publication_identifier":{"issn":["0022-0396"],"eissn":["1090-2732"]},"publication":"Journal of Differential Equations","title":"On a non-isothermal Cahn-Hilliard model based on a microforce balance","day":"15","isi":1,"department":[{"_id":"JuFi"}],"author":[{"first_name":"Alice","id":"25647992-AA84-11E9-9D75-8427E6697425","last_name":"Marveggio","full_name":"Marveggio, Alice"},{"first_name":"Giulio","last_name":"Schimperna","full_name":"Schimperna, Giulio"}],"date_updated":"2025-07-10T12:01:25Z","intvolume":"       274","oa_version":"Preprint","abstract":[{"lang":"eng","text":"This paper is concerned with a non-isothermal Cahn-Hilliard model based on a microforce balance. The model was derived by A. Miranville and G. Schimperna starting from the two fundamental laws of Thermodynamics, following M. Gurtin's two-scale approach. The main working assumptions are made on the behaviour of the heat flux as the absolute temperature tends to zero and to infinity. A suitable Ginzburg-Landau free energy is considered. Global-in-time existence for the initial-boundary value problem associated to the entropy formulation and, in a subcase, also to the weak formulation of the model is proved by deriving suitable a priori estimates and by showing weak sequential stability of families of approximating solutions. At last, some highlights are given regarding a possible approximation scheme compatible with the a-priori estimates available for the system."}],"oa":1,"issue":"2","date_published":"2021-02-15T00:00:00Z","publisher":"Elsevier","doi":"10.1016/j.jde.2020.10.030","language":[{"iso":"eng"}],"article_type":"original","external_id":{"arxiv":["2004.02618"],"isi":["000600845300023"]},"page":"924-970","year":"2021","quality_controlled":"1","arxiv":1,"month":"02","scopus_import":"1","_id":"8792","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"A. Marveggio and G. Schimperna, “On a non-isothermal Cahn-Hilliard model based on a microforce balance,” <i>Journal of Differential Equations</i>, vol. 274, no. 2. Elsevier, pp. 924–970, 2021.","apa":"Marveggio, A., &#38; Schimperna, G. (2021). On a non-isothermal Cahn-Hilliard model based on a microforce balance. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2020.10.030\">https://doi.org/10.1016/j.jde.2020.10.030</a>","ama":"Marveggio A, Schimperna G. On a non-isothermal Cahn-Hilliard model based on a microforce balance. <i>Journal of Differential Equations</i>. 2021;274(2):924-970. doi:<a href=\"https://doi.org/10.1016/j.jde.2020.10.030\">10.1016/j.jde.2020.10.030</a>","ista":"Marveggio A, Schimperna G. 2021. On a non-isothermal Cahn-Hilliard model based on a microforce balance. Journal of Differential Equations. 274(2), 924–970.","mla":"Marveggio, Alice, and Giulio Schimperna. “On a Non-Isothermal Cahn-Hilliard Model Based on a Microforce Balance.” <i>Journal of Differential Equations</i>, vol. 274, no. 2, Elsevier, 2021, pp. 924–70, doi:<a href=\"https://doi.org/10.1016/j.jde.2020.10.030\">10.1016/j.jde.2020.10.030</a>.","chicago":"Marveggio, Alice, and Giulio Schimperna. “On a Non-Isothermal Cahn-Hilliard Model Based on a Microforce Balance.” <i>Journal of Differential Equations</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jde.2020.10.030\">https://doi.org/10.1016/j.jde.2020.10.030</a>.","short":"A. Marveggio, G. Schimperna, Journal of Differential Equations 274 (2021) 924–970."},"publication_status":"published","volume":274,"type":"journal_article"},{"acknowledgement":"We are grateful to Matthias Függer and Thomas Nowak for having raised our interest in the problem studied in this paper.\r\nThis work has been supported the Austrian Science Fund (FWF) projects S11405, S11407 (RiSE), and P28182 (ADynNet).","date_created":"2020-11-22T23:01:26Z","file_date_updated":"2021-02-04T11:28:42Z","status":"public","article_processing_charge":"No","publication_identifier":{"eissn":["1872-6771"],"issn":["0166-218X"]},"publication":"Discrete Applied Mathematics","ddc":["510"],"day":"31","title":"Optimal strategies for selecting coordinators","department":[{"_id":"KrCh"}],"project":[{"name":"Rigorous Systems Engineering","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"}],"isi":1,"has_accepted_license":"1","author":[{"first_name":"Martin","full_name":"Zeiner, Martin","last_name":"Zeiner"},{"first_name":"Ulrich","full_name":"Schmid, Ulrich","last_name":"Schmid"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"abstract":[{"text":"We study optimal election sequences for repeatedly selecting a (very) small group of leaders among a set of participants (players) with publicly known unique ids. In every time slot, every player has to select exactly one player that it considers to be the current leader, oblivious to the selection of the other players, but with the overarching goal of maximizing a given parameterized global (“social”) payoff function in the limit. We consider a quite generic model, where the local payoff achieved by a given player depends, weighted by some arbitrary but fixed real parameter, on the number of different leaders chosen in a round, the number of players that choose the given player as the leader, and whether the chosen leader has changed w.r.t. the previous round or not. The social payoff can be the maximum, average or minimum local payoff of the players. Possible applications include quite diverse examples such as rotating coordinator-based distributed algorithms and long-haul formation flying of social birds. Depending on the weights and the particular social payoff, optimal sequences can be very different, from simple round-robin where all players chose the same leader alternatingly every time slot to very exotic patterns, where a small group of leaders (at most 2) is elected in every time slot. Moreover, we study the question if and when a single player would not benefit w.r.t. its local payoff when deviating from the given optimal sequence, i.e., when our optimal sequences are Nash equilibria in the restricted strategy space of oblivious strategies. As this is the case for many parameterizations of our model, our results reveal that no punishment is needed to make it rational for the players to optimize the social payoff.","lang":"eng"}],"oa_version":"Published Version","intvolume":"       289","date_updated":"2026-04-16T09:15:13Z","publisher":"Elsevier","language":[{"iso":"eng"}],"doi":"10.1016/j.dam.2020.10.022","date_published":"2021-01-31T00:00:00Z","issue":"1","file":[{"success":1,"creator":"dernst","relation":"main_file","date_created":"2021-02-04T11:28:42Z","file_size":652739,"content_type":"application/pdf","date_updated":"2021-02-04T11:28:42Z","file_name":"2021_DiscreteApplMath_Zeiner.pdf","checksum":"f1039ff5a2d6ca116720efdb84ee9d5e","access_level":"open_access","file_id":"9089"}],"oa":1,"article_type":"original","page":"392-415","external_id":{"isi":["000596823800035"]},"quality_controlled":"1","year":"2021","month":"01","scopus_import":"1","_id":"8793","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","type":"journal_article","volume":289,"publication_status":"published","citation":{"ieee":"M. Zeiner, U. Schmid, and K. Chatterjee, “Optimal strategies for selecting coordinators,” <i>Discrete Applied Mathematics</i>, vol. 289, no. 1. Elsevier, pp. 392–415, 2021.","apa":"Zeiner, M., Schmid, U., &#38; Chatterjee, K. (2021). Optimal strategies for selecting coordinators. <i>Discrete Applied Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dam.2020.10.022\">https://doi.org/10.1016/j.dam.2020.10.022</a>","ama":"Zeiner M, Schmid U, Chatterjee K. Optimal strategies for selecting coordinators. <i>Discrete Applied Mathematics</i>. 2021;289(1):392-415. doi:<a href=\"https://doi.org/10.1016/j.dam.2020.10.022\">10.1016/j.dam.2020.10.022</a>","short":"M. Zeiner, U. Schmid, K. Chatterjee, Discrete Applied Mathematics 289 (2021) 392–415.","chicago":"Zeiner, Martin, Ulrich Schmid, and Krishnendu Chatterjee. “Optimal Strategies for Selecting Coordinators.” <i>Discrete Applied Mathematics</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.dam.2020.10.022\">https://doi.org/10.1016/j.dam.2020.10.022</a>.","mla":"Zeiner, Martin, et al. “Optimal Strategies for Selecting Coordinators.” <i>Discrete Applied Mathematics</i>, vol. 289, no. 1, Elsevier, 2021, pp. 392–415, doi:<a href=\"https://doi.org/10.1016/j.dam.2020.10.022\">10.1016/j.dam.2020.10.022</a>.","ista":"Zeiner M, Schmid U, Chatterjee K. 2021. Optimal strategies for selecting coordinators. Discrete Applied Mathematics. 