[{"status":"public","publication":"Journal of Machine Learning Research","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"date_published":"2022-04-01T00:00:00Z","acknowledgement":"We would like to thank Mert Pilanci for several exploratory discussions in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765 Research Center for Informatics.\r\n","related_material":{"link":[{"url":"https://www.jmlr.org/papers/v23/21-1365.html","relation":"other"}]},"external_id":{"arxiv":["2111.02278"]},"year":"2022","ddc":["000"],"page":"1-55","quality_controlled":"1","publisher":"Journal of Machine Learning Research","article_processing_charge":"No","type":"journal_article","_id":"11420","date_updated":"2024-09-10T13:03:17Z","language":[{"iso":"eng"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise linear solutions for wide ReLU networks,” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55.","ama":"Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. 2022;23(130):1-55.","apa":"Shevchenko, A., Kungurtsev, V., &#38; Mondelli, M. (2022). Mean-field analysis of piecewise linear solutions for wide ReLU networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","mla":"Shevchenko, Aleksandr, et al. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>, vol. 23, no. 130, Journal of Machine Learning Research, 2022, pp. 1–55.","ista":"Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 23(130), 1–55.","chicago":"Shevchenko, Aleksandr, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2022."},"issue":"130","arxiv":1,"month":"04","file":[{"file_size":1521701,"date_created":"2022-05-30T08:22:55Z","creator":"cchlebak","date_updated":"2022-05-30T08:22:55Z","file_id":"11422","success":1,"file_name":"21-1365.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"d4ff5d1affb34848b5c5e4002483fc62"}],"department":[{"_id":"MaMo"},{"_id":"DaAl"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory.","lang":"eng"}],"intvolume":"        23","has_accepted_license":"1","file_date_updated":"2022-05-30T08:22:55Z","publication_identifier":{"eissn":["1533-7928"],"issn":["1532-4435"]},"publication_status":"published","title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","oa_version":"Published Version","day":"01","scopus_import":"1","author":[{"first_name":"Aleksandr","last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","full_name":"Shevchenko, Aleksandr"},{"full_name":"Kungurtsev, Vyacheslav","last_name":"Kungurtsev","first_name":"Vyacheslav"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","first_name":"Marco"}],"date_created":"2022-05-29T22:01:54Z","article_type":"original","volume":23},{"year":"2022","project":[{"grant_number":"M03073","name":"Learning and triangulating manifolds via collapses","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"},{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"status":"public","publication":"38th International Symposium on Computational Geometry","conference":{"location":"Berlin, Germany","end_date":"2022-06-10","start_date":"2022-06-07","name":"SoCG: Symposium on Computational Geometry"},"date_published":"2022-06-01T00:00:00Z","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,"editor":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"first_name":"Michael","full_name":"Kerber, Michael","last_name":"Kerber"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","doi":"10.4230/LIPIcs.SoCG.2022.66","article_processing_charge":"No","type":"conference","series_title":"LIPIcs","date_updated":"2023-02-21T09:50:52Z","_id":"11428","ddc":["510"],"page":"66:1-66:9","quality_controlled":"1","month":"06","file":[{"checksum":"b25ce40fade4ebc0bcaae176db4f5f1f","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2022_LIPICs_Chambers.pdf","success":1,"file_id":"11437","creator":"dernst","date_updated":"2022-06-07T07:58:30Z","file_size":17580705,"date_created":"2022-06-07T07:58:30Z"}],"department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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>.","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>","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.","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>.","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.","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.","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>"},"oa_version":"Published Version","title":"A cautionary tale: Burning the medial axis is unstable","author":[{"last_name":"Chambers","full_name":"Chambers, Erin","first_name":"Erin"},{"first_name":"Christopher D","full_name":"Fillmore, Christopher D","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","last_name":"Fillmore"},{"orcid":"0000-0002-6862-208X","first_name":"Elizabeth R","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87","full_name":"Stephenson, Elizabeth R"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","last_name":"Wintraecken","orcid":"0000-0002-7472-2220","first_name":"Mathijs"}],"day":"01","scopus_import":"1","date_created":"2022-06-01T14:18:04Z","volume":224,"abstract":[{"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.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       224","has_accepted_license":"1","publication_status":"published","publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-95977-227-3"]},"file_date_updated":"2022-06-07T07:58:30Z"},{"abstract":[{"lang":"eng","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."}],"intvolume":"     13238","page":"153","publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"eisbn":["9783031062452"],"isbn":["9783031062445"],"issn":["0302-9743"]},"quality_controlled":"1","publisher":"Springer Nature","oa_version":"None","title":"Web and Wireless Geographical Information Systems","editor":[{"id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","full_name":"Karimipour, Farid","last_name":"Karimipour","first_name":"Farid","orcid":"0000-0001-6746-4174"},{"first_name":"Sabine","full_name":"Storandt, Sabine","last_name":"Storandt"}],"day":"01","article_processing_charge":"No","alternative_title":["LNCS"],"doi":"10.1007/978-3-031-06245-2","date_created":"2022-06-02T05:40:53Z","type":"book_editor","edition":"1","_id":"11429","volume":13238,"date_updated":"2022-06-02T05:56:22Z","status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-05-01T00:00:00Z","citation":{"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>","short":"F. Karimipour, S. Storandt, eds., Web and Wireless Geographical Information Systems, 1st ed., Springer Nature, Cham, 2022.","ieee":"F. Karimipour and S. Storandt, Eds., <i>Web and Wireless Geographical