[{"date_updated":"2023-08-03T07:16:20Z","publication":"Applied Physics Letters","article_type":"letter_note","article_number":"190401","oa":1,"year":"2022","main_file_link":[{"url":"https://doi.org/10.1063/5.0097339","open_access":"1"}],"intvolume":"       120","publisher":"American Institute of Physics","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JoFi"}],"scopus_import":"1","date_created":"2022-05-29T22:01:53Z","external_id":{"isi":["000796002100002"]},"date_published":"2022-05-12T00:00:00Z","publication_identifier":{"issn":["0003-6951"]},"status":"public","publication_status":"published","acknowledgement":"We would like to thank all of the authors who contributed to\r\nthis Special Topic. We would also like to thank the editorial team at\r\nAPL including Jessica Trudeau, Emma Van Burns, Martin Weides,\r\nand Lesley Cohen.","_id":"11417","author":[{"first_name":"Anthony J.","full_name":"Sigillito, Anthony J.","last_name":"Sigillito"},{"last_name":"Covey","full_name":"Covey, Jacob P.","first_name":"Jacob P."},{"last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"},{"full_name":"Petersson, Karl","last_name":"Petersson","first_name":"Karl"},{"first_name":"Stefan","last_name":"Preble","full_name":"Preble, Stefan"}],"title":"Emerging qubit systems: Guest editorial","doi":"10.1063/5.0097339","issue":"19","abstract":[{"lang":"eng","text":"Over the past few years, the field of quantum information science has seen tremendous progress toward realizing large-scale quantum computers. With demonstrations of quantum computers outperforming classical computers for a select range of problems,1–3 we have finally entered the noisy, intermediate-scale quantum (NISQ) computing era. While the quantum computers of today are technological marvels, they are not yet error corrected, and it is unclear whether any system will scale beyond a few hundred logical qubits without significant changes to architecture and control schemes. Today's quantum systems are analogous to the ENIAC (Electronic Numerical Integrator And Computer) and EDVAC (Electronic Discrete Variable Automatic Computer) systems of the 1940s, which ran on vacuum tubes. These machines were built on a solid, nominally scalable architecture and when they were developed, nobody could have predicted the development of the transistor and the impact of the resulting semiconductor industry. Simply put, the computers of today are nothing like the early computers of the 1940s. We believe that the qubits of future fault-tolerant quantum systems will look quite different from the qubits of the NISQ machines in operation today. This Special Topic issue is devoted to new and emerging quantum systems with a focus on enabling technologies that can eventually lead to the quantum analog to the transistor. We have solicited both research4–18 and perspective articles19–21 to discuss new and emerging qubit systems with a focus on novel materials, encodings, and architectures. We are proud to present a collection that touches on a wide range of technologies including superconductors,7–13,21 semiconductors,15–17,19 and individual atomic qubits.18\r\n"}],"volume":120,"article_processing_charge":"No","month":"05","day":"12","citation":{"chicago":"Sigillito, Anthony J., Jacob P. Covey, Johannes M Fink, Karl Petersson, and Stefan Preble. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>. American Institute of Physics, 2022. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>.","mla":"Sigillito, Anthony J., et al. “Emerging Qubit Systems: Guest Editorial.” <i>Applied Physics Letters</i>, vol. 120, no. 19, 190401, American Institute of Physics, 2022, doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>.","ama":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. 2022;120(19). doi:<a href=\"https://doi.org/10.1063/5.0097339\">10.1063/5.0097339</a>","short":"A.J. Sigillito, J.P. Covey, J.M. Fink, K. Petersson, S. Preble, Applied Physics Letters 120 (2022).","ista":"Sigillito AJ, Covey JP, Fink JM, Petersson K, Preble S. 2022. Emerging qubit systems: Guest editorial. Applied Physics Letters. 120(19), 190401.","ieee":"A. J. Sigillito, J. P. Covey, J. M. Fink, K. Petersson, and S. Preble, “Emerging qubit systems: Guest editorial,” <i>Applied Physics Letters</i>, vol. 120, no. 19. American Institute of Physics, 2022.","apa":"Sigillito, A. J., Covey, J. P., Fink, J. M., Petersson, K., &#38; Preble, S. (2022). Emerging qubit systems: Guest editorial. <i>Applied Physics Letters</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/5.0097339\">https://doi.org/10.1063/5.0097339</a>"},"oa_version":"Published Version"},{"date_published":"2022-05-01T00:00:00Z","external_id":{"isi":["000793963400005"],"arxiv":["2103.06730"]},"date_created":"2022-05-29T22:01:53Z","scopus_import":"1","department":[{"_id":"LaEr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Institute of Mathematical Statistics","main_file_link":[{"url":"https://arxiv.org/abs/2103.06730","open_access":"1"}],"intvolume":"        50","year":"2022","oa":1,"page":"984-1012","article_type":"original","publication":"Annals of Probability","date_updated":"2023-08-03T07:16:53Z","oa_version":"Preprint","citation":{"ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. Normal fluctuation in quantum ergodicity for Wigner matrices. Annals of Probability. 50(3), 984–1012.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Annals of Probability 50 (2022) 984–1012.","ama":"Cipolloni G, Erdös L, Schröder DJ. Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. 2022;50(3):984-1012. doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2022). Normal fluctuation in quantum ergodicity for Wigner matrices. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Normal fluctuation in quantum ergodicity for Wigner matrices,” <i>Annals of Probability</i>, vol. 50, no. 3. Institute of Mathematical Statistics, pp. 984–1012, 2022.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AOP1552\">https://doi.org/10.1214/21-AOP1552</a>.","mla":"Cipolloni, Giorgio, et al. “Normal Fluctuation in Quantum Ergodicity for Wigner Matrices.” <i>Annals of Probability</i>, vol. 50, no. 3, Institute of Mathematical Statistics, 2022, pp. 984–1012, doi:<a href=\"https://doi.org/10.1214/21-AOP1552\">10.1214/21-AOP1552</a>."