[{"scopus_import":"1","external_id":{"isi":["000798461500001"],"arxiv":["2006.08836"]},"date_updated":"2023-08-03T07:17:37Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"article_type":"original","year":"2022","oa_version":"Preprint","volume":375,"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2006.08836"}],"date_published":"2022-06-01T00:00:00Z","_id":"11443","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"}],"arxiv":1,"article_processing_charge":"No","issue":"6","language":[{"iso":"eng"}],"doi":"10.1090/tran/8614","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. ","day":"01","type":"journal_article","author":[{"orcid":"0000-0002-4003-7567","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3","last_name":"Kwan","full_name":"Kwan, Matthew Alan","first_name":"Matthew Alan"},{"last_name":"Sauermann","full_name":"Sauermann, Lisa","first_name":"Lisa"},{"first_name":"Yufei","full_name":"Zhao, Yufei","last_name":"Zhao"}],"citation":{"mla":"Kwan, Matthew Alan, et al. “Extension Complexity of Low-Dimensional Polytopes.” <i>Transactions of the American Mathematical Society</i>, vol. 375, no. 6, American Mathematical Society, 2022, pp. 4209–50, doi:<a href=\"https://doi.org/10.1090/tran/8614\">10.1090/tran/8614</a>.","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.","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>.","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>","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."},"title":"Extension complexity of low-dimensional polytopes","publication":"Transactions of the American Mathematical Society","quality_controlled":"1","department":[{"_id":"MaKw"}],"intvolume":"       375","status":"public","publisher":"American Mathematical Society","isi":1,"month":"06","date_created":"2022-06-12T22:01:45Z","page":"4209-4250"},{"publication_identifier":{"issn":["1758-3489"],"eissn":["1758-3497"]},"scopus_import":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2023-02-21T09:51:29Z","year":"2022","oa_version":"Submitted Version","article_type":"original","volume":38,"oa":1,"main_file_link":[{"open_access":"1","url":"https://rgu-repository.worktribe.com/output/1635939"}],"publication_status":"published","_id":"11444","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"}],"date_published":"2022-04-01T00:00:00Z","article_processing_charge":"No","issue":"1","doi":"10.3366/lih.2022.0097","language":[{"iso":"eng"}],"type":"journal_article","author":[{"first_name":"Clara A","full_name":"Chlebak, Clara A","last_name":"Chlebak","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","orcid":"0000-0002-3385-3865"},{"full_name":"Reid, Peter H.","first_name":"Peter H.","last_name":"Reid"}],"day":"01","title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","citation":{"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.","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.","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>.","short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","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>","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>"},"intvolume":"        38","status":"public","publication":"Library and Information History","department":[{"_id":"E-Lib"}],"quality_controlled":"1","publisher":"Edinburgh University Press","date_created":"2022-06-12T22:01:45Z","month":"04","page":"23-41"},{"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"],"language":[{"iso":"eng"}],"doi":"10.1007/s11538-022-01029-z","ddc":["510","570"],"related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"project":[{"_id":"26580278-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales"},{"_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","name":"Evolutionary analysis of gene regulation","grant_number":"I05127"}],"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.","day":"17","type":"journal_article","author":[{"orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","full_name":"Saona Urmeneta, Raimundo J","first_name":"Raimundo J"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","full_name":"Khudiakova, Kseniia","first_name":"Kseniia"}],"citation":{"short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (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>","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>","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>.","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.","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.","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>."},"ec_funded":1,"title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","publication":"Bulletin of Mathematical Biology","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"quality_controlled":"1","intvolume":"        84","status":"public","publisher":"Springer Nature","isi":1,"month":"06","date_created":"2022-06-17T16:16:15Z","external_id":{"isi":["000812509800001"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T07:20:53Z","publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"article_type":"original","year":"2022","has_accepted_license":"1","oa_version":"Published Version","file_date_updated":"2022-06-20T07:51:32Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":84,"publication_status":"published","oa":1,"article_number":"74","file":[{"file_id":"11455","relation":"main_file","content_type":"application/pdf","success":1,"date_created":"2022-06-20T07:51:32Z","file_size":463025,"creator":"dernst","file_name":"2022_BulletinMathBiology_Saona.pdf","access_level":"open_access","date_updated":"2022-06-20T07:51:32Z","checksum":"05a1fe7d10914a00c2bca9b447993a65"}],"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"}],"_id":"11447","date_published":"2022-06-17T00:00:00Z","article_processing_charge":"Yes (via OA deal)","issue":"8"},{"oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":11,"file_date_updated":"2022-06-20T07:44:19Z","article_processing_charge":"No","_id":"11448","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."}],"date_published":"2022-05-05T00:00:00Z","article_number":"75842","file":[{"creator":"dernst","file_size":5297213,"file_name":"2022_eLife_Somermeyer.pdf","access_level":"open_access","date_updated":"2022-06-20T07:44:19Z","checksum":"7573c28f44028ab0cc81faef30039e44","relation":"main_file","file_id":"11454","content_type":"application/pdf","success":1,"date_created":"2022-06-20T07:44:19Z"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_identifier":{"issn":["2050-084X"]},"external_id":{"isi":["000799197200001"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T07:20:15Z","has_accepted_license":"1","oa_version":"Published Version","year":"2022","article_type":"original","isi":1,"publisher":"eLife Sciences Publications","status":"public","intvolume":"        11","publication":"eLife","department":[{"_id":"GradSch"},{"_id":"FyKo"}],"quality_controlled":"1","date_created":"2022-06-18T09:06:59Z","month":"05","project":[{"grant_number":"771209","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"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.","ddc":["570"],"doi":"10.7554/elife.75842","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"language":[{"iso":"eng"}],"title":"Heterogeneity of the GFP fitness landscape and data-driven protein design","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>","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>","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).","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>.","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.","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."},"ec_funded":1,"author":[{"first_name":"Louisa","full_name":"Gonzalez Somermeyer, Louisa","last_name":"Gonzalez Somermeyer","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9139-5383"},{"last_name":"Fleiss","full_name":"Fleiss, Aubin","first_name":"Aubin"},{"last_name":"Mishin","full_name":"Mishin, Alexander S","first_name":"Alexander S"},{"first_name":"Nina G","full_name":"Bozhanova, Nina G","last_name":"Bozhanova"},{"full_name":"Igolkina, Anna A","first_name":"Anna A","last_name":"Igolkina"},{"first_name":"Jens","full_name":"Meiler, Jens","last_name":"Meiler"},{"last_name":"Alaball Pujol","full_name":"Alaball Pujol, Maria-Elisenda","first_name":"Maria-Elisenda"},{"first_name":"Ekaterina V","full_name":"Putintseva, Ekaterina V","last_name":"Putintseva"},{"last_name":"Sarkisyan","first_name":"Karen S","full_name":"Sarkisyan, Karen S"},{"first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","day":"05"},{"title":"Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development","ec_funded":1,"citation":{"chicago":"Anderson, Donovan J., Florian Pauler, Aaron Mckenna, Jay Shendure, Simon Hippenmeyer, and Marshall S. Horwitz. “Simultaneous Brain Cell Type and Lineage Determined by ScRNA-Seq Reveals Stereotyped Cortical Development.” <i>Cell Systems</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>.","ista":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. 2022. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. Cell Systems. 13(6), 438–453.e5.","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>.","short":"D.J. Anderson, F. Pauler, A. Mckenna, J. Shendure, S. Hippenmeyer, M.S. Horwitz, Cell Systems 13 (2022) 438–453.e5.","ama":"Anderson DJ, Pauler F, Mckenna A, Shendure J, Hippenmeyer S, Horwitz MS. Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. 2022;13(6):438-453.e5. doi:<a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">10.1016/j.cels.2022.03.006</a>","apa":"Anderson, D. J., Pauler, F., Mckenna, A., Shendure, J., Hippenmeyer, S., &#38; Horwitz, M. S. (2022). Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development. <i>Cell Systems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cels.2022.03.006\">https://doi.org/10.1016/j.cels.2022.03.006</a>"},"author":[{"last_name":"Anderson","first_name":"Donovan J.","full_name":"Anderson, Donovan J."},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mckenna","first_name":"Aaron","full_name":"Mckenna, Aaron"},{"first_name":"Jay","full_name":"Shendure, Jay","last_name":"Shendure"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon"},{"last_name":"Horwitz","first_name":"Marshall S.","full_name":"Horwitz, Marshall S."