[{"issue":"3","date_created":"2022-05-29T22:01:53Z","acknowledgement":"L.E. would like to thank Zhigang Bao for many illuminating discussions in an early stage of this research. The authors are also grateful to Paul Bourgade for his comments on the manuscript and the anonymous referee for several useful suggestions.","publication":"Annals of Probability","volume":50,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2103.06730","open_access":"1"}],"article_type":"original","date_updated":"2023-08-03T07:16:53Z","publisher":"Institute of Mathematical Statistics","type":"journal_article","page":"984-1012","publication_identifier":{"eissn":["2168-894X"],"issn":["0091-1798"]},"isi":1,"year":"2022","month":"05","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity for Wigner matrices. Annals of Probability. 50(3), 984–1012.","mla":"Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>, vol. 50, no. 3, Institute of Mathematical Statistics, 2022, pp. 984–1012, doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum ergodicity for Wigner matrices,” <i>Annals of Probability</i>, vol. 50, no. 3. Institute of Mathematical Statistics, pp. 984–1012, 2022.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012.","ama":"Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. 2022;50(3):984-1012. doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>."},"title":"Normal fluctuation in quantum ergodicity for Wigner matrices","date_published":"2022-05-01T00:00:00Z","abstract":[{"text":"We consider the quadratic form of a general high-rank deterministic matrix on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian fluctuation for each bulk eigenvector in the large N limit. The proof is a combination of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau (2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021) 1005–1048).","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"day":"01","department":[{"_id":"LaEr"}],"publication_status":"published","external_id":{"isi":["000793963400005"],"arxiv":["2103.06730"]},"scopus_import":"1","arxiv":1,"article_processing_charge":"No","oa_version":"Preprint","status":"public","_id":"11418","author":[{"first_name":"Giorgio","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J","first_name":"Dominik J"}],"quality_controlled":"1","doi":"10.1214/21-AOP1552","intvolume":"        50","fulldoi":"https://doi.org/10.1214/21-AOP1552"},{"oa_version":"Published Version","_id":"11419","status":"public","author":[{"first_name":"Tetsuya","full_name":"Hori, Tetsuya","last_name":"Hori"},{"first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546","last_name":"Eguchi"},{"full_name":"Wang, Han Ying","first_name":"Han Ying","last_name":"Wang"},{"full_name":"Miyasaka, Tomohiro","first_name":"Tomohiro","last_name":"Miyasaka"},{"full_name":"Guillaud, Laurent","first_name":"Laurent","last_name":"Guillaud"},{"last_name":"Taoufiq","first_name":"Zacharie","full_name":"Taoufiq, Zacharie"},{"first_name":"Satyajit","full_name":"Mahapatra, Satyajit","last_name":"Mahapatra"},{"first_name":"Hiroshi","full_name":"Yamada, Hiroshi","last_name":"Yamada"},{"full_name":"Takei, Kohji","first_name":"Kohji","last_name":"Takei"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"quality_controlled":"1","intvolume":"        11","doi":"10.7554/eLife.73542","fulldoi":"https://doi.org/10.7554/eLife.73542","ddc":["616"],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"e73542","external_id":{"pmid":["35471147 "],"isi":["000876231600001"]},"scopus_import":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"day":"05","department":[{"_id":"RySh"}],"file_date_updated":"2022-05-30T08:09:16Z","publication_status":"published","year":"2022","citation":{"ista":"Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S, Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. eLife. 11, e73542.","mla":"Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>, vol. 11, e73542, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>.","short":"T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra, H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022).","apa":"Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z., … Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>","ieee":"T. Hori <i>et al.</i>, “Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ama":"Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>","chicago":"Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>."},"month":"05","title":"Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer's disease synapse model","abstract":[{"lang":"eng","text":"Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased MT-bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin 1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission."}],"date_published":"2022-05-05T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"eLife Sciences Publications","type":"journal_article","isi":1,"publication_identifier":{"eissn":["2050-084X"]},"pmid":1,"article_type":"original","file":[{"creator":"cchlebak","relation":"main_file","checksum":"ccddbd167e00ff8375f12998af497152","content_type":"application/pdf","file_size":2466296,"access_level":"open_access","success":1,"date_created":"2022-05-30T08:09:16Z","date_updated":"2022-05-30T08:09:16Z","file_id":"11421","file_name":"elife-73542-v2.pdf"}],"date_updated":"2023-08-03T07:15:49Z","oa":1,"date_created":"2022-05-29T22:01:54Z","acknowledgement":"We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda for technical assistant with in vitro analysis of tau. This research was supported by funding from Okinawa Institute of Science and Technology and from Technology (OIST) and Core Research for the Evolutional Science and Technology of Japan Science and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas to TM (Brain Protein Aging and Dementia Control 26117004).","has_accepted_license":"1","publication":"eLife","volume":11},{"publication":"38th International Symposium on Computational Geometry","has_accepted_license":"1","acknowledgement":"Partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics” and the European Research Council (ERC), grant no. 788183, “Alpha Shape Theory Extended”. Erin Chambers: Supported in part by the National Science Foundation through grants DBI-1759807, CCF-1907612, and CCF-2106672. Mathijs Wintraecken: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073 Acknowledgements We thank André Lieutier, David Letscher, Ellen Gasparovic, Kathryn Leonard, and Tao Ju for early discussions on this work. We also thank Lu Liu, Yajie Yan and Tao Ju for sharing code to generate the examples.","ec_funded":1,"volume":224,"date_created":"2022-06-01T14:18:04Z","oa":1,"date_updated":"2025-04-14T07:43:57Z","file":[{"relation":"main_file","creator":"dernst","checksum":"b25ce40fade4ebc0bcaae176db4f5f1f","content_type":"application/pdf","file_size":17580705,"success":1,"access_level":"open_access","date_created":"2022-06-07T07:58:30Z","date_updated":"2022-06-07T07:58:30Z","file_id":"11437","file_name":"2022_LIPICs_Chambers.pdf"}],"publication_identifier":{"isbn":["978-3-95977-227-3"],"issn":["1868-8969"]},"type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","page":"66:1-66:9","citation":{"ista":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. 2022. A cautionary tale: Burning the medial axis is unstable. 38th International Symposium on Computational Geometry. SoCG: Symposium on Computational GeometryLIPIcs vol. 224, 66:1-66:9.","mla":"Chambers, Erin, et al. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, vol. 224, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>.","ieee":"E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “A cautionary tale: Burning the medial axis is unstable,” in <i>38th International Symposium on Computational Geometry</i>, Berlin, Germany, 2022, vol. 224, p. 66:1-66:9.","apa":"Chambers, E., Fillmore, C. D., Stephenson, E. R., &#38; Wintraecken, M. (2022). A cautionary tale: Burning the medial axis is unstable. In X. Goaoc &#38; M. Kerber (Eds.), <i>38th International Symposium on Computational Geometry</i> (Vol. 224, p. 66:1-66:9). Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>","short":"E. Chambers, C.D. Fillmore, E.R. Stephenson, M. Wintraecken, in:, X. Goaoc, M. Kerber (Eds.), 38th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022, p. 66:1-66:9.","ama":"Chambers E, Fillmore CD, Stephenson ER, Wintraecken M. A cautionary tale: Burning the medial axis is unstable. In: Goaoc X, Kerber M, eds. <i>38th International Symposium on Computational Geometry</i>. Vol 224. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2022:66:1-66:9. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">10.4230/LIPIcs.SoCG.2022.66</a>","chicago":"Chambers, Erin, Christopher D Fillmore, Elizabeth R Stephenson, and Mathijs Wintraecken. “A Cautionary Tale: Burning the Medial Axis Is Unstable.” In <i>38th International Symposium on Computational Geometry</i>, edited by Xavier Goaoc and Michael Kerber, 224:66:1-66:9. LIPIcs. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>."},"month":"06","title":"A cautionary tale: Burning the medial axis is unstable","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The medial axis of a set consists of the points in the ambient space without a unique closest point on the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a topologically equivalent skeleton. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities various prunings of the medial axis have been proposed. Here, we examine one type of pruning, called burning. Because of the good experimental results, it was hoped that the burning method of simplifying the medial axis would be stable. In this work we show a simple example that dashes such hopes based on Bing’s house with two rooms, demonstrating an isotopy of a shape where the medial axis goes from collapsible to non-collapsible."}],"date_published":"2022-06-01T00:00:00Z","year":"2022","department":[{"_id":"HeEd"}],"series_title":"LIPIcs","file_date_updated":"2022-06-07T07:58:30Z","publication_status":"published","editor":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael"}],"day":"01","language":[{"iso":"eng"}],"project":[{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"},{"call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"conference":{"location":"Berlin, Germany","end_date":"2022-06-10","start_date":"2022-06-07","name":"SoCG: Symposium on Computational Geometry"},"fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2022.66","ddc":["510"],"corr_author":"1","oa_version":"Published Version","doi":"10.4230/LIPIcs.SoCG.2022.66","intvolume":"       224","_id":"11428","author":[{"first_name":"Erin","full_name":"Chambers, Erin","last_name":"Chambers"},{"first_name":"Christopher D","full_name":"Fillmore, Christopher D","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","last_name":"Fillmore"},{"orcid":"0000-0002-6862-208X","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","last_name":"Stephenson","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R"},{"last_name":"Wintraecken","orcid":"0000-0002-7472-2220","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","full_name":"Wintraecken, Mathijs","first_name":"Mathijs"}],"status":"public","quality_controlled":"1"},{"article_processing_charge":"No","fulldoi":"https://doi.org/10.1007/978-3-031-06245-2","corr_author":"1","oa_version":"None","intvolume":"     13238","doi":"10.1007/978-3-031-06245-2","_id":"11429","quality_controlled":"1","status":"public","month":"05","citation":{"ieee":"F. Karimipour and S. Storandt, Eds., <i>Web and Wireless Geographical Information Systems</i>, 1st ed., vol. 13238. Cham: Springer Nature, 2022.","apa":"Karimipour, F., &#38; Storandt, S. (Eds.). (2022). <i>Web and Wireless Geographical Information Systems</i> (1st ed., Vol. 13238). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>","short":"F. Karimipour, S. Storandt, eds., Web and Wireless Geographical Information Systems, 1st ed., Springer Nature, Cham, 2022.","chicago":"Karimipour, Farid, and Sabine Storandt, eds. <i>Web and Wireless Geographical Information Systems</i>. 1st ed. Vol. 13238. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>.","ama":"Karimipour F, Storandt S, eds. <i>Web and Wireless Geographical Information Systems</i>. Vol 13238. 1st ed. Cham: Springer Nature; 2022. doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>","mla":"Karimipour, Farid, and Sabine Storandt, editors. <i>Web and Wireless Geographical Information Systems</i>. 1st ed., vol. 13238, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/978-3-031-06245-2\">10.1007/978-3-031-06245-2</a>.","ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p."},"title":"Web and Wireless Geographical Information Systems","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-05-01T00:00:00Z","abstract":[{"text":"This book constitutes the refereed proceedings of the 18th International Symposium on Web and Wireless Geographical Information Systems, W2GIS 2022, held in Konstanz, Germany, in April 2022.\r\nThe 7 full papers presented together with 6 short papers in the volume were carefully reviewed and selected from 16 submissions.  The papers cover topics that range from mobile GIS and Location-Based Services to Spatial Information Retrieval and Wireless Sensor Networks.","lang":"eng"}],"year":"2022","department":[{"_id":"HeEd"}],"publication_status":"published","editor":[{"first_name":"Farid","full_name":"Karimipour, Farid","orcid":"0000-0001-6746-4174","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","last_name":"Karimipour"},{"first_name":"Sabine","full_name":"Storandt, Sabine","last_name":"Storandt"}],"day":"01","language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:02:30Z","place":"Cham","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031062445"],"eisbn":["9783031062452"]},"type":"book_editor","publisher":"Springer Nature","page":"153","alternative_title":["LNCS"],"volume":13238,"date_created":"2022-06-02T05:40:53Z","edition":"1"},{"fulldoi":"https://doi.org/10.1111/cgf.14478","_id":"11432","status":"public","quality_controlled":"1","author":[{"full_name":"Schreck, Camille","first_name":"Camille","last_name":"Schreck","id":"2B14B676-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J"}],"intvolume":"        41","doi":"10.1111/cgf.14478","oa_version":"Submitted Version","corr_author":"1","article_processing_charge":"No","scopus_import":"1","external_id":{"isi":["000802723900027"]},"publication_status":"published","department":[{"_id":"ChWo"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"day":"01","abstract":[{"lang":"eng","text":"This paper proposes a method for simulating liquids in large bodies of water by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator. The surface wave simulation uses the equivalent sources method (ESM) to efficiently animate large bodies of water with precisely controllable wave propagation behavior. The 3D liquid simulator animates complex non-linear fluid behaviors like splashes and breaking waves using off-the-shelf simulators using FLIP or the level set method with semi-Lagrangian advection.\r\nWe combine the two approaches by using the 3D solver to animate localized non-linear behaviors, and the 2D wave solver to animate larger regions with linear surface physics. We use the surface motion from the 3D solver as boundary conditions for 2D surface wave simulator, and we use the velocity and surface heights from the 2D surface wave simulator as boundary conditions for the 3D fluid simulation. We also introduce a novel technique for removing visual artifacts caused by numerical errors in 3D fluid solvers: we use experimental data to estimate the artificial dispersion caused by the 3D solver and we then carefully tune the wave speeds of the 2D solver to match it, effectively eliminating any differences in wave behavior across the boundary. To the best of our knowledge, this is the first time such a empirically driven error compensation approach has been used to remove coupling errors from a physics simulator.\r\nOur coupled simulation approach leverages the strengths of each simulation technique, animating large environments with seamless transitions between 2D and 3D physics."}],"date_published":"2022-05-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","month":"05","citation":{"mla":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>, vol. 41, no. 2, Wiley, 2022, pp. 343–53, doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>.","ista":"Schreck C, Wojtan C. 2022. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. Computer Graphics Forum. 41(2), 343–353.","ama":"Schreck C, Wojtan C. Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. 2022;41(2):343-353. doi:<a href=\"https://doi.org/10.1111/cgf.14478\">10.1111/cgf.14478</a>","chicago":"Schreck, Camille, and Chris Wojtan. “Coupling 3D Liquid Simulation with 2D Wave Propagation for Large Scale Water Surface Animation Using the Equivalent Sources Method.” <i>Computer Graphics Forum</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>.","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 343–353.","ieee":"C. Schreck and C. Wojtan, “Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method,” <i>Computer Graphics Forum</i>, vol. 41, no. 2. Wiley, pp. 343–353, 2022.","apa":"Schreck, C., &#38; Wojtan, C. (2022). Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.14478\">https://doi.org/10.1111/cgf.14478</a>"},"year":"2022","isi":1,"publication_identifier":{"issn":["0167-7055"],"eissn":["1467-8659"]},"page":"343-353","publisher":"Wiley","type":"journal_article","date_updated":"2024-10-22T09:58:19Z","article_type":"original","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-03641349/"}],"oa":1,"volume":41,"ec_funded":1,"acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria and MFX Team at INRIA for their valuable feedback. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176.","publication":"Computer Graphics Forum","issue":"2","date_created":"2022-06-05T22:01:49Z"},{"issue":"2","date_created":"2022-06-05T22:01:50Z","volume":36,"acknowledgement":"G.I. acknowledges the financial support from the Ministry of Educational and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and\r\nKKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI.","publication":"SIAM Journal on Discrete Mathematics","oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2103.04122"}],"article_type":"original","date_updated":"2023-10-18T06:58:03Z","page":"951-957","publisher":"Society for Industrial and Applied Mathematics","type":"journal_article","publication_identifier":{"issn":["0895-4801"]},"isi":1,"year":"2022","date_published":"2022-04-11T00:00:00Z","abstract":[{"text":"We introduce a new variant of quantitative Helly-type theorems: the minimal homothetic distance of the intersection of a family of convex sets to the intersection of a subfamily of a fixed size. As an application, we establish the following quantitative Helly-type result for the diameter. If $K$ is the intersection of finitely many convex bodies in $\\mathbb{R}^d$, then one can select $2d$ of these bodies whose intersection is of diameter at most $(2d)^3{diam}(K)$. The best previously known estimate, due to Brazitikos [Bull. Hellenic Math. Soc., 62 (2018), pp. 19--25], is $c d^{11/2}$. Moreover, we confirm that the multiplicative factor $c d^{1/2}$ conjectured by Bárány, Katchalski, and Pach [Proc. Amer. Math. Soc., 86 (1982), pp. 109--114] cannot be improved. The bounds above follow from our key result that concerns sparse approximation of a convex polytope by the convex hull of a well-chosen subset of its vertices: Assume that $Q \\subset {\\mathbb R}^d$ is a polytope whose centroid is the origin. Then there exist at most 2d vertices of $Q$ whose convex hull $Q^{\\prime \\prime}$ satisfies $Q \\subset - 8d^3 Q^{\\prime \\prime}.$","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A quantitative Helly-type theorem: Containment in a homothet","month":"04","citation":{"ista":"Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.","mla":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2, Society for Industrial and Applied Mathematics, 2022, pp. 951–57, doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>.","ama":"Ivanov G, Naszodi M. A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. 2022;36(2):951-957. doi:<a href=\"https://doi.org/10.1137/21M1403308\">10.1137/21M1403308</a>","chicago":"Ivanov, Grigory, and Marton Naszodi. “A Quantitative Helly-Type Theorem: Containment in a Homothet.” <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics, 2022. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>.","ieee":"G. Ivanov and M. Naszodi, “A quantitative Helly-type theorem: Containment in a homothet,” <i>SIAM Journal on Discrete Mathematics</i>, vol. 36, no. 2. Society for Industrial and Applied Mathematics, pp. 951–957, 2022.","short":"G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957.","apa":"Ivanov, G., &#38; Naszodi, M. (2022). A quantitative Helly-type theorem: Containment in a homothet. <i>SIAM Journal on Discrete Mathematics</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1403308\">https://doi.org/10.1137/21M1403308</a>"},"day":"11","language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"UlWa"}],"external_id":{"arxiv":["2103.04122"],"isi":["000793158200002"]},"arxiv":1,"article_processing_charge":"No","scopus_import":"1","quality_controlled":"1","_id":"11435","author":[{"last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory","first_name":"Grigory"},{"full_name":"Naszodi, Marton","first_name":"Marton","last_name":"Naszodi"}],"status":"public","doi":"10.1137/21M1403308","intvolume":"        36","oa_version":"Preprint","fulldoi":"https://doi.org/10.1137/21M1403308"},{"ddc":["000"],"fulldoi":"https://doi.org/10.1145/3528223.3530144","intvolume":"        41","doi":"10.1145/3528223.3530144","status":"public","_id":"11442","quality_controlled":"1","author":[{"last_name":"Piovarci","orcid":"0000-0002-5062-4474","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael","first_name":"Michael"},{"first_name":"Michael","full_name":"Foshey, Michael","last_name":"Foshey"},{"last_name":"Xu","full_name":"Xu, Jie","first_name":"Jie"},{"last_name":"Erps","full_name":"Erps, Timothy","first_name":"Timothy"},{"last_name":"Babaei","first_name":"Vahid","full_name":"Babaei, Vahid"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"last_name":"Rusinkiewicz","full_name":"Rusinkiewicz, Szymon","first_name":"Szymon"},{"first_name":"Wojciech","full_name":"Matusik, Wojciech","last_name":"Matusik"},{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd"}],"corr_author":"1","oa_version":"Submitted Version","OA_place":"publisher","article_processing_charge":"No","arxiv":1,"PlanS_conform":"1","scopus_import":"1","external_id":{"isi":["000830989200091"],"arxiv":["2201.11819"]},"article_number":"112","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","file_date_updated":"2022-06-28T08:32:58Z","department":[{"_id":"BeBi"}],"language":[{"iso":"eng"}],"day":"01","project":[{"grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020"}],"OA_type":"hybrid","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2022-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"Enabling additive manufacturing to employ a wide range of novel, functional materials can be a major boost to this technology. However, making such materials printable requires painstaking trial-and-error by an expert operator,\r\nas they typically tend to exhibit peculiar rheological or hysteresis properties. Even in the case of successfully finding the process parameters, there is no guarantee of print-to-print consistency due to material differences between batches. These challenges make closed-loop feedback an attractive option where the process parameters are adjusted on-the-fly. There are several challenges for designing an efficient controller: the deposition parameters are complex and highly coupled, artifacts occur after long time horizons, simulating the deposition is computationally costly, and learning on hardware is intractable. In this work, we demonstrate the feasibility of learning a closed-loop control policy for additive manufacturing using reinforcement learning. We show that approximate, but efficient, numerical simulation is\r\nsufficient as long as it allows learning the behavioral patterns of deposition that translate to real-world experiences. In combination with reinforcement learning, our model can be used to discover control policies that outperform\r\nbaseline controllers. Furthermore, the recovered policies have a minimal sim-to-real gap. We showcase this by applying our control policy in-vivo on a single-layer, direct ink writing printer. "}],"citation":{"ista":"Piovarci M, Foshey M, Xu J, Erps T, Babaei V, Didyk P, Rusinkiewicz S, Matusik W, Bickel B. 2022. Closed-loop control of direct ink writing via reinforcement learning. ACM Transactions on Graphics. 41(4), 112.","mla":"Piovarci, Michael, et al. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4, 112, Association for Computing Machinery, 2022, doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>.","chicago":"Piovarci, Michael, Michael Foshey, Jie Xu, Timothy Erps, Vahid Babaei, Piotr Didyk, Szymon Rusinkiewicz, Wojciech Matusik, and Bernd Bickel. “Closed-Loop Control of Direct Ink Writing via Reinforcement Learning.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>.","ama":"Piovarci M, Foshey M, Xu J, et al. Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. 2022;41(4). doi:<a href=\"https://doi.org/10.1145/3528223.3530144\">10.1145/3528223.3530144</a>","short":"M. Piovarci, M. Foshey, J. Xu, T. Erps, V. Babaei, P. Didyk, S. Rusinkiewicz, W. Matusik, B. Bickel, ACM Transactions on Graphics 41 (2022).","apa":"Piovarci, M., Foshey, M., Xu, J., Erps, T., Babaei, V., Didyk, P., … Bickel, B. (2022). Closed-loop control of direct ink writing via reinforcement learning. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3528223.3530144\">https://doi.org/10.1145/3528223.3530144</a>","ieee":"M. Piovarci <i>et al.</i>, “Closed-loop control of direct ink writing via reinforcement learning,” <i>ACM Transactions on Graphics</i>, vol. 41, no. 4. Association for Computing Machinery, 2022."