289(1), 392–415."}},{"type":"journal_article","volume":381,"publication_status":"published","citation":{"ama":"Runkel I, Szegedy L. Area-dependent quantum field theory. <i>Communications in Mathematical Physics</i>. 2021;381(1):83–117. doi:<a href=\"https://doi.org/10.1007/s00220-020-03902-1\">10.1007/s00220-020-03902-1</a>","apa":"Runkel, I., &#38; Szegedy, L. (2021). Area-dependent quantum field theory. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-020-03902-1\">https://doi.org/10.1007/s00220-020-03902-1</a>","ieee":"I. Runkel and L. Szegedy, “Area-dependent quantum field theory,” <i>Communications in Mathematical Physics</i>, vol. 381, no. 1. Springer Nature, pp. 83–117, 2021.","mla":"Runkel, Ingo, and Lorant Szegedy. “Area-Dependent Quantum Field Theory.” <i>Communications in Mathematical Physics</i>, vol. 381, no. 1, Springer Nature, 2021, pp. 83–117, doi:<a href=\"https://doi.org/10.1007/s00220-020-03902-1\">10.1007/s00220-020-03902-1</a>.","ista":"Runkel I, Szegedy L. 2021. Area-dependent quantum field theory. Communications in Mathematical Physics. 381(1), 83–117.","chicago":"Runkel, Ingo, and Lorant Szegedy. “Area-Dependent Quantum Field Theory.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00220-020-03902-1\">https://doi.org/10.1007/s00220-020-03902-1</a>.","short":"I. Runkel, L. Szegedy, Communications in Mathematical Physics 381 (2021) 83–117."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8816","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"scopus_import":"1","month":"01","quality_controlled":"1","year":"2021","page":"83–117","external_id":{"isi":["000591139000001"]},"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1007/s00220-020-03902-1","publisher":"Springer Nature","date_published":"2021-01-01T00:00:00Z","issue":"1","file":[{"date_updated":"2021-02-03T15:00:30Z","content_type":"application/pdf","file_size":790526,"file_id":"9081","checksum":"6f451f9c2b74bedbc30cf884a3e02670","access_level":"open_access","file_name":"2021_CommMathPhys_Runkel.pdf","creator":"dernst","relation":"main_file","success":1,"date_created":"2021-02-03T15:00:30Z"}],"oa":1,"abstract":[{"text":"Area-dependent quantum field theory is a modification of two-dimensional topological quantum field theory, where one equips each connected component of a bordism with a positive real number—interpreted as area—which behaves additively under glueing. As opposed to topological theories, in area-dependent theories the state spaces can be infinite-dimensional. We introduce the notion of regularised Frobenius algebras in Hilbert spaces and show that area-dependent theories are in one-to-one correspondence to commutative regularised Frobenius algebras. We also provide a state sum construction for area-dependent theories. Our main example is two-dimensional Yang–Mills theory with compact gauge group, which we treat in detail.","lang":"eng"}],"oa_version":"Published Version","intvolume":"       381","date_updated":"2025-07-10T12:01:25Z","author":[{"last_name":"Runkel","full_name":"Runkel, Ingo","first_name":"Ingo"},{"full_name":"Szegedy, Lorant","last_name":"Szegedy","orcid":"0000-0003-2834-5054","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","first_name":"Lorant"}],"department":[{"_id":"MiLe"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"has_accepted_license":"1","isi":1,"ddc":["510"],"day":"01","title":"Area-dependent quantum field theory","publication":"Communications in Mathematical Physics","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"The authors thank Yuki Arano, Nils Carqueville, Alexei Davydov, Reiner Lauterbach, Pau Enrique Moliner, Chris Heunen, André Henriques, Ehud Meir, Catherine Meusburger, Gregor Schaumann, Richard Szabo and Stefan Wagner for helpful discussions and comments. We also thank the referees for their detailed comments which significantly improved the exposition of this paper. LS is supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory”. Open access funding provided by Institute of Science and Technology (IST Austria).","date_created":"2020-11-29T23:01:17Z","file_date_updated":"2021-02-03T15:00:30Z","status":"public"},{"scopus_import":"1","month":"04","_id":"8817","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Shehu Y, Iyiola OS, Thong DV, Van NTC. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. <i>Mathematical Methods of Operations Research</i>. 2021;93(2):213-242. doi:<a href=\"https://doi.org/10.1007/s00186-020-00730-w\">10.1007/s00186-020-00730-w</a>","apa":"Shehu, Y., Iyiola, O. S., Thong, D. V., &#38; Van, N. T. C. (2021). An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. <i>Mathematical Methods of Operations Research</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00186-020-00730-w\">https://doi.org/10.1007/s00186-020-00730-w</a>","ieee":"Y. Shehu, O. S. Iyiola, D. V. Thong, and N. T. C. Van, “An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems,” <i>Mathematical Methods of Operations Research</i>, vol. 93, no. 2. Springer Nature, pp. 213–242, 2021.","short":"Y. Shehu, O.S. Iyiola, D.V. Thong, N.T.C. Van, Mathematical Methods of Operations Research 93 (2021) 213–242.","mla":"Shehu, Yekini, et al. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” <i>Mathematical Methods of Operations Research</i>, vol. 93, no. 2, Springer Nature, 2021, pp. 213–42, doi:<a href=\"https://doi.org/10.1007/s00186-020-00730-w\">10.1007/s00186-020-00730-w</a>.","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Duong Viet Thong, and Nguyen Thi Cam Van. “An Inertial Subgradient Extragradient Algorithm Extended to Pseudomonotone Equilibrium Problems.” <i>Mathematical Methods of Operations Research</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00186-020-00730-w\">https://doi.org/10.1007/s00186-020-00730-w</a>.","ista":"Shehu Y, Iyiola OS, Thong DV, Van NTC. 2021. An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems. Mathematical Methods of Operations Research. 93(2), 213–242."},"publication_status":"published","type":"journal_article","volume":93,"issue":"2","publisher":"Springer Nature","date_published":"2021-04-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1007/s00186-020-00730-w","article_type":"original","external_id":{"isi":["000590497300001"]},"page":"213-242","year":"2021","quality_controlled":"1","title":"An inertial subgradient extragradient algorithm extended to pseudomonotone equilibrium problems","day":"01","isi":1,"project":[{"call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"department":[{"_id":"VlKo"}],"author":[{"first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9224-7139","last_name":"Shehu","full_name":"Shehu, Yekini"},{"first_name":"Olaniyi S.","last_name":"Iyiola","full_name":"Iyiola, Olaniyi S."},{"first_name":"Duong Viet","full_name":"Thong, Duong Viet","last_name":"Thong"},{"full_name":"Van, Nguyen Thi Cam","last_name":"Van","first_name":"Nguyen Thi Cam"}],"intvolume":"        93","date_updated":"2024-11-04T13:52:33Z","oa_version":"None","abstract":[{"lang":"eng","text":"The paper introduces an inertial extragradient subgradient method with self-adaptive step sizes for solving equilibrium problems in real Hilbert spaces. Weak convergence of the proposed method is obtained under the condition that the bifunction is pseudomonotone and Lipchitz continuous. Linear convergence is also given when the bifunction is strongly pseudomonotone and Lipchitz continuous. Numerical implementations and comparisons with other related inertial methods are given using test problems including a real-world application to Nash–Cournot oligopolistic electricity market equilibrium model."