[{"quality_controlled":"1","ddc":["510"],"page":"343-411","type":"journal_article","_id":"10772","date_updated":"2023-08-02T14:29:50Z","publisher":"London Mathematical Society","article_processing_charge":"Yes (via OA deal)","doi":"10.1112/jlms.12515","date_published":"2022-02-05T00:00:00Z","acknowledgement":"This paper is based on my PhD thesis, which would not be possible without the support of my advisor Bernd Siebert. I also thank Dan Abramovich, Mohammed Abouzaid, Mark Gross, Tom Coates and Dimitri Zvonkine for many useful conversations. Finally, I thank the anonymous referees for their many insightful comments and valuable suggestions which have resulted in major improvements to this article. This project has received funding from the EuropeanResearch Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement Number: 682603), and from Fondation Mathématique Jacques Hadamard. ","status":"public","publication":"Journal of the London Mathematical Society","external_id":{"arxiv":["1712.10260"],"isi":["000751600600001"]},"year":"2022","isi":1,"file_date_updated":"2022-02-21T11:22:58Z","publication_status":"published","publication_identifier":{"eissn":["1469-7750"],"issn":["0024-6107"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","text":"We introduce tropical corals, balanced trees in a half-space, and show that they correspond to holomorphic polygons capturing the product rule in Lagrangian Floer theory for the elliptic curve. We then prove a correspondence theorem equating counts of tropical corals to punctured log Gromov–Witten invariants of the Tate curve. This implies that the homogeneous coordinate ring of the mirror to the Tate curve is isomorphic to the degree-zero part of symplectic cohomology, confirming a prediction of homological mirror symmetry."}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":"       105","has_accepted_license":"1","date_created":"2022-02-20T23:01:33Z","article_type":"original","volume":105,"title":"Mirror symmetry for the Tate curve via tropical and log corals","oa_version":"Published Version","day":"05","scopus_import":"1","author":[{"id":"3c26b22e-c843-11eb-aa56-d38ffa0bdd08","full_name":"Arguez, Nuroemuer Huelya","last_name":"Arguez","first_name":"Nuroemuer Huelya"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Arguez NH. Mirror symmetry for the Tate curve via tropical and log corals. <i>Journal of the London Mathematical Society</i>. 2022;105(1):343-411. doi:<a href=\"https://doi.org/10.1112/jlms.12515\">10.1112/jlms.12515</a>","ieee":"N. H. Arguez, “Mirror symmetry for the Tate curve via tropical and log corals,” <i>Journal of the London Mathematical Society</i>, vol. 105, no. 1. London Mathematical Society, pp. 343–411, 2022.","short":"N.H. Arguez, Journal of the London Mathematical Society 105 (2022) 343–411.","chicago":"Arguez, Nuroemuer Huelya. “Mirror Symmetry for the Tate Curve via Tropical and Log Corals.” <i>Journal of the London Mathematical Society</i>. London Mathematical Society, 2022. <a href=\"https://doi.org/10.1112/jlms.12515\">https://doi.org/10.1112/jlms.12515</a>.","ista":"Arguez NH. 2022. Mirror symmetry for the Tate curve via tropical and log corals. Journal of the London Mathematical Society. 105(1), 343–411.","apa":"Arguez, N. H. (2022). Mirror symmetry for the Tate curve via tropical and log corals. <i>Journal of the London Mathematical Society</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/jlms.12515\">https://doi.org/10.1112/jlms.12515</a>","mla":"Arguez, Nuroemuer Huelya. “Mirror Symmetry for the Tate Curve via Tropical and Log Corals.” <i>Journal of the London Mathematical Society</i>, vol. 105, no. 1, London Mathematical Society, 2022, pp. 343–411, doi:<a href=\"https://doi.org/10.1112/jlms.12515\">10.1112/jlms.12515</a>."},"issue":"1","language":[{"iso":"eng"}],"oa":1,"file":[{"date_created":"2022-02-21T11:22:58Z","file_size":936873,"creator":"dernst","date_updated":"2022-02-21T11:22:58Z","file_id":"10783","success":1,"file_name":"2022_JournLondonMathSociety_Arguez.