}],"type":"journal_article","day":"15","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.","pmid":1,"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002"}],"doi":"10.1016/j.cels.2022.03.006","language":[{"iso":"eng"}],"page":"438-453.e5","date_created":"2022-06-19T22:01:57Z","month":"06","isi":1,"publisher":"Elsevier","status":"public","intvolume":"        13","quality_controlled":"1","department":[{"_id":"SiHi"}],"publication":"Cell Systems","oa_version":"Published Version","year":"2022","article_type":"original","publication_identifier":{"eissn":["2405-4720"],"issn":["2405-4712"]},"date_updated":"2023-08-03T07:19:43Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"pmid":["35452605"],"isi":["000814124400002"]},"issue":"6","article_processing_charge":"No","_id":"11449","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"}],"date_published":"2022-06-15T00:00:00Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cels.2022.03.006","open_access":"1"}],"publication_status":"published","volume":13},{"date_created":"2022-06-19T22:01:58Z","month":"08","status":"public","intvolume":"        61","quality_controlled":"1","department":[{"_id":"MaIb"}],"publication":"Angewandte Chemie - International Edition","isi":1,"publisher":"Wiley","author":[{"first_name":"Mahsa","full_name":"Parvizian, Mahsa","last_name":"Parvizian"},{"first_name":"Alejandra","full_name":"Duràn Balsa, Alejandra","last_name":"Duràn Balsa"},{"full_name":"Pokratath, Rohan","first_name":"Rohan","last_name":"Pokratath"},{"full_name":"Kalha, Curran","first_name":"Curran","last_name":"Kalha"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598","first_name":"Seungho","full_name":"Lee, Seungho","last_name":"Lee"},{"first_name":"Dietger","full_name":"Van Den Eynden, Dietger","last_name":"Van Den Eynden"},{"first_name":"Maria","full_name":"Ibáñez, Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843"},{"last_name":"Regoutz","first_name":"Anna","full_name":"Regoutz, Anna"},{"full_name":"De Roo, Jonathan","first_name":"Jonathan","last_name":"De Roo"}],"type":"journal_article","day":"01","title":"The chemistry of Cu₃N and Cu₃PdN nanocrystals","citation":{"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).","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>","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>","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.","ieee":"M. Parvizian <i>et al.</i>, “The chemistry of Cu₃N and Cu₃PdN nanocrystals,” <i>Angewandte Chemie - International Edition</i>, vol. 61, no. 31. Wiley, 2022.","chicago":"Parvizian, Mahsa, Alejandra Duràn Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van Den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “The Chemistry of Cu₃N and Cu₃PdN Nanocrystals.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/anie.202207013\">https://doi.org/10.1002/anie.202207013</a>.","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>."},"doi":"10.1002/anie.202207013","ddc":["540"],"language":[{"iso":"eng"}],"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.","related_material":{"record":[{"status":"public","id":"11695","relation":"research_data"}]},"pmid":1,"date_published":"2022-08-01T00:00:00Z","_id":"11451","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."}],"file":[{"file_name":"2022_AngewandteChemieInternat_Parvizian.pdf","creator":"dernst","file_size":1303202,"checksum":"2a3ee0bb59e044b808ebe85cd94ac899","date_updated":"2022-07-29T09:29:20Z","access_level":"open_access","content_type":"application/pdf","file_id":"11696","relation":"main_file","date_created":"2022-07-29T09:29:20Z","success":1}],"article_number":"e202207013","issue":"31","article_processing_charge":"No","volume":61,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2022-07-29T09:29:20Z","oa":1,"publication_status":"published","has_accepted_license":"1","year":"2022","oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"date_updated":"2023-08-03T07:19:12Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"pmid":["35612297"],"isi":["000811084000001"]},"scopus_import":"1"},{"editor":[{"first_name":"Daisuke","full_name":"Yamamoto, Daisuke","last_name":"Yamamoto"}],"oa_version":"None","year":"2022","publication_identifier":{"eisbn":["9781071623213"],"eissn":["1940-6045"],"isbn":["9781071623206"],"issn":["0893-2336"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-21T09:51:55Z","article_processing_charge":"No","date_published":"2022-06-04T00:00:00Z","_id":"11456","abstract":[{"lang":"eng","text":"The proteomes of specialized structures, and the interactomes of proteins of interest, provide entry points to elucidate the functions of molecular machines. Here, we review a proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes. Although the focus is on C. elegans neurons, the method is applicable regardless of cell type. We describe detailed extraction procedures that solubilize the bulk of C. elegans proteins and highlight the importance of tagging endogenous genes, to ensure physiological expression levels. We review issues associated with non-specific background noise and the importance of appropriate controls. As proof of principle, we review our analysis of the interactome of a presynaptic active zone protein, ELKS-1. Our aim is to provide a detailed protocol for TurboID-based proximity labeling in C. elegans and to highlight its potential and its limitations to characterize protein complexes and subcellular compartments in this animal."}],"publication_status":"published","volume":181,"title":"Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling","citation":{"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>","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>","short":"M. Artan, M. de Bono, in:, D. Yamamoto (Ed.), Behavioral Neurogenetics, Springer Nature, New York, 2022, pp. 277–294.","mla":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, vol. 181, Springer Nature, 2022, pp. 277–94, doi:<a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">10.1007/978-1-0716-2321-3_15</a>.","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.","ista":"Artan M, de Bono M. 2022.Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling. In: Behavioral Neurogenetics. Neuromethods, vol. 181, 277–294.","chicago":"Artan, Murat, and Mario de Bono. “Proteomic Analysis of C. Elegans Neurons Using TurboID-Based Proximity Labeling.” In <i>Behavioral Neurogenetics</i>, edited by Daisuke Yamamoto, 181:277–94. NM. New York: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-1-0716-2321-3_15\">https://doi.org/10.1007/978-1-0716-2321-3_15</a>."},"ec_funded":1,"type":"book_chapter","author":[{"first_name":"Murat","full_name":"Artan, Murat","last_name":"Artan","id":"C407B586-6052-11E9-B3AE-7006E6697425"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","first_name":"Mario","last_name":"de Bono"}],"alternative_title":["Neuromethods"],"day":"04","project":[{"_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"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).","doi":"10.1007/978-1-0716-2321-3_15","language":[{"iso":"eng"}],"page":"277-294","series_title":"NM","date_created":"2022-06-20T08:10:34Z","month":"06","place":"New York","publisher":"Springer Nature","intvolume":"       181","status":"public","publication":"Behavioral Neurogenetics","quality_controlled":"1","department":[{"_id":"MaDe"}]},{"oa_version":"Published Version","has_accepted_license":"1","year":"2022","publication_identifier":{"isbn":["9781450392655"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-07-14T09:09:54Z","external_id":{"isi":["000850435600030"],"arxiv":["2204.00870"]},"scopus_import":"1","article_processing_charge":"No","arxiv":1,"_id":"11459","date_published":"2022-06-09T00:00:00Z","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."}],"file":[{"content_type":"application/pdf","file_id":"11466","relation":"main_file","success":1,"date_created":"2022-06-27T07:38:21Z","file_name":"2022_PLDI_Zikelic.pdf","file_size":318697,"creator":"dernst","date_updated":"2022-06-27T07:38:21Z","access_level":"open_access","checksum":"7eb915a2ca5b5ce4729321f33b2e16e1"}],"oa":1,"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2022-06-27T07:38:21Z","conference":{"location":"San Diego, CA, United States","name":"PLDI: Programming Language Design and Implementation","end_date":"2022-06-17","start_date":"2022-06-13"},"title":"Differential cost analysis with simultaneous potentials and anti-potentials","ec_funded":1,"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>.","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.","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.","chicago":"Zikelic, Dorde, Bor-Yuh Evan Chang, Pauline Bolignano, and Franco Raimondi. “Differential Cost Analysis with Simultaneous Potentials and Anti-Potentials.” In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i>, 442–57. Association for Computing Machinery, 2022. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>.","apa":"Zikelic, D., Chang, B.-Y. E., Bolignano, P., &#38; Raimondi, F. (2022). Differential cost analysis with simultaneous potentials and anti-potentials. In <i>Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation</i> (pp. 442–457). San Diego, CA, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3519939.3523435\">https://doi.org/10.1145/3519939.3523435</a>","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."},"type":"conference","author":[{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic"},{"last_name":"Chang","first_name":"Bor-Yuh Evan","full_name":"Chang, Bor-Yuh Evan"},{"full_name":"Bolignano, Pauline","first_name":"Pauline","last_name":"Bolignano"},{"first_name":"Franco","full_name":"Raimondi, Franco","last_name":"Raimondi"}],"day":"09","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":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"ddc":["000"],"doi":"10.1145/3519939.3523435","language":[{"iso":"eng"}],"page":"442-457","date_created":"2022-06-21T09:26:15Z","month":"06","isi":1,"publisher":"Association for Computing Machinery","status":"public","quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publication":"Proceedings of the 43rd ACM SIGPLAN International Conference on Programming Language Design and Implementation"},{"article_processing_charge":"No","_id":"11460","date_published":"2022-06-22T00:00:00Z","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."}],"file":[{"content_type":"application/pdf","relation":"main_file","file_id":"11461","date_created":"2022-06-24T08:22:59Z","success":1,"file_name":"2022_MolecularAutism_Schaaf.pdf","creator":"dernst","file_size":7552298,"checksum":"525d2618e855139089bbfc3e3d49d1b2","date_updated":"2022-06-24T08:22:59Z","access_level":"open_access"}],"article_number":"27","oa":1,"publication_status":"published","volume":13,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2022-06-24T08:22:59Z","has_accepted_license":"1","year":"2022","oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["2040-2392"]},"date_updated":"2023-08-03T07:21:32Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000814641400001"]},"date_created":"2022-06-23T14:28:55Z","month":"06","isi":1,"publisher":"Springer Nature","status":"public","intvolume":"        13","quality_controlled":"1","department":[{"_id":"SiHi"}],"publication":"Molecular Autism","title":"WDFY3 mutation alters laminar position and morphology of cortical neurons","citation":{"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>","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>","short":"Z.A. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K.S. Zarbalis, Molecular Autism 13 (2022).","mla":"Schaaf, Zachary A., et al. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>, vol. 13, 27, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1186/s13229-022-00508-3\">10.1186/s13229-022-00508-3</a>.","chicago":"Schaaf, Zachary A., Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and Konstantinos S. Zarbalis. “WDFY3 Mutation Alters Laminar Position and Morphology of Cortical Neurons.” <i>Molecular Autism</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1186/s13229-022-00508-3\">https://doi.org/10.1186/s13229-022-00508-3</a>.","ista":"Schaaf ZA, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis KS. 2022. WDFY3 mutation alters laminar position and morphology of cortical neurons. Molecular Autism. 13, 27.","ieee":"Z. A. Schaaf <i>et al.</i>, “WDFY3 mutation alters laminar position and morphology of cortical neurons,” <i>Molecular Autism</i>, vol. 13. Springer Nature, 2022."},"author":[{"last_name":"Schaaf","first_name":"Zachary A.","full_name":"Schaaf, Zachary A."},{"last_name":"Tat","first_name":"Lyvin","full_name":"Tat, Lyvin"},{"first_name":"Noemi","full_name":"Cannizzaro, Noemi","last_name":"Cannizzaro"},{"full_name":"Green, Ralph","first_name":"Ralph","last_name":"Green"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"last_name":"Zarbalis","full_name":"Zarbalis, Konstantinos S.","first_name":"Konstantinos S."}],"type":"journal_article","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.","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1186/s13229-023-00539-4"}]},"doi":"10.1186/s13229-022-00508-3","ddc":["570"],"language":[{"iso":"eng"}],"keyword":["Psychiatry and Mental health","Developmental Biology","Developmental Neuroscience","Molecular Biology"]},{"_id":"11462","date_published":"2022-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"Nanobodies (VHH) from camelid antibody libraries hold great promise as therapeutic agents and components of immunoassay systems. Synthetic antibody libraries that could be designed and generated once and for various applications could yield binders to virtually any targets, even for non-immunogenic or toxic ones, in a short term. One of the most difficult tasks is to obtain antibodies with a high affinity and specificity to polyglycosylated proteins. It requires antibody libraries with extremely high functional diversity and the use of sophisticated selection techniques. Here we report a development of a novel sandwich immunoassay involving a combination of the synthetic library-derived VHH-Fc fusion protein as a capture antibody and the immune single-chain fragment variable (scFv) as a tracer for the detection of pregnancy-associated glycoprotein (PAG) of cattle (Bos taurus). We succeeded in the generation of a number of specific scFv antibodies against PAG from the mouse immune library. Subsequent selection using the immobilized scFv-Fc capture antibody allowed to isolate 1.9 nM VHH binder from the diverse synthetic library without any overlapping with the capture antibody binding site. The prototype sandwich ELISA based on the synthetic VHH and the immune scFv was established. This is the first successful example of the combination of synthetic and immune antibody libraries in a single sandwich immunoassay. Thus, our approach could be used for the express isolation of antibody pairs and the development of sandwich immunoassays for challenging antigens."}],"article_processing_charge":"No","volume":106,"publication_status":"published","article_type":"original","year":"2022","oa_version":"None","date_updated":"2023-10-10T07:15:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","external_id":{"pmid":["35723693"],"isi":["000813677500001"]},"publication_identifier":{"eissn":["1432-0614"],"issn":["0175-7598"]},"month":"08","date_created":"2022-06-26T22:01:34Z","page":"5093-5103","quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"LeSa"}],"publication":"Applied Microbiology and Biotechnology","intvolume":"       106","status":"public","publisher":"Springer Nature","isi":1,"day":"01","author":[{"full_name":"Dormeshkin, Dmitri","first_name":"Dmitri","last_name":"Dormeshkin"},{"full_name":"Shapira, Michail","first_name":"Michail","last_name":"Shapira"},{"full_name":"Karputs, Alena","first_name":"Alena","last_name":"Karputs"},{"full_name":"Kavaleuski, Anton","first_name":"Anton","last_name":"Kavaleuski","id":"62304f89-eb97-11eb-a6c2-8903dd183976","orcid":"0000-0003-2091-526X"},{"last_name":"Kuzminski","full_name":"Kuzminski, Ivan","first_name":"Ivan"},{"last_name":"Stepanova","first_name":"Elena","full_name":"Stepanova, Elena"},{"full_name":"Gilep, Andrei","first_name":"Andrei","last_name":"Gilep"}],"type":"journal_article","citation":{"chicago":"Dormeshkin, Dmitri, Michail Shapira, Alena Karputs, Anton Kavaleuski, Ivan Kuzminski, Elena Stepanova, and Andrei Gilep. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>.","ieee":"D. Dormeshkin <i>et al.</i>, “Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development,” <i>Applied Microbiology and Biotechnology</i>, vol. 106. Springer Nature, pp. 5093–5103, 2022.","ista":"Dormeshkin D, Shapira M, Karputs A, Kavaleuski A, Kuzminski I, Stepanova E, Gilep A. 2022. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. Applied Microbiology and Biotechnology. 106, 5093–5103.","mla":"Dormeshkin, Dmitri, et al. “Combining of Synthetic VHH and Immune ScFv Libraries for Pregnancy-Associated Glycoproteins ELISA Development.” <i>Applied Microbiology and Biotechnology</i>, vol. 106, Springer Nature, 2022, pp. 5093–103, doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>.","short":"D. Dormeshkin, M. Shapira, A. Karputs, A. Kavaleuski, I. Kuzminski, E. Stepanova, A. Gilep, Applied Microbiology and Biotechnology 106 (2022) 5093–5103.","ama":"Dormeshkin D, Shapira M, Karputs A, et al. Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. 2022;106:5093-5103. doi:<a href=\"https://doi.org/10.1007/s00253-022-12022-w\">10.1007/s00253-022-12022-w</a>","apa":"Dormeshkin, D., Shapira, M., Karputs, A., Kavaleuski, A., Kuzminski, I., Stepanova, E., &#38; Gilep, A. (2022). Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development. <i>Applied Microbiology and Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00253-022-12022-w\">https://doi.org/10.1007/s00253-022-12022-w</a>"},"title":"Combining of synthetic VHH and immune scFv libraries for pregnancy-associated glycoproteins ELISA development","language":[{"iso":"eng"}],"doi":"10.1007/s00253-022-12022-w","acknowledgement":"This study was financially supported by the State Committee on Science and Technology. We would like to thank Elena Tumar and Elena Kisileva at the Institute of Bioorganic Chemistry of NASB for their kind assistance with mouse immunizations.","pmid":1},{"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2111.08603 Focus to learn more"}],"publication_status":"published","volume":105,"article_processing_charge":"No","issue":"22","arxiv":1,"_id":"11469","abstract":[{"lang":"eng","text":"Thermalizing and localized many-body quantum systems present two distinct dynamical phases of matter. Recently the fate of a localized system coupled to a thermalizing system viewed as a quantum bath received significant theoretical and experimental attention. In this work, we study a mobile impurity, representing a small quantum bath, that interacts locally with an Anderson insulator with a finite density of localized particles. Using static Hartree approximation to obtain an effective disorder strength, we formulate an analytic criterion for the perturbative stability of the localization. Next, we use an approximate dynamical Hartree method and the quasi-exact time-evolved block decimation (TEBD) algorithm to study the dynamics of the system. We find that the dynamical Hartree approach which completely ignores entanglement between the impurity and localized particles predicts the delocalization of the system. In contrast, the full numerical simulation of the unitary dynamics with TEBD suggests the stability of localization on numerically accessible timescales. Finally, using an extension of the density matrix renormalization group algorithm to excited states (DMRG-X), we approximate the highly excited eigenstates of the system. We find that the impurity remains localized in the eigenstates and entanglement is enhanced in a finite region around the position of the impurity, confirming the dynamical predictions. Dynamics and the DMRG-X results provide compelling evidence for the stability of localization."}],"date_published":"2022-06-27T00:00:00Z","article_number":"224208","acknowledged_ssus":[{"_id":"ScienComp"}],"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"external_id":{"isi":["000823050000001"],"arxiv":["2111.08603"]},"date_updated":"2023-09-05T12:12:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","year":"2022","article_type":"original","isi":1,"publisher":"American Physical Society","intvolume":"       105","status":"public","publication":"Physical Review B","department":[{"_id":"MaSe"}],"quality_controlled":"1","date_created":"2022-06-29T20:19:51Z","month":"06","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"related_material":{"record":[{"status":"public","id":"12732","relation":"dissertation_contains"}]},"acknowledgement":"We thank M. Ljubotina for insightful discussions. P. B., A. M. and M. S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D. A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","doi":"10.1103/physrevb.105.224208","language":[{"iso":"eng"}],"title":"Localization of a mobile impurity interacting with an Anderson insulator","citation":{"mla":"Brighi, Pietro, et al. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, 224208, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>.","chicago":"Brighi, Pietro, Alexios Michailidis, Kristina Kirova, Dmitry A. Abanin, and Maksym Serbyn. “Localization of a Mobile Impurity Interacting with an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>.","ieee":"P. Brighi, A. Michailidis, K. Kirova, D. A. Abanin, and M. Serbyn, “Localization of a mobile impurity interacting with an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","ista":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. 2022. Localization of a mobile impurity interacting with an Anderson insulator. Physical Review B. 105(22), 224208.","ama":"Brighi P, Michailidis A, Kirova K, Abanin DA, Serbyn M. Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.224208\">10.1103/physrevb.105.224208</a>","apa":"Brighi, P., Michailidis, A., Kirova, K., Abanin, D. A., &#38; Serbyn, M. (2022). Localization of a mobile impurity interacting with an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.224208\">https://doi.org/10.1103/physrevb.105.224208</a>","short":"P. Brighi, A. Michailidis, K. Kirova, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022)."},"ec_funded":1,"author":[{"orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","first_name":"Pietro","full_name":"Brighi, Pietro","last_name":"Brighi"},{"first_name":"Alexios","full_name":"Michailidis, Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064"},{"last_name":"Kirova","first_name":"Kristina","full_name":"Kirova, Kristina","id":"4aeda2ae-f847-11ec-98e0-c4a66fe174d4"},{"last_name":"Abanin","first_name":"Dmitry A.","full_name":"Abanin, Dmitry A."},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"type":"journal_article","day":"27"},{"department":[{"_id":"MaSe"}],"quality_controlled":"1","publication":"Physical Review B","intvolume":"       105","status":"public","publisher":"American Physical Society","isi":1,"month":"06","date_created":"2022-06-29T20:20:47Z","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.105.l220203","acknowledgement":"We acknowledge useful discussions with M. Ljubotina. P. B., A. M., and M. S. were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was supported by the Swiss National Science Foundation and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597). The development of parallel TEBD code was was supported by S. Elefante from the Scientific Computing (SciComp) that is part of Scientific Service Units (SSU) of IST Austria. Some of the computations were performed on the Baobab cluster of the University of Geneva.","project":[{"grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E"}],"related_material":{"record":[{"id":"12732","relation":"dissertation_contains","status":"public"}]},"day":"27","type":"journal_article","author":[{"orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi","first_name":"Pietro","full_name":"Brighi, Pietro"},{"full_name":"Michailidis, Alexios A.","first_name":"Alexios A.","last_name":"Michailidis"},{"full_name":"Abanin, Dmitry A.","first_name":"Dmitry A.","last_name":"Abanin"},{"last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"}],"ec_funded":1,"citation":{"chicago":"Brighi, Pietro, Alexios A. Michailidis, Dmitry A. Abanin, and Maksym Serbyn. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>.","ieee":"P. Brighi, A. A. Michailidis, D. A. Abanin, and M. Serbyn, “Propagation of many-body localization in an Anderson insulator,” <i>Physical Review B</i>, vol. 105, no. 22. American Physical Society, 2022.","ista":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. 2022. Propagation of many-body localization in an Anderson insulator. Physical Review B. 105(22), L220203.","mla":"Brighi, Pietro, et al. “Propagation of Many-Body Localization in an Anderson Insulator.” <i>Physical Review B</i>, vol. 105, no. 22, L220203, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>.","short":"P. Brighi, A.A. Michailidis, D.A. Abanin, M. Serbyn, Physical Review B 105 (2022).","ama":"Brighi P, Michailidis AA, Abanin DA, Serbyn M. Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. 2022;105(22). doi:<a href=\"https://doi.org/10.1103/physrevb.105.l220203\">10.1103/physrevb.105.l220203</a>","apa":"Brighi, P., Michailidis, A. A., Abanin, D. A., &#38; Serbyn, M. (2022). Propagation of many-body localization in an Anderson insulator. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.105.l220203\">https://doi.org/10.1103/physrevb.105.l220203</a>"},"title":"Propagation of many-body localization in an Anderson insulator","volume":105,"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2109.07332"}],"article_number":"L220203","date_published":"2022-06-27T00:00:00Z","_id":"11470","abstract":[{"text":"Many-body localization (MBL) is an example of a dynamical phase of matter that avoids thermalization. While the MBL phase is robust to weak local perturbations, the fate of an MBL system coupled to a thermalizing quantum system that represents a “heat bath” is an open question that is actively investigated theoretically and experimentally. In this work, we consider the stability of an Anderson insulator with a finite density of particles interacting with a single mobile impurity—a small quantum bath. We give perturbative arguments that support the stability of localization in the strong interaction regime. Large-scale tensor network simulations of dynamics are employed to corroborate the presence of the localized phase and give quantitative predictions in the thermodynamic limit. We develop a phenomenological description of the dynamics in the strong interaction regime, and we demonstrate that the impurity effectively turns the Anderson insulator into an MBL phase, giving rise to nontrivial entanglement dynamics well captured by our phenomenology.","lang":"eng"}],"arxiv":1,"issue":"22","article_processing_charge":"No","date_updated":"2023-08-03T07:23:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000823050000012"],"arxiv":["2109.07332"]},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"article_type":"original","year":"2022","oa_version":"Preprint"},{"arxiv":1,"article_processing_charge":"No","issue":"2","file":[{"success":1,"date_created":"2022-06-30T07:14:48Z","relation":"main_file","file_id":"11472","content_type":"application/pdf","access_level":"open_access","date_updated":"2022-06-30T07:14:48Z","checksum":"a7706b28d24a0e32a55ea04b82a2df43","creator":"dernst","file_size":4231591,"file_name":"2022_PRXQuantum_Sack.pdf"}],"article_number":"020365","_id":"11471","abstract":[{"text":"Variational quantum algorithms are promising algorithms for achieving quantum advantage on nearterm devices. The quantum hardware is used to implement a variational wave function and measure observables, whereas the classical computer is used to store and update the variational parameters. The optimization landscape of expressive variational ansätze is however dominated by large regions in parameter space, known as barren plateaus, with vanishing gradients, which prevents efficient optimization. In this work we propose a general algorithm to avoid barren plateaus in the initialization and throughout the optimization. To this end we define a notion of weak barren plateaus (WBPs) based on the entropies of local reduced density matrices. The presence of WBPs can be efficiently quantified using recently introduced shadow tomography of the quantum state with a classical computer. We demonstrate that avoidance of WBPs suffices to ensure sizable gradients in the initialization. In addition, we demonstrate that decreasing the gradient step size, guided by the entropies allows WBPs to be avoided during the optimization process. This paves the way for efficient barren plateau-free optimization on near-term devices. ","lang":"eng"}],"date_published":"2022-06-29T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2022-06-30T07:14:48Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":3,"article_type":"original","has_accepted_license":"1","year":"2022","oa_version":"Published Version","external_id":{"arxiv":["2201.08194"],"isi":["000822564300001"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-12-13T14:47:24Z","publication_identifier":{"issn":["2691-3399"]},"month":"06","date_created":"2022-06-29T20:21:32Z","publisher":"American Physical Society","isi":1,"publication":"PRX Quantum","quality_controlled":"1","department":[{"_id":"MaSe"}],"intvolume":"         3","status":"public","citation":{"short":"S. Sack, R.A. Medina Ramos, A. Michailidis, R. Kueng, M. Serbyn, PRX Quantum 3 (2022).","apa":"Sack, S., Medina Ramos, R. A., Michailidis, A., Kueng, R., &#38; Serbyn, M. (2022). Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>","ama":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. Avoiding barren plateaus using classical shadows. <i>PRX Quantum</i>. 2022;3(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>","ista":"Sack S, Medina Ramos RA, Michailidis A, Kueng R, Serbyn M. 2022. Avoiding barren plateaus using classical shadows. PRX Quantum. 3(2), 020365.","ieee":"S. Sack, R. A. Medina Ramos, A. Michailidis, R. Kueng, and M. Serbyn, “Avoiding barren plateaus using classical shadows,” <i>PRX Quantum</i>, vol. 3, no. 2. American Physical Society, 2022.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Alexios Michailidis, Richard Kueng, and Maksym Serbyn. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/prxquantum.3.020365\">https://doi.org/10.1103/prxquantum.3.020365</a>.","mla":"Sack, Stefan, et al. “Avoiding Barren Plateaus Using Classical Shadows.” <i>PRX Quantum</i>, vol. 3, no. 2, 020365, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/prxquantum.3.020365\">10.1103/prxquantum.3.020365</a>."},"ec_funded":1,"title":"Avoiding barren plateaus using classical shadows","day":"29","author":[{"full_name":"Sack, Stefan","first_name":"Stefan","last_name":"Sack","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508"},{"first_name":"Raimel A","full_name":"Medina Ramos, Raimel A","last_name":"Medina Ramos","id":"CE680B90-D85A-11E9-B684-C920E6697425","orcid":"0000-0002-5383-2869"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","first_name":"Alexios","last_name":"Michailidis"},{"full_name":"Kueng, Richard","first_name":"Richard","last_name":"Kueng"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","related_material":{"record":[{"relation":"dissertation_contains","id":"14622","status":"public"}]},"project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}],"acknowledgement":"We thank Marco Cerezo, Zoe Holmes, and Nicholas Hunter-Jones for fruitful discussion and valuable feedback. We also acknowledge Adam Smith, Johannes Jakob Meyer, and Victor V. Albert for comments on the paper. The simulations were performed in the Julia programming\r\nlanguage [65] using the Yao module [66]. S.H.S., R.A.M., A.A.M. and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","keyword":["General Medicine"],"language":[{"iso":"eng"}],"doi":"10.1103/prxquantum.3.020365","ddc":["530"]},{"article_processing_charge":"No","file":[{"date_updated":"2022-07-05T08:12:56Z","access_level":"open_access","checksum":"7970714a20a6052f75fb27a6c3e9976e","file_name":"thes1_no_isbn_2_1b.pdf","file_size":1830973,"creator":"kmysliwy","success":1,"date_created":"2022-07-05T08:12:56Z","content_type":"application/pdf","file_id":"11486","relation":"main_file"},{"checksum":"647a2011fdf56277096c9350fefe1097","access_level":"closed","date_updated":"2022-07-05T08:17:12Z","creator":"kmysliwy","file_size":5831060,"file_name":"thes_source.zip","date_created":"2022-07-05T08:15:52Z","file_id":"11487","relation":"source_file","content_type":"application/zip"}],"abstract":[{"lang":"eng","text":"The polaron model is a basic model of quantum field theory describing a single particle\r\ninteracting with a bosonic field. It arises in many physical contexts. We are mostly concerned\r\nwith models applicable in the context of an impurity atom in a Bose-Einstein condensate as\r\nwell as the problem of electrons moving in polar crystals.