}],"status":"public","date_created":"2020-11-29T23:01:18Z","acknowledgement":"The authors are grateful to the two referees and the Associate Editor for their comments and suggestions which have improved the earlier version of the paper greatly. The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","article_processing_charge":"No","ec_funded":1,"publication_identifier":{"eissn":["1432-5217"],"issn":["1432-2994"]},"publication":"Mathematical Methods of Operations Research"},{"publication":"Nature","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-020-03068-9"}]},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"article_processing_charge":"No","acknowledgement":"We thank O. Eschenko and M. Constantinou for providing feedback on earlier versions of this work, and J. Werner and M. Schnabel for technical support during the development of this study. This research was supported by the Max Planck Society.","date_created":"2020-11-29T23:01:19Z","status":"public","abstract":[{"text":"The hippocampus has a major role in encoding and consolidating long-term memories, and undergoes plastic changes during sleep1. These changes require precise homeostatic control by subcortical neuromodulatory structures2. The underlying mechanisms of this phenomenon, however, remain unknown. Here, using multi-structure recordings in macaque monkeys, we show that the brainstem transiently modulates hippocampal network events through phasic pontine waves known as pontogeniculooccipital waves (PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially, selectively influencing high-frequency ripples and low-frequency theta events, respectively. The two types of PGO wave are associated with opposite hippocampal spike-field coupling, prompting periods of high neural synchrony of neural populations during periods of ripple and theta instances. The coupling between PGO waves and ripples, classically associated with distinct sleep stages, supports the notion that a global coordination mechanism of hippocampal sleep dynamics by cholinergic pontine transients may promote systems and synaptic memory consolidation as well as synaptic homeostasis.","lang":"eng"}],"oa_version":"None","intvolume":"       589","date_updated":"2025-07-10T12:01:26Z","author":[{"last_name":"Ramirez Villegas","full_name":"Ramirez Villegas, Juan F","first_name":"Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michel","full_name":"Besserve, Michel","last_name":"Besserve"},{"first_name":"Yusuke","full_name":"Murayama, Yusuke","last_name":"Murayama"},{"first_name":"Henry C.","full_name":"Evrard, Henry C.","last_name":"Evrard"},{"full_name":"Oeltermann, Axel","last_name":"Oeltermann","first_name":"Axel"},{"last_name":"Logothetis","full_name":"Logothetis, Nikos K.","first_name":"Nikos K."}],"department":[{"_id":"JoCs"}],"isi":1,"day":"07","title":"Coupling of hippocampal theta and ripples with pontogeniculooccipital waves","quality_controlled":"1","year":"2021","page":"96-102","external_id":{"isi":["000591047800005"],"pmid":["33208951"]},"article_type":"original","publisher":"Springer Nature","language":[{"iso":"eng"}],"doi":"10.1038/s41586-020-2914-4","date_published":"2021-01-07T00:00:00Z","issue":"7840","volume":589,"type":"journal_article","publication_status":"published","citation":{"short":"J.F. Ramirez Villegas, M. Besserve, Y. Murayama, H.C. Evrard, A. Oeltermann, N.K. Logothetis, Nature 589 (2021) 96–102.","mla":"Ramirez Villegas, Juan F., et al. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” <i>Nature</i>, vol. 589, no. 7840, Springer Nature, 2021, pp. 96–102, doi:<a href=\"https://doi.org/10.1038/s41586-020-2914-4\">10.1038/s41586-020-2914-4</a>.","ista":"Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. 2021. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. Nature. 589(7840), 96–102.","chicago":"Ramirez Villegas, Juan F, Michel Besserve, Yusuke Murayama, Henry C. Evrard, Axel Oeltermann, and Nikos K. Logothetis. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-020-2914-4\">https://doi.org/10.1038/s41586-020-2914-4</a>.","ieee":"J. F. Ramirez Villegas, M. Besserve, Y. Murayama, H. C. Evrard, A. Oeltermann, and N. K. Logothetis, “Coupling of hippocampal theta and ripples with pontogeniculooccipital waves,” <i>Nature</i>, vol. 589, no. 7840. Springer Nature, pp. 96–102, 2021.","apa":"Ramirez Villegas, J. F., Besserve, M., Murayama, Y., Evrard, H. C., Oeltermann, A., &#38; Logothetis, N. K. (2021). Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2914-4\">https://doi.org/10.1038/s41586-020-2914-4</a>","ama":"Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. <i>Nature</i>. 2021;589(7840):96-102. doi:<a href=\"https://doi.org/10.1038/s41586-020-2914-4\">10.1038/s41586-020-2914-4</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8818","pmid":1,"scopus_import":"1","month":"01"},{"oa_version":"Published Version","intvolume":"        31","date_updated":"2024-10-21T06:02:09Z","abstract":[{"text":"Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1,  2,  3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1,  2,  3,  4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7,  8,  9,  10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface.","lang":"eng"}],"author":[{"first_name":"MM","last_name":"Marquès-Bueno","full_name":"Marquès-Bueno, MM"},{"first_name":"L","full_name":"Armengot, L","last_name":"Armengot"},{"first_name":"LC","last_name":"Noack","full_name":"Noack, LC"},{"first_name":"J","last_name":"Bareille","full_name":"Bareille, J"},{"first_name":"Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7244-7237","last_name":"Rodriguez Solovey","full_name":"Rodriguez Solovey, Lesia"},{"first_name":"MP","last_name":"Platre","full_name":"Platre, MP"},{"first_name":"V","last_name":"Bayle","full_name":"Bayle, V"},{"first_name":"M","last_name":"Liu","full_name":"Liu, M"},{"first_name":"D","full_name":"Opdenacker, D","last_name":"Opdenacker"},{"full_name":"Vanneste, S","last_name":"Vanneste","first_name":"S"},{"last_name":"Möller","full_name":"Möller, BK","first_name":"BK"},{"first_name":"ZL","full_name":"Nimchuk, ZL","last_name":"Nimchuk"},{"first_name":"T","last_name":"Beeckman","full_name":"Beeckman, T"},{"full_name":"Caño-Delgado, AI","last_name":"Caño-Delgado","first_name":"AI"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml"},{"full_name":"Jaillais, Y","last_name":"Jaillais","first_name":"Y"}],"has_accepted_license":"1","isi":1,"department":[{"_id":"JiFr"}],"title":"Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism","ddc":["570"],"day":"11","publication":"Current Biology","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"article_processing_charge":"Yes (via OA deal)","date_created":"2020-12-01T13:39:46Z","file_date_updated":"2021-02-04T11:37:50Z","status":"public","acknowledgement":"We thank the SiCE group for discussions and comments; S. Yalovsky, B. Scheres, and the NASC/ABRC collection for providing transgenic Arabidopsis lines and plasmids; L. Kalmbach and M. Barberon for the gift of pLOK180_pFR7m34GW; A. Lacroix, J. Berger, and P. Bolland for plant care; and M. Fendrych for help with microfluidics in the J.F. lab. We acknowledge\r\nthe contribution of the SFR Biosciences (UMS3444/CNRS, US8/Inser m, ENS de Lyon, UCBL) facilities: C. Lionet, E. Chatre, and J. Brocard at LBIPLATIM-MICROSCOPY for assistance with imaging, and V. GuegenChaignon and A. Page at the Protein Science Facility (PSF) for assistance with protein purification and mass spectrometry. Y.J. was funded by ERC\r\ngrant 3363360-APPL under FP/2007–2013. Y.J. and Z.L.N. were funded by an ANR- and NSF-supported ERA-CAPS project (SICOPID: ANR-17-CAPS0003-01/NSF PGRP IOS-1841917). A.I.C.-D. is funded by an ERC consolidator grant (ERC-2015-CoG–683163) and BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness. Exchanges between the Y.J. and T.B. laboratories were funded by Tournesol grant 35656NB. B.K.M. was\r\nfunded by the Omics@vib Marie Curie COFUND and Research Foundation Flanders for a postdoctoral fellowship.","publication_status":"published","citation":{"ieee":"M. Marquès-Bueno <i>et al.</i>, “Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism,” <i>Current Biology</i>, vol. 31, no. 1. Elsevier, 2021.","apa":"Marquès-Bueno, M., Armengot, L., Noack, L., Bareille, J., Rodriguez Solovey, L., Platre, M., … Jaillais, Y. (2021). Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">https://doi.org/10.1016/j.cub.2020.10.011</a>","ama":"Marquès-Bueno M, Armengot L, Noack L, et al. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. <i>Current Biology</i>. 