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"8bd0fd9694be894a191857ddf27678f0"}],"department":[{"_id":"TaHa"}],"month":"02","arxiv":1},{"publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00454-022-00371-2","type":"journal_article","_id":"10773","date_updated":"2023-08-02T14:31:25Z","ddc":["510"],"page":"811-842","quality_controlled":"1","external_id":{"isi":["000752175300002"]},"isi":1,"year":"2022","status":"public","publication":"Discrete and Computational Geometry","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria).","date_published":"2022-04-01T00:00:00Z","oa_version":"Published Version","title":"Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics","scopus_import":"1","day":"01","author":[{"orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera Di Montesano","full_name":"Cultrera Di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"}],"date_created":"2022-02-20T23:01:34Z","article_type":"original","volume":67,"abstract":[{"lang":"eng","text":"The Voronoi tessellation in Rd is defined by locally minimizing the power distance to given weighted points. Symmetrically, the Delaunay mosaic can be defined by locally maximizing the negative power distance to other such points. We prove that the average of the two piecewise quadratic functions is piecewise linear, and that all three functions have the same critical points and values. Discretizing the two piecewise quadratic functions, we get the alpha shapes as sublevel sets of the discrete function on the Delaunay mosaic, and analogous shapes as superlevel sets of the discrete function on the Voronoi tessellation. For the same non-critical value, the corresponding shapes are disjoint, separated by a narrow channel that contains no critical points but the entire level set of the piecewise linear function."}],"license":"https://creativecommons.org/licenses/by/4.0/","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        67","has_accepted_license":"1","file_date_updated":"2022-08-02T06:07:55Z","publication_status":"published","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"04","file":[{"creator":"dernst","date_updated":"2022-08-02T06:07:55Z","file_size":2518111,"date_created":"2022-08-02T06:07:55Z","file_id":"11718","content_type":"application/pdf","access_level":"open_access","file_name":"2022_DiscreteCompGeometry_Biswas.pdf","success":1,"checksum":"9383d3b70561bacee905e335dc922680","relation":"main_file"}],"department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics. <i>Discrete and Computational Geometry</i>. 2022;67:811-842. doi:<a href=\"https://doi.org/10.1007/s00454-022-00371-2\">10.1007/s00454-022-00371-2</a>","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics,” <i>Discrete and Computational Geometry</i>, vol. 67. Springer Nature, pp. 811–842, 2022.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Discrete and Computational Geometry 67 (2022) 811–842.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2022. Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics. Discrete and Computational Geometry. 67, 811–842.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Continuous and Discrete Radius Functions on Voronoi Tessellations and Delaunay Mosaics.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-022-00371-2\">https://doi.org/10.1007/s00454-022-00371-2</a>.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (2022). Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00371-2\">https://doi.org/10.1007/s00454-022-00371-2</a>","mla":"Biswas, Ranita, et al. “Continuous and Discrete Radius Functions on Voronoi Tessellations and Delaunay Mosaics.” <i>Discrete and Computational Geometry</i>, vol. 67, Springer Nature, 2022, pp. 811–42, doi:<a href=\"https://doi.org/10.1007/s00454-022-00371-2\">10.1007/s00454-022-00371-2</a>."}},{"year":"2022","external_id":{"arxiv":["2105.02013"]},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","status":"public","conference":{"name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation","end_date":"2022-01-18","start_date":"2022-01-16","location":"Philadelphia, PA, United States"},"acknowledgement":"This work was funded in part by the Wittgenstein Award Z211-N23 of the Austrian Science Fund (FWF) and by the FWF project W1255-N23.","date_published":"2022-01-14T00:00:00Z","doi":"10.1007/978-3-030-94583-1_1","alternative_title":["LNCS"],"article_processing_charge":"No","publisher":"Springer Nature","date_updated":"2022-08-05T09:02:56Z","_id":"10774","type":"conference","page":"1-19","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.02013","open_access":"1"}],"quality_controlled":"1","arxiv":1,"month":"01","department":[{"_id":"ToHe"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"short":"E. Bartocci, T. Ferrere, T.A. Henzinger, D. Nickovic, A.O. Da