\r\nThe model has a simple structure in which the interaction of the particle with the field is given\r\nby a term linear in the field’s creation and annihilation operators. In this work, we investigate\r\nthe properties of this model by providing rigorous estimates on various energies relevant to the\r\nproblem. The estimates are obtained, for the most part, by suitable operator techniques which\r\nconstitute the principal mathematical substance of the thesis.\r\nThe first application of these techniques is to derive the polaron model rigorously from first\r\nprinciples, i.e., from a full microscopic quantum-mechanical many-body problem involving an\r\nimpurity in an otherwise homogeneous system. We accomplish this for the N + 1 Bose gas\r\nin the mean-field regime by showing that a suitable polaron-type Hamiltonian arises at weak\r\ninteractions as a low-energy effective theory for this problem.\r\nIn the second part, we investigate rigorously the ground state of the model at fixed momentum\r\nand for large values of the coupling constant. Qualitatively, the system is expected to display\r\na transition from the quasi-particle behavior at small momenta, where the dispersion relation\r\nis parabolic and the particle moves through the medium dragging along a cloud of phonons, to\r\nthe radiative behavior at larger momenta where the polaron decelerates and emits free phonons.\r\nAt the same time, in the strong coupling regime, the bosonic field is expected to behave purely\r\nclassically. Accordingly, the effective mass of the polaron at strong coupling is conjectured to\r\nbe asymptotically equal to the one obtained from the semiclassical counterpart of the problem,\r\nfirst studied by Landau and Pekar in the 1940s. For polaron models with regularized form\r\nfactors and phonon dispersion relations of superfluid type, i.e., bounded below by a linear\r\nfunction of the wavenumbers for all phonon momenta as in the interacting Bose gas, we prove\r\nthat for a large window of momenta below the radiation threshold, the energy-momentum\r\nrelation at strong coupling is indeed essentially a parabola with semi-latus rectum equal to the\r\nLandau–Pekar effective mass, as expected.\r\nFor the Fröhlich polaron describing electrons in polar crystals where the dispersion relation is\r\nof the optical type and the form factor is formally UV–singular due to the nature of the point\r\ncharge-dipole interaction, we are able to give the corresponding upper bound. In contrast to\r\nthe regular case, this requires the inclusion of the quantum fluctuations of the phonon field,\r\nwhich makes the problem considerably more difficult.\r\nThe results are supplemented by studies on the absolute ground-state energy at strong coupling,\r\na proof of the divergence of the effective mass with the coupling constant for a wide class of\r\npolaron models, as well as the discussion of the apparent UV singularity of the Fröhlich model\r\nand the application of the techniques used for its removal for the energy estimates.\r\n"}],"_id":"11473","date_published":"2022-07-01T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2022-07-05T08:17:12Z","has_accepted_license":"1","year":"2022","oa_version":"Published Version","date_updated":"2023-09-07T13:43:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledged_ssus":[{"_id":"SSU"}],"publication_identifier":{"issn":["2663-337X"]},"page":"138","month":"07","date_created":"2022-06-30T12:15:03Z","supervisor":[{"first_name":"Robert","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","department":[{"_id":"GradSch"},{"_id":"RoSe"}],"status":"public","ec_funded":1,"citation":{"short":"K. Mysliwy, Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates, Institute of Science and Technology Austria, 2022.","ama":"Mysliwy K. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>","apa":"Mysliwy, K. (2022). <i>Polarons in Bose gases and polar crystals: Some rigorous energy estimates</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>","chicago":"Mysliwy, Krzysztof. “Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11473\">https://doi.org/10.15479/at:ista:11473</a>.","ieee":"K. Mysliwy, “Polarons in Bose gases and polar crystals: Some rigorous energy estimates,” Institute of Science and Technology Austria, 2022.","ista":"Mysliwy K. 2022. Polarons in Bose gases and polar crystals: Some rigorous energy estimates. Institute of Science and Technology Austria.","mla":"Mysliwy, Krzysztof. <i>Polarons in Bose Gases and Polar Crystals: Some Rigorous Energy Estimates</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11473\">10.15479/at:ista:11473</a>."},"title":"Polarons in Bose gases and polar crystals: Some rigorous energy estimates","day":"01","alternative_title":["ISTA Thesis"],"author":[{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","last_name":"Mysliwy","first_name":"Krzysztof","full_name":"Mysliwy, Krzysztof"}],"type":"dissertation","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"10564"},{"status":"public","id":"8705","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"ddc":["515","539"],"doi":"10.15479/at:ista:11473"},{"acknowledgement":"We thank Marta Mularczyk and Yiannis Tselekounis for their very helpful feedback on an earlier draft of this paper.","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"doi":"10.1007/978-3-031-07085-3_28","language":[{"iso":"eng"}],"conference":{"location":"Trondheim, Norway","end_date":"2022-06-03","start_date":"2022-05-30","name":"EUROCRYPT: Annual International Conference on the Theory and Applications of Cryptology and Information Security"},"title":"CoCoA: Concurrent continuous group key agreement","ec_funded":1,"citation":{"short":"J. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, Advances in Cryptology – EUROCRYPT 2022, Springer Nature, Cham, 2022, pp. 815–844.","apa":"Alwen, J., Auerbach, B., Cueto Noval, M., Klein, K., Pascual Perez, G., Pietrzak, K. Z., &#38; Walter, M. (2022). CoCoA: Concurrent continuous group key agreement. In <i>Advances in Cryptology – EUROCRYPT 2022</i> (Vol. 13276, pp. 815–844). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">https://doi.org/10.1007/978-3-031-07085-3_28</a>","ama":"Alwen J, Auerbach B, Cueto Noval M, et al. CoCoA: Concurrent continuous group key agreement. In: <i>Advances in Cryptology – EUROCRYPT 2022</i>. Vol 13276. Cham: Springer Nature; 2022:815–844. doi:<a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">10.1007/978-3-031-07085-3_28</a>","ieee":"J. Alwen <i>et al.</i>, “CoCoA: Concurrent continuous group key agreement,” in <i>Advances in Cryptology – EUROCRYPT 2022</i>, Trondheim, Norway, 2022, vol. 13276, pp. 815–844.","ista":"Alwen J, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2022. CoCoA: Concurrent continuous group key agreement. Advances in Cryptology – EUROCRYPT 2022. EUROCRYPT: Annual International Conference on the Theory and Applications of Cryptology and Information Security, LNCS, vol. 13276, 815–844.","chicago":"Alwen, Joël, Benedikt Auerbach, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “CoCoA: Concurrent Continuous Group Key Agreement.” In <i>Advances in Cryptology – EUROCRYPT 2022</i>, 13276:815–844. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">https://doi.org/10.1007/978-3-031-07085-3_28</a>.","mla":"Alwen, Joël, et al. “CoCoA: Concurrent Continuous Group Key Agreement.” <i>Advances in Cryptology – EUROCRYPT 2022</i>, vol. 13276, Springer Nature, 2022, pp. 815–844, doi:<a href=\"https://doi.org/10.1007/978-3-031-07085-3_28\">10.1007/978-3-031-07085-3_28</a>."},"alternative_title":["LNCS"],"type":"conference","author":[{"last_name":"Alwen","first_name":"Joël","full_name":"Alwen, Joël"},{"last_name":"Auerbach","full_name":"Auerbach, Benedikt","first_name":"Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","orcid":"0000-0002-7553-6606"},{"id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","last_name":"Cueto Noval","first_name":"Miguel","full_name":"Cueto Noval, Miguel"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","full_name":"Klein, Karen","last_name":"Klein"},{"id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","last_name":"Pascual Perez","full_name":"Pascual Perez, Guillermo","first_name":"Guillermo"},{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Walter","full_name":"Walter, Michael","first_name":"Michael"}],"day":"25","isi":1,"publisher":"Springer Nature","status":"public","intvolume":"     13276","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"quality_controlled":"1","publication":"Advances in Cryptology – EUROCRYPT 2022","page":"815–844","date_created":"2022-06-30T16:48:00Z","place":"Cham","month":"05","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031070846"],"eissn":["1611-3349"],"eisbn":["9783031070853"]},"date_updated":"2023-08-03T07:25:02Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","external_id":{"isi":["000832305300028"]},"oa_version":"Preprint","year":"2022","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/251"}],"oa":1,"publication_status":"published","volume":13276,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"Messaging platforms like Signal are widely deployed and provide strong security in an asynchronous setting. It is a challenging problem to construct a protocol with similar security guarantees that can efficiently scale to large groups. A major bottleneck are the frequent key rotations users need to perform to achieve post compromise forward security.\r\n\r\nIn current proposals – most notably in TreeKEM (which is part of the IETF’s Messaging Layer Security (MLS) protocol draft) – for users in a group of size n to rotate their keys, they must each craft a message of size log(n) to be broadcast to the group using an (untrusted) delivery server.\r\n\r\nIn larger groups, having users sequentially rotate their keys requires too much bandwidth (or takes too long), so variants allowing any T≤n users to simultaneously rotate their keys in just 2 communication rounds have been suggested (e.g. “Propose and Commit” by MLS). Unfortunately, 2-round concurrent updates are either damaging or expensive (or both); i.e. they either result in future operations being more costly (e.g. via “blanking” or “tainting”) or are costly themselves requiring Ω(T) communication for each user [Bienstock et al., TCC’20].