},"day":"01","month":"05","volume":50,"article_processing_charge":"No","arxiv":1,"abstract":[{"text":"We consider the quadratic form of a general high-rank deterministic matrix on the eigenvectors of an N×N\r\nWigner matrix and prove that it has Gaussian fluctuation for each bulk eigenvector in the large N limit. The proof is a combination of the energy method for the Dyson Brownian motion inspired by Marcinek and Yau (2021) and our recent multiresolvent local laws (Comm. Math. Phys. 388 (2021) 1005–1048).","lang":"eng"}],"issue":"3","doi":"10.1214/21-AOP1552","title":"Normal fluctuation in quantum ergodicity for Wigner matrices","author":[{"last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4901-7992"},{"full_name":"Erdös, László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856"}],"_id":"11418","acknowledgement":"L.E. would like to thank Zhigang Bao for many illuminating discussions in an early stage of this research. The authors are also grateful to Paul Bourgade for his comments on the manuscript and the anonymous referee for several useful suggestions.","publication_status":"published","status":"public","publication_identifier":{"eissn":["2168-894X"],"issn":["0091-1798"]}},{"article_processing_charge":"No","volume":11,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2022-05-30T08:09:16Z","file_id":"11421","relation":"main_file","creator":"cchlebak","file_size":2466296,"file_name":"elife-73542-v2.pdf","date_updated":"2022-05-30T08:09:16Z","success":1,"content_type":"application/pdf","checksum":"ccddbd167e00ff8375f12998af497152","access_level":"open_access"}],"oa_version":"Published Version","ddc":["616"],"file_date_updated":"2022-05-30T08:09:16Z","pmid":1,"month":"05","citation":{"ama":"Hori T, Eguchi K, Wang HY, et al. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>","short":"T. Hori, K. Eguchi, H.Y. Wang, T. Miyasaka, L. Guillaud, Z. Taoufiq, S. Mahapatra, H. Yamada, K. Takei, T. Takahashi, ELife 11 (2022).","ista":"Hori T, Eguchi K, Wang HY, Miyasaka T, Guillaud L, Taoufiq Z, Mahapatra S, Yamada H, Takei K, Takahashi T. 2022. Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. eLife. 11, e73542.","ieee":"T. Hori <i>et al.</i>, “Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","apa":"Hori, T., Eguchi, K., Wang, H. Y., Miyasaka, T., Guillaud, L., Taoufiq, Z., … Takahashi, T. (2022). Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer’s disease synapse model. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>","mla":"Hori, Tetsuya, et al. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>, vol. 11, e73542, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.73542\">10.7554/eLife.73542</a>.","chicago":"Hori, Tetsuya, Kohgaku Eguchi, Han Ying Wang, Tomohiro Miyasaka, Laurent Guillaud, Zacharie Taoufiq, Satyajit Mahapatra, Hiroshi Yamada, Kohji Takei, and Tomoyuki Takahashi. “Microtubule Assembly by Tau Impairs Endocytosis and Neurotransmission via Dynamin Sequestration in Alzheimer’s Disease Synapse Model.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.73542\">https://doi.org/10.7554/eLife.73542</a>."},"day":"05","acknowledgement":"We thank Yasuo Ihara, Nobuyuki Nukina, and Takeshi Sakaba for comments and Patrick Stoney for editing this paper. We also thank Shota Okuda and Mikako Matsubara for their contributions in the early stage of this study, and Satoko Wada-Kakuda for technical assistant with in vitro analysis of tau. This research was supported by funding from Okinawa Institute of Science and Technology and from Technology (OIST) and Core Research for the Evolutional Science and Technology of Japan Science and Technology Agency (CREST) to TT, and by Scientific Research on Innovative Areas to TM (Brain Protein Aging and Dementia Control 26117004).","publication_status":"published","status":"public","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/eLife.73542","abstract":[{"text":"Elevation of soluble wild-type (WT) tau occurs in synaptic compartments in Alzheimer’s disease. We addressed whether tau elevation affects synaptic transmission at the calyx of Held in slices from mice brainstem. Whole-cell loading of WT human tau (h-tau) in presynaptic terminals at 10–20 µM caused microtubule (MT) assembly and activity-dependent rundown of excitatory neurotransmission. Capacitance measurements revealed that the primary target of WT h-tau is vesicle endocytosis. Blocking MT assembly using nocodazole prevented tau-induced impairments of endocytosis and neurotransmission. Immunofluorescence imaging analyses revealed that MT assembly by WT h-tau loading was associated with an increased MT-bound fraction of the endocytic protein dynamin. A synthetic dodecapeptide corresponding to dynamin 1-pleckstrin-homology domain inhibited MT-dynamin interaction and rescued tau-induced impairments of endocytosis and neurotransmission. We conclude that elevation of presynaptic WT tau induces de novo assembly of MTs, thereby sequestering free dynamins. As a result, endocytosis and subsequent vesicle replenishment are impaired, causing activity-dependent rundown of neurotransmission.","lang":"eng"}],"_id":"11419","title":"Microtubule assembly by tau impairs endocytosis and neurotransmission via dynamin sequestration in Alzheimer's disease synapse model","author":[{"full_name":"Hori, Tetsuya","last_name":"Hori","first_name":"Tetsuya"},{"orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","last_name":"Eguchi"},{"first_name":"Han Ying","last_name":"Wang","full_name":"Wang, Han Ying"},{"first_name":"Tomohiro","full_name":"Miyasaka, Tomohiro","last_name":"Miyasaka"},{"full_name":"Guillaud, Laurent","last_name":"Guillaud","first_name":"Laurent"},{"first_name":"Zacharie","full_name":"Taoufiq, Zacharie","last_name":"Taoufiq"},{"first_name":"Satyajit","last_name":"Mahapatra","full_name":"Mahapatra, Satyajit"},{"full_name":"Yamada, Hiroshi","last_name":"Yamada","first_name":"Hiroshi"},{"first_name":"Kohji","last_name":"Takei","full_name":"Takei, Kohji"},{"first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki","last_name":"Takahashi"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"eLife Sciences Publications","intvolume":"        11","date_created":"2022-05-29T22:01:54Z","scopus_import":"1","external_id":{"pmid":["35471147 "],"isi":["000876231600001"]},"date_published":"2022-05-05T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"RySh"}],"article_number":"e73542","article_type":"original","date_updated":"2023-08-03T07:15:49Z","publication":"eLife","year":"2022","oa":1},{"day":"01","citation":{"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.","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.","short":"A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 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.","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.","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.","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."