Information Systems</i>, 1st ed., vol. 13238. Cham: Springer Nature, 2022.","ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p.","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>.","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>.","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>"},"place":"Cham","month":"05","year":"2022","department":[{"_id":"HeEd"}]},{"date_published":"2022-05-01T00:00:00Z","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.","ec_funded":1,"project":[{"call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"Computer Graphics Forum","external_id":{"isi":["000802723900027"]},"isi":1,"year":"2022","quality_controlled":"1","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03641349/","open_access":"1"}],"page":"343-353","type":"journal_article","date_updated":"2023-08-02T06:44:05Z","_id":"11432","publisher":"Wiley","doi":"10.1111/cgf.14478","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"2","citation":{"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.","short":"C. Schreck, C. Wojtan, Computer Graphics Forum 41 (2022) 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>","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>","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.","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>."},"language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"ChWo"}],"month":"05","publication_status":"published","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"abstract":[{"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.","lang":"eng"}],"intvolume":"        41","acknowledged_ssus":[{"_id":"ScienComp"}],"article_type":"original","date_created":"2022-06-05T22:01:49Z","volume":41,"title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","oa_version":"Submitted Version","author":[{"first_name":"Camille","full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546"}],"day":"01","scopus_import":"1"},{"_id":"11435","date_updated":"2023-10-18T06:58:03Z","type":"journal_article","article_processing_charge":"No","doi":"10.1137/21M1403308","publisher":"Society for Industrial and Applied Mathematics","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2103.04122"}],"quality_controlled":"1","page":"951-957","isi":1,"year":"2022","external_id":{"isi":["000793158200002"],"arxiv":["2103.04122"]},"date_published":"2022-04-11T00:00:00Z","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","status":"public","volume":36,"date_created":"2022-06-05T22:01:50Z","article_type":"original","day":"11","scopus_import":"1","author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","first_name":"Grigory"},{"first_name":"Marton","full_name":"Naszodi, Marton","last_name":"Naszodi"}],"oa_version":"Preprint","title":"A quantitative Helly-type theorem: Containment in a homothet","publication_status":"published","publication_identifier":{"issn":["0895-4801"]},"intvolume":"        36","abstract":[{"lang":"eng","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 $Q \\subset - 8d^3 Q^{\\prime \\prime}.$"}],"department":[{"_id":"UlWa"}],"arxiv":1,"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.","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>.","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>","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>","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."},"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["2331-7019"]},"publication_status":"published","abstract":[{"text":"Lasers with well-controlled relative frequencies are indispensable for many applications in science and technology. We present a frequency-offset locking method for lasers based on beat-frequency discrimination utilizing hybrid electronic LC filters. The method is specifically designed for decoupling the tightness of the lock from the broadness of its capture range. The presented demonstration locks two free-running diode lasers at 780 nm with a 5.5-GHz offset. It displays an offset frequency instability below 55 Hz for time scales in excess of 1000 s and a minimum of 12 Hz at 10-s averaging. The performance is complemented with a 190-MHz lock-capture range, a tuning range of up to 1 GHz, and a frequency ramp agility of 200kHz/μs.","lang":"eng"}],"intvolume":"        17","volume":17,"article_type":"original","date_created":"2022-06-07T08:07:59Z","author":[{"id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Vyacheslav","last_name":"Li","first_name":"Vyacheslav"},{"first_name":"Fritz R","full_name":"Diorico, Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","last_name":"Diorico"},{"last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur","first_name":"Onur","orcid":"0000-0002-2031-204X"}],"day":"19","oa_version":"Preprint","title":"Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters","issue":"5","citation":{"apa":"Li, V., Diorico, F. R., &#38; Hosten, O. (2022). Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. <i>Physical Review Applied</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">https://doi.org/10.1103/physrevapplied.17.054031</a>","mla":"Li, Vyacheslav, et al. “Laser Frequency-Offset Locking at 10-Hz-Level Instability Using Hybrid Electronic Filters.” <i>Physical Review Applied</i>, vol. 17, no. 5, 054031, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">10.1103/physrevapplied.17.054031</a>.","ista":"Li V, Diorico FR, Hosten O. 2022. Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. Physical Review Applied. 17(5), 054031.","chicago":"Li, Vyacheslav, Fritz R Diorico, and Onur Hosten. “Laser Frequency-Offset Locking at 10-Hz-Level Instability Using Hybrid Electronic Filters.” <i>Physical Review Applied</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">https://doi.org/10.1103/physrevapplied.17.054031</a>.","ieee":"V. Li, F. R. Diorico, and O. Hosten, “Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters,” <i>Physical Review Applied</i>, vol. 17, no. 5. American Physical Society, 2022.","short":"V. Li, F.R. Diorico, O. Hosten, Physical Review Applied 17 (2022).","ama":"Li V, Diorico FR, Hosten O. Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters. <i>Physical Review Applied</i>. 