Costa, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2022, pp. 1–19.","ieee":"E. Bartocci, T. Ferrere, T. A. Henzinger, D. Nickovic, and A. O. Da Costa, “Flavors of sequential information flow,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Philadelphia, PA, United States, 2022, vol. 13182, pp. 1–19.","ama":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. Flavors of sequential information flow. In: <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 13182. Springer Nature; 2022:1-19. doi:<a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">10.1007/978-3-030-94583-1_1</a>","mla":"Bartocci, Ezio, et al. “Flavors of Sequential Information Flow.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, vol. 13182, Springer Nature, 2022, pp. 1–19, doi:<a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">10.1007/978-3-030-94583-1_1</a>.","apa":"Bartocci, E., Ferrere, T., Henzinger, T. A., Nickovic, D., &#38; Da Costa, A. O. (2022). Flavors of sequential information flow. In <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 13182, pp. 1–19). Philadelphia, PA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">https://doi.org/10.1007/978-3-030-94583-1_1</a>","ista":"Bartocci E, Ferrere T, Henzinger TA, Nickovic D, Da Costa AO. 2022. Flavors of sequential information flow. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 13182, 1–19.","chicago":"Bartocci, Ezio, Thomas Ferrere, Thomas A Henzinger, Dejan Nickovic, and Ana Oliveira Da Costa. “Flavors of Sequential Information Flow.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, 13182:1–19. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-94583-1_1\">https://doi.org/10.1007/978-3-030-94583-1_1</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"first_name":"Thomas","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere"},{"first_name":"Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"first_name":"Ana Oliveira","last_name":"Da Costa","full_name":"Da Costa, Ana Oliveira"}],"scopus_import":"1","day":"14","oa_version":"Preprint","title":"Flavors of sequential information flow","volume":13182,"date_created":"2022-02-20T23:01:34Z","intvolume":"     13182","abstract":[{"lang":"eng","text":"We study the problem of specifying sequential information-flow properties of systems. Information-flow properties are hyperproperties, as they compare different traces of a system. Sequential information-flow properties can express changes, over time, in the information-flow constraints. For example, information-flow constraints during an initialization phase of a system may be different from information-flow constraints that are required during the operation phase. We formalize several variants of interpreting sequential information-flow constraints, which arise from different assumptions about what can be observed of the system. For this purpose, we introduce a first-order logic, called Hypertrace Logic, with both trace and time quantifiers for specifying linear-time hyperproperties. We prove that HyperLTL, which corresponds to a fragment of Hypertrace Logic with restricted quantifier prefixes, cannot specify the majority of the studied variants of sequential information flow, including all variants in which the transition between sequential phases (such as initialization and operation) happens asynchronously. Our results rely on new equivalences between sets of traces that cannot be distinguished by certain classes of formulas from Hypertrace Logic. This presents a new approach to proving inexpressiveness results for HyperLTL."}],"publication_identifier":{"eissn":["16113349"],"issn":["03029743"],"isbn":["9783030945824"]},"publication_status":"published"},{"date_updated":"2023-08-03T06:57:01Z","_id":"10775","type":"journal_article","doi":"10.1109/TIT.2022.3148779","article_processing_charge":"No","publisher":"IEEE","main_file_link":[{"url":"https://arxiv.org/abs/2012.10584","open_access":"1"}],"quality_controlled":"1","page":"3823-3828","isi":1,"year":"2022","external_id":{"arxiv":["2012.10584"],"isi":["000799622500022"]},"related_material":{"record":[{"id":"11145","status":"public","relation":"earlier_version"}]},"acknowledgement":"Research supported by NSF Award DMS-1953990.","date_published":"2022-06-01T00:00:00Z","publication":"IEEE Transactions on Information