},"month":"06","title":"Closed-loop control of direct ink writing via reinforcement learning","year":"2022","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"isi":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/","relation":"press_release","description":"News on ISTA website"}]},"type":"journal_article","publisher":"Association for Computing Machinery","date_updated":"2025-09-10T09:36:45Z","file":[{"success":1,"access_level":"open_access","file_size":33994829,"content_type":"application/pdf","checksum":"27f6fe41c6ff84d50445cc9b0176d45b","relation":"main_file","creator":"dernst","file_name":"2022_ACM_acceptedversion_Piovarci.pdf","file_id":"11467","date_updated":"2022-06-28T08:32:58Z","date_created":"2022-06-28T08:32:58Z"}],"article_type":"original","oa":1,"ec_funded":1,"volume":41,"publication":"ACM Transactions on Graphics","acknowledgement":"This work is graciously supported by the following grant agencies: FWF Lise Meitner (Grant M 3319), SNSF (Grant 200502), ERC Starting Grant (MATERIALIZABLE-715767), NSF (Grant IIS-181507).\r\n","has_accepted_license":"1","date_created":"2022-06-10T06:41:47Z","issue":"4"},{"date_created":"2022-06-12T22:01:45Z","issue":"6","publication":"Transactions of the American Mathematical Society","acknowledgement":"The research of the first author was supported by SNSF Project 178493 and NSF Award DMS-1953990. The research of the second author supported by NSF Award DMS-1953772.\r\nThe research of the third author was supported by NSF Award DMS-1764176, NSF CAREER Award DMS-2044606, a Sloan Research Fellowship, and the MIT Solomon Buchsbaum Fund. ","volume":375,"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2006.08836"}],"article_type":"original","date_updated":"2024-10-09T21:02:31Z","type":"journal_article","publisher":"American Mathematical Society","page":"4209-4250","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"isi":1,"year":"2022","citation":{"mla":"Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6, American Mathematical Society, 2022, pp. 4209–50, doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>.","ista":"Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.","short":"M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical Society 375 (2022) 4209–4250.","apa":"Kwan, M. A., Sauermann, L., &#38; Zhao, Y. (2022). Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>","ieee":"M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional polytopes,” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6. American Mathematical Society, pp. 4209–4250, 2022.","chicago":"Kwan, Matthew Alan, Lisa Sauermann, and Yufei Zhao. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2022. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>.","ama":"Kwan MA, Sauermann L, Zhao Y. Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. 2022;375(6):4209-4250. doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>"},"month":"06","title":"Extension complexity of low-dimensional polytopes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-06-01T00:00:00Z","abstract":[{"lang":"eng","text":"Sometimes, it is possible to represent a complicated polytope as a projection of a much simpler polytope. To quantify this phenomenon, the extension complexity of a polytope P is defined to be the minimum number of facets of a (possibly higher-dimensional) polytope from which P can be obtained as a (linear) projection. This notion is motivated by its relevance to combinatorial optimisation, and has been studied intensively for various specific polytopes associated with important optimisation problems. In this paper we study extension complexity as a parameter of general polytopes, more specifically considering various families of low-dimensional polytopes. First, we prove that for a fixed dimension d, the extension complexity of a random d-dimensional polytope (obtained as the convex hull of random points in a ball or on a sphere) is typically on the order of the square root of its number of vertices. Second, we prove that any cyclic n-vertex polygon (whose vertices lie on a circle) has extension complexity at most 24√n. This bound is tight up to the constant factor 24. Finally, we show that there exists an no(1)-dimensional polytope with at most n vertices and extension complexity n1−o(1). Our theorems are proved with a range of different techniques, which we hope will be of further interest."}],"day":"01","language":[{"iso":"eng"}],"department":[{"_id":"MaKw"}],"publication_status":"published","external_id":{"arxiv":["2006.08836"],"isi":["000798461500001"]},"scopus_import":"1","article_processing_charge":"No","arxiv":1,"corr_author":"1","oa_version":"Preprint","intvolume":"       375","doi":"10.1090/tran/8614","quality_controlled":"1","_id":"11443","status":"public","author":[{"first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan"},{"last_name":"Sauermann","full_name":"Sauermann, Lisa","first_name":"Lisa"},{"last_name":"Zhao","full_name":"Zhao, Yufei","first_name":"Yufei"}],"fulldoi":"https://doi.org/10.1090/tran/8614"},{"doi":"10.3366/lih.2022.0097","intvolume":"        38","_id":"11444","author":[{"first_name":"Clara A","full_name":"Chlebak, Clara A","orcid":"0000-0002-3385-3865","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","last_name":"Chlebak"},{"first_name":"Peter H.","full_name":"Reid, Peter H.","last_name":"Reid"}],"quality_controlled":"1","status":"public","corr_author":"1","oa_version":"Submitted Version","fulldoi":"https://doi.org/10.3366/lih.2022.0097","article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"day":"01","publication_status":"published","department":[{"_id":"E-Lib"}],"year":"2022","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2022-04-01T00:00:00Z","abstract":[{"text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride.","lang":"eng"}],"title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","month":"04","citation":{"apa":"Chlebak, C. A., &#38; Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. Edinburgh University Press. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” <i>Library and Information History</i>, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>. Edinburgh University Press, 2022. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>.","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. 2022;38(1):23-41. doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>."},"page":"23-41","type":"journal_article","publisher":"Edinburgh University Press","publication_identifier":{"eissn":["1758-3497"],"issn":["1758-3489"]},"article_type":"original","date_updated":"2024-10-09T21:02:31Z","oa":1,"main_file_link":[{"url":"https://rgu-repository.worktribe.com/output/1635939","open_access":"1"}],"date_created":"2022-06-12T22:01:45Z","issue":"1","volume":38,"publication":"Library and Information History"},{"external_id":{"pmid":["35713756"],"isi":["000812509800001"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"74","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","doi":"10.1007/s11538-022-01029-z","intvolume":"        84","_id":"11447","status":"public","quality_controlled":"1","author":[{"id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","last_name":"Saona Urmeneta","first_name":"Raimundo J","full_name":"Saona Urmeneta, Raimundo J"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov"},{"full_name":"Khudiakova, Kseniia","first_name":"Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465"}],"corr_author":"1","oa_version":"Published Version","ddc":["510","570"],"fulldoi":"https://doi.org/10.1007/s11538-022-01029-z","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"date_published":"2022-06-17T00:00:00Z","citation":{"chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022.","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>."},"title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","month":"06","day":"17","language":[{"iso":"eng"}],"project":[{"grant_number":"771209","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales"},{"_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","name":"Evolutionary analysis of gene regulation","grant_number":"I05127"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"file_date_updated":"2022-06-20T07:51:32Z","file":[{"relation":"main_file","creator":"dernst","checksum":"05a1fe7d10914a00c2bca9b447993a65","content_type":"application/pdf","file_size":463025,"success":1,"access_level":"open_access","date_created":"2022-06-20T07:51:32Z","date_updated":"2022-06-20T07:51:32Z","file_name":"2022_BulletinMathBiology_Saona.pdf","file_id":"11455"}],"article_type":"original","date_updated":"2026-06-12T12:43:34Z","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}],"record":[{"relation":"dissertation_contains","status":"public","id":"21918"}]},"type":"journal_article","publisher":"Springer Nature","pmid":1,"publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"isi":1,"date_created":"2022-06-17T16:16:15Z","issue":"8","ec_funded":1,"volume":84,"publication":"Bulletin of Mathematical Biology","has_accepted_license":"1","acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","oa":1},{"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-15T00:00:00Z","abstract":[{"lang":"eng","text":"Mutations are acquired frequently, such that each cell's genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide variants (SNVs). We simultaneously inferred cell lineage and marked developmental time points based on X chromosome inactivation and the total number of LOH events while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared with experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans."}],"title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","citation":{"ista":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. 13(6), 438–453.e5.","mla":"Anderson, Donovan J., et al. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>, vol. 13, no. 6, Elsevier, 2022, p. 438–453.e5, doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>.","ama":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. 2022;13(6):438-453.e5. doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>","chicago":"Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>.","ieee":"D. J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, and M. S. Horwitz, “Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development,” <i>Cell Systems</i>, vol. 13, no. 6. Elsevier, p. 438–453.e5, 2022.","apa":"Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>","short":"D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, Cell Systems 13 (2022) 438–453.e5."},"month":"06","language":[{"iso":"eng"}],"day":"15","project":[{"grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002"}],"publication_status":"published","department":[{"_id":"SiHi"}],"external_id":{"pmid":["35452605"],"isi":["000814124400002"]},"article_processing_charge":"No","scopus_import":"1","intvolume":"        13","doi":"10.1016/j.cels.2022.03.006","_id":"11449","status":"public","author":[{"last_name":"Anderson","first_name":"Donovan J.","full_name":"Anderson, Donovan J."},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mckenna","full_name":"Mckenna, Aaron","first_name":"Aaron"},{"full_name":"Shendure, Jay","first_name":"Jay","last_name":"Shendure"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"full_name":"Horwitz, Marshall S.","first_name":"Marshall S.","last_name":"Horwitz"}],"quality_controlled":"1","oa_version":"Published Version","ddc":["570"],"fulldoi":"https://doi.org/10.1016/j.cels.2022.03.006","date_created":"2022-06-19T22:01:57Z","issue":"6","ec_funded":1,"volume":13,"publication":"Cell Systems","acknowledgement":"D.J.A. thanks Wayne K. Potts, Alan R. Rogers, Kristen Hawkes, Ryk Ward, and Jon Seger for inspiring a young undergraduate to apply evolutionary theory to intraorganism development. Supported by the Paul G. Allen Frontiers Group (University of Washington); NIH R00HG010152 (Dartmouth); and NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program 725780 LinPro to S.H.","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cels.2022.03.006"}],"article_type":"original","date_updated":"2026-06-18T17:15:22Z","page":"438-453.e5","type":"journal_article","publisher":"Elsevier","pmid":1,"publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"isi":1},{"day":"04","language":[{"iso":"eng"}],"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z"},{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"editor":[{"last_name":"Yamamoto","first_name":"Daisuke","full_name":"Yamamoto, Daisuke"}],"publication_status":"published","department":[{"_id":"MaDe"}],"series_title":"NM","year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-04T00:00:00Z","abstract":[{"lang":"eng","text":"The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal."}],"citation":{"ista":"Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.","mla":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>.","apa":"Artan, M., &#38; de Bono, M. (2022). Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In D. Yamamoto (Ed.), <i>Behavioral Neurogenetics</i> (Vol. 181, pp. 277–294). New York: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>","ieee":"M. Artan and M. de Bono, “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling,” in <i>Behavioral Neurogenetics</i>, vol. 181, D. Yamamoto, Ed. New York: Springer Nature, 2022, pp. 277–294.","short":"M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer Nature, New York, 2022, pp. 277–294.","ama":"Artan M, de Bono M. Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Yamamoto D, ed. <i>Behavioral Neurogenetics</i>. Vol 181. NM. New York: Springer Nature; 2022:277-294. doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>","chicago":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” In <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>."},"title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","month":"06","intvolume":"       181","doi":"10.1007/978-1-0716-2321-3_15","quality_controlled":"1","_id":"11456","status":"public","author":[{"first_name":"Murat","full_name":"Artan, Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","orcid":"0000-0001-8945-6992","last_name":"Artan"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","last_name":"de Bono","first_name":"Mario","full_name":"de Bono, Mario"}],"corr_author":"1","oa_version":"None","fulldoi":"https://doi.org/10.1007/978-1-0716-2321-3_15","article_processing_charge":"No","scopus_import":"1","date_created":"2022-06-20T08:10:34Z","ec_funded":1,"alternative_title":["Neuromethods"],"volume":181,"publication":"Behavioral Neurogenetics","acknowledgement":"We thank de Bono lab members for the helpful comments on the manuscript. The biotin-auxotrophic E. coli strain MG1655bioB:kan was a generous gift from J. Cronan (University of Illinois) and was kindly sent to us by Jessica Feldman and Ariana Sanchez (Stanford University). dg398 pEntryslot2_mNeongreen::3XFLAG::stop and dg397 pEntryslot3_mNeongreen::3XFLAG::stop::unc-54 3’UTR entry vector were kindly sent by Dr. Dominique Glauser (University of Fribourg). This work was supported by an Advanced ERC Grant (269058 ACMO) and a Wellcome Investigator Award (209504/Z/17/Z) to MdB and an ISTplus Fellowship to MA (Marie Sklodowska-Curie agreement No 754411).","page":"277-294","type":"book_chapter","publisher":"Springer Nature","publication_identifier":{"issn":["0893-2336"],"eissn":["1940-6045"],"isbn":["9781071623206"],"eisbn":["9781071623213"]},"place":"New York","date_updated":"2025-04-14T07:43:58Z"},{"publisher":"Association for Computing Machinery","type":"conference","page":"442-457","publication_identifier":{"isbn":["9781450392655"]},"isi":1,"file":[{"date_updated":"2022-06-27T07:38:21Z","file_id":"11466","file_name":"2022_PLDI_Zikelic.pdf","date_created":"2022-06-27T07:38:21Z","file_size":318697,"content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","creator":"dernst","checksum":"7eb915a2ca5b5ce4729321f33b2e16e1"}],"date_updated":"2025-04-14T07:52:47Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa":1,"date_created":"2022-06-21T09:26:15Z","acknowledgement":"We thank Shaun Willows, Thomas Lugnet, and the Living Room Application Vending team for suggesting threshold\r\nbounds as a developer-friendly way to interact with a differential cost analyzer, and we thank Jim Christy, Daniel\r\nSchoepe, and the Prime Video Automated Reasoning team for their support and helpful suggestions throughout the\r\nproject. We also thank Michael Emmi for feedback on an earlier version of this paper. And finally, we thank the anonymous reviewers for their useful feedback and Aws Albarghouthi for shepherding the final version of the paper. Ðorđe Žikelić was also partially supported by ERC CoG 863818 (FoRM-SMArt).","has_accepted_license":"1","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","ec_funded":1,"oa_version":"Published Version","corr_author":"1","quality_controlled":"1","_id":"11459","status":"public","author":[{"full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chang","first_name":"Bor-Yuh Evan","full_name":"Chang, Bor-Yuh Evan"},{"full_name":"Bolignano, Pauline","first_name":"Pauline","last_name":"Bolignano"},{"last_name":"Raimondi","first_name":"Franco","full_name":"Raimondi, Franco"}],"doi":"10.1145/3519939.3523435","fulldoi":"https://doi.org/10.1145/3519939.3523435","ddc":["000"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"external_id":{"arxiv":["2204.00870"],"isi":["000850435600030"]},"conference":{"location":"San Diego, CA, United States","end_date":"2022-06-17","start_date":"2022-06-13","name":"PLDI: Programming Language Design and Implementation"},"scopus_import":"1","arxiv":1,"article_processing_charge":"No","project":[{"call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"language":[{"iso":"eng"}],"day":"09","file_date_updated":"2022-06-27T07:38:21Z","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication_status":"published","year":"2022","citation":{"ama":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. Differential cost analysis with simultaneous potentials and anti-potentials. In: <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2022:442-457. doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>.","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>","short":"D. Zikelic, B.