2022;17(5). doi:<a href=\"https://doi.org/10.1103/physrevapplied.17.054031\">10.1103/physrevapplied.17.054031</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"GradSch"},{"_id":"OnHo"}],"article_number":"054031","arxiv":1,"month":"05","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2111.13194"}],"quality_controlled":"1","date_updated":"2023-08-03T07:18:34Z","_id":"11438","type":"journal_article","doi":"10.1103/physrevapplied.17.054031","article_processing_charge":"No","publisher":"American Physical Society","acknowledgement":"This work was supported by IST Austria. The authors thank Yueheng Shi for technical contributions.","date_published":"2022-05-19T00:00:00Z","status":"public","publication":"Physical Review Applied","keyword":["General Physics and Astronomy"],"year":"2022","isi":1,"external_id":{"isi":["000880670300001"],"arxiv":["2111.13194"]}},{"publication_identifier":{"isbn":["9783030955182"],"eisbn":["9783030955199"]},"publication_status":"published","intvolume":"        30","abstract":[{"lang":"eng","text":"To compute the persistent homology of a grayscale digital image one needs to build a simplicial or cubical complex from it. For cubical complexes, the two commonly used constructions (corresponding to direct and indirect digital adjacencies) can give different results for the same image. The two constructions are almost dual to each other, and we use this relationship to extend and modify the cubical complexes to become dual filtered cell complexes. We derive a general relationship between the persistent homology of two dual filtered cell complexes, and also establish how various modifications to a filtered complex change the persistence diagram. Applying these results to images, we derive a method to transform the persistence diagram computed using one type of cubical complex into a persistence diagram for the other construction. This means software for computing persistent homology from images can now be easily adapted to produce results for either of the two cubical complex constructions without additional low-level code implementation."}],"volume":30,"date_created":"2022-06-07T08:21:11Z","author":[{"last_name":"Bleile","full_name":"Bleile, Bea","first_name":"Bea"},{"first_name":"Adélie","full_name":"Garin, Adélie","last_name":"Garin"},{"last_name":"Heiss","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","full_name":"Heiss, Teresa","first_name":"Teresa","orcid":"0000-0002-1780-2689"},{"full_name":"Maggs, Kelly","last_name":"Maggs","first_name":"Kelly"},{"first_name":"Vanessa","full_name":"Robins, Vanessa","last_name":"Robins"}],"scopus_import":"1","day":"27","oa_version":"Preprint","title":"The persistent homology of dual digital image constructions","citation":{"ieee":"B. Bleile, A. Garin, T. Heiss, K. Maggs, and V. Robins, “The persistent homology of dual digital image constructions,” in <i>Research in Computational Topology 2</i>, 1st ed., vol. 30, E. Gasparovic, V. Robins, and K. Turner, Eds. Cham: Springer Nature, 2022, pp. 1–26.","short":"B. Bleile, A. Garin, T. Heiss, K. Maggs, V. Robins, in:, E. Gasparovic, V. Robins, K. Turner (Eds.), Research in Computational Topology 2, 1st ed., Springer Nature, Cham, 2022, pp. 1–26.","ama":"Bleile B, Garin A, Heiss T, Maggs K, Robins V. The persistent homology of dual digital image constructions. In: Gasparovic E, Robins V, Turner K, eds. <i>Research in Computational Topology 2</i>. Vol 30. 1st ed. AWMS. Cham: Springer Nature; 2022:1-26. doi:<a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">10.1007/978-3-030-95519-9_1</a>","apa":"Bleile, B., Garin, A., Heiss, T., Maggs, K., &#38; Robins, V. (2022). The persistent homology of dual digital image constructions. In E. Gasparovic, V. Robins, &#38; K. Turner (Eds.), <i>Research in Computational Topology 2</i> (1st ed., Vol. 30, pp. 1–26). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">https://doi.org/10.1007/978-3-030-95519-9_1</a>","mla":"Bleile, Bea, et al. “The Persistent Homology of Dual Digital Image Constructions.” <i>Research in Computational Topology 2</i>, edited by Ellen Gasparovic et al., 1st ed., vol. 30, Springer Nature, 2022, pp. 1–26, doi:<a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">10.1007/978-3-030-95519-9_1</a>.","chicago":"Bleile, Bea, Adélie Garin, Teresa Heiss, Kelly Maggs, and Vanessa Robins. “The Persistent Homology of Dual Digital Image Constructions.” In <i>Research in Computational Topology 2</i>, edited by Ellen Gasparovic, Vanessa Robins, and Katharine Turner, 1st ed., 30:1–26. AWMS. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-95519-9_1\">https://doi.org/10.1007/978-3-030-95519-9_1</a>.","ista":"Bleile B, Garin A, Heiss T, Maggs K, Robins V. 2022.The persistent homology of dual digital image constructions. In: Research in Computational Topology 2. Association for Women in Mathematics Series, vol. 30, 1–26."},"place":"Cham","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"month":"01","arxiv":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2102.11397"}],"quality_controlled":"1","page":"1-26","date_updated":"2022-06-07T08:32:42Z","edition":"1","_id":"11440","type":"book_chapter","series_title":"AWMS","doi":"10.1007/978-3-030-95519-9_1","article_processing_charge":"No","alternative_title":["Association for Women in Mathematics Series"],"editor":[{"last_name":"Gasparovic","full_name":"Gasparovic, Ellen","first_name":"Ellen"},{"first_name":"Vanessa","full_name":"Robins, Vanessa","last_name":"Robins"},{"first_name":"Katharine","last_name":"Turner","full_name":"Turner, Katharine"}],"publisher":"Springer Nature","ec_funded":1,"acknowledgement":"This project started during the Women in Computational Topology workshop held in Canberra in July of 2019. All authors are very grateful for its organisation and the financial support for the workshop from the Mathematical Sciences Institute at ANU, the US National Science Foundation through the award CCF-1841455, the Australian Mathematical Sciences Institute and the Association for Women in Mathematics. AG is supported by the Swiss National Science Foundation grant CRSII5_177237. TH is supported by the European Research Council (ERC) Horizon 2020 project “Alpha Shape Theory Extended” No. 788183. KM is supported by the ERC Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 859860. VR was supported by Australian Research Council Future Fellowship FT140100604 during the early stages of this project.","date_published":"2022-01-27T00:00:00Z","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended"}],"publication":"Research in Computational Topology 2","status":"public","year":"2022","external_id":{"arxiv":["2102.11397"]}},{"year":"2022","external_id":{"arxiv":["2201.11819"]},"related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/"}]},"project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","grant_number":"M03319","name":"Perception-Aware Appearance Fabrication"},{"call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"status":"public","publication":"ACM Transactions on Graphics","ec_funded":1,"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","date_published":"2022-06-01T00:00:00Z","doi":"10.1145/3528223.3530144","article_processing_charge":"No","publisher":"Association for Computing Machinery","date_updated":"2023-05-31T12:38:21Z","_id":"11442","type":"journal_article","ddc":["000"],"quality_controlled":"1","month":"06","arxiv":1,"department":[{"_id":"BeBi"}],"file":[{"date_created":"2022-06-28T08:32:58Z","file_size":33994829,"date_updated":"2022-06-28T08:32:58Z","creator":"dernst","file_id":"11467","success":1,"file_name":"2022_ACM_acceptedversion_Piovarci.