},"month":"04","file_date_updated":"2022-05-30T08:22:55Z","ddc":["000"],"oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"d4ff5d1affb34848b5c5e4002483fc62","success":1,"date_updated":"2022-05-30T08:22:55Z","file_name":"21-1365.pdf","file_size":1521701,"relation":"main_file","creator":"cchlebak","file_id":"11422","date_created":"2022-05-30T08:22:55Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"has_accepted_license":"1","article_processing_charge":"No","volume":23,"author":[{"id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr","last_name":"Shevchenko"},{"first_name":"Vyacheslav","last_name":"Kungurtsev","full_name":"Kungurtsev, Vyacheslav"},{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"}],"title":"Mean-field analysis of piecewise linear solutions for wide ReLU networks","_id":"11420","issue":"130","abstract":[{"lang":"eng","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."}],"publication_identifier":{"eissn":["1533-7928"],"issn":["1532-4435"]},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"status":"public","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","publication_status":"published","department":[{"_id":"MaMo"},{"_id":"DaAl"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["2111.02278"]},"date_published":"2022-04-01T00:00:00Z","scopus_import":"1","date_created":"2022-05-29T22:01:54Z","intvolume":"        23","publisher":"Journal of Machine Learning Research","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"year":"2022","publication":"Journal of Machine Learning Research","date_updated":"2024-09-10T13:03:17Z","related_material":{"link":[{"relation":"other","url":"https://www.jmlr.org/papers/v23/21-1365.html"}]},"article_type":"original","page":"1-55"},{"file":[{"date_created":"2022-06-07T07:58:30Z","file_id":"11437","relation":"main_file","file_size":17580705,"creator":"dernst","file_name":"2022_LIPICs_Chambers.pdf","checksum":"b25ce40fade4ebc0bcaae176db4f5f1f","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-06-07T07:58:30Z","success":1}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","volume":224,"has_accepted_license":"1","ddc":["510"],"file_date_updated":"2022-06-07T07:58:30Z","month":"06","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>.","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.","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.","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>","ieee":"E. Chambers, C. D. Fillmore, E. R. Stephenson, and M. Wintraecken, “A cautionary tale: Burning the medial axis is unstable,” in <i>38th International Symposium on Computational Geometry</i>, Berlin, Germany, 2022, vol. 224, p. 66:1-66:9.","apa":"Chambers, E., Fillmore, C. D., Stephenson, E. R., &#38; Wintraecken, M. (2022). A cautionary tale: Burning the medial axis is unstable. In X. Goaoc &#38; M. Kerber (Eds.), <i>38th International Symposium on Computational Geometry</i> (Vol. 224, p. 66:1-66:9). Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2022.66\">https://doi.org/10.4230/LIPIcs.SoCG.2022.66</a>"},"day":"01","oa_version":"Published Version","conference":{"location":"Berlin, Germany","start_date":"2022-06-07","end_date":"2022-06-10","name":"SoCG: Symposium on Computational Geometry"},"project":[{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"},{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"isbn":["978-3-95977-227-3"],"issn":["1868-8969"]},"ec_funded":1,"publication_status":"published","status":"public","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.","editor":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"last_name":"Kerber","full_name":"Kerber, Michael","first_name":"Michael"}],"_id":"11428","title":"A cautionary tale: Burning the medial axis is unstable","author":[{"full_name":"Chambers, Erin","last_name":"Chambers","first_name":"Erin"},{"last_name":"Fillmore","full_name":"Fillmore, Christopher D","first_name":"Christopher D","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425"},{"id":"2D04F932-F248-11E8-B48F-1D18A9856A87","first_name":"Elizabeth R","full_name":"Stephenson, Elizabeth R","last_name":"Stephenson","orcid":"0000-0002-6862-208X"},{"id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","orcid":"0000-0002-7472-2220"}],"doi":"10.4230/LIPIcs.SoCG.2022.66","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"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"       224","series_title":"LIPIcs","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"date_created":"2022-06-01T14:18:04Z","scopus_import":"1","date_published":"2022-06-01T00:00:00Z","date_updated":"2023-02-21T09:50:52Z","publication":"38th International Symposium on Computational Geometry","page":"66:1-66:9","oa":1,"year":"2022"},{"date_updated":"2022-06-02T05:56:22Z","edition":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031062445"],"eisbn":["9783031062452"],"issn":["0302-9743"]},"page":"153","place":"Cham","status":"public","publication_status":"published","_id":"11429","editor":[{"last_name":"Karimipour","full_name":"Karimipour, Farid","first_name":"Farid","id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","orcid":"0000-0001-6746-4174"},{"last_name":"Storandt","full_name":"Storandt, Sabine","first_name":"Sabine"}],"title":"Web and Wireless Geographical Information Systems","doi":"10.1007/978-3-031-06245-2","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."}],"year":"2022","alternative_title":["LNCS"],"publisher":"Springer Nature","intvolume":"     13238","article_processing_charge":"No","volume":13238,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"book_editor","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Karimipour F, Storandt S eds. 2022. Web and Wireless Geographical Information Systems 1st ed., Cham: Springer Nature, 153p.","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.","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>","ieee":"F. Karimipour and S. Storandt, Eds., <i>Web and Wireless Geographical Information Systems</i>, 1st ed., vol. 13238. Cham: Springer Nature, 2022.","chicago":"Karimipour, Farid, and Sabine Storandt, eds. <i>Web and Wireless Geographical Information Systems</i>. 1st ed. Vol. 13238. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-06245-2\">https://doi.org/10.1007/978-3-031-06245-2</a>.","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>."},"day":"01","department":[{"_id":"HeEd"}],"date_created":"2022-06-02T05:40:53Z","oa_version":"None","date_published":"2022-05-01T00:00:00Z"},{"volume":41,"article_processing_charge":"No","day":"01","citation":{"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>.","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>.","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>","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>","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."