Theory","status":"public","volume":68,"article_type":"original","date_created":"2022-02-20T23:01:34Z","author":[{"full_name":"Ferber, Asaf","last_name":"Ferber","first_name":"Asaf"},{"first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","last_name":"Kwan","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sauermann","full_name":"Sauermann, Lisa","first_name":"Lisa"}],"day":"01","scopus_import":"1","title":"List-decodability with large radius for Reed-Solomon codes","oa_version":"Preprint","publication_status":"published","publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"abstract":[{"lang":"eng","text":"List-decodability of Reed–Solomon codes has received a lot of attention, but the best-possible dependence between the parameters is still not well-understood. In this work, we focus on the case where the list-decoding radius is of the form r = 1-ε for ε tending to zero. Our main result states that there exist Reed–Solomon codes with rate Ω(ε) which are (1 - ε, O(1/ε))-list-decodable, meaning that any Hamming ball of radius 1-ε contains at most O(1/ε) codewords. This trade-off between rate and list-decoding radius is best-possible for any code with list size less than exponential in the block length. By achieving this trade-off between rate and list-decoding radius we improve a recent result of Guo, Li, Shangguan, Tamo, and Wootters, and resolve the main motivating question of their work. Moreover, while their result requires the field to be exponentially large in the block length, we only need the field size to be polynomially large (and in fact, almost-linear suffices). We deduce our main result from a more general theorem, in which we prove good list-decodability properties of random puncturings of any given code with very large distance."}],"intvolume":"        68","department":[{"_id":"MaKw"}],"month":"06","arxiv":1,"issue":"6","citation":{"short":"A. Ferber, M.A. Kwan, L. Sauermann, IEEE Transactions on Information Theory 68 (2022) 3823–3828.","ieee":"A. Ferber, M. A. Kwan, and L. Sauermann, “List-decodability with large radius for Reed-Solomon codes,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 6. IEEE, pp. 3823–3828, 2022.","ama":"Ferber A, Kwan MA, Sauermann L. List-decodability with large radius for Reed-Solomon codes. <i>IEEE Transactions on Information Theory</i>. 2022;68(6):3823-3828. doi:<a href=\"https://doi.org/10.1109/TIT.2022.3148779\">10.1109/TIT.2022.3148779</a>","mla":"Ferber, Asaf, et al. “List-Decodability with Large Radius for Reed-Solomon Codes.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 6, IEEE, 2022, pp. 3823–28, doi:<a href=\"https://doi.org/10.1109/TIT.2022.3148779\">10.1109/TIT.2022.3148779</a>.","apa":"Ferber, A., Kwan, M. A., &#38; Sauermann, L. (2022). List-decodability with large radius for Reed-Solomon codes. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2022.3148779\">https://doi.org/10.1109/TIT.2022.3148779</a>","ista":"Ferber A, Kwan MA, Sauermann L. 2022. List-decodability with large radius for Reed-Solomon codes. IEEE Transactions on Information Theory. 68(6), 3823–3828.","chicago":"Ferber, Asaf, Matthew Alan Kwan, and Lisa Sauermann. “List-Decodability with Large Radius for Reed-Solomon Codes.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/TIT.2022.3148779\">https://doi.org/10.1109/TIT.2022.3148779</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}]},{"date_updated":"2023-08-02T14:38:58Z","_id":"10776","type":"journal_article","doi":"10.1007/s00454-021-00364-7","article_processing_charge":"No","publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.13536"}],"quality_controlled":"1","page":"1133-1154","isi":1,"year":"2022","external_id":{"isi":["000750681500001"],"arxiv":["2003.13536"]},"acknowledgement":"The work by Zuzana Patáková has been partially supported by Charles University Research Center Program No. UNCE/SCI/022, and part of it was done during her research stay at IST Austria. The work by Martin Tancer is supported by the GAČR Grant 19-04113Y and by the Charles University Projects PRIMUS/17/SCI/3 and UNCE/SCI/004.","date_published":"2022-12-01T00:00:00Z","publication":"Discrete and Computational