-Y.E. Chang, P. Bolignano, F. Raimondi, in:, Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2022, pp. 442–457.","ieee":"D. Zikelic, B.-Y. E. Chang, P. Bolignano, and F. Raimondi, “Differential cost analysis with simultaneous potentials and anti-potentials,” in <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, San Diego, CA, United States, 2022, pp. 442–457.","ista":"Zikelic D, Chang B-YE, Bolignano P, Raimondi F. 2022. Differential cost analysis with simultaneous potentials and anti-potentials. Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 442–457.","mla":"Zikelic, Dorde, et al. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2022, pp. 442–57, doi:<a href=\"https://doi.org/10.1145/3519939.3523435\">10.1145/3519939.3523435</a>."},"title":"Differential cost analysis with simultaneous potentials and anti-potentials","month":"06","abstract":[{"lang":"eng","text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples."}],"date_published":"2022-06-09T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"volume":13,"has_accepted_license":"1","acknowledgement":"This study was funded by NIMH R21MH115347 to KSZ. KSZ is further supported by Shriners Hospitals for Children.\r\nWe would like to thank Angelo Harlan de Crescenzo for early contributions to this project.","publication":"Molecular Autism","date_created":"2022-06-23T14:28:55Z","oa":1,"date_updated":"2025-06-11T13:34:57Z","file":[{"date_created":"2022-06-24T08:22:59Z","date_updated":"2022-06-24T08:22:59Z","file_name":"2022_MolecularAutism_Schaaf.pdf","file_id":"11461","relation":"main_file","creator":"dernst","checksum":"525d2618e855139089bbfc3e3d49d1b2","file_size":7552298,"content_type":"application/pdf","success":1,"access_level":"open_access"}],"article_type":"original","pmid":1,"publication_identifier":{"issn":["2040-2392"]},"isi":1,"related_material":{"link":[{"url":"https://doi.org/10.1186/s13229-023-00539-4","relation":"erratum"}]},"keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"publisher":"Springer Nature","type":"journal_article","abstract":[{"lang":"eng","text":"Background: Proper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology.\r\nMethods: Here, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild-type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults: We revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages.\r\nLimitations: While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients or some of the other neurodevelopmental conditions associated with WDFY3 mutation.\r\nConclusions: Our genetic approach revealed several cell autonomous requirements of WDFY3 in neuronal development that could underlie the pathogenic mechanisms of WDFY3-related neurodevelopmental conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for WDFY3 in regulating neuronal function and interconnectivity in postnatal life."}],"date_published":"2022-06-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","apa":"Schaaf, Z. A., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. S. (2022). WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022."},"month":"06","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","year":"2022","publication_status":"published","department":[{"_id":"SiHi"}],"file_date_updated":"2022-06-24T08:22:59Z","language":[{"iso":"eng"}],"day":"22","article_processing_charge":"No","scopus_import":"1","article_number":"27","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"isi":["000814641400001"],"pmid":["35733184"]},"ddc":["570"],"fulldoi":"https://doi.org/10.1186/s13229-022-00508-3","_id":"11460","quality_controlled":"1","status":"public","author":[{"last_name":"Schaaf","first_name":"Zachary A.","full_name":"Schaaf, Zachary A."},{"last_name":"Tat","full_name":"Tat, Lyvin","first_name":"Lyvin"},{"last_name":"Cannizzaro","full_name":"Cannizzaro, Noemi","first_name":"Noemi"},{"last_name":"Green","full_name":"Green, Ralph","first_name":"Ralph"},{"last_name":"Rülicke","full_name":"Rülicke, Thomas","first_name":"Thomas"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"first_name":"Konstantinos S.","full_name":"Zarbalis, Konstantinos S.","last_name":"Zarbalis"}],"doi":"10.1186/s13229-022-00508-3","intvolume":"        13","oa_version":"Published Version"},{"article_type":"original","date_updated":"2023-10-10T07:15:02Z","page":"5093-5103","publisher":"Springer Nature","type":"journal_article","pmid":1,"isi":1,"publication_identifier":{"eissn":["1432-0614"],"issn":["0175-7598"]},"date_created":"2022-06-26T22:01:34Z","volume":106,"acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","publication":"Applied Microbiology and Biotechnology","external_id":{"isi":["000813677500001"],"pmid":["35723693"]},"article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Dormeshkin, Dmitri","first_name":"Dmitri","last_name":"Dormeshkin"},{"first_name":"Michail","full_name":"Shapira, Michail","last_name":"Shapira"},{"last_name":"Karputs","first_name":"Alena","full_name":"Karputs, Alena"},{"last_name":"Kavaleuski","id":"62304f89-eb97-11eb-a6c2-8903dd183976","orcid":"0000-0003-2091-526X","full_name":"Kavaleuski, Anton","first_name":"Anton"},{"last_name":"Kuzminski","first_name":"Ivan","full_name":"Kuzminski, Ivan"},{"last_name":"Stepanova","full_name":"Stepanova, Elena","first_name":"Elena"},{"full_name":"Gilep, Andrei","first_name":"Andrei","last_name":"Gilep"}],"_id":"11462","quality_controlled":"1","status":"public","intvolume":"       106","doi":"10.1007/s00253-022-12022-w","oa_version":"None","fulldoi":"https://doi.org/10.1007/s00253-022-12022-w","year":"2022","date_published":"2022-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>","chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>.","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>","ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022.","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103."},"month":"08","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","day":"01","language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"LeSa"}]},{"corr_author":"1","oa_version":"Preprint","intvolume":"       105","doi":"10.1103/physrevb.105.224208","author":[{"last_name":"Brighi","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","full_name":"Brighi, Pietro","first_name":"Pietro"},{"first_name":"Alexios","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis"},{"last_name":"Kirova","id":"4aeda2ae-f847-11ec-98e0-c4a66fe174d4","full_name":"Kirova, Kristina","first_name":"Kristina"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","last_name":"Serbyn"}],"_id":"11469","quality_controlled":"1","status":"public","fulldoi":"https://doi.org/10.1103/physrevb.105.224208","external_id":{"arxiv":["2111.08603"],"isi":["000823050000001"]},"article_number":"224208","scopus_import":"1","article_processing_charge":"No","arxiv":1,"day":"27","language":[{"iso":"eng"}],"project":[{"grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"department":[{"_id":"MaSe"}],"publication_status":"published","year":"2022","citation":{"ista":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. 2022. Localization of a mobile impurity interacting with an Anderson insulator. Physical Review B. 105(22), 224208.","mla":"Brighi, Pietro, et al. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, 224208, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>.","ama":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>","chicago":"Brighi, Pietro, Alexios Michailidis, Kristina Kirova, Dmitry A. Abanin, and Maksym Serbyn. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>.","ieee":"P. Brighi, A. Michailidis, K. Kirova, D. A. Abanin, and M. Serbyn, “Localization of a mobile impurity interacting with an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","short":"P. Brighi, A. Michailidis, K. Kirova, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022).","apa":"Brighi, P., Michailidis, A., Kirova, K., Abanin, D. A., &#38; Serbyn, M. (2022). Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>"},"month":"06","title":"Localization of a mobile impurity interacting with an Anderson insulator","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-27T00:00:00Z","abstract":[{"text":"Thermalizing and localized many-body quantum systems present two distinct dynamical phases of matter. Recently the fate of a localized system coupled to a thermalizing system viewed as a quantum bath received significant theoretical and experimental attention. In this work, we study a mobile impurity, representing a small quantum bath, that interacts locally with an Anderson insulator with a finite density of localized particles. Using static Hartree approximation to obtain an effective disorder strength, we formulate an analytic criterion for the perturbative stability of the localization. Next, we use an approximate dynamical Hartree method and the quasi-exact time-evolved block decimation (TEBD) algorithm to study the dynamics of the system. We find that the dynamical Hartree approach which completely ignores entanglement between the impurity and localized particles predicts the delocalization of the system. In contrast, the full numerical simulation of the unitary dynamics with TEBD suggests the stability of localization on numerically accessible timescales. Finally, using an extension of the density matrix renormalization group algorithm to excited states (DMRG-X), we approximate the highly excited eigenstates of the system. We find that the impurity remains localized in the eigenstates and entanglement is enhanced in a finite region around the position of the impurity, confirming the dynamical predictions. Dynamics and the DMRG-X results provide compelling evidence for the stability of localization.","lang":"eng"}],"type":"journal_article","publisher":"American Physical Society","related_material":{"record":[{"relation":"dissertation_contains","id":"12732","status":"public"}]},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"isi":1,"article_type":"original","date_updated":"2026-04-07T13:26:31Z","oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2111.08603","open_access":"1"}],"date_created":"2022-06-29T20:19:51Z","issue":"22","publication":"Physical Review B","acknowledgement":"We thank M. Ljubotina for insightful discussions. P. B., A. M. and M. S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D. A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","ec_funded":1,"volume":105},{"year":"2022","month":"06","citation":{"ieee":"P. Brighi, A. A. Michailidis, D. A. Abanin, and M. Serbyn, “Propagation of many-body localization in an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","short":"P. Brighi, A.A. Michailidis, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022).","apa":"Brighi, P., Michailidis, A. A., Abanin, D. A., &#38; Serbyn, M. (2022). Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>","chicago":"Brighi, Pietro, Alexios A. Michailidis, Dmitry A. Abanin, and Maksym Serbyn. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>.","ama":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>","mla":"Brighi, Pietro, et al. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, L220203, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>.","ista":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. 2022. Propagation of many-body localization in an Anderson insulator. Physical Review B. 105(22), L220203."},"title":"Propagation of many-body localization in an Anderson insulator","abstract":[{"text":"Many-body localization (MBL) is an example of a dynamical phase of matter that avoids thermalization. While the MBL phase is robust to weak local perturbations, the fate of an MBL system coupled to a thermalizing quantum system that represents a “heat bath” is an open question that is actively investigated theoretically and experimentally. In this work, we consider the stability of an Anderson insulator with a finite density of particles interacting with a single mobile impurity—a small quantum bath. We give perturbative arguments that support the stability of localization in the strong interaction regime. Large-scale tensor network simulations of dynamics are employed to corroborate the presence of the localized phase and give quantitative predictions in the thermodynamic limit. We develop a phenomenological description of the dynamics in the strong interaction regime, and we demonstrate that the impurity effectively turns the Anderson insulator into an MBL phase, giving rise to nontrivial entanglement dynamics well captured by our phenomenology.","lang":"eng"}],"date_published":"2022-06-27T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"grant_number":"850899","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"language":[{"iso":"eng"}],"day":"27","department":[{"_id":"MaSe"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_status":"published","article_number":"L220203","external_id":{"arxiv":["2109.07332"],"isi":["000823050000012"]},"scopus_import":"1","arxiv":1,"article_processing_charge":"No","oa_version":"Preprint","corr_author":"1","_id":"11470","status":"public","quality_controlled":"1","author":[{"first_name":"Pietro","full_name":"Brighi, Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7969-2729","last_name":"Brighi"},{"full_name":"Michailidis, Alexios A.","first_name":"Alexios A.","last_name":"Michailidis"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"doi":"10.1103/physrevb.105.l220203","intvolume":"       105","fulldoi":"https://doi.org/10.1103/physrevb.105.l220203","issue":"22","date_created":"2022-06-29T20:20:47Z","acknowledgement":"We acknowledge useful discussions with M. Ljubotina. P. B., A. M., and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","publication":"Physical Review B","volume":105,"ec_funded":1,"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.07332"}],"article_type":"original","date_updated":"2026-04-07T13:26:31Z","publisher":"American Physical Society","type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12732"}]},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"isi":1},{"date_created":"2022-06-30T12:15:03Z","ec_funded":1,"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","oa":1,"file":[{"file_name":"thes1_no_isbn_2_1b.pdf","file_id":"11486","date_updated":"2022-07-05T08:12:56Z","date_created":"2022-07-05T08:12:56Z","access_level":"open_access","success":1,"content_type":"application/pdf","file_size":1830973,"checksum":"7970714a20a6052f75fb27a6c3e9976e","creator":"kmysliwy","relation":"main_file"},{"checksum":"647a2011fdf56277096c9350fefe1097","creator":"kmysliwy","relation":"source_file","access_level":"closed","file_size":5831060,"content_type":"application/zip","date_created":"2022-07-05T08:15:52Z","file_id":"11487","file_name":"thes_source.zip","date_updated":"2022-07-05T08:17:12Z"}],"date_updated":"2026-04-07T14:14:52Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"10564","status":"public"},{"id":"8705","status":"public","relation":"part_of_dissertation"}]},"page":"138","type":"dissertation","publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"year":"2022","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2022-07-01T00:00:00Z","abstract":[{"lang":"eng","text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n"}],"citation":{"ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","apa":"Mysliwy, K. (2022). <i>Polarons in Bose gases and polar crystals: Some rigorous energy estimates</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>.","mla":"Mysliwy, Krzysztof. <i>Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>.","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria."},"title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","month":"07","day":"01","language":[{"iso":"eng"}],"project":[{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","acknowledged_ssus":[{"_id":"SSU"}],"file_date_updated":"2022-07-05T08:17:12Z","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"article_processing_charge":"No","OA_place":"publisher","doi":"10.15479/at:ista:11473","status":"public","_id":"11473","author":[{"last_name":"Mysliwy","id":"316457FC-F248-11E8-B48F-1D18A9856A87","full_name":"Mysliwy, Krzysztof","first_name":"Krzysztof"}],"corr_author":"1","oa_version":"Published Version","supervisor":[{"first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"ddc":["515","539"],"fulldoi":"https://doi.org/10.15479/at:ista:11473"},{"publisher":"EDP Sciences","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations"],"publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"article_type":"original","date_updated":"2022-07-19T09:33:24Z","extern":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2201.07257"}],"date_created":"2022-07-05T14:27:26Z","acknowledgement":"We thank the anonymous referee for constructive comments and suggestions. We would like to express our gratitude to Edmund Christian Herenz, Leindert Boogard, Miroslava Dessauges, Moupiya Maji, Valentin Mauerhofer, Charlotte Paola Simmonds Wagemann, Masami Ouchi, Kazuhiro Shimasaku, Akio Inoue, and Rieko Momose for giving insightful comments and suggestions. H.K. is grateful to Liam