2021;31(1). doi:<a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">10.1016/j.cub.2020.10.011</a>","short":"M. Marquès-Bueno, L. Armengot, L. Noack, J. Bareille, L. Rodriguez Solovey, M. Platre, V. Bayle, M. Liu, D. Opdenacker, S. Vanneste, B. Möller, Z. Nimchuk, T. Beeckman, A. Caño-Delgado, J. Friml, Y. Jaillais, Current Biology 31 (2021).","ista":"Marquès-Bueno M, Armengot L, Noack L, Bareille J, Rodriguez Solovey L, Platre M, Bayle V, Liu M, Opdenacker D, Vanneste S, Möller B, Nimchuk Z, Beeckman T, Caño-Delgado A, Friml J, Jaillais Y. 2021. Auxin-regulated reversible inhibition of TMK1 signaling by MAKR2 modulates the dynamics of root gravitropism. Current Biology. 31(1).","mla":"Marquès-Bueno, MM, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” <i>Current Biology</i>, vol. 31, no. 1, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">10.1016/j.cub.2020.10.011</a>.","chicago":"Marquès-Bueno, MM, L Armengot, LC Noack, J Bareille, Lesia Rodriguez Solovey, MP Platre, V Bayle, et al. “Auxin-Regulated Reversible Inhibition of TMK1 Signaling by MAKR2 Modulates the Dynamics of Root Gravitropism.” <i>Current Biology</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cub.2020.10.011\">https://doi.org/10.1016/j.cub.2020.10.011</a>."},"volume":31,"type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"8824","pmid":1,"month":"01","scopus_import":"1","quality_controlled":"1","year":"2021","external_id":{"isi":["000614361000039"],"pmid":["33157019"]},"article_type":"original","file":[{"content_type":"application/pdf","date_updated":"2021-02-04T11:37:50Z","file_size":3458646,"file_id":"9090","file_name":"2021_CurrentBiology_MarquesBueno.pdf","checksum":"30b3393d841fb2b1e2b22fb42b5c8fff","access_level":"open_access","relation":"main_file","creator":"dernst","success":1,"date_created":"2021-02-04T11:37:50Z"}],"oa":1,"date_published":"2021-01-11T00:00:00Z","doi":"10.1016/j.cub.2020.10.011","publisher":"Elsevier","language":[{"iso":"eng"}],"issue":"1"},{"month":"07","scopus_import":"1","pmid":1,"arxiv":1,"_id":"8910","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":373,"citation":{"ista":"Valentini M, Peñaranda F, Hofmann AC, Brauns M, Hauschild R, Krogstrup P, San-Jose P, Prada E, Aguado R, Katsaros G. 2021. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. Science. 373(6550), 82–88.","mla":"Valentini, Marco, et al. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” <i>Science</i>, vol. 373, no. 6550, 82–88, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/science.abf1513\">10.1126/science.abf1513</a>.","chicago":"Valentini, Marco, Fernando Peñaranda, Andrea C Hofmann, Matthias Brauns, Robert Hauschild, Peter Krogstrup, Pablo San-Jose, Elsa Prada, Ramón Aguado, and Georgios Katsaros. “Nontopological Zero-Bias Peaks in Full-Shell Nanowires Induced by Flux-Tunable Andreev States.” <i>Science</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/science.abf1513\">https://doi.org/10.1126/science.abf1513</a>.","short":"M. Valentini, F. Peñaranda, A.C. Hofmann, M. Brauns, R. Hauschild, P. Krogstrup, P. San-Jose, E. Prada, R. Aguado, G. Katsaros, Science 373 (2021).","ama":"Valentini M, Peñaranda F, Hofmann AC, et al. Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. <i>Science</i>. 2021;373(6550). doi:<a href=\"https://doi.org/10.1126/science.abf1513\">10.1126/science.abf1513</a>","apa":"Valentini, M., Peñaranda, F., Hofmann, A. C., Brauns, M., Hauschild, R., Krogstrup, P., … Katsaros, G. (2021). Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abf1513\">https://doi.org/10.1126/science.abf1513</a>","ieee":"M. Valentini <i>et al.</i>, “Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states,” <i>Science</i>, vol. 373, no. 6550. American Association for the Advancement of Science, 2021."},"publication_status":"published","issue":"6550","doi":"10.1126/science.abf1513","language":[{"iso":"eng"}],"date_published":"2021-07-02T00:00:00Z","publisher":"American Association for the Advancement of Science","oa":1,"article_type":"original","external_id":{"isi":["000677843100034"],"arxiv":["2008.02348"],"pmid":["34210881"]},"year":"2021","quality_controlled":"1","day":"02","title":"Nontopological zero-bias peaks in full-shell nanowires induced by flux-tunable Andreev states","project":[{"_id":"262116AA-B435-11E9-9278-68D0E5697425","name":"Hybrid Semiconductor - Superconductor Quantum Devices"},{"name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511"}],"department":[{"_id":"GeKa"},{"_id":"Bio"}],"isi":1,"author":[{"first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","full_name":"Valentini, Marco"},{"full_name":"Peñaranda, Fernando","last_name":"Peñaranda","first_name":"Fernando"},{"id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C","full_name":"Hofmann, Andrea C","last_name":"Hofmann"},{"id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","full_name":"Brauns, Matthias","last_name":"Brauns"},{"orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild"},{"first_name":"Peter","full_name":"Krogstrup, Peter","last_name":"Krogstrup"},{"first_name":"Pablo","full_name":"San-Jose, Pablo","last_name":"San-Jose"},{"last_name":"Prada","full_name":"Prada, Elsa","first_name":"Elsa"},{"first_name":"Ramón","last_name":"Aguado","full_name":"Aguado, Ramón"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","last_name":"Katsaros","full_name":"Katsaros, Georgios"}],"abstract":[{"text":"A semiconducting nanowire fully wrapped by a superconducting shell has been proposed as a platform for obtaining Majorana modes at small magnetic fields. In this study, we demonstrate that the appearance of subgap states in such structures is actually governed by the junction region in tunneling spectroscopy measurements and not the full-shell nanowire itself. Short tunneling regions never show subgap states, whereas longer junctions always do. This can be understood in terms of quantum dots forming in the junction and hosting Andreev levels in the Yu-Shiba-Rusinov regime. The intricate magnetic field dependence of the Andreev levels, through both the Zeeman and Little-Parks effects, may result in robust zero-bias peaks—features that could be easily misinterpreted as originating from Majorana zero modes but are unrelated to topological superconductivity.","lang":"eng"}],"date_updated":"2026-04-07T13:27:22Z","intvolume":"       373","oa_version":"Submitted Version","article_number":"82-88","acknowledgement":"The authors thank A. Higginbotham, E. J. H. Lee and F. R. Martins for helpful discussions. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility; the NOMIS Foundation and Microsoft; the European Union’s Horizon 2020 research and innovation program under the Marie SklodowskaCurie grant agreement No 844511; the FETOPEN Grant Agreement No. 828948; the European Research Commission through the grant agreement HEMs-DAM No 716655; the Spanish Ministry of Science and Innovation through Grants PGC2018-097018-B-I00, PCI2018-093026, FIS2016-80434-P (AEI/FEDER, EU), RYC2011-09345 (Ram´on y Cajal Programme), and the Mar´ıa de Maeztu Programme for Units of Excellence in R&D (CEX2018-000805-M); the CSIC Research Platform on Quantum Technologies PTI-001.","status":"public","date_created":"2020-12-02T10:51:52Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2008.02348"}],"article_processing_charge":"No","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"related_material":{"record":[{"status":"public","id":"9389","relation":"research_data"},{"status":"public","id":"13286","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/unfinding-a-split-electron/"}]},"publication":"Science"},{"article_type":"original","date_published":"2021-10-01T00:00:00Z","publisher":"Springer Nature","doi":"10.1038/s41578-020-00262-z","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","year":"2021","page":"926–943 ","external_id":{"isi":["000600826100003"],"arxiv":["2004.08133"]},"_id":"8911","month":"10","scopus_import":"1","arxiv":1,"volume":6,"type":"journal_article","publication_status":"published","citation":{"short":"G. Scappucci, C. Kloeffel, F.A. Zwanenburg, D. Loss, M. Myronov, J.-J. Zhang, S.D. Franceschi, G. Katsaros, M. Veldhorst, Nature Reviews Materials 6 (2021) 926–943.","ista":"Scappucci G, Kloeffel C, Zwanenburg FA, Loss D, Myronov M, Zhang J-J, Franceschi SD, Katsaros G, Veldhorst M. 2021. The germanium quantum information route. Nature Reviews Materials. 