\r\n\r\nIn this paper we propose CoCoA; a new scheme that allows for T concurrent updates that are neither damaging nor costly. That is, they add no cost to future operations yet they only require Ω(log2(n)) communication per user. To circumvent the [Bienstock et al.] lower bound, CoCoA increases the number of rounds needed to complete all updates from 2 up to (at most) log(n); though typically fewer rounds are needed.\r\n\r\nThe key insight of our protocol is the following: in the (non-concurrent version of) TreeKEM, a delivery server which gets T concurrent update requests will approve one and reject the remaining T−1. In contrast, our server attempts to apply all of them. If more than one user requests to rotate the same key during a round, the server arbitrarily picks a winner. Surprisingly, we prove that regardless of how the server chooses the winners, all previously compromised users will recover after at most log(n) such update rounds.\r\n\r\nTo keep the communication complexity low, CoCoA is a server-aided CGKA. That is, the delivery server no longer blindly forwards packets, but instead actively computes individualized packets tailored to each user. As the server is untrusted, this change requires us to develop new mechanisms ensuring robustness of the protocol."}],"_id":"11476","date_published":"2022-05-25T00:00:00Z"},{"citation":{"mla":"Bartalska, Katarina, et al. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>, vol. 25, no. 7, 104580, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>.","ista":"Bartalska K, Hübschmann V, Korkut M, Cubero RJ, Venturino A, Rössler K, Czech T, Siegert S. 2022. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. iScience. 25(7), 104580.","ieee":"K. Bartalska <i>et al.</i>, “A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation,” <i>iScience</i>, vol. 25, no. 7. Elsevier, 2022.","chicago":"Bartalska, Katarina, Verena Hübschmann, Medina Korkut, Ryan J Cubero, Alessandro Venturino, Karl Rössler, Thomas Czech, and Sandra Siegert. “A Systematic Characterization of Microglia-like Cell Occurrence during Retinal Organoid Differentiation.” <i>IScience</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>.","apa":"Bartalska, K., Hübschmann, V., Korkut, M., Cubero, R. J., Venturino, A., Rössler, K., … Siegert, S. (2022). A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2022.104580\">https://doi.org/10.1016/j.isci.2022.104580</a>","ama":"Bartalska K, Hübschmann V, Korkut M, et al. A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation. <i>iScience</i>. 2022;25(7). doi:<a href=\"https://doi.org/10.1016/j.isci.2022.104580\">10.1016/j.isci.2022.104580</a>","short":"K. Bartalska, V. Hübschmann, M. Korkut, R.J. Cubero, A. Venturino, K. Rössler, T. Czech, S. Siegert, IScience 25 (2022)."},"ec_funded":1,"title":"A systematic characterization of microglia-like cell occurrence during retinal organoid differentiation","day":"15","author":[{"id":"4D883232-F248-11E8-B48F-1D18A9856A87","last_name":"Bartalska","full_name":"Bartalska, Katarina","first_name":"Katarina"},{"last_name":"Hübschmann","full_name":"Hübschmann, Verena","first_name":"Verena","id":"32B7C918-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Korkut","first_name":"Medina","full_name":"Korkut, Medina","orcid":"0000-0003-4309-2251","id":"4B51CE74-F248-11E8-B48F-1D18A9856A87"},{"id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","last_name":"Cubero","first_name":"Ryan J","full_name":"Cubero, Ryan J"},{"last_name":"Venturino","first_name":"Alessandro","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karl","full_name":"Rössler, Karl","last_name":"Rössler"},{"last_name":"Czech","full_name":"Czech, Thomas","first_name":"Thomas"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","full_name":"Siegert, Sandra","last_name":"Siegert"}],"type":"journal_article","related_material":{"record":[{"relation":"other","id":"12117","status":"public"}]},"project":[{"call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"How human microglia shape developing neurons during health and inflammation","grant_number":"SC19-017","_id":"9B99D380-BA93-11EA-9121-9846C619BF3A"}],"acknowledgement":"We thank the scientific service units at ISTA, specifically the lab support facility and imaging & optics facility for their support; Nicolas Armel for performing the Mass Spectrometry. We thank Alexandra Lang and Tanja Peilnsteiner for their help in human brain tissue collection, Rouven Schulz for his insights into the functional assays We thank all members of the Siegert group for constant feedback on the project and Margaret Maes, Rouven Schulz, and Marco Benevento for feedback on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant No. 715571 to S.S.) and from the Gesellschaft für Forschungsförderung Niederösterreich (grant No. Sc19-017 to V.H.).","language":[{"iso":"eng"}],"doi":"10.1016/j.isci.2022.104580","ddc":["610"],"month":"07","date_created":"2022-07-03T22:01:33Z","publisher":"Elsevier","isi":1,"publication":"iScience","quality_controlled":"1","department":[{"_id":"SaSi"}],"status":"public","intvolume":"        25","article_type":"original","oa_version":"Published Version","has_accepted_license":"1","year":"2022","external_id":{"isi":["000830428500005"]},"scopus_import":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-02T12:21:33Z","publication_identifier":{"eissn":["2589-0042"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"article_processing_charge":"Yes","issue":"7","article_number":"104580","file":[{"date_created":"2022-07-04T08:19:25Z","success":1,"relation":"main_file","file_id":"11480","content_type":"application/pdf","checksum":"a470b74e1b3796c710189c81a4cd4329","access_level":"open_access","date_updated":"2022-07-04T08:19:25Z","file_size":19400048,"creator":"cchlebak","file_name":"2022_iScience_Bartalska.pdf"}],"abstract":[{"text":"Cerebral organoids differentiated from human-induced pluripotent stem cells (hiPSC) provide a unique opportunity to investigate brain development. However, organoids usually lack microglia, brain-resident immune cells, which are present in the early embryonic brain and participate in neuronal circuit development. Here, we find IBA1+ microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture with an unguided retinal organoid differentiation protocol. Microglia do not infiltrate the neuroectoderm and instead enrich within non-pigmented, 3D-cystic compartments that develop in parallel to the 3D-retinal organoids. When we guide the retinal organoid differentiation with low-dosed BMP4, we prevent cup development and enhance microglia and 3D-cysts formation. Mass spectrometry identifies these 3D-cysts to express mesenchymal and epithelial markers. We confirmed this microglia-preferred environment also within the unguided protocol, providing insight into microglial behavior and migration and offer a model to study how they enter and distribute within the human brain.","lang":"eng"}],"_id":"11478","date_published":"2022-07-15T00:00:00Z","publication_status":"published","oa":1,"file_date_updated":"2022-07-04T08:19:25Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":25},{"citation":{"short":"H. Kusakabe, A. Verhamme, J. Blaizot, T. Garel, L. Wisotzki, F. Leclercq, R. Bacon, J. Schaye, S.G. Gallego, J. Kerutt, J.J. Matthee, M. Maseda, T. Nanayakkara, R. Pelló, J. Richard, L. Tresse, T. Urrutia, E. Vitte, Astronomy &#38; Astrophysics 660 (2022).","ama":"Kusakabe H, Verhamme A, Blaizot J, et al. The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. <i>Astronomy &#38; Astrophysics</i>. 2022;660. doi:<a href=\"https://doi.org/10.1051/0004-6361/202142302\">10.1051/0004-6361/202142302</a>","apa":"Kusakabe, H., Verhamme, A., Blaizot, J., Garel, T., Wisotzki, L., Leclercq, F., … Vitte, E. (2022). The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202142302\">https://doi.org/10.1051/0004-6361/202142302</a>","chicago":"Kusakabe, Haruka, Anne Verhamme, Jérémy Blaizot, Thibault Garel, Lutz Wisotzki, Floriane Leclercq, Roland Bacon, et al. “The MUSE EXtremely Deep Field: Individual Detections of Ly<i>α</i> Haloes around Rest-Frame UV-Selected Galaxies at <i>z</i> ≃ 2.9–4.4.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202142302\">https://doi.org/10.1051/0004-6361/202142302</a>.","ieee":"H. Kusakabe <i>et al.</i>, “The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4,” <i>Astronomy &#38; Astrophysics</i>, vol. 660. EDP Sciences, 2022.","ista":"Kusakabe H, Verhamme A, Blaizot J, Garel T, Wisotzki L, Leclercq F, Bacon R, Schaye J, Gallego SG, Kerutt J, Matthee JJ, Maseda M, Nanayakkara T, Pelló R, Richard J, Tresse L, Urrutia T, Vitte E. 2022. The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4. Astronomy &#38; Astrophysics. 660, A44.","mla":"Kusakabe, Haruka, et al. “The MUSE EXtremely Deep Field: Individual Detections of Ly<i>α</i> Haloes around Rest-Frame UV-Selected Galaxies at <i>z</i> ≃ 2.9–4.4.” <i>Astronomy &#38; Astrophysics</i>, vol. 660, A44, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202142302\">10.1051/0004-6361/202142302</a>."},"title":"The MUSE eXtremely Deep Field: Individual detections of Ly<i>α</i> haloes around rest-frame UV-selected galaxies at <i>z</i> ≃ 2.9–4.4","day":"07","type":"journal_article","author":[{"last_name":"Kusakabe","first_name":"Haruka","full_name":"Kusakabe, Haruka"},{"full_name":"Verhamme, Anne","first_name":"Anne","last_name":"Verhamme"},{"first_name":"Jérémy","full_name":"Blaizot, Jérémy","last_name":"Blaizot"},{"first_name":"Thibault","full_name":"Garel, Thibault","last_name":"Garel"},{"full_name":"Wisotzki, Lutz","first_name":"Lutz","last_name":"Wisotzki"},{"full_name":"Leclercq, Floriane","first_name":"Floriane","last_name":"Leclercq"},{"last_name":"Bacon","full_name":"Bacon, Roland","first_name":"Roland"},{"full_name":"Schaye, Joop","first_name":"Joop","last_name":"Schaye"},{"full_name":"Gallego, Sofia G.","first_name":"Sofia G.","last_name":"Gallego"},{"full_name":"Kerutt, Josephine","first_name":"Josephine","last_name":"Kerutt"},{"first_name":"Jorryt J","full_name":"Matthee, Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720"},{"last_name":"Maseda","first_name":"Michael","full_name":"Maseda, Michael"},{"first_name":"Themiya","full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara"},{"last_name":"Pelló","first_name":"Roser","full_name":"Pelló, Roser"},{"first_name":"Johan","full_name":"Richard, Johan","last_name":"Richard"},{"full_name":"Tresse, Laurence","first_name":"Laurence","last_name":"Tresse"},{"last_name":"Urrutia","full_name":"Urrutia, Tanya","first_name":"Tanya"},{"first_name":"Eloïse","full_name":"Vitte, Eloïse","last_name":"Vitte"}],"acknowledgement":"We thank the anonymous referee for constructive comments and suggestions. We would like to express our gratitude to Edmund Christian Herenz, Leindert Boogard, Miroslava Dessauges, Moupiya Maji, Valentin Mauerhofer, Charlotte Paola Simmonds Wagemann, Masami