McCarney for useful suggestions on English writing through the UniGE’s Tandems linguistiques. H.K. acknowledges support from Swiss Government Excellence Scholarships and Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship. H.K., F.L., and A.V. are supported by the SNF grant PP00P2 176808. A.V. and T.G. are supported by the ERC Starting Grant 757258“TRIPLE”. This work was supported by the Programme National Cosmology et Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, co-funded by CEA and CNES. This work is based on observations taken by VLT, which is operated by European Southern Observatory. This research made use of Astropy, which is a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018), and other software and packages: MARZ, MPDAF (Piqueras et al. 2019), PHOTUTILS, Numpy (Harris et al. 2020), Scipy (Virtanen et al. 2020), and matplotlib (Hunter 2007).","publication":"Astronomy & Astrophysics","volume":660,"oa_version":"Published Version","quality_controlled":"1","_id":"11488","status":"public","author":[{"full_name":"Kusakabe, Haruka","first_name":"Haruka","last_name":"Kusakabe"},{"full_name":"Verhamme, Anne","first_name":"Anne","last_name":"Verhamme"},{"last_name":"Blaizot","first_name":"Jérémy","full_name":"Blaizot, Jérémy"},{"full_name":"Garel, Thibault","first_name":"Thibault","last_name":"Garel"},{"first_name":"Lutz","full_name":"Wisotzki, Lutz","last_name":"Wisotzki"},{"first_name":"Floriane","full_name":"Leclercq, Floriane","last_name":"Leclercq"},{"full_name":"Bacon, Roland","first_name":"Roland","last_name":"Bacon"},{"first_name":"Joop","full_name":"Schaye, Joop","last_name":"Schaye"},{"full_name":"Gallego, Sofia G.","first_name":"Sofia G.","last_name":"Gallego"},{"first_name":"Josephine","full_name":"Kerutt, Josephine","last_name":"Kerutt"},{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"last_name":"Maseda","full_name":"Maseda, Michael","first_name":"Michael"},{"full_name":"Nanayakkara, Themiya","first_name":"Themiya","last_name":"Nanayakkara"},{"first_name":"Roser","full_name":"Pelló, Roser","last_name":"Pelló"},{"first_name":"Johan","full_name":"Richard, Johan","last_name":"Richard"},{"last_name":"Tresse","full_name":"Tresse, Laurence","first_name":"Laurence"},{"last_name":"Urrutia","full_name":"Urrutia, Tanya","first_name":"Tanya"},{"last_name":"Vitte","first_name":"Eloïse","full_name":"Vitte, Eloïse"}],"intvolume":"       660","doi":"10.1051/0004-6361/202142302","fulldoi":"https://doi.org/10.1051/0004-6361/202142302","article_number":"A44","external_id":{"arxiv":["2201.07257"]},"scopus_import":"1","arxiv":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"day":"07","publication_status":"published","year":"2022","title":"The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4","month":"04","citation":{"ieee":"H. Kusakabe <i>et al.</i>, “The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4,” <i>Astronomy &#38; Astrophysics</i>, vol. 660. EDP Sciences, 2022.","short":"H. Kusakabe, A. Verhamme, J. Blaizot, T. Garel, L. Wisotzki, F. Leclercq, R. Bacon, J. Schaye, S.G. Gallego, J. Kerutt, J.J. Matthee, M. Maseda, T. Nanayakkara, R. Pelló, J. Richard, L. Tresse, T. Urrutia, E. Vitte, Astronomy &#38; Astrophysics 660 (2022).","apa":"Kusakabe, H., Verhamme, A., Blaizot, J., Garel, T., Wisotzki, L., Leclercq, F., … Vitte, E. (2022). The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202142302\">https://doi.org/10.1051/0004-6361/202142302</a>","chicago":"Kusakabe, Haruka, Anne Verhamme, Jérémy Blaizot, Thibault Garel, Lutz Wisotzki, Floriane Leclercq, Roland Bacon, et al. “The MUSE EXtremely Deep Field: Individual Detections of Ly<i>α</i> Haloes around Rest-Frame UV-Selected Galaxies at <i>z</i> ≃ 2.9–4.4.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202142302\">https://doi.org/10.1051/0004-6361/202142302</a>.","ama":"Kusakabe H, Verhamme A, Blaizot J, et al. The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. <i>Astronomy &#38; Astrophysics</i>. 2022;660. doi:<a href=\"https://doi.org/10.1051/0004-6361/202142302\">10.1051/0004-6361/202142302</a>","ista":"Kusakabe H, Verhamme A, Blaizot J, Garel T, Wisotzki L, Leclercq F, Bacon R, Schaye J, Gallego SG, Kerutt J, Matthee JJ, Maseda M, Nanayakkara T, Pelló R, Richard J, Tresse L, Urrutia T, Vitte E. 2022. The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. Astronomy &#38; Astrophysics. 660, A44.","mla":"Kusakabe, Haruka, et al. “The MUSE EXtremely Deep Field: Individual Detections of Ly<i>α</i> Haloes around Rest-Frame UV-Selected Galaxies at <i>z</i> ≃ 2.9–4.4.” <i>Astronomy &#38; Astrophysics</i>, vol. 660, A44, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202142302\">10.1051/0004-6361/202142302</a>."},"abstract":[{"text":"Hydrogen Lyα haloes (LAHs) are commonly used as a tracer of the circumgalactic medium (CGM) at high redshifts. In this work, we aim to explore the existence of Lyα haloes around individual UV-selected galaxies, rather than around Lyα emitters (LAEs), at high redshifts. Our sample was continuum-selected with F775W ≤ 27.5, and spectroscopic redshifts were assigned or constrained for all the sources thanks to the deepest (100- to 140-h) existing Very Large Telescope (VLT)/Multi-Unit Spectroscopic Explorer (MUSE) data with adaptive optics. The final sample includes 21 galaxies that are purely F775W-magnitude selected within the redshift range z ≈ 2.9 − 4.4 and within a UV magnitude range −20 ≤ M1500 ≤ −18, thus avoiding any bias toward LAEs. We tested whether galaxy’s Lyα emission is significantly more extended than the MUSE PSF-convolved continuum component. We find 17 LAHs and four non-LAHs. We report the first individual detections of extended Lyα emission around non-LAEs. The Lyα halo fraction is thus as high as 81.0−11.2+10.3%, which is close to that for LAEs at z = 3 − 6 in the literature. This implies that UV-selected galaxies generally have a large amount of hydrogen in their CGM. We derived the mean surface brightness (SB) profile for our LAHs with cosmic dimming corrections and find that Lyα emission extends to 5.4 arcsec (≃40 physical kpc at the midpoint redshift z = 3.6) above the typical 1σ SB limit. The incidence rate of surrounding gas detected in Lyα per one-dimensional line of sight per unit redshift, dn/dz, is estimated to be 0.76−0.09+0.09 for galaxies with M1500 ≤ −18 mag at z ≃ 3.7. Assuming that Lyα emission and absorption arise in the same gas, this suggests, based on abundance matching, that LAHs trace the same gas as damped Lyα systems (DLAs) and sub-DLAs.","lang":"eng"}],"date_published":"2022-04-07T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"corr_author":"1","oa_version":"Published Version","intvolume":"        23","doi":"10.3390/ijms23116352","status":"public","_id":"11489","author":[{"first_name":"V","full_name":"Bilanovičová, V","last_name":"Bilanovičová"},{"first_name":"N","full_name":"Rýdza, N","last_name":"Rýdza"},{"first_name":"L","full_name":"Koczka, L","last_name":"Koczka"},{"last_name":"Hess","full_name":"Hess, M","first_name":"M"},{"full_name":"Feraru, E","first_name":"E","last_name":"Feraru"},{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"T","full_name":"Nodzyński, T","last_name":"Nodzyński"}],"quality_controlled":"1","fulldoi":"https://doi.org/10.3390/ijms23116352","ddc":["570"],"external_id":{"isi":["000808733300001"],"pmid":["35683031"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":"1","article_processing_charge":"Yes","day":"06","language":[{"iso":"eng"}],"project":[{"_id":"262EF96E-B435-11E9-9278-68D0E5697425","name":"RNA-directed DNA methylation in plant development","grant_number":"P29988","call_identifier":"FWF"}],"file_date_updated":"2022-07-06T07:36:59Z","department":[{"_id":"JiFr"}],"publication_status":"published","year":"2022","title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","month":"06","citation":{"short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>","chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>.","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.","lang":"eng"}],"date_published":"2022-06-06T00:00:00Z","type":"journal_article","publisher":"MDPI","page":"6352","isi":1,"publication_identifier":{"issn":["1422-0067"]},"pmid":1,"article_type":"original","file":[{"checksum":"e997a57a928ec9d51fad8ce824a05935","creator":"cchlebak","relation":"main_file","access_level":"open_access","success":1,"file_size":2324542,"content_type":"application/pdf","date_created":"2022-07-06T07:36:59Z","file_id":"11492","file_name":"2022_IntJMolSci_Bilanovicova.pdf","date_updated":"2022-07-06T07:36:59Z"}],"date_updated":"2025-04-15T08:12:07Z","oa":1,"date_created":"2022-07-05T15:14:34Z","issue":"11","publication":"International Journal of Molecular Sciences","has_accepted_license":"1","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","volume":23}]