6, 926–943.","mla":"Scappucci, Giordano, et al. “The Germanium Quantum Information Route.” <i>Nature Reviews Materials</i>, vol. 6, Springer Nature, 2021, pp. 926–943, doi:<a href=\"https://doi.org/10.1038/s41578-020-00262-z\">10.1038/s41578-020-00262-z</a>.","chicago":"Scappucci, Giordano, Christoph Kloeffel, Floris A. Zwanenburg, Daniel Loss, Maksym Myronov, Jian-Jun Zhang, Silvano De Franceschi, Georgios Katsaros, and Menno Veldhorst. “The Germanium Quantum Information Route.” <i>Nature Reviews Materials</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41578-020-00262-z\">https://doi.org/10.1038/s41578-020-00262-z</a>.","ieee":"G. Scappucci <i>et al.</i>, “The germanium quantum information route,” <i>Nature Reviews Materials</i>, vol. 6. Springer Nature, pp. 926–943, 2021.","ama":"Scappucci G, Kloeffel C, Zwanenburg FA, et al. The germanium quantum information route. <i>Nature Reviews Materials</i>. 2021;6:926–943. doi:<a href=\"https://doi.org/10.1038/s41578-020-00262-z\">10.1038/s41578-020-00262-z</a>","apa":"Scappucci, G., Kloeffel, C., Zwanenburg, F. A., Loss, D., Myronov, M., Zhang, J.-J., … Veldhorst, M. (2021). The germanium quantum information route. <i>Nature Reviews Materials</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41578-020-00262-z\">https://doi.org/10.1038/s41578-020-00262-z</a>"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","acknowledgement":"G.S., M.W.,F.A.Z acknowledge financial support from The Netherlands Organization for Scientific Research (NWO). F.Z., D.L., G.K. acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under Grand Agreement Nr. 862046. G.K. acknowledges funding from FP7 ERC Starting Grant 335497, FWF Y 715-N30, FWF P-30207. S.D. acknowledges support from the European Union’s Horizon 2020 program under Grant\r\nAgreement No. 81050 and from the Agence Nationale de la Recherche through the TOPONANO and CMOSQSPIN projects. J.Z. acknowledges support from the National Key R&D Program of China (Grant No. 2016YFA0301701) and Strategic Priority Research Program of CAS (Grant No. XDB30000000). D.L. and C.K. acknowledge the Swiss National Science Foundation and NCCR QSIT.","date_created":"2020-12-02T10:52:51Z","main_file_link":[{"url":"https://arxiv.org/abs/2004.08133","open_access":"1"}],"status":"public","publication":"Nature Reviews Materials","publication_identifier":{"eissn":["2058-8437"]},"ec_funded":1,"department":[{"_id":"GeKa"}],"project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","grant_number":"335497","call_identifier":"FP7","_id":"25517E86-B435-11E9-9278-68D0E5697425"},{"name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","_id":"2552F888-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y00715"},{"name":"Hole spin orbit qubits in Ge quantum wells","call_identifier":"FWF","grant_number":"P30207","_id":"2641CE5E-B435-11E9-9278-68D0E5697425"}],"isi":1,"day":"01","title":"The germanium quantum information route","abstract":[{"lang":"eng","text":"In the worldwide endeavor for disruptive quantum technologies, germanium is emerging as a versatile material to realize devices capable of encoding, processing, or transmitting quantum information. These devices leverage special properties of the germanium valence-band states, commonly known as holes, such as their inherently strong spin-orbit coupling and the ability to host superconducting pairing correlations. In this Review, we initially introduce the physics of holes in low-dimensional germanium structures with key insights from a theoretical perspective. We then examine the material science progress underpinning germanium-based planar heterostructures and nanowires. We review the most significant experimental results demonstrating key building blocks for quantum technology, such as an electrically driven universal quantum gate set with spin qubits in quantum dots and superconductor-semiconductor devices for hybrid quantum systems. We conclude by identifying the most promising prospects\r\ntoward scalable quantum information processing. "}],"oa_version":"Preprint","date_updated":"2024-10-22T09:41:03Z","intvolume":"         6","author":[{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"last_name":"Kloeffel","full_name":"Kloeffel, Christoph","first_name":"Christoph"},{"full_name":"Zwanenburg, Floris A.","last_name":"Zwanenburg","first_name":"Floris A."},{"first_name":"Daniel","full_name":"Loss, Daniel","last_name":"Loss"},{"full_name":"Myronov, Maksym","last_name":"Myronov","first_name":"Maksym"},{"first_name":"Jian-Jun","full_name":"Zhang, Jian-Jun","last_name":"Zhang"},{"first_name":"Silvano De","last_name":"Franceschi","full_name":"Franceschi, Silvano De"},{"orcid":"0000-0001-8342-202X","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros"},{"last_name":"Veldhorst","full_name":"Veldhorst, Menno","first_name":"Menno"}]},{"has_accepted_license":"1","isi":1,"department":[{"_id":"ToHe"}],"project":[{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"}],"title":"Boosting expensive synchronizing heuristics","ddc":["000"],"day":"01","oa_version":"Submitted Version","article_number":"114203","intvolume":"       167","date_updated":"2026-04-16T09:15:47Z","abstract":[{"lang":"eng","text":"For automata, synchronization, the problem of bringing an automaton to a particular state regardless of its initial state, is important. It has several applications in practice and is related to a fifty-year-old conjecture on the length of the shortest synchronizing word. Although using shorter words increases the effectiveness in practice, finding a shortest one (which is not necessarily unique) is NP-hard. For this reason, there exist various heuristics in the literature. However, high-quality heuristics such as SynchroP producing relatively shorter sequences are very expensive and can take hours when the automaton has tens of thousands of states. The SynchroP heuristic has been frequently used as a benchmark to evaluate the performance of the new heuristics. In this work, we first improve the runtime of SynchroP and its variants by using algorithmic techniques. We then focus on adapting SynchroP for many-core architectures,\r\nand overall, we obtain more than 1000× speedup on GPUs compared to naive sequential implementation that has been frequently used as a benchmark to evaluate new heuristics in the literature. We also propose two SynchroP variants and evaluate their performance."}],"author":[{"id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","first_name":"Naci E","full_name":"Sarac, Naci E","last_name":"Sarac"},{"last_name":"Altun","full_name":"Altun, Ömer Faruk","first_name":"Ömer Faruk"},{"full_name":"Atam, Kamil Tolga","last_name":"Atam","first_name":"Kamil Tolga"},{"first_name":"Sertac","last_name":"Karahoda","full_name":"Karahoda, Sertac"},{"last_name":"Kaya","full_name":"Kaya, Kamer","first_name":"Kamer"},{"first_name":"Hüsnü","last_name":"Yenigün","full_name":"Yenigün, Hüsnü"}],"article_processing_charge":"No","date_created":"2020-12-02T13:34:25Z","file_date_updated":"2020-12-02T13:33:51Z","status":"public","acknowledgement":"This work was supported by The Scientific and Technological Research Council of Turkey (TUBITAK) [grant number 114E569]. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). We would like to thank the authors of (Roman & Szykula, 2015) for providing their heuristics implementations, which we used to compare our SynchroP implementation as given in Table 11.","publication":"Expert Systems with Applications","publication_identifier":{"eissn":["1873-6793"],"issn":["0957-4174"]},"_id":"8912","scopus_import":"1","month":"04","publication_status":"published","citation":{"ama":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. Boosting expensive synchronizing heuristics. <i>Expert Systems with Applications</i>. 