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"27f6fe41c6ff84d50445cc9b0176d45b"}],"article_number":"112","oa":1,"language":[{"iso":"eng"}],"issue":"4","citation":{"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>","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>.","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.","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.","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).","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","last_name":"Piovarci","first_name":"Michael"},{"last_name":"Foshey","full_name":"Foshey, Michael","first_name":"Michael"},{"last_name":"Xu","full_name":"Xu, Jie","first_name":"Jie"},{"first_name":"Timothy","full_name":"Erps, Timothy","last_name":"Erps"},{"first_name":"Vahid","full_name":"Babaei, Vahid","last_name":"Babaei"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"full_name":"Rusinkiewicz, Szymon","last_name":"Rusinkiewicz","first_name":"Szymon"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"},{"orcid":"0000-0001-6511-9385","first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"}],"day":"01","title":"Closed-loop control of direct ink writing via reinforcement learning","oa_version":"Submitted Version","volume":41,"article_type":"original","date_created":"2022-06-10T06:41:47Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        41","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. "}],"publication_status":"published","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"file_date_updated":"2022-06-28T08:32:58Z"},{"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. ","date_published":"2022-06-01T00:00:00Z","status":"public","publication":"Transactions of the American Mathematical Society","external_id":{"isi":["000798461500001"],"arxiv":["2006.08836"]},"year":"2022","isi":1,"quality_controlled":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2006.08836","open_access":"1"}],"page":"4209-4250","type":"journal_article","_id":"11443","date_updated":"2023-08-03T07:17:37Z","publisher":"American Mathematical Society","article_processing_charge":"No","doi":"10.1090/tran/8614","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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>","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>.","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>.","ista":"Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional polytopes. Transactions of the American Mathematical Society. 375(6), 4209–4250.","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.","short":"M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical Society 375 (2022) 4209–4250.","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>"},"issue":"6","language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"MaKw"}],"arxiv":1,"month":"06","publication_status":"published","publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"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."}],"intvolume":"       375","date_created":"2022-06-12T22:01:45Z","article_type":"original","volume":375,"oa_version":"Preprint","title":"Extension complexity of low-dimensional polytopes","day":"01","scopus_import":"1","author":[{"full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567"},{"first_name":"Lisa","full_name":"Sauermann, Lisa","last_name":"Sauermann"},{"first_name":"Yufei","full_name":"Zhao, Yufei","last_name":"Zhao"}]},{"file_date_updated":"2022-06-20T07:51:32Z","publication_status":"published","publication_identifier":{"eissn":["1522-9602"],"issn":["0092-8240"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        84","abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","date_created":"2022-06-17T16:16:15Z","article_type":"original","volume":84,"oa_version":"Published Version","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","scopus_import":"1","day":"17","author":[{"first_name":"Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kseniia","orcid":"0000-0002-6246-1465","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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>","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>.","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.","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>."},"issue":"8","language":[{"iso":"eng"}],"oa":1,"article_number":"74","file":[{"file_id":"11455","creator":"dernst","date_updated":"2022-06-20T07:51:32Z","date_created":"2022-06-20T07:51:32Z","file_size":463025,"checksum":"05a1fe7d10914a00c2bca9b447993a65","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2022_BulletinMathBiology_Saona.pdf","success":1}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"month":"06","quality_controlled":"1","ddc":["510","570"],"type":"journal_article","_id":"11447","date_updated":"2023-08-03T07:20:53Z","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s11538-022-01029-z","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.","date_published":"2022-06-17T00:00:00Z","ec_funded":1,"status":"public","publication":"Bulletin of Mathematical Biology","project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"grant_number":"I05127","name":"Evolutionary analysis of gene regulation","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f"}],"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":[{"relation":"erratum","url":"https://doi.org/10.1007/s11538-022-01118-z"}]},"external_id":{"isi":["000812509800001"]},"year":"2022","isi":1},{"quality_controlled":"1","ddc":["570"],"type":"journal_article","date_updated":"2023-08-03T07:20:15Z","_id":"11448","publisher":"eLife Sciences Publications","doi":"10.7554/elife.75842","article_processing_charge":"No","acknowledgement":"We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com) for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova for technical assistance and data interpretation. Core facility Biomolecular Interactions and Crystallization of CEITEC Masaryk University is gratefully acknowledged for the obtaining of the scientific data presented in this paper. This research was supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF). MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC), Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility in the Vanderbilt University Center for Structural Biology. We are grateful to Joel M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4, the Imperial College Research Fellowship and the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\"). Experiments were partially carried out using equipment provided by the Institute of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH). This work was supported by a Russian Science Foundation grant 19-74-10102.