},"month":"05","oa_version":"Submitted Version","publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"status":"public","publication_status":"published","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,"author":[{"full_name":"Schreck, Camille","last_name":"Schreck","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"title":"Coupling 3D liquid simulation with 2D wave propagation for large scale water surface animation using the equivalent sources method","_id":"11432","issue":"2","abstract":[{"lang":"eng","text":"This paper proposes a method for simulating liquids in large bodies of water by coupling together a water surface wave simulator with a 3D Navier-Stokes simulator. The surface wave simulation uses the equivalent sources method (ESM) to efficiently animate large bodies of water with precisely controllable wave propagation behavior. The 3D liquid simulator animates complex non-linear fluid behaviors like splashes and breaking waves using off-the-shelf simulators using FLIP or the level set method with semi-Lagrangian advection.\r\nWe combine the two approaches by using the 3D solver to animate localized non-linear behaviors, and the 2D wave solver to animate larger regions with linear surface physics. We use the surface motion from the 3D solver as boundary conditions for 2D surface wave simulator, and we use the velocity and surface heights from the 2D surface wave simulator as boundary conditions for the 3D fluid simulation. We also introduce a novel technique for removing visual artifacts caused by numerical errors in 3D fluid solvers: we use experimental data to estimate the artificial dispersion caused by the 3D solver and we then carefully tune the wave speeds of the 2D solver to match it, effectively eliminating any differences in wave behavior across the boundary. To the best of our knowledge, this is the first time such a empirically driven error compensation approach has been used to remove coupling errors from a physics simulator.\r\nOur coupled simulation approach leverages the strengths of each simulation technique, animating large environments with seamless transitions between 2D and 3D physics."}],"doi":"10.1111/cgf.14478","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-03641349/","open_access":"1"}],"intvolume":"        41","publisher":"Wiley","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"ChWo"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000802723900027"]},"date_published":"2022-05-01T00:00:00Z","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2022-06-05T22:01:49Z","publication":"Computer Graphics Forum","date_updated":"2023-08-02T06:44:05Z","article_type":"original","page":"343-353","oa":1,"year":"2022"},{"publication_identifier":{"issn":["0895-4801"]},"status":"public","publication_status":"published","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.","title":"A quantitative Helly-type theorem: Containment in a homothet","author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"first_name":"Marton","last_name":"Naszodi","full_name":"Naszodi, Marton"}],"_id":"11435","abstract":[{"text":"We introduce a new variant of quantitative Helly-type theorems: the minimal homothetic distance of the intersection of a family of convex sets to the intersection of a subfamily of a fixed size. As an application, we establish the following quantitative Helly-type result for the diameter. If $K$ is the intersection of finitely many convex bodies in $\\mathbb{R}^d$, then one can select $2d$ of these bodies whose intersection is of diameter at most $(2d)^3{diam}(K)$. The best previously known estimate, due to Brazitikos [Bull. Hellenic Math. Soc., 62 (2018), pp. 19--25], is $c d^{11/2}$. Moreover, we confirm that the multiplicative factor $c d^{1/2}$ conjectured by Bárány, Katchalski, and Pach [Proc. Amer. Math. Soc., 86 (1982), pp. 109--114] cannot be improved. The bounds above follow from our key result that concerns sparse approximation of a convex polytope by the convex hull of a well-chosen subset of its vertices: Assume that $Q \\subset {\\mathbb R}^d$ is a polytope whose centroid is the origin. Then there exist at most 2d vertices of $Q$ whose convex hull $Q^{\\prime \\prime}$ satisfies $Q \\subset - 8d^3 Q^{\\prime \\prime}.$","lang":"eng"}],"issue":"2","doi":"10.1137/21M1403308","arxiv":1,"article_processing_charge":"No","volume":36,"citation":{"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>","short":"G. Ivanov, M. Naszodi, SIAM Journal on Discrete Mathematics 36 (2022) 951–957.","ista":"Ivanov G, Naszodi M. 2022. A quantitative Helly-type theorem: Containment in a homothet. SIAM Journal on Discrete Mathematics. 36(2), 951–957.","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.","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>","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>.","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>."},"day":"11","month":"04","oa_version":"Preprint","publication":"SIAM Journal on Discrete Mathematics","date_updated":"2023-10-18T06:58:03Z","page":"951-957","article_type":"original","oa":1,"year":"2022","publisher":"Society for Industrial and Applied Mathematics","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2103.04122","open_access":"1"}],"intvolume":"        36","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-04-11T00:00:00Z","external_id":{"isi":["000793158200002"],"arxiv":["2103.04122"]},"date_created":"2022-06-05T22:01:50Z","scopus_import":"1"},{"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2111.13194"}],"intvolume":"        17","publisher":"American Physical Society","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"date_created":"2022-06-07T08:07:59Z","external_id":{"isi":["000880670300001"],"arxiv":["2111.13194"]},"date_published":"2022-05-19T00:00:00Z","date_updated":"2023-08-03T07:18:34Z","publication":"Physical Review Applied","article_type":"original","article_number":"054031","oa":1,"keyword":["General Physics and Astronomy"],"year":"2022","arxiv":1,"volume":17,"article_processing_charge":"No","month":"05","day":"19","citation":{"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>","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.","short":"V. Li, F.R. Diorico, O. Hosten, Physical Review Applied 17 (2022).","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>","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.","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>.","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>."