2021;167(4). doi:<a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">10.1016/j.eswa.2020.114203</a>","apa":"Sarac, N. E., Altun, Ö. F., Atam, K. T., Karahoda, S., Kaya, K., &#38; Yenigün, H. (2021). Boosting expensive synchronizing heuristics. <i>Expert Systems with Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">https://doi.org/10.1016/j.eswa.2020.114203</a>","ieee":"N. E. Sarac, Ö. F. Altun, K. T. Atam, S. Karahoda, K. Kaya, and H. Yenigün, “Boosting expensive synchronizing heuristics,” <i>Expert Systems with Applications</i>, vol. 167, no. 4. Elsevier, 2021.","short":"N.E. Sarac, Ö.F. Altun, K.T. Atam, S. Karahoda, K. Kaya, H. Yenigün, Expert Systems with Applications 167 (2021).","chicago":"Sarac, Naci E, Ömer Faruk Altun, Kamil Tolga Atam, Sertac Karahoda, Kamer Kaya, and Hüsnü Yenigün. “Boosting Expensive Synchronizing Heuristics.” <i>Expert Systems with Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">https://doi.org/10.1016/j.eswa.2020.114203</a>.","ista":"Sarac NE, Altun ÖF, Atam KT, Karahoda S, Kaya K, Yenigün H. 2021. Boosting expensive synchronizing heuristics. Expert Systems with Applications. 167(4), 114203.","mla":"Sarac, Naci E., et al. “Boosting Expensive Synchronizing Heuristics.” <i>Expert Systems with Applications</i>, vol. 167, no. 4, 114203, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.eswa.2020.114203\">10.1016/j.eswa.2020.114203</a>."},"corr_author":"1","type":"journal_article","volume":167,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_type":"original","file":[{"file_id":"8913","access_level":"open_access","checksum":"600c2f81bc898a725bcfa7cf26ff4fed","file_name":"synchroPaperRevised.pdf","date_updated":"2020-12-02T13:33:51Z","content_type":"application/pdf","file_size":634967,"date_created":"2020-12-02T13:33:51Z","creator":"esarac","relation":"main_file"}],"oa":1,"publisher":"Elsevier","date_published":"2021-04-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1016/j.eswa.2020.114203","issue":"4","quality_controlled":"1","year":"2021","external_id":{"isi":["000640531100038"]}},{"publication":"Liver International","publication_identifier":{"issn":["1478-3223"],"eissn":["1478-3231"]},"article_processing_charge":"No","file_date_updated":"2021-02-04T12:01:45Z","status":"public","date_created":"2020-12-06T23:01:16Z","acknowledgement":"This work was supported by grant F7310‐B21 from the Austrian Science Foundation (to MT). We thank Jelena Remetic, Claudia D. Fuchs, Veronika Mlitz and Daniel Steinacher, for their valuable input and discussion. Figure 1 and Figure 2 have been created with BioRender.com.","date_updated":"2025-06-12T06:33:00Z","intvolume":"        41","oa_version":"Published Version","abstract":[{"text":"The recent outbreak of coronavirus disease 2019 (COVID‐19), caused by the Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) has resulted in a world‐wide pandemic. Disseminated lung injury with the development of acute respiratory distress syndrome (ARDS) is the main cause of mortality in COVID‐19. Although liver failure does not seem to occur in the absence of pre‐existing liver disease, hepatic involvement in COVID‐19 may correlate with overall disease severity and serve as a prognostic factor for the development of ARDS. The spectrum of liver injury in COVID‐19 may range from direct infection by SARS‐CoV‐2, indirect involvement by systemic inflammation, hypoxic changes, iatrogenic causes such as drugs and ventilation to exacerbation of underlying liver disease. This concise review discusses the potential pathophysiological mechanisms for SARS‐CoV‐2 hepatic tropism as well as acute and possibly long‐term liver injury in COVID‐19.","lang":"eng"}],"author":[{"first_name":"Alexander D.","full_name":"Nardo, Alexander D.","last_name":"Nardo"},{"first_name":"Mathias","full_name":"Schneeweiss-Gleixner, Mathias","last_name":"Schneeweiss-Gleixner"},{"last_name":"Bakail","full_name":"Bakail, May M","first_name":"May M","id":"FB3C3F8E-522F-11EA-B186-22963DDC885E","orcid":"0000-0002-9592-1587"},{"last_name":"Dixon","full_name":"Dixon, Emmanuel D.","first_name":"Emmanuel D."},{"last_name":"Lax","full_name":"Lax, Sigurd F.","first_name":"Sigurd F."},{"first_name":"Michael","full_name":"Trauner, Michael","last_name":"Trauner"}],"isi":1,"has_accepted_license":"1","department":[{"_id":"CampIT"}],"title":"Pathophysiological mechanisms of liver injury in COVID-19","day":"01","ddc":["570"],"year":"2021","quality_controlled":"1","external_id":{"isi":["000594239200001"],"pmid":["33190346"]},"page":"20-32","article_type":"original","oa":1,"file":[{"date_created":"2021-02-04T12:01:45Z","success":1,"relation":"main_file","creator":"dernst","file_name":"2021_Liver_Nardo.pdf","access_level":"open_access","checksum":"6e4f21b77ef22c854e016240974fc473","file_id":"9091","file_size":930414,"content_type":"application/pdf","date_updated":"2021-02-04T12:01:45Z"}],"issue":"1","language":[{"iso":"eng"}],"doi":"10.1111/liv.14730","date_published":"2021-01-01T00:00:00Z","publisher":"Wiley","citation":{"chicago":"Nardo, Alexander D., Mathias Schneeweiss-Gleixner, May M Bakail, Emmanuel D. Dixon, Sigurd F. Lax, and Michael Trauner. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” <i>Liver International</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/liv.14730\">https://doi.org/10.1111/liv.14730</a>.","mla":"Nardo, Alexander D., et al. “Pathophysiological Mechanisms of Liver Injury in COVID-19.” <i>Liver International</i>, vol. 41, no. 1, Wiley, 2021, pp. 20–32, doi:<a href=\"https://doi.org/10.1111/liv.14730\">10.1111/liv.14730</a>.","ista":"Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. 2021. Pathophysiological mechanisms of liver injury in COVID-19. Liver International. 41(1), 20–32.","short":"A.D. Nardo, M. Schneeweiss-Gleixner, M.M. Bakail, E.D. Dixon, S.F. Lax, M. Trauner, Liver International 41 (2021) 20–32.","ieee":"A. D. Nardo, M. Schneeweiss-Gleixner, M. M. Bakail, E. D. Dixon, S. F. Lax, and M. Trauner, “Pathophysiological mechanisms of liver injury in COVID-19,” <i>Liver International</i>, vol. 41, no. 1. Wiley, pp. 20–32, 2021.","ama":"Nardo AD, Schneeweiss-Gleixner M, Bakail MM, Dixon ED, Lax SF, Trauner M. Pathophysiological mechanisms of liver injury in COVID-19. <i>Liver International</i>. 2021;41(1):20-32. doi:<a href=\"https://doi.org/10.1111/liv.14730\">10.1111/liv.14730</a>","apa":"Nardo, A. D., Schneeweiss-Gleixner, M., Bakail, M. M., Dixon, E. D., Lax, S. F., &#38; Trauner, M. (2021). Pathophysiological mechanisms of liver injury in COVID-19. <i>Liver International</i>. Wiley. <a href=\"https://doi.org/10.1111/liv.14730\">https://doi.org/10.1111/liv.14730</a>"},"publication_status":"published","type":"journal_article","volume":41,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"8927","scopus_import":"1","month":"01","pmid":1},{"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"related_material":{"record":[{"id":"13065","relation":"research_data","status":"public"}]},"publication":"Journal of Evolutionary Biology","date_created":"2020-12-06T23:01:16Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"status":"public","acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","article_processing_charge":"No","author":[{"last_name":"Arnoux","full_name":"Arnoux, Stéphanie","first_name":"Stéphanie"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"first_name":"Christopher","last_name":"Sauvage","full_name":"Sauvage, Christopher"}],"oa_version":"Published Version","date_updated":"2026-06-18T19:37:17Z","intvolume":"        34","abstract":[{"lang":"eng","text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available."}],"title":"Genomic inference of complex domestication histories in three Solanaceae species","ddc":["570"],"day":"01","isi":1,"department":[{"_id":"NiBa"}],"project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","call_identifier":"FWF","name":"Sex chromosomes and species barriers"}],"external_id":{"isi":["000587769700001"],"pmid":["33107098"]},"page":"270-283","quality_controlled":"1","year":"2021","oa":1,"date_published":"2021-02-01T00:00:00Z","doi":"10.1111/jeb.13723","publisher":"Wiley","language":[{"iso":"eng"}],"issue":"2","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","citation":{"short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>.","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>.","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. 