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385.","date_published":"2022-05-05T00:00:00Z","ec_funded":1,"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"publication":"eLife","status":"public","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"external_id":{"isi":["000799197200001"]},"isi":1,"year":"2022","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"file_date_updated":"2022-06-20T07:44:19Z","abstract":[{"text":"Studies of protein fitness landscapes reveal biophysical constraints guiding protein evolution and empower prediction of functional proteins. However, generalisation of these findings is limited due to scarceness of systematic data on fitness landscapes of proteins with a defined evolutionary relationship. We characterized the fitness peaks of four orthologous fluorescent proteins with a broad range of sequence divergence. While two of the four studied fitness peaks were sharp, the other two were considerably flatter, being almost entirely free of epistatic interactions. Mutationally robust proteins, characterized by a flat fitness peak, were not optimal templates for machine-learning-driven protein design – instead, predictions were more accurate for fragile proteins with epistatic landscapes. Our work paves insights for practical application of fitness landscape heterogeneity in protein engineering.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        11","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"has_accepted_license":"1","article_type":"original","date_created":"2022-06-18T09:06:59Z","volume":11,"oa_version":"Published Version","title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","author":[{"last_name":"Gonzalez Somermeyer","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","first_name":"Louisa"},{"last_name":"Fleiss","full_name":"Fleiss, Aubin","first_name":"Aubin"},{"full_name":"Mishin, Alexander S","last_name":"Mishin","first_name":"Alexander S"},{"first_name":"Nina G","last_name":"Bozhanova","full_name":"Bozhanova, Nina G"},{"first_name":"Anna A","full_name":"Igolkina, Anna A","last_name":"Igolkina"},{"full_name":"Meiler, Jens","last_name":"Meiler","first_name":"Jens"},{"first_name":"Maria-Elisenda","last_name":"Alaball Pujol","full_name":"Alaball Pujol, Maria-Elisenda"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V"},{"first_name":"Karen S","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S"},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","orcid":"0000-0001-8243-4694"}],"scopus_import":"1","day":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova, Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva, Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>.","ista":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.","mla":"Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape and Data-Driven Protein Design.” <i>ELife</i>, vol. 11, 75842, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>.","apa":"Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina, A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.75842\">https://doi.org/10.7554/elife.75842</a>","ama":"Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP fitness landscape and data-driven protein design. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.75842\">10.7554/elife.75842</a>","short":"L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina, J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov, ELife 11 (2022).","ieee":"L. Gonzalez Somermeyer <i>et al.</i>, “Heterogeneity of the GFP fitness landscape and data-driven protein design,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022."},"language":[{"iso":"eng"}],"oa":1,"file":[{"creator":"dernst","date_updated":"2022-06-20T07:44:19Z","file_size":5297213,"date_created":"2022-06-20T07:44:19Z","file_id":"11454","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_eLife_Somermeyer.pdf","checksum":"7573c28f44028ab0cc81faef30039e44","relation":"main_file"}],"article_number":"75842","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"month":"05"},{"date_created":"2022-06-19T22:01:57Z","article_type":"original","volume":13,"oa_version":"Published Version","title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","scopus_import":"1","day":"15","author":[{"first_name":"Donovan J.","full_name":"Anderson, Donovan J.","last_name":"Anderson"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","last_name":"Pauler"},{"last_name":"Mckenna","full_name":"Mckenna, Aaron","first_name":"Aaron"},{"first_name":"Jay","last_name":"Shendure","full_name":"Shendure, Jay"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marshall S.","last_name":"Horwitz","full_name":"Horwitz, Marshall S."}],"publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"publication_status":"published","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."}],"intvolume":"        13","department":[{"_id":"SiHi"}],"month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","short":"D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, Cell Systems 13 (2022) 438–453.e5.","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>","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>","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>.","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>.","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."