},"oa_version":"Preprint","publication_identifier":{"issn":["2331-7019"]},"status":"public","publication_status":"published","acknowledgement":"This work was supported by IST Austria. The authors thank Yueheng Shi for technical contributions.","_id":"11438","author":[{"id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","first_name":"Vyacheslav","full_name":"Li, Vyacheslav","last_name":"Li"},{"last_name":"Diorico","full_name":"Diorico, Fritz R","first_name":"Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"}],"title":"Laser frequency-offset locking at 10-Hz-level instability using hybrid electronic filters","doi":"10.1103/physrevapplied.17.054031","issue":"5","abstract":[{"lang":"eng","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."}]},{"page":"1-26","publication":"Research in Computational Topology 2","date_updated":"2022-06-07T08:32:42Z","alternative_title":["Association for Women in Mathematics Series"],"year":"2022","oa":1,"type":"book_chapter","quality_controlled":"1","language":[{"iso":"eng"}],"series_title":"AWMS","publisher":"Springer Nature","intvolume":"        30","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2102.11397"}],"external_id":{"arxiv":["2102.11397"]},"date_published":"2022-01-27T00:00:00Z","date_created":"2022-06-07T08:21:11Z","scopus_import":"1","department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","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.","status":"public","place":"Cham","ec_funded":1,"publication_identifier":{"isbn":["9783030955182"],"eisbn":["9783030955199"]},"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"}],"edition":"1","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."}],"doi":"10.1007/978-3-030-95519-9_1","title":"The persistent homology of dual digital image constructions","author":[{"first_name":"Bea","last_name":"Bleile","full_name":"Bleile, Bea"},{"first_name":"Adélie","last_name":"Garin","full_name":"Garin, Adélie"},{"first_name":"Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss","full_name":"Heiss, Teresa","orcid":"0000-0002-1780-2689"},{"first_name":"Kelly","full_name":"Maggs, Kelly","last_name":"Maggs"},{"first_name":"Vanessa","last_name":"Robins","full_name":"Robins, Vanessa"}],"_id":"11440","editor":[{"first_name":"Ellen","last_name":"Gasparovic","full_name":"Gasparovic, Ellen"},{"first_name":"Vanessa","last_name":"Robins","full_name":"Robins, Vanessa"},{"full_name":"Turner, Katharine","last_name":"Turner","first_name":"Katharine"}],"article_processing_charge":"No","volume":30,"arxiv":1,"oa_version":"Preprint","citation":{"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>","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.","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>","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.","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.","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>."},"day":"27","month":"01"},{"publication_status":"published","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","status":"public","ec_funded":1,"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"project":[{"grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"abstract":[{"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. ","lang":"eng"}],"issue":"4","doi":"10.1145/3528223.3530144","title":"Closed-loop control of direct ink writing via reinforcement learning","author":[{"last_name":"Piovarci","full_name":"Piovarci, Michael","first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E"},{"last_name":"Foshey","full_name":"Foshey, Michael","first_name":"Michael"},{"first_name":"Jie","full_name":"Xu, Jie","last_name":"Xu"},{"full_name":"Erps, Timothy","last_name":"Erps","first_name":"Timothy"},{"first_name":"Vahid","full_name":"Babaei, Vahid","last_name":"Babaei"},{"first_name":"Piotr","full_name":"Didyk, Piotr","last_name":"Didyk"},{"last_name":"Rusinkiewicz","full_name":"Rusinkiewicz, Szymon","first_name":"Szymon"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385"}],"_id":"11442","has_accepted_license":"1","article_processing_charge":"No","volume":41,"file":[{"success":1,"date_updated":"2022-06-28T08:32:58Z","access_level":"open_access","checksum":"27f6fe41c6ff84d50445cc9b0176d45b","content_type":"application/pdf","file_name":"2022_ACM_acceptedversion_Piovarci.pdf","file_size":33994829,"relation":"main_file","creator":"dernst","file_id":"11467","date_created":"2022-06-28T08:32:58Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"oa_version":"Submitted Version","citation":{"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>.","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.","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>","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>","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."},"day":"01","ddc":["000"],"file_date_updated":"2022-06-28T08:32:58Z","month":"06","related_material":{"link":[{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/machine-learning-3d-printing-fluids/"}]},"article_number":"112","article_type":"original","publication":"ACM Transactions on Graphics","date_updated":"2023-05-31T12:38:21Z","year":"2022","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","intvolume":"        41","date_published":"2022-06-01T00:00:00Z","external_id":{"arxiv":["2201.11819"]},"date_created":"2022-06-10T06:41:47Z","department":[{"_id":"BeBi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"page":"4209-4250","article_type":"original","publication":"Transactions of the American Mathematical Society","date_updated":"2023-08-03T07:17:37Z","year":"2022","oa":1,"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"American Mathematical Society","intvolume":"       375","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2006.08836"}],"date_published":"2022-06-01T00:00:00Z","external_id":{"arxiv":["2006.08836"],"isi":["000798461500001"]},"date_created":"2022-06-12T22:01:45Z","scopus_import":"1","department":[{"_id":"MaKw"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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. ","publication_status":"published","status":"public","publication_identifier":{"issn":["0002-9947"],"eissn":["1088-6850"]},"abstract":[{"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.","lang":"eng"}],"issue":"6","doi":"10.1090/tran/8614","title":"Extension complexity of low-dimensional polytopes","author":[{"orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","first_name":"Matthew Alan","full_name":"Kwan, Matthew Alan","last_name":"Kwan"},{"first_name":"Lisa","full_name":"Sauermann, Lisa","last_name":"Sauermann"},{"last_name":"Zhao","full_name":"Zhao, Yufei","first_name":"Yufei"}],"_id":"11443","volume":375,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","citation":{"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>.","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>.","apa":"Kwan, M. A., Sauermann, L., &#38; Zhao, Y. (2022). Extension complexity of low-dimensional polytopes. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8614\">https://doi.org/10.1090/tran/8614</a>","ieee":"M. A. Kwan, L. Sauermann, and Y. Zhao, “Extension complexity of low-dimensional polytopes,” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6. American Mathematical Society, pp. 4209–4250, 2022.","ista":"Kwan MA, Sauermann L, Zhao Y. 2022. Extension complexity of low-dimensional polytopes. Transactions of the American Mathematical Society. 375(6), 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>","short":"M.A. Kwan, L. Sauermann, Y. Zhao, Transactions of the American Mathematical Society 375 (2022) 4209–4250."},"day":"01","month":"06"},{"publication_identifier":{"issn":["1758-3489"],"eissn":["1758-3497"]},"status":"public","publication_status":"published","_id":"11444","author":[{"id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","first_name":"Clara A","full_name":"Chlebak, Clara A","last_name":"Chlebak","orcid":"0000-0002-3385-3865"},{"first_name":"Peter H.","full_name":"Reid, Peter H.","last_name":"Reid"}],"title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","doi":"10.3366/lih.2022.0097","issue":"1","abstract":[{"text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride.","lang":"eng"}],"article_processing_charge":"No","volume":38,"month":"04","day":"01","citation":{"apa":"Chlebak, C. A., &#38; Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. Edinburgh University Press. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” <i>Library and Information History</i>, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41.","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. <i>Library and Information History</i>. 2022;38(1):23-41. doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>. Edinburgh University Press, 2022. <a href=\"https://doi.org/10.3366/lih.2022.0097\">https://doi.org/10.3366/lih.2022.0097</a>.","mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” <i>Library and Information History</i>, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:<a href=\"https://doi.org/10.3366/lih.2022.0097\">10.3366/lih.2022.0097</a>."},"oa_version":"Submitted Version","date_updated":"2023-02-21T09:51:29Z","publication":"Library and Information History","article_type":"original","page":"23-41","oa":1,"year":"2022","main_file_link":[{"url":"https://rgu-repository.worktribe.com/output/1635939","open_access":"1"}],"intvolume":"        38","publisher":"Edinburgh University Press","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"E-Lib"}],"scopus_import":"1","date_created":"2022-06-12T22:01:45Z","date_published":"2022-04-01T00:00:00Z"},{"isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":"        84","publisher":"Springer Nature","external_id":{"isi":["000812509800001"]},"date_published":"2022-06-17T00:00:00Z","scopus_import":"1","date_created":"2022-06-17T16:16:15Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11538-022-01118-z"}]},"article_type":"original","article_number":"74","publication":"Bulletin of Mathematical Biology","date_updated":"2023-08-03T07:20:53Z","year":"2022","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"],"oa":1,"has_accepted_license":"1","volume":84,"article_processing_charge":"Yes (via OA deal)","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11455","date_created":"2022-06-20T07:51:32Z","file_name":"2022_BulletinMathBiology_Saona.pdf","creator":"dernst","relation":"main_file","file_size":463025,"success":1,"date_updated":"2022-06-20T07:51:32Z","access_level":"open_access","checksum":"05a1fe7d10914a00c2bca9b447993a65","content_type":"application/pdf"}],"oa_version":"Published Version","day":"17","citation":{"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>.","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>.","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>","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>","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.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022)."},"ddc":["510","570"],"month":"06","file_date_updated":"2022-06-20T07:51:32Z","publication_status":"published","status":"public","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.","ec_funded":1,"publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"name":"Evolutionary analysis of gene regulation","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","grant_number":"I05127"}],"issue":"8","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"doi":"10.1007/s11538-022-01029-z","author":[{"orcid":"0000-0001-5103-038X","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov"},{"full_name":"Khudiakova, Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","first_name":"Kseniia","orcid":"0000-0002-6246-1465"}],"title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","_id":"11447"},{"project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"publication_identifier":{"issn":["2050-084X"]},"ec_funded":1,"publication_status":"published","status":"public","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.","_id":"11448","author":[{"orcid":"0000-0001-9139-5383","first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","full_name":"Gonzalez Somermeyer, 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","full_name":"Bozhanova, Nina G","last_name":"Bozhanova"},{"full_name":"Igolkina, Anna A","last_name":"Igolkina","first_name":"Anna A"},{"first_name":"Jens","full_name":"Meiler, Jens","last_name":"Meiler"},{"last_name":"Alaball Pujol","full_name":"Alaball Pujol, Maria-Elisenda","first_name":"Maria-Elisenda"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V","first_name":"Ekaterina V"},{"last_name":"Sarkisyan","full_name":"Sarkisyan, Karen S","first_name":"Karen S"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"}],"title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","doi":"10.7554/elife.75842","abstract":[{"lang":"eng","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."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"success":1,"date_updated":"2022-06-20T07:44:19Z","access_level":"open_access","content_type":"application/pdf","checksum":"7573c28f44028ab0cc81faef30039e44","file_name":"2022_eLife_Somermeyer.pdf","file_size":5297213,"relation":"main_file","creator":"dernst","file_id":"11454","date_created":"2022-06-20T07:44:19Z"}],"volume":11,"article_processing_charge":"No","has_accepted_license":"1","ddc":["570"],"month":"05","file_date_updated":"2022-06-20T07:44:19Z","day":"05","citation":{"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).","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.","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>","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.","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>.","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>."