Geometry","status":"public","volume":68,"article_type":"original","date_created":"2022-02-20T23:01:35Z","author":[{"orcid":"0000-0002-3975-1683","first_name":"Zuzana","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova"},{"last_name":"Tancer","full_name":"Tancer, Martin","first_name":"Martin"},{"orcid":"0000-0002-1494-0568","first_name":"Uli","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner"}],"scopus_import":"1","day":"01","title":"Barycentric cuts through a convex body","oa_version":"Preprint","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"publication_status":"published","intvolume":"        68","abstract":[{"text":"Let K be a convex body in Rn (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K∩h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p0 is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n≥2, there are always at least three distinct barycentric cuts through the point p0∈K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p0 are guaranteed if n≥3.","lang":"eng"}],"department":[{"_id":"UlWa"}],"month":"12","arxiv":1,"citation":{"short":"Z. Patakova, M. Tancer, U. Wagner, Discrete and Computational Geometry 68 (2022) 1133–1154.","ieee":"Z. Patakova, M. Tancer, and U. Wagner, “Barycentric cuts through a convex body,” <i>Discrete and Computational Geometry</i>, vol. 68. Springer Nature, pp. 1133–1154, 2022.","ama":"Patakova Z, Tancer M, Wagner U. Barycentric cuts through a convex body. <i>Discrete and Computational Geometry</i>. 2022;68:1133-1154. doi:<a href=\"https://doi.org/10.1007/s00454-021-00364-7\">10.1007/s00454-021-00364-7</a>","mla":"Patakova, Zuzana, et al. “Barycentric Cuts through a Convex Body.” <i>Discrete and Computational Geometry</i>, vol. 68, Springer Nature, 2022, pp. 1133–54, doi:<a href=\"https://doi.org/10.1007/s00454-021-00364-7\">10.1007/s00454-021-00364-7</a>.","apa":"Patakova, Z., Tancer, M., &#38; Wagner, U. (2022). Barycentric cuts through a convex body. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-021-00364-7\">https://doi.org/10.1007/s00454-021-00364-7</a>","ista":"Patakova Z, Tancer M, Wagner U. 2022. Barycentric cuts through a convex body. Discrete and Computational Geometry. 68, 1133–1154.","chicago":"Patakova, Zuzana, Martin Tancer, and Uli Wagner. “Barycentric Cuts through a Convex Body.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-021-00364-7\">https://doi.org/10.1007/s00454-021-00364-7</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>.","apa":"Barton, N. H., &#38; Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2021.0009\">https://doi.org/10.1098/rstb.2021.0009</a>","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848, The Royal Society, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>.","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1848). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0009\">10.1098/rstb.2021.0009</a>","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1848. The Royal Society, 2022.","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022)."},"issue":"1848","language":[{"iso":"eng"}],"oa":1,"file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","relation":"main_file","creator":"dernst","date_updated":"2022-08-02T06:14:32Z","file_size":1349672,"date_created":"2022-08-02T06:14:32Z","file_id":"11719"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"month":"04","file_date_updated":"2022-08-02T06:14:32Z","publication_status":"published","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"intvolume":"       377","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.","lang":"eng"}],"has_accepted_license":"1","date_created":"2022-02-21T16:08:10Z","article_type":"original","volume":377,"oa_version":"Published Version","title":"The response of a metapopulation to a changing environment","day":"11","scopus_import":"1","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"},{"first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","last_name":"Olusanya","full_name":"Olusanya, Oluwafunmilola O","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2022-04-11T00:00:00Z","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","pmid":1,"status":"public","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","project":[{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"related_material":{"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}]},"external_id":{"isi":["000758140300001"],"pmid":["35184588"]},"year":"2022","isi":1,"quality_controlled":"1","ddc":["570"],"type":"journal_article","_id":"10787","date_updated":"2025-05-26T09:05:09Z","publisher":"The Royal Society","article_processing_charge":"No","doi":"10.1098/rstb.2021.0009"},{"department":[{"_id":"TiBr"}],"article_number":"2202.10909","keyword":["Integral point","toric variety","Manin's conjecture"],"year":"2022","month":"02","arxiv":1,"external_id":{"arxiv":["2202.10909"]},"citation":{"short":"F.A. Wilsch, ArXiv (n.d.).","ieee":"F. A. Wilsch, “Integral points of bounded height on a certain toric variety,” <i>arXiv</i>. .","ama":"Wilsch FA. Integral points of bounded height on a certain toric variety. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2202.10909\">10.48550/arXiv.2202.10909</a>","mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Certain Toric Variety.” <i>ArXiv</i>, 2202.10909, doi:<a href=\"https://doi.org/10.48550/arXiv.2202.10909\">10.48550/arXiv.2202.10909</a>.","apa":"Wilsch, F. A. (n.d.). Integral points of bounded height on a certain toric variety. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2202.10909\">https://doi.org/10.48550/arXiv.2202.10909</a>","ista":"Wilsch FA. Integral points of bounded height on a certain toric variety. arXiv, 2202.10909.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Certain Toric Variety.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2202.10909\">https://doi.org/10.48550/arXiv.2202.10909</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-02-22T00:00:00Z","acknowledgement":"Part of this work was conducted as a guest at the Institut de Mathématiques de Jussieu–Paris Rive Gauche invited by Antoine Chambert-Loir and funded by DAAD.\r\nDuring this time, I had interesting and fruitful discussions on the interpretation of the result for\r\nthe toric variety discussed in Section 3 with Antoine Chambert-Loir. I wish to thank him for these\r\nopportunities and for his useful remarks on earlier versions of this article. This work was partly\r\nfunded by FWF grant P 32428-N35.","oa":1,"language":[{"iso":"eng"}],"publication":"arXiv","status":"public","project":[{"_id":"26AEDAB2-B435-11E9-9278-68D0E5697425","name":"New frontiers of the Manin conjecture","grant_number":"P32428","call_identifier":"FWF"}],"_id":"10788","date_updated":"2023-05-03T07:46:35Z","date_created":"2022-02-23T09:04:43Z","type":"preprint","article_processing_charge":"No","day":"22","doi":"10.48550/arXiv.2202.10909","author":[{"last_name":"Wilsch","id":"560601DA-8D36-11E9-A136-7AC1E5697425","full_name":"Wilsch, Florian Alexander","orcid":"0000-0001-7302-8256","first_name":"Florian Alexander"}],"title":"Integral points of bounded height on a certain toric variety","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2202.10909"}],"publication_status":"submitted","abstract":[{"text":"We determine an asymptotic formula for the number of integral points of\r\nbounded height on a certain toric variety, which is incompatible with part of a\r\npreprint by Chambert-Loir and Tschinkel. We provide an alternative\r\ninterpretation of the asymptotic formula we get. To do so, we construct an\r\nanalogue of Peyre's constant $\\alpha$ and describe its relation to a new\r\nobstruction to the Zariski density of integral points in certain regions of\r\nvarieties.","lang":"eng"}]},{"department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"article_number":"kvac009","file":[{"relation":"main_file","checksum":"822e76e056c07099d1fb27d1ece5941b","file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","file_id":"14061","date_created":"2023-08-16T08:00:30Z","file_size":4846551,"creator":"dernst","date_updated":"2023-08-16T08:00:30Z"}],"month":"07","issue":"1","citation":{"chicago":"Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>.","ista":"Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM, Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 1(1), kvac009.","apa":"Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter, S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>","mla":"Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1, kvac009, Oxford Academic, 2022, doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>.","ama":"Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. 2022;1(1). doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>","ieee":"A. H. Hansen <i>et al.