},"issue":"6","language":[{"iso":"eng"}],"oa":1,"type":"journal_article","_id":"11449","date_updated":"2023-08-03T07:19:43Z","publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.cels.2022.03.006","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2022.03.006","open_access":"1"}],"page":"438-453.e5","external_id":{"pmid":["35452605"],"isi":["000814124400002"]},"isi":1,"year":"2022","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.","date_published":"2022-06-15T00:00:00Z","ec_funded":1,"pmid":1,"publication":"Cell Systems","status":"public","project":[{"call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425"},{"grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","_id":"25D92700-B435-11E9-9278-68D0E5697425"}]},{"file_date_updated":"2022-07-29T09:29:20Z","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"The precursor conversion chemistry and surface chemistry of Cu3N and Cu3PdN nanocrystals are unknown or contested. Here, we first obtain phase-pure, colloidally stable nanocubes. Second, we elucidate the pathway by which copper(II) nitrate and oleylamine form Cu3N. We find that oleylamine is both a reductant and a nitrogen source. Oleylamine is oxidized by nitrate to a primary aldimine, which reacts further with excess oleylamine to a secondary aldimine, eliminating ammonia. Ammonia reacts with CuI to form Cu3N. Third, we investigated the surface chemistry and find a mixed ligand shell of aliphatic amines and carboxylates (formed in situ). While the carboxylates appear tightly bound, the amines are easily desorbed from the surface. Finally, we show that doping with palladium decreases the band gap and the material becomes semi-metallic. These results bring insight into the chemistry of metal nitrides and might help the development of other metal nitride nanocrystals."}],"intvolume":"        61","has_accepted_license":"1","date_created":"2022-06-19T22:01:58Z","article_type":"original","volume":61,"oa_version":"Published Version","title":"The chemistry of Cu₃N and Cu₃PdN nanocrystals","day":"01","scopus_import":"1","author":[{"first_name":"Mahsa","full_name":"Parvizian, Mahsa","last_name":"Parvizian"},{"first_name":"Alejandra","last_name":"Duràn Balsa","full_name":"Duràn Balsa, Alejandra"},{"last_name":"Pokratath","full_name":"Pokratath, Rohan","first_name":"Rohan"},{"full_name":"Kalha, Curran","last_name":"Kalha","first_name":"Curran"},{"orcid":"0000-0002-6962-8598","first_name":"Seungho","last_name":"Lee","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Dietger","last_name":"Van Den Eynden","full_name":"Van Den Eynden, Dietger"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","full_name":"Regoutz, Anna","last_name":"Regoutz"},{"full_name":"De Roo, Jonathan","last_name":"De Roo","first_name":"Jonathan"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Parvizian M, Duràn Balsa A, Pokratath R, et al. The chemistry of Cu₃N and Cu₃PdN nanocrystals. <i>Angewandte Chemie - International Edition</i>. 2022;61(31). doi:<a href=\"https://doi.org/10.1002/anie.202207013\">10.1002/anie.202207013</a>","short":"M. Parvizian, A. Duràn Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van Den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, Angewandte Chemie - International Edition 61 (2022).","ieee":"M. Parvizian <i>et al.</i>, “The chemistry of Cu₃N and Cu₃PdN nanocrystals,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31. Wiley, 2022.","chicago":"Parvizian, Mahsa, Alejandra Duràn Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van Den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>.","ista":"Parvizian M, Duràn Balsa A, Pokratath R, Kalha C, Lee S, Van Den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. The chemistry of Cu₃N and Cu₃PdN nanocrystals. Angewandte Chemie - International Edition. 61(31), e202207013.","mla":"Parvizian, Mahsa, et al. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31, e202207013, Wiley, 2022, doi:<a href=\"https://doi.org/10.1002/anie.202207013\">10.1002/anie.202207013</a>.","apa":"Parvizian, M., Duràn Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van Den Eynden, D., … De Roo, J. (2022). The chemistry of Cu₃N and Cu₃PdN nanocrystals. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>"},"issue":"31","language":[{"iso":"eng"}],"oa":1,"file":[{"relation":"main_file","checksum":"2a3ee0bb59e044b808ebe85cd94ac899","success":1,"file_name":"2022_AngewandteChemieInternat_Parvizian.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"11696","file_size":1303202,"date_created":"2022-07-29T09:29:20Z","creator":"dernst","date_updated":"2022-07-29T09:29:20Z"}],"article_number":"e202207013","department":[{"_id":"MaIb"}],"month":"08","quality_controlled":"1","ddc":["540"],"type":"journal_article","_id":"11451","date_updated":"2023-08-03T07:19:12Z","publisher":"Wiley","article_processing_charge":"No","doi":"10.1002/anie.202207013","date_published":"2022-08-01T00:00:00Z","acknowledgement":"J.D.R. and M.P. acknowledge the SNF Eccellenza funding scheme (project number: 194172). We acknowledge DESY (Hamburg, Germany), a member of the Helmholtz Association HGF, for the provision of experimental facilities. Parts of this research were carried out at beamline P21.1, PETRA III. We thank Dr. Soham Banerjee for acquiring the PDF data and helpful advice. A.R. acknowledges the support from the Analytical Chemistry Trust Fund for her CAMS-UK Fellowship. C.K. acknowledges the support from the Department of Chemistry, UCL. The authors acknowledge Dr Stephan Lany from NREL for providing the Cu3N DFT calculations. The authors thank Prof. Raymond Schaak and Dr. Robert William Lord for helpful advice and suggestions regarding the purification procedure. Open access funding provided by Universitat Basel.","pmid":1,"publication":"Angewandte Chemie - International Edition","status":"public","related_material":{"record":[{"id":"11695","status":"public","relation":"research_data"}]},"external_id":{"pmid":["35612297"],"isi":["000811084000001"]},"isi":1,"year":"2022"},{"title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","oa_version":"None","scopus_import":"1","day":"04","author":[{"last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat","first_name":"Murat"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","last_name":"de Bono","orcid":"0000-0001-8347-0443","first_name":"Mario"}],"date_created":"2022-06-20T08:10:34Z","volume":181,"intvolume":"       181","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."}],"publication_status":"published","publication_identifier":{"isbn":["9781071623206"],"issn":["0893-2336"],"eisbn":["9781071623213"],"eissn":["1940-6045"]},"month":"06","department":[{"_id":"MaDe"}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>","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.","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.","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>.","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>","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>."