},"oa_version":"Published Version","date_updated":"2023-08-03T07:20:15Z","publication":"eLife","article_type":"original","article_number":"75842","oa":1,"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"year":"2022","intvolume":"        11","publisher":"eLife Sciences Publications","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"scopus_import":"1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"date_created":"2022-06-18T09:06:59Z","external_id":{"isi":["000799197200001"]},"date_published":"2022-05-05T00:00:00Z"},{"oa_version":"Published Version","citation":{"ista":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. 13(6), 438–453.e5.","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>","short":"D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, Cell Systems 13 (2022) 438–453.e5.","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>","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.","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>."},"day":"15","pmid":1,"month":"06","volume":13,"article_processing_charge":"No","abstract":[{"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.","lang":"eng"}],"issue":"6","doi":"10.1016/j.cels.2022.03.006","title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","author":[{"first_name":"Donovan J.","last_name":"Anderson","full_name":"Anderson, Donovan J."},{"last_name":"Pauler","full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mckenna, Aaron","last_name":"Mckenna","first_name":"Aaron"},{"full_name":"Shendure, Jay","last_name":"Shendure","first_name":"Jay"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Marshall S.","last_name":"Horwitz","full_name":"Horwitz, Marshall S."}],"_id":"11449","publication_status":"published","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.","status":"public","ec_funded":1,"publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","grant_number":"LS13-002","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"}],"external_id":{"pmid":["35452605"],"isi":["000814124400002"]},"date_published":"2022-06-15T00:00:00Z","date_created":"2022-06-19T22:01:57Z","scopus_import":"1","department":[{"_id":"SiHi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Elsevier","intvolume":"        13","main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2022.03.006","open_access":"1"}],"year":"2022","oa":1,"page":"438-453.e5","article_type":"original","publication":"Cell Systems","date_updated":"2023-08-03T07:19:43Z"},{"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Wiley","intvolume":"        61","external_id":{"isi":["000811084000001"],"pmid":["35612297"]},"date_published":"2022-08-01T00:00:00Z","date_created":"2022-06-19T22:01:58Z","scopus_import":"1","department":[{"_id":"MaIb"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"relation":"research_data","status":"public","id":"11695"}]},"article_number":"e202207013","article_type":"original","publication":"Angewandte Chemie - International Edition","date_updated":"2023-08-03T07:19:12Z","year":"2022","oa":1,"has_accepted_license":"1","article_processing_charge":"No","volume":61,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2022-07-29T09:29:20Z","file_id":"11696","date_updated":"2022-07-29T09:29:20Z","success":1,"checksum":"2a3ee0bb59e044b808ebe85cd94ac899","content_type":"application/pdf","access_level":"open_access","file_size":1303202,"relation":"main_file","creator":"dernst","file_name":"2022_AngewandteChemieInternat_Parvizian.pdf"}],"oa_version":"Published Version","citation":{"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.","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>","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).","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.","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>","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>.","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>."},"day":"01","ddc":["540"],"file_date_updated":"2022-07-29T09:29:20Z","month":"08","pmid":1,"publication_status":"published","status":"public","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.","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"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."}],"issue":"31","doi":"10.1002/anie.202207013","title":"The chemistry of Cu₃N and Cu₃PdN nanocrystals","author":[{"last_name":"Parvizian","full_name":"Parvizian, Mahsa","first_name":"Mahsa"},{"full_name":"Duràn Balsa, Alejandra","last_name":"Duràn Balsa","first_name":"Alejandra"},{"first_name":"Rohan","last_name":"Pokratath","full_name":"Pokratath, Rohan"},{"full_name":"Kalha, Curran","last_name":"Kalha","first_name":"Curran"},{"orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho"},{"full_name":"Van Den Eynden, Dietger","last_name":"Van Den Eynden","first_name":"Dietger"},{"orcid":"0000-0001-5013-2843","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","full_name":"Ibáñez, Maria"},{"first_name":"Anna","last_name":"Regoutz","full_name":"Regoutz, Anna"},{"first_name":"Jonathan","last_name":"De Roo","full_name":"De Roo, Jonathan"}],"_id":"11451"},{"publication":"Behavioral Neurogenetics","date_updated":"2023-02-21T09:51:55Z","page":"277-294","year":"2022","alternative_title":["Neuromethods"],"series_title":"NM","publisher":"Springer Nature","intvolume":"       181","type":"book_chapter","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"MaDe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-04T00:00:00Z","date_created":"2022-06-20T08:10:34Z","scopus_import":"1","publication_identifier":{"eissn":["1940-6045"],"issn":["0893-2336"],"eisbn":["9781071623213"],"isbn":["9781071623206"]},"project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"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).","publication_status":"published","status":"public","place":"New York","ec_funded":1,"title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","author":[{"id":"C407B586-6052-11E9-B3AE-7006E6697425","first_name":"Murat","full_name":"Artan, Murat","last_name":"Artan"},{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"_id":"11456","editor":[{"full_name":"Yamamoto, Daisuke","last_name":"Yamamoto","first_name":"Daisuke"}],"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."