</i>, “Tissue-wide effects override cell-intrinsic gene function in radial neuron migration,” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1. Oxford Academic, 2022.","short":"A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter, C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford Open Neuroscience 1 (2022)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":1,"article_type":"original","date_created":"2022-02-25T07:52:11Z","author":[{"first_name":"Andi H","last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048"},{"last_name":"Riedl","full_name":"Riedl, Michael","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4844-6311","first_name":"Michael"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen"},{"first_name":"Anna-Magdalena","id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","full_name":"Heger, Anna-Magdalena","last_name":"Heger"},{"last_name":"Laukoter","full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010","first_name":"Susanne"},{"last_name":"Sommer","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","orcid":"0000-0003-1216-9105"},{"last_name":"Nicolas","full_name":"Nicolas, Armel","id":"2A103192-F248-11E8-B48F-1D18A9856A87","first_name":"Armel"},{"first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","last_name":"Hof"},{"first_name":"Li Huei","full_name":"Tsai, Li Huei","last_name":"Tsai"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"}],"day":"07","title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","oa_version":"Published Version","publication_identifier":{"eissn":["2753-149X"]},"publication_status":"published","file_date_updated":"2023-08-16T08:00:30Z","has_accepted_license":"1","abstract":[{"text":"The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"         1","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"year":"2022","related_material":{"record":[{"id":"12726","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"14530"}]},"ec_funded":1,"date_published":"2022-07-07T00:00:00Z","acknowledgement":"A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer lab for discussion. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics Facility, Lab Support Facility and Preclinical Facility.","project":[{"name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444","call_identifier":"FP7","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"}],"status":"public","publication":"Oxford Open Neuroscience","date_updated":"2023-11-30T10:55:12Z","_id":"10791","type":"journal_article","doi":"10.1093/oons/kvac009","article_processing_charge":"No","publisher":"Oxford Academic","quality_controlled":"1","ddc":["570"]},{"department":[{"_id":"SiHi"}],"year":"2022","month":"02","external_id":{"pmid":["PPR454733"]},"citation":{"ama":"Schaaf Z, Tat L, Cannizzaro N, et al. WDFY3 cell autonomously controls neuronal migration. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>","ieee":"Z. Schaaf <i>et al.</i>, “WDFY3 cell autonomously controls neuronal migration.” Research Square.","short":"Z. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K. Zarbalis, (n.d.).","chicago":"Schaaf, Zachary, Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and K Zarbalis. “WDFY3 Cell Autonomously Controls Neuronal Migration.” Research Square, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">https://doi.org/10.21203/rs.3.rs-1316167/v1</a>.","ista":"Schaaf Z, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis K. WDFY3 cell autonomously controls neuronal migration. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>.","apa":"Schaaf, Z., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. (n.d.). WDFY3 cell autonomously controls neuronal migration. Research Square. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">https://doi.org/10.21203/rs.3.rs-1316167/v1</a>","mla":"Schaaf, Zachary, et al. <i>WDFY3 Cell Autonomously Controls Neuronal Migration</i>. Research Square, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>."