},"place":"New York","publisher":"Springer Nature","editor":[{"full_name":"Yamamoto, Daisuke","last_name":"Yamamoto","first_name":"Daisuke"}],"article_processing_charge":"No","alternative_title":["Neuromethods"],"doi":"10.1007/978-1-0716-2321-3_15","series_title":"NM","type":"book_chapter","_id":"11456","date_updated":"2023-02-21T09:51:55Z","page":"277-294","quality_controlled":"1","year":"2022","publication":"Behavioral Neurogenetics","status":"public","project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"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).","date_published":"2022-06-04T00:00:00Z","ec_funded":1},{"external_id":{"arxiv":["2204.00870"],"isi":["000850435600030"]},"year":"2022","isi":1,"status":"public","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"date_published":"2022-06-09T00:00:00Z","conference":{"name":"PLDI: Programming Language Design and Implementation","end_date":"2022-06-17","start_date":"2022-06-13","location":"San Diego, CA, United States"},"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).","ec_funded":1,"publisher":"Association for Computing Machinery","article_processing_charge":"No","doi":"10.1145/3519939.3523435","type":"conference","_id":"11459","date_updated":"2025-07-14T09:09:54Z","ddc":["000"],"page":"442-457","quality_controlled":"1","month":"06","arxiv":1,"file":[{"relation":"main_file","checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","file_name":"2022_PLDI_Zikelic.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"11466","date_created":"2022-06-27T07:38:21Z","file_size":318697,"creator":"dernst","date_updated":"2022-06-27T07:38:21Z"}],"department":[{"_id":"GradSch"},{"_id":"KrCh"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","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>.","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>.","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>","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>","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."},"title":"Differential cost analysis with simultaneous potentials and anti-potentials","oa_version":"Published Version","day":"09","scopus_import":"1","author":[{"orcid":"0000-0002-4681-1699","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","last_name":"Zikelic"},{"first_name":"Bor-Yuh Evan","full_name":"Chang, Bor-Yuh Evan","last_name":"Chang"},{"last_name":"Bolignano","full_name":"Bolignano, Pauline","first_name":"Pauline"},{"first_name":"Franco","last_name":"Raimondi","full_name":"Raimondi, Franco"}],"date_created":"2022-06-21T09:26:15Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2022-06-27T07:38:21Z","publication_status":"published","publication_identifier":{"isbn":["9781450392655"]}},{"file_date_updated":"2022-06-24T08:22:59Z","publication_identifier":{"issn":["2040-2392"]},"publication_status":"published","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"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."}],"intvolume":"        13","volume":13,"date_created":"2022-06-23T14:28:55Z","article_type":"original","day":"22","author":[{"last_name":"Schaaf","full_name":"Schaaf, Zachary A.","first_name":"Zachary A."},{"full_name":"Tat, Lyvin","last_name":"Tat","first_name":"Lyvin"},{"full_name":"Cannizzaro, Noemi","last_name":"Cannizzaro","first_name":"Noemi"},{"first_name":"Ralph","last_name":"Green","full_name":"Green, Ralph"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Konstantinos S.","last_name":"Zarbalis","full_name":"Zarbalis, Konstantinos S."}],"title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","oa_version":"Published Version","citation":{"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>","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>.","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.","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.","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","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>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"SiHi"}],"file":[{"relation":"main_file","checksum":"525d2618e855139089bbfc3e3d49d1b2","file_name":"2022_MolecularAutism_Schaaf.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"11461","file_size":7552298,"date_created":"2022-06-24T08:22:59Z","creator":"dernst","date_updated":"2022-06-24T08:22:59Z"}],"article_number":"27","month":"06","quality_controlled":"1","ddc":["570"],"_id":"11460","date_updated":"2023-08-03T07:21:32Z","type":"journal_article","article_processing_charge":"No","doi":"10.1186/s13229-022-00508-3","publisher":"Springer Nature","date_published":"2022-06-22T00:00:00Z","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","status":"public","keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"isi":1,"year":"2022","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13229-023-00539-4"}]},"external_id":{"isi":["000814641400001"]}},{"status":"public","publication":"Applied Microbiology and Biotechnology","date_published":"2022-08-01T00:00:00Z","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.","pmid":1,"external_id":{"isi":["000813677500001"],"pmid":["35723693"]},"year":"2022","isi":1,"page":"5093-5103","quality_controlled":"1","publisher":"Springer Nature","doi":"10.1007/s00253-022-12022-w","article_processing_charge":"No","type":"journal_article","date_updated":"2023-10-10T07:15:02Z","_id":"11462","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>.","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.","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>.","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>","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>","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","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."},"month":"08","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"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."