2021;34(2):270-283. doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>"},"type":"journal_article","volume":34,"pmid":1,"month":"02","scopus_import":"1","_id":"8928"},{"keyword":["Theoretical Computer Science","Computational Theory and Mathematics","Geometry and Topology","Discrete Mathematics and Combinatorics"],"article_type":"original","publisher":"Springer Nature","date_published":"2021-07-01T00:00:00Z","doi":"10.1007/s00454-020-00250-8","language":[{"iso":"eng"}],"issue":"1","file":[{"file_id":"9795","access_level":"open_access","checksum":"c848986091e56699dc12de85adb1e39c","file_name":"2021_DescreteCompGeopmetry_Boissonnat.pdf","date_updated":"2021-08-06T09:52:29Z","content_type":"application/pdf","file_size":983307,"date_created":"2021-08-06T09:52:29Z","relation":"main_file","creator":"kschuh","success":1}],"oa":1,"quality_controlled":"1","year":"2021","page":"386-434","external_id":{"isi":["000597770300001"]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"8940","scopus_import":"1","month":"07","type":"journal_article","corr_author":"1","volume":66,"publication_status":"published","citation":{"short":"J.-D. Boissonnat, S. Kachanovich, M. Wintraecken, Discrete &#38; Computational Geometry 66 (2021) 386–434.","ista":"Boissonnat J-D, Kachanovich S, Wintraecken M. 2021. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. Discrete &#38; Computational Geometry. 66(1), 386–434.","chicago":"Boissonnat, Jean-Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” <i>Discrete &#38; Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00250-8\">https://doi.org/10.1007/s00454-020-00250-8</a>.","mla":"Boissonnat, Jean-Daniel, et al. “Triangulating Submanifolds: An Elementary and Quantified Version of Whitney’s Method.” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no. 1, Springer Nature, 2021, pp. 386–434, doi:<a href=\"https://doi.org/10.1007/s00454-020-00250-8\">10.1007/s00454-020-00250-8</a>.","ieee":"J.-D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Triangulating submanifolds: An elementary and quantified version of Whitney’s method,” <i>Discrete &#38; Computational Geometry</i>, vol. 66, no. 1. Springer Nature, pp. 386–434, 2021.","apa":"Boissonnat, J.-D., Kachanovich, S., &#38; Wintraecken, M. (2021). Triangulating submanifolds: An elementary and quantified version of Whitney’s method. <i>Discrete &#38; Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00250-8\">https://doi.org/10.1007/s00454-020-00250-8</a>","ama":"Boissonnat J-D, Kachanovich S, Wintraecken M. Triangulating submanifolds: An elementary and quantified version of Whitney’s method. <i>Discrete &#38; Computational Geometry</i>. 2021;66(1):386-434. doi:<a href=\"https://doi.org/10.1007/s00454-020-00250-8\">10.1007/s00454-020-00250-8</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (via OA deal)","acknowledgement":"This work has been funded by the European Research Council under the European Union’s ERC Grant Agreement Number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. Open access funding provided by the Institute of Science and Technology (IST Austria).","date_created":"2020-12-12T11:07:02Z","status":"public","file_date_updated":"2021-08-06T09:52:29Z","publication":"Discrete & Computational Geometry","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"ec_funded":1,"department":[{"_id":"HeEd"}],"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"has_accepted_license":"1","isi":1,"ddc":["516"],"day":"01","title":"Triangulating submanifolds: An elementary and quantified version of Whitney’s method","abstract":[{"text":"We quantise Whitney’s construction to prove the existence of a triangulation for any C^2 manifold, so that we get an algorithm with explicit bounds. We also give a new elementary proof, which is completely geometric.","lang":"eng"}],"oa_version":"Published Version","intvolume":"        66","date_updated":"2025-04-14T07:43:50Z","author":[{"first_name":"Jean-Daniel","full_name":"Boissonnat, Jean-Daniel","last_name":"Boissonnat"},{"full_name":"Kachanovich, Siargey","last_name":"Kachanovich","first_name":"Siargey"},{"full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}]},{"corr_author":"1","type":"journal_article","volume":118,"publication_status":"published","citation":{"short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>.","chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>.","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2010054118.","ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., &#38; Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8988","pmid":1,"month":"01","scopus_import":"1","quality_controlled":"1","year":"2021","external_id":{"isi":["000607270100018"],"pmid":["33443153"]},"article_type":"original","date_published":"2021-01-05T00:00:00Z","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","doi":"10.1073/pnas.2010054118","issue":"1","oa":1,"abstract":[{"text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.","lang":"eng"}],"oa_version":"Published Version","article_number":"e2010054118","intvolume":"       118","date_updated":"2026-06-18T19:37:53Z","author":[{"full_name":"Düllberg, Christian F","last_name":"Düllberg","orcid":"0000-0001-6335-9748","first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Auer","full_name":"Auer, Albert","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","first_name":"Albert","orcid":"0000-0002-3580-2906"},{"first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","last_name":"Canigova","full_name":"Canigova, Nikola"},{"full_name":"Loibl, Katrin","last_name":"Loibl","orcid":"0000-0002-2429-7668","id":"3760F32C-F248-11E8-B48F-1D18A9856A87","first_name":"Katrin"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","full_name":"Loose, Martin"}],"department":[{"_id":"MaLo"},{"_id":"MiSi"}],"project":[{"_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"isi":1,"ddc":["570"],"day":"05","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"article_processing_charge":"No","acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","date_created":"2021-01-03T23:01:23Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2010054118","open_access":"1"}],"status":"public"},{"_id":"8992","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"month":"01","scopus_import":"1","pmid":1,"citation":{"ieee":"S. Tan, C. Luschnig, and J. Friml, “Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling,” <i>Molecular Plant</i>, vol. 14, no. 1. Elsevier, pp. 151–165, 2021.","apa":"Tan, S., Luschnig, C., &#38; Friml, J. (2021). Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">https://doi.org/10.1016/j.molp.2020.11.004</a>","ama":"Tan S, Luschnig C, Friml J. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. <i>Molecular Plant</i>. 2021;14(1):151-165. doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>","short":"S. Tan, C. Luschnig, J. Friml, Molecular Plant 14 (2021) 151–165.","ista":"Tan S, Luschnig C, Friml J. 2021. Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling. Molecular Plant. 14(1), 151–165.","mla":"Tan, Shutang, et al. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>, vol. 14, no. 1, Elsevier, 2021, pp. 151–65, doi:<a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">10.1016/j.molp.2020.11.004</a>.","chicago":"Tan, Shutang, Christian Luschnig, and Jiří Friml. “Pho-View of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling.” <i>Molecular Plant</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.molp.2020.11.004\">https://doi.org/10.1016/j.molp.2020.11.004</a>."