}],"doi":"10.1007/978-1-0716-2321-3_15","article_processing_charge":"No","volume":181,"citation":{"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>.","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>.","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.","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.","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>"},"day":"04","month":"06","oa_version":"None"},{"article_processing_charge":"No","has_accepted_license":"1","file":[{"relation":"main_file","creator":"dernst","file_size":318697,"file_name":"2022_PLDI_Zikelic.pdf","date_updated":"2022-06-27T07:38:21Z","success":1,"checksum":"7eb915a2ca5b5ce4729321f33b2e16e1","content_type":"application/pdf","access_level":"open_access","date_created":"2022-06-27T07:38:21Z","file_id":"11466"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"arxiv":1,"oa_version":"Published Version","conference":{"end_date":"2022-06-17","location":"San Diego, CA, United States","start_date":"2022-06-13","name":"PLDI: Programming Language Design and Implementation"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ddc":["000"],"month":"06","file_date_updated":"2022-06-27T07:38:21Z","citation":{"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>.","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>.","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.","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.","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>","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."},"day":"09","ec_funded":1,"status":"public","publication_status":"published","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).","project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"publication_identifier":{"isbn":["9781450392655"]},"doi":"10.1145/3519939.3523435","abstract":[{"lang":"eng","text":"We present a novel approach to differential cost analysis that, given a program revision, attempts to statically bound the difference in resource usage, or cost, between the two program versions. Differential cost analysis is particularly interesting because of the many compelling applications for it, such as detecting resource-use regressions at code-review time or proving the absence of certain side-channel vulnerabilities. One prior approach to differential cost analysis is to apply relational reasoning that conceptually constructs a product program on which one can over-approximate the difference in costs between the two program versions. However, a significant challenge in any relational approach is effectively aligning the program versions to get precise results. In this paper, our key insight is that we can avoid the need for and the limitations of program alignment if, instead, we bound the difference of two cost-bound summaries rather than directly bounding the concrete cost difference. In particular, our method computes a threshold value for the maximal difference in cost between two program versions simultaneously using two kinds of cost-bound summaries---a potential function that evaluates to an upper bound for the cost incurred in the first program and an anti-potential function that evaluates to a lower bound for the cost incurred in the second. Our method has a number of desirable properties: it can be fully automated, it allows optimizing the threshold value on relative cost, it is suitable for programs that are not syntactically similar, and it supports non-determinism. We have evaluated an implementation of our approach on a number of program pairs collected from the literature, and we find that our method computes tight threshold values on relative cost in most examples."}],"_id":"11459","title":"Differential cost analysis with simultaneous potentials and anti-potentials","author":[{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"},{"first_name":"Bor-Yuh Evan","full_name":"Chang, Bor-Yuh Evan","last_name":"Chang"},{"first_name":"Pauline","full_name":"Bolignano, Pauline","last_name":"Bolignano"},{"full_name":"Raimondi, Franco","last_name":"Raimondi","first_name":"Franco"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","isi":1,"publisher":"Association for Computing Machinery","date_created":"2022-06-21T09:26:15Z","scopus_import":"1","external_id":{"isi":["000850435600030"],"arxiv":["2204.00870"]},"date_published":"2022-06-09T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"page":"442-457","date_updated":"2025-07-14T09:09:54Z","publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation","year":"2022","oa":1},{"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1,"publisher":"Springer Nature","intvolume":"        13","date_created":"2022-06-23T14:28:55Z","external_id":{"isi":["000814641400001"]},"date_published":"2022-06-22T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"SiHi"}],"article_number":"27","article_type":"original","related_material":{"link":[{"url":"https://doi.org/10.1186/s13229-023-00539-4","relation":"erratum"}]},"date_updated":"2023-08-03T07:21:32Z","publication":"Molecular Autism","keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"],"year":"2022","oa":1,"volume":13,"article_processing_charge":"No","has_accepted_license":"1","file":[{"checksum":"525d2618e855139089bbfc3e3d49d1b2","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-06-24T08:22:59Z","success":1,"relation":"main_file","file_size":7552298,"creator":"dernst","file_name":"2022_MolecularAutism_Schaaf.pdf","date_created":"2022-06-24T08:22:59Z","file_id":"11461"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","month":"06","file_date_updated":"2022-06-24T08:22:59Z","ddc":["570"],"citation":{"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>.","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>.","ama":"Schaaf ZA, Tat L, Cannizzaro N, et al. WDFY3 mutation alters laminar position and morphology of cortical neurons. <i>Molecular Autism</i>. 2022;13. doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","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.","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>"},"day":"22","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_status":"published","status":"public","publication_identifier":{"issn":["2040-2392"]},"doi":"10.1186/s13229-022-00508-3","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."}],"_id":"11460","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","author":[{"full_name":"Schaaf, Zachary A.","last_name":"Schaaf","first_name":"Zachary A."},{"first_name":"Lyvin","full_name":"Tat, Lyvin","last_name":"Tat"},{"last_name":"Cannizzaro","full_name":"Cannizzaro, Noemi","first_name":"Noemi"},{"first_name":"Ralph","full_name":"Green, Ralph","last_name":"Green"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"last_name":"Zarbalis","full_name":"Zarbalis, Konstantinos S.","first_name":"Konstantinos S."}]}]