}],"intvolume":"       106","publication_identifier":{"eissn":["1432-0614"],"issn":["0175-7598"]},"publication_status":"published","oa_version":"None","title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"full_name":"Karputs, Alena","last_name":"Karputs","first_name":"Alena"},{"first_name":"Anton","orcid":"0000-0003-2091-526X","id":"62304f89-eb97-11eb-a6c2-8903dd183976","full_name":"Kavaleuski, Anton","last_name":"Kavaleuski"},{"first_name":"Ivan","last_name":"Kuzminski","full_name":"Kuzminski, Ivan"},{"last_name":"Stepanova","full_name":"Stepanova, Elena","first_name":"Elena"},{"first_name":"Andrei","last_name":"Gilep","full_name":"Gilep, Andrei"}],"scopus_import":"1","day":"01","article_type":"original","date_created":"2022-06-26T22:01:34Z","volume":106},{"project":[{"call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"status":"public","publication":"Physical Review B","ec_funded":1,"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.","date_published":"2022-06-27T00:00:00Z","year":"2022","isi":1,"external_id":{"arxiv":["2111.08603"],"isi":["000823050000001"]},"related_material":{"record":[{"id":"12732","relation":"dissertation_contains","status":"public"}]},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2111.08603 Focus to learn more"}],"quality_controlled":"1","doi":"10.1103/physrevb.105.224208","article_processing_charge":"No","publisher":"American Physical Society","date_updated":"2023-09-05T12:12:52Z","_id":"11469","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"issue":"22","citation":{"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>","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).","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>.","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.","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>","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>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"month":"06","department":[{"_id":"MaSe"}],"article_number":"224208","intvolume":"       105","abstract":[{"lang":"eng","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."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","author":[{"orcid":"0000-0002-7969-2729","first_name":"Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","full_name":"Brighi, Pietro","last_name":"Brighi"},{"orcid":"0000-0002-8443-1064","first_name":"Alexios","last_name":"Michailidis","full_name":"Michailidis, Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kristina","full_name":"Kirova, Kristina","id":"4aeda2ae-f847-11ec-98e0-c4a66fe174d4","last_name":"Kirova"},{"last_name":"Abanin","full_name":"Abanin, Dmitry A.","first_name":"Dmitry A."},{"orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"day":"27","oa_version":"Preprint","title":"Localization of a mobile impurity interacting with an Anderson insulator","volume":105,"article_type":"original","date_created":"2022-06-29T20:19:51Z"},{"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","intvolume":"       105","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"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"volume":105,"article_type":"original","date_created":"2022-06-29T20:20:47Z","author":[{"first_name":"Pietro","orcid":"0000-0002-7969-2729","last_name":"Brighi","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","full_name":"Brighi, Pietro"},{"last_name":"Michailidis","full_name":"Michailidis, Alexios A.","first_name":"Alexios A."},{"first_name":"Dmitry A.","last_name":"Abanin","full_name":"Abanin, Dmitry A."},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"}],"day":"27","title":"Propagation of many-body localization in an Anderson insulator","oa_version":"Preprint","issue":"22","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).","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>","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>","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.","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>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MaSe"}],"article_number":"L220203","arxiv":1,"month":"06","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2109.07332","open_access":"1"}],"quality_controlled":"1","date_updated":"2023-08-03T07:23:52Z","_id":"11470","type":"journal_article","doi":"10.1103/physrevb.105.l220203","article_processing_charge":"No","publisher":"American Physical Society","ec_funded":1,"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.","date_published":"2022-06-27T00:00:00Z","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"status":"public","publication":"Physical Review B","isi":1,"year":"2022","external_id":{"arxiv":["2109.07332"],"isi":["000823050000012"]},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12732"}]}},{"status":"public","publication":"PRX Quantum","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"ec_funded":1,"acknowledgement":"We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S., R.A.M., A.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).","date_published":"2022-06-29T00:00:00Z","isi":1,"year":"2022","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14622"}]},"external_id":{"isi":["000822564300001"],"arxiv":["2201.08194"]},"keyword":["General Medicine"],"ddc":["530"],"quality_controlled":"1","article_processing_charge":"No","doi":"10.1103/prxquantum.3.020365","publisher":"American Physical Society","_id":"11471","date_updated":"2023-12-13T14:47:24Z","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"citation":{"ama":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>","short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022).","ieee":"S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding barren plateaus using classical shadows,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng, and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>.","ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.","mla":"Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>.","apa":"Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., &#38; Serbyn, M. (2022). Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>"},"issue":"2","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"06","arxiv":1,"department":[{"_id":"MaSe"}],"article_number":"020365","file":[{"relation":"main_file","checksum":"a7706b28d24a0e32a55ea04b82a2df43","file_name":"2022_PRXQuantum_Sack.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"11472","file_size":4231591,"date_created":"2022-06-30T07:14:48Z","date_updated":"2022-06-30T07:14:48Z","creator":"dernst"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"         3","abstract":[{"lang":"eng","text":"Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. "}],"file_date_updated":"2022-06-30T07:14:48Z","publication_status":"published","publication_identifier":{"issn":["2691-3399"]},"day":"29","author":[{"full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","orcid":"0000-0001-5400-8508","first_name":"Stefan"},{"full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","first_name":"Raimel A"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","full_name":"Michailidis, Alexios","last_name":"Michailidis","first_name":"Alexios","orcid":"0000-0002-8443-1064"},{"full_name":"Kueng, Richard","last_name":"Kueng","first_name":"Richard"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym"}],"title":"Avoiding barren plateaus using classical shadows","oa_version":"Published Version","volume":3,"date_created":"2022-06-29T20:21:32Z","article_type":"original"}]