},"publication_status":"published","volume":14,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"file":[{"file_id":"8995","file_name":"2020_MolecularPlant_Tan.pdf","access_level":"open_access","checksum":"917e60e57092f22e16beac70b1775ea6","content_type":"application/pdf","date_updated":"2021-01-07T14:03:53Z","file_size":871088,"date_created":"2021-01-07T14:03:53Z","creator":"dernst","relation":"main_file","success":1}],"issue":"1","doi":"10.1016/j.molp.2020.11.004","language":[{"iso":"eng"}],"publisher":"Elsevier","date_published":"2021-01-04T00:00:00Z","year":"2021","quality_controlled":"1","external_id":{"pmid":["33186755"],"isi":["000605359400014"]},"page":"151-165","isi":1,"has_accepted_license":"1","project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis"}],"department":[{"_id":"JiFr"}],"title":"Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling","day":"04","ddc":["580"],"intvolume":"        14","date_updated":"2025-07-10T12:01:28Z","oa_version":"Published Version","abstract":[{"text":"The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.","lang":"eng"}],"author":[{"full_name":"Tan, Shutang","last_name":"Tan","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","last_name":"Friml"}],"article_processing_charge":"No","status":"public","file_date_updated":"2021-01-07T14:03:53Z","date_created":"2021-01-03T23:01:23Z","acknowledgement":"This work was supported by the European Union’s Horizon 2020 Program (ERC grant agreement no. 742985 to J.F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). C.L. is supported by the Austrian Science Fund (FWF; P 31493).","publication":"Molecular Plant","ec_funded":1,"publication_identifier":{"eissn":["1752-9867"],"issn":["1674-2052"]}},{"_id":"8993","pmid":1,"month":"01","scopus_import":"1","publication_status":"published","citation":{"short":"L. Abas, M. Kolb, J. Stadlmann, D.P. Janacek, K. Lukic, C. Schwechheimer, L.A. Sazanov, L. Mach, J. Friml, U.Z. Hammes, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","chicago":"Abas, Lindy, Martina Kolb, Johannes Stadlmann, Dorina P. Janacek, Kristina Lukic, Claus Schwechheimer, Leonid A Sazanov, Lukas Mach, Jiří Friml, and Ulrich Z. Hammes. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>.","mla":"Abas, Lindy, et al. “Naphthylphthalamic Acid Associates with and Inhibits PIN Auxin Transporters.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1, e2020857118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>.","ista":"Abas L, Kolb M, Stadlmann J, Janacek DP, Lukic K, Schwechheimer C, Sazanov LA, Mach L, Friml J, Hammes UZ. 2021. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2020857118.","ieee":"L. Abas <i>et al.</i>, “Naphthylphthalamic acid associates with and inhibits PIN auxin transporters,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","ama":"Abas L, Kolb M, Stadlmann J, et al. Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2020857118\">10.1073/pnas.2020857118</a>","apa":"Abas, L., Kolb, M., Stadlmann, J., Janacek, D. P., Lukic, K., Schwechheimer, C., … Hammes, U. Z. (2021). Naphthylphthalamic acid associates with and inhibits PIN auxin transporters. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2020857118\">https://doi.org/10.1073/pnas.2020857118</a>"},"volume":118,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"language":[{"iso":"eng"}],"date_published":"2021-01-05T00:00:00Z","publisher":"National Academy of Sciences","doi":"10.1073/pnas.2020857118","issue":"1","quality_controlled":"1","year":"2021","external_id":{"pmid":["33443187"],"isi":["000607270100073"]},"isi":1,"department":[{"_id":"JiFr"},{"_id":"LeSa"}],"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"title":"Naphthylphthalamic acid associates with and inhibits PIN auxin transporters","ddc":["580"],"day":"05","oa_version":"Published Version","article_number":"e2020857118","date_updated":"2026-06-18T19:38:20Z","intvolume":"       118","abstract":[{"text":"N-1-naphthylphthalamic acid (NPA) is a key inhibitor of directional (polar) transport of the hormone auxin in plants. For decades, it has been a pivotal tool in elucidating the unique polar auxin transport-based processes underlying plant growth and development. Its exact mode of action has long been sought after and is still being debated, with prevailing mechanistic schemes describing only indirect connections between NPA and the main transporters responsible for directional transport, namely PIN auxin exporters. Here we present data supporting a model in which NPA associates with PINs in a more direct manner than hitherto postulated. We show that NPA inhibits PIN activity in a heterologous oocyte system and that expression of NPA-sensitive PINs in plant, yeast, and oocyte membranes leads to specific saturable NPA binding. We thus propose that PINs are a bona fide NPA target. This offers a straightforward molecular basis for NPA inhibition of PIN-dependent auxin transport and a logical parsimonious explanation for the known physiological effects of NPA on plant growth, as well as an alternative hypothesis to interpret past and future results. We also introduce PIN dimerization and describe an effect of NPA on this, suggesting that NPA binding could be exploited to gain insights into structural aspects of PINs related to their transport mechanism.","lang":"eng"}],"author":[{"full_name":"Abas, Lindy","last_name":"Abas","first_name":"Lindy"},{"first_name":"Martina","last_name":"Kolb","full_name":"Kolb, Martina"},{"first_name":"Johannes","full_name":"Stadlmann, Johannes","last_name":"Stadlmann"},{"first_name":"Dorina P.","last_name":"Janacek","full_name":"Janacek, Dorina P."},{"full_name":"Lukic, Kristina","last_name":"Lukic","orcid":"0000-0003-1581-881X","id":"2B04DB84-F248-11E8-B48F-1D18A9856A87","first_name":"Kristina"},{"first_name":"Claus","last_name":"Schwechheimer","full_name":"Schwechheimer, Claus"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A"},{"last_name":"Mach","full_name":"Mach, Lukas","first_name":"Lukas"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"first_name":"Ulrich Z.","full_name":"Hammes, Ulrich Z.","last_name":"Hammes"}],"article_processing_charge":"No","date_created":"2021-01-03T23:01:23Z","main_file_link":[{"url":"https://doi.org/10.1073/pnas.2020857118","open_access":"1"}],"status":"public","acknowledgement":"This work was supported by Austrian Science Fund Grant FWF P21533-B20 (to L.A.); German Research Foundation Grant DFG HA3468/6-1 (to U.Z.H.); and European Research Council Grant 742985 (to J.F.). We thank Herta Steinkellner and Alexandra Castilho for N. benthamiana plants, Fabian Nagelreiter for statistical advice, Lanassa Bassukas for help with [ɣ32P]-\r\nATP assays, and Josef Penninger for providing access to mass spectrometry instruments at the Vienna BioCenter Core Facilities. We thank PNAS reviewers for the many comments and suggestions that helped to improve this manuscript.","publication":"Proceedings of the National Academy of Sciences of the United States of America","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1073/pnas.2102232118"}]},"ec_funded":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]}},{"abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"intvolume":"        17","date_updated":"2025-06-12T06:33:18Z","oa_version":"Published Version","article_number":"e1008529","author":[{"full_name":"Kavcic, Bor","last_name":"Kavcic","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"last_name":"Bollenbach","full_name":"Bollenbach, Tobias","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GaTk"}],"isi":1,"has_accepted_license":"1","day":"07","ddc":["570"],"title":"Minimal biophysical model of combined antibiotic action","publication":"PLOS Computational Biology","related_material":{"record":[{"relation":"research_data","id":"8930","status":"public"},{"id":"7673","relation":"earlier_version","status":"public"}]},"publication_identifier":{"issn":["1553-7358"]},"article_processing_charge":"Yes","acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","status":"public","file_date_updated":"2021-02-04T12:30:48Z","date_created":"2021-01-08T07:16:18Z","volume":17,"type":"journal_article","citation":{"ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” <i>PLOS Computational Biology</i>, vol. 17. Public Library of Science, 2021.","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. 2021;17. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>.","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>, vol. 17, e1008529, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>."},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"_id":"8997","scopus_import":"1","month":"01","pmid":1,"year":"2021","quality_controlled":"1","external_id":{"isi":["000608045000010"],"pmid":["33411759"]},"keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"article_type":"original","language":[{"iso":"eng"}],"date_published":"2021-01-07T00:00:00Z","doi":"10.1371/journal.pcbi.1008529","publisher":"Public Library of Science","oa":1,"file":[{"relation":"main_file","creator":"dernst","success":1,"date_created":"2021-02-04T12:30:48Z","date_updated":"2021-02-04T12:30:48Z","content_type":"application/pdf","file_size":3690053,"file_id":"9092","access_level":"open_access","checksum":"e29f2b42651bef8e034781de8781ffac","file_name":"2021_PlosComBio_Kavcic.pdf"}]}]