Ouchi, Kazuhiro Shimasaku, Akio Inoue, and Rieko Momose for giving insightful comments and suggestions. H.K. is grateful to Liam McCarney for useful suggestions on English writing through the UniGE’s Tandems linguistiques. H.K. acknowledges support from Swiss Government Excellence Scholarships and Japan Society for the Promotion of Science (JSPS) Overseas Research Fellowship. H.K., F.L., and A.V. are supported by the SNF grant PP00P2 176808. A.V. and T.G. are supported by the ERC Starting Grant 757258“TRIPLE”. This work was supported by the Programme National Cosmology et Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, co-funded by CEA and CNES. This work is based on observations taken by VLT, which is operated by European Southern Observatory. This research made use of Astropy, which is a community-developed core Python package for Astronomy (Astropy Collaboration 2013, 2018), and other software and packages: MARZ, MPDAF (Piqueras et al. 2019), PHOTUTILS, Numpy (Harris et al. 2020), Scipy (Virtanen et al. 2020), and matplotlib (Hunter 2007).","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations"],"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/202142302","month":"04","extern":"1","date_created":"2022-07-05T14:27:26Z","publisher":"EDP Sciences","publication":"Astronomy & Astrophysics","quality_controlled":"1","status":"public","intvolume":"       660","article_type":"original","oa_version":"Published Version","year":"2022","scopus_import":"1","external_id":{"arxiv":["2201.07257"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-07-19T09:33:24Z","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"arxiv":1,"article_processing_charge":"No","article_number":"A44","_id":"11488","date_published":"2022-04-07T00:00:00Z","abstract":[{"text":"Hydrogen Lyα haloes (LAHs) are commonly used as a tracer of the circumgalactic medium (CGM) at high redshifts. In this work, we aim to explore the existence of Lyα haloes around individual UV-selected galaxies, rather than around Lyα emitters (LAEs), at high redshifts. Our sample was continuum-selected with F775W ≤ 27.5, and spectroscopic redshifts were assigned or constrained for all the sources thanks to the deepest (100- to 140-h) existing Very Large Telescope (VLT)/Multi-Unit Spectroscopic Explorer (MUSE) data with adaptive optics. The final sample includes 21 galaxies that are purely F775W-magnitude selected within the redshift range z ≈ 2.9 − 4.4 and within a UV magnitude range −20 ≤ M1500 ≤ −18, thus avoiding any bias toward LAEs. We tested whether galaxy’s Lyα emission is significantly more extended than the MUSE PSF-convolved continuum component. We find 17 LAHs and four non-LAHs. We report the first individual detections of extended Lyα emission around non-LAEs. The Lyα halo fraction is thus as high as 81.0−11.2+10.3%, which is close to that for LAEs at z = 3 − 6 in the literature. This implies that UV-selected galaxies generally have a large amount of hydrogen in their CGM. We derived the mean surface brightness (SB) profile for our LAHs with cosmic dimming corrections and find that Lyα emission extends to 5.4 arcsec (≃40 physical kpc at the midpoint redshift z = 3.6) above the typical 1σ SB limit. The incidence rate of surrounding gas detected in Lyα per one-dimensional line of sight per unit redshift, dn/dz, is estimated to be 0.76−0.09+0.09 for galaxies with M1500 ≤ −18 mag at z ≃ 3.7. Assuming that Lyα emission and absorption arise in the same gas, this suggests, based on abundance matching, that LAHs trace the same gas as damped Lyα systems (DLAs) and sub-DLAs.","lang":"eng"}],"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/2201.07257","open_access":"1"}],"oa":1,"volume":660},{"oa":1,"publication_status":"published","volume":23,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2022-07-06T07:36:59Z","issue":"11","article_processing_charge":"Yes","_id":"11489","abstract":[{"lang":"eng","text":"Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors."}],"date_published":"2022-06-06T00:00:00Z","file":[{"relation":"main_file","file_id":"11492","content_type":"application/pdf","success":1,"date_created":"2022-07-06T07:36:59Z","creator":"cchlebak","file_size":2324542,"file_name":"2022_IntJMolSci_Bilanovicova.pdf","access_level":"open_access","date_updated":"2022-07-06T07:36:59Z","checksum":"e997a57a928ec9d51fad8ce824a05935"}],"publication_identifier":{"issn":["1422-0067"]},"date_updated":"2023-08-09T10:13:57Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["35683031"],"isi":["000808733300001"]},"has_accepted_license":"1","year":"2022","oa_version":"Published Version","article_type":"original","isi":1,"publisher":"MDPI","status":"public","intvolume":"        23","quality_controlled":"1","department":[{"_id":"JiFr"}],"publication":"International Journal of Molecular Sciences","page":"6352","date_created":"2022-07-05T15:14:34Z","month":"06","acknowledgement":"We thank Charo del Genio from Coventry University and Richard Napier from the University of Warwick for helpful discussion concerning protein modeling and inspiration concerning CD spectroscopy, respectively. We thank Jan Hejatko for sharing the published AHP2 construct. We also thank Josef Houser from the core facility BIC CEITEC for valuable assistance, discussions, and ideas relating to CD. We acknowledge the: Core Facility CELLIM of CEITEC supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR), part of the Euro-BioImaging (www.eurobioimaging.eu accessed on 1 January 2016) ALM and medical imaging Node (Brno, CZ), CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127) and European Regional Development Fund-Project “UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974) for their support with obtaining scientific data presented in this paper; Plant Sciences Core Facility of CEITEC Masaryk University for technical support. Open Access Funding by the Austrian Science Fund (FWF).","project":[{"grant_number":"P29988","name":"RNA-directed DNA methylation in plant development","_id":"262EF96E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"pmid":1,"ddc":["570"],"doi":"10.3390/ijms23116352","language":[{"iso":"eng"}],"title":"The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein","citation":{"chicago":"Bilanovičová, V, N Rýdza, L Koczka, M Hess, E Feraru, Jiří Friml, and T Nodzyński. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>. MDPI, 2022. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>.","ista":"Bilanovičová V, Rýdza N, Koczka L, Hess M, Feraru E, Friml J, Nodzyński T. 2022. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. International Journal of Molecular Sciences. 23(11), 6352.","ieee":"V. Bilanovičová <i>et al.</i>, “The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein,” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11. MDPI, p. 6352, 2022.","mla":"Bilanovičová, V., et al. “The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.” <i>International Journal of Molecular Sciences</i>, vol. 23, no. 11, MDPI, 2022, p. 6352, doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>.","short":"V. Bilanovičová, N. Rýdza, L. Koczka, M. Hess, E. Feraru, J. Friml, T. Nodzyński, International Journal of Molecular Sciences 23 (2022) 6352.","ama":"Bilanovičová V, Rýdza N, Koczka L, et al. The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. 2022;23(11):6352. doi:<a href=\"https://doi.org/10.3390/ijms23116352\">10.3390/ijms23116352</a>","apa":"Bilanovičová, V., Rýdza, N., Koczka, L., Hess, M., Feraru, E., Friml, J., &#38; Nodzyński, T. (2022). The hydrophilic loop of Arabidopsis PIN1 auxin efflux carrier harbors hallmarks of an intrinsically disordered protein. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms23116352\">https://doi.org/10.3390/ijms23116352</a>"},"author":[{"full_name":"Bilanovičová, V","first_name":"V","last_name":"Bilanovičová"},{"full_name":"Rýdza, N","first_name":"N","last_name":"Rýdza"},{"full_name":"Koczka, L","first_name":"L","last_name":"Koczka"},{"last_name":"Hess","first_name":"M","full_name":"Hess, M"},{"last_name":"Feraru","first_name":"E","full_name":"Feraru, E"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří"},{"full_name":"Nodzyński, T","first_name":"T","last_name":"Nodzyński"}],"type":"journal_article","day":"06"},{"keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / techniques: spectroscopic / galaxies: stellar content / galaxies: formation"],"language":[{"iso":"eng"}],"doi":"10.1051/0004-6361/202142187","acknowledgement":"We thank the referee for thoughtful and constructive comments that have improved the quality of this manuscript. Based on observations collected at the European Southern Observatory under ESO programme 1101.A-0127. This work made use of v2.2.1 of the Binary Population and Spectral Synthesis (BPASS) models as described in Eldridge et al. (2017) and Stanway & Eldridge (2018). A.F. acknowledges the support from grant PRIN MIUR2017-20173ML3WW_001. T.N. acknowledges support from Australian Research Council Laureate Fellowship FL180100060.","day":"30","author":[{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"full_name":"Feltre, Anna","first_name":"Anna","last_name":"Feltre"},{"last_name":"Maseda","first_name":"Michael","full_name":"Maseda, Michael"},{"first_name":"Themiya","full_name":"Nanayakkara, Themiya","last_name":"Nanayakkara"},{"first_name":"Leindert","full_name":"Boogaard, Leindert","last_name":"Boogaard"},{"last_name":"Bacon","full_name":"Bacon, Roland","first_name":"Roland"},{"last_name":"Verhamme","first_name":"Anne","full_name":"Verhamme, Anne"},{"last_name":"Leclercq","full_name":"Leclercq, Floriane","first_name":"Floriane"},{"full_name":"Kusakabe, Haruka","first_name":"Haruka","last_name":"Kusakabe"},{"full_name":"Urrutia, Tanya","first_name":"Tanya","last_name":"Urrutia"},{"full_name":"Wisotzki, Lutz","first_name":"Lutz","last_name":"Wisotzki"}],"type":"journal_article","citation":{"apa":"Matthee, J. J., Feltre, A., Maseda, M., Nanayakkara, T., Boogaard, L., Bacon, R., … Wisotzki, L. (2022). Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202142187\">https://doi.org/10.1051/0004-6361/202142187</a>","ama":"Matthee JJ, Feltre A, Maseda M, et al. Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field. <i>Astronomy &#38; Astrophysics</i>. 2022;660. doi:<a href=\"https://doi.org/10.1051/0004-6361/202142187\">10.1051/0004-6361/202142187</a>","short":"J.J. Matthee, A. Feltre, M. Maseda, T. Nanayakkara, L. Boogaard, R. Bacon, A. Verhamme, F. Leclercq, H. Kusakabe, T. Urrutia, L. Wisotzki, Astronomy &#38; Astrophysics 660 (2022).","mla":"Matthee, Jorryt J., et al. “Deciphering Stellar Metallicities in the Early Universe: Case Study of a Young Galaxy at z = 4.77 in the MUSE EXtremely Deep Field.” <i>Astronomy &#38; Astrophysics</i>, vol. 660, A10, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202142187\">10.1051/0004-6361/202142187</a>.","ista":"Matthee JJ, Feltre A, Maseda M, Nanayakkara T, Boogaard L, Bacon R, Verhamme A, Leclercq F, Kusakabe H, Urrutia T, Wisotzki L. 2022. Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field. Astronomy &#38; Astrophysics. 660, A10.","ieee":"J. J. Matthee <i>et al.</i>, “Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field,” <i>Astronomy &#38; Astrophysics</i>, vol. 660. EDP Sciences, 2022.","chicago":"Matthee, Jorryt J, Anna Feltre, Michael Maseda, Themiya Nanayakkara, Leindert Boogaard, Roland Bacon, Anne Verhamme, et al. “Deciphering Stellar Metallicities in the Early Universe: Case Study of a Young Galaxy at z = 4.77 in the MUSE EXtremely Deep Field.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202142187\">https://doi.org/10.1051/0004-6361/202142187</a>."},"title":"Deciphering stellar metallicities in the early universe: Case study of a young galaxy at z = 4.77 in the MUSE eXtremely Deep Field","publication":"Astronomy & Astrophysics","quality_controlled":"1","intvolume":"       660","status":"public","publisher":"EDP Sciences","month":"03","extern":"1","date_created":"2022-07-05T15:25:35Z","scopus_import":"1","external_id":{"arxiv":["2111.14855"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-07-19T09:33:46Z","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"article_type":"original","year":"2022","oa_version":"Published Version","volume":660,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2111.14855"}],"oa":1,"article_number":"A10","_id":"11490","abstract":[{"lang":"eng","text":"Directly characterising the first generations of stars in distant galaxies is a key quest of observational cosmology. We present a case study of ID53 at z = 4.77, the UV-brightest (but L⋆) star-forming galaxy at z > 3 in the MUSE eXtremely Deep Field with a mass of ≈109 M⊙. In addition to very strong Lyman-α (Lyα) emission, we clearly detect the (stellar) continuum and an N V P Cygni feature, interstellar absorption, fine-structure emission and nebular C IV emission lines in the 140 h spectrum. Continuum emission from two spatially resolved components in Hubble Space Telescope data are blended in the MUSE data, but we show that the nebular C IV emission originates from a subcomponent of the galaxy. The UV spectrum can be fit with recent BPASS stellar population models combined with single-burst or continuous star formation histories (SFHs), a standard initial mass function, and an attenuation law. Models with a young age and low metallicity (log10(age/yr) = 6.5–7.6 and [Z/H] = −2.15 to −1.15) are preferred, but the details depend on the assumed SFH. The intrinsic Hα luminosity of the best-fit models is an order of magnitude higher than the Hα luminosity inferred from Spitzer/IRAC data, which either suggests a high escape fraction of ionising photons, a high relative attenuation of nebular to stellar dust, or a complex SFH. The metallicity appears lower than the metallicity in more massive galaxies at z = 3 − 5, consistent with the scenario according to which younger galaxies have lower metallicities. This chemical immaturity likely facilitates Lyα escape, explaining why the Lyα equivalent width is anti-correlated with stellar metallicity. Finally, we stress that uncertainties in SFHs impose a challenge for future inferences of the stellar metallicity of young galaxies. This highlights the need for joint (spatially resolved) analyses of stellar spectra and photo-ionisation models."}],"date_published":"2022-03-30T00:00:00Z","arxiv":1,"article_processing_charge":"No"},{"_id":"11497","abstract":[{"lang":"eng","text":"Context. The hydrogen Lyman α line is often the only measurable feature in optical spectra of high-redshift galaxies. Its shape and strength are influenced by radiative transfer processes and the properties of the underlying stellar population. High equivalent widths of several hundred Å are especially hard to explain by models and could point towards unusual stellar populations, for example with low metallicities, young stellar ages, and a top-heavy initial mass function. Other aspects influencing equivalent widths are the morphology of the galaxy and its gas properties.\r\nAims. The aim of this study is to better understand the connection between the Lyman α rest-frame equivalent width (EW0) and spectral properties as well as ultraviolet (UV) continuum morphology by obtaining reliable EW0 histograms for a statistical sample of galaxies and by assessing the fraction of objects with large equivalent widths.\r\nMethods. We used integral field spectroscopy from the Multi Unit Spectroscopic Explorer (MUSE) combined with broad-band data from the Hubble Space Telescope (HST) to measure EW0. We analysed the emission lines of 1920 Lyman α emitters (LAEs) detected in the full MUSE-Wide (one hour exposure time) and MUSE-Deep (ten hour exposure time) surveys and found UV continuum counterparts in archival HST data. We fitted the UV continuum photometric images using the Galfit software to gain morphological information on the rest-UV emission and fitted the spectra obtained from MUSE to determine the double peak fraction, asymmetry, full-width at half maximum, and flux of the Lyman α line.\r\nResults. The two surveys show different histograms of Lyman α EW0. In MUSE-Wide, 20% of objects have EW0 > 240 Å, while this fraction is only 11% in MUSE-Deep and ≈16% for the full sample. This includes objects without HST continuum counterparts (one-third of our sample), for which we give lower limits for EW0. The object with the highest securely measured EW0 has EW0 = 589 ± 193 Å (the highest lower limit being EW0 = 4464 Å). We investigate the connection between EW0 and Lyman α spectral or UV continuum morphological properties.\r\nConclusions. The survey depth has to be taken into account when studying EW0 distributions. We find that in general, high EW0 objects can have a wide range of spectral and UV morphological properties, which might reflect that the underlying causes for high EW0 values are equally varied."}],"date_published":"2022-03-25T00:00:00Z","article_number":"183","article_processing_charge":"No","arxiv":1,"volume":659,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2202.06642"}],"oa":1,"publication_status":"published","year":"2022","oa_version":"Published Version","article_type":"original","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"external_id":{"arxiv":["2202.06642"]},"scopus_import":"1","date_updated":"2022-07-19T09:47:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-07-06T08:17:27Z","month":"03","extern":"1","intvolume":"       659","status":"public","publication":"Astronomy & Astrophysics","quality_controlled":"1","publisher":"EDP Sciences","author":[{"first_name":"J.","full_name":"Kerutt, J.","last_name":"Kerutt"},{"full_name":"Wisotzki, L.","first_name":"L.","last_name":"Wisotzki"},{"first_name":"A.","full_name":"Verhamme, A.","last_name":"Verhamme"},{"last_name":"Schmidt","full_name":"Schmidt, K. B.","first_name":"K. B."},{"last_name":"Leclercq","first_name":"F.","full_name":"Leclercq, F."},{"first_name":"E. C.","full_name":"Herenz, E. C.","last_name":"Herenz"},{"last_name":"Urrutia","first_name":"T.","full_name":"Urrutia, T."},{"first_name":"T.","full_name":"Garel, T.","last_name":"Garel"},{"last_name":"Hashimoto","full_name":"Hashimoto, T.","first_name":"T."},{"first_name":"M.","full_name":"Maseda, M.","last_name":"Maseda"},{"full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X"},{"last_name":"Kusakabe","first_name":"H.","full_name":"Kusakabe, H."},{"last_name":"Schaye","full_name":"Schaye, J.","first_name":"J."},{"first_name":"J.","full_name":"Richard, J.","last_name":"Richard"},{"last_name":"Guiderdoni","full_name":"Guiderdoni, B.","first_name":"B."},{"last_name":"Mauerhofer","first_name":"V.","full_name":"Mauerhofer, V."},{"full_name":"Nanayakkara, T.","first_name":"T.","last_name":"Nanayakkara"},{"last_name":"Vitte","first_name":"E.","full_name":"Vitte, E."}],"type":"journal_article","day":"25","title":"Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep","citation":{"mla":"Kerutt, J., et al. “Equivalent Widths of Lyman α Emitters in MUSE-Wide and MUSE-Deep.” <i>Astronomy &#38; Astrophysics</i>, vol. 659, 183, EDP Sciences, 2022, doi:<a href=\"https://doi.org/10.1051/0004-6361/202141900\">10.1051/0004-6361/202141900</a>.","chicago":"Kerutt, J., L. Wisotzki, A. Verhamme, K. B. Schmidt, F. Leclercq, E. C. Herenz, T. Urrutia, et al. “Equivalent Widths of Lyman α Emitters in MUSE-Wide and MUSE-Deep.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2022. <a href=\"https://doi.org/10.1051/0004-6361/202141900\">https://doi.org/10.1051/0004-6361/202141900</a>.","ista":"Kerutt J, Wisotzki L, Verhamme A, Schmidt KB, Leclercq F, Herenz EC, Urrutia T, Garel T, Hashimoto T, Maseda M, Matthee JJ, Kusakabe H, Schaye J, Richard J, Guiderdoni B, Mauerhofer V, Nanayakkara T, Vitte E. 2022. Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep. Astronomy &#38; Astrophysics. 659, 183.","ieee":"J. Kerutt <i>et al.</i>, “Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep,” <i>Astronomy &#38; Astrophysics</i>, vol. 659. EDP Sciences, 2022.","ama":"Kerutt J, Wisotzki L, Verhamme A, et al. Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep. <i>Astronomy &#38; Astrophysics</i>. 2022;659. doi:<a href=\"https://doi.org/10.1051/0004-6361/202141900\">10.1051/0004-6361/202141900</a>","apa":"Kerutt, J., Wisotzki, L., Verhamme, A., Schmidt, K. B., Leclercq, F., Herenz, E. C., … Vitte, E. (2022). Equivalent widths of Lyman α emitters in MUSE-Wide and MUSE-Deep. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202141900\">https://doi.org/10.1051/0004-6361/202141900</a>","short":"J. Kerutt, L. Wisotzki, A. Verhamme, K.B. Schmidt, F. Leclercq, E.C. Herenz, T. Urrutia, T. Garel, T. Hashimoto, M. Maseda, J.J. Matthee, H. Kusakabe, J. Schaye, J. Richard, B. Guiderdoni, V. Mauerhofer, T. Nanayakkara, E. Vitte, Astronomy &#38; Astrophysics 659 (2022)."},"doi":"10.1051/0004-6361/202141900","keyword":["Space and Planetary Science","Astronomy and Astrophysics","galaxies: high-redshift / galaxies: formation / galaxies: evolution / cosmology: observations"],"language":[{"iso":"eng"}],"acknowledgement":"We thank the referee for thoughtful and constructive comments that have improved the quality of this manuscript. Based on observations collected at the European Southern Observatory under ESO programme 1101.A-0127. This work made use of v2.2.1 of the Binary Population and Spectral Synthesis (BPASS) models as described in Eldridge et al. (2017) and Stanway & Eldridge (2018). A.F. acknowledges the support from grant PRIN MIUR2017-20173ML3WW_001. T.N. acknowledges support from Australian Research Council Laureate Fellowship FL180100060."}]