},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-02-16T00:00:00Z","oa":1,"status":"public","language":[{"iso":"eng"}],"_id":"10792","date_updated":"2023-10-17T13:06:52Z","date_created":"2022-02-25T07:53:26Z","type":"preprint","day":"16","article_processing_charge":"No","doi":"10.21203/rs.3.rs-1316167/v1","author":[{"first_name":"Zachary","last_name":"Schaaf","full_name":"Schaaf, Zachary"},{"first_name":"Lyvin","full_name":"Tat, Lyvin","last_name":"Tat"},{"last_name":"Cannizzaro","full_name":"Cannizzaro, Noemi","first_name":"Noemi"},{"last_name":"Green","full_name":"Green, Ralph","first_name":"Ralph"},{"full_name":"Rülicke, Thomas","last_name":"Rülicke","first_name":"Thomas"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"K","last_name":"Zarbalis","full_name":"Zarbalis, K"}],"title":"WDFY3 cell autonomously controls neuronal migration","publisher":"Research Square","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.21203/rs.3.rs-1316167/v1"}],"publication_identifier":{"eissn":["2693-5015"]},"publication_status":"submitted","page":"30","abstract":[{"lang":"eng","text":"Background\r\nProper 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\r\nHere, 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\r\nWe 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. Limitations 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.\r\nConclusions\r\nOur genetic approach revealed several cell autonomous requirements of Wdfy3 in neuronal development that could underly the pathogenic mechanisms of WDFY3-related ASD 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."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"}},{"acknowledgement":"The authors would like to thank Gioia Carinci and Cristian Giardinà for useful discussions. F.R. and S.F. thank Jean-René Chazottes for a stay at CPHT (Institut Polytechnique de Paris), in the realm of Chaire d’Alembert (Paris-Saclay University), where part of this work was performed. S.F. acknowledges Simona Villa for her support in creating the picture. S.F. acknowledges financial support from NWO via the grant TOP1.17.019. F.S. acknowledges financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.","date_published":"2022-02-01T00:00:00Z","ec_funded":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","status":"public","external_id":{"isi":["000752489300010"],"arxiv":["2007.08272"]},"isi":1,"year":"2022","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.08272"}],"page":"220-247","type":"journal_article","date_updated":"2023-10-17T12:49:43Z","_id":"10797","publisher":"Institute of Mathematical Statistics","doi":"10.1214/21-AIHP1163","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","citation":{"ista":"Floreani S, Redig F, Sau F. 2022. Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. Annales de l’institut Henri Poincare (B) Probability and Statistics. 58(1), 220–247.","chicago":"Floreani, Simone, Frank Redig, and Federico Sau. “Orthogonal Polynomial Duality of Boundary Driven Particle Systems and Non-Equilibrium Correlations.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AIHP1163\">https://doi.org/10.1214/21-AIHP1163</a>.","apa":"Floreani, S., Redig, F., &#38; Sau, F. (2022). Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AIHP1163\">https://doi.org/10.1214/21-AIHP1163</a>","mla":"Floreani, Simone, et al. “Orthogonal Polynomial Duality of Boundary Driven Particle Systems and Non-Equilibrium Correlations.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 58, no. 1, Institute of Mathematical Statistics, 2022, pp. 220–47, doi:<a href=\"https://doi.org/10.1214/21-AIHP1163\">10.1214/21-AIHP1163</a>.","ama":"Floreani S, Redig F, Sau F. Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2022;58(1):220-247. doi:<a href=\"https://doi.org/10.1214/21-AIHP1163\">10.1214/21-AIHP1163</a>","ieee":"S. Floreani, F. Redig, and F. Sau, “Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 58, no. 1. Institute of Mathematical Statistics, pp. 220–247, 2022.","short":"S. Floreani, F. Redig, F. Sau, Annales de l’institut Henri Poincare (B) Probability and Statistics 58 (2022) 220–247."},"language":[{"iso":"eng"}],"oa":1,"department":[{"_id":"JaMa"}],"arxiv":1,"month":"02","publication_status":"published","publication_identifier":{"issn":["0246-0203"]},"abstract":[{"text":"We consider symmetric partial exclusion and inclusion processes in a general graph in contact with reservoirs, where we allow both for edge disorder and well-chosen site disorder. We extend the classical dualities to this context and then we derive new orthogonal polynomial dualities. From the classical dualities, we derive the uniqueness of the non-equilibrium steady state and obtain correlation inequalities. Starting from the orthogonal polynomial dualities, we show universal properties of n-point correlation functions in the non-equilibrium steady state for systems with at most two different reservoir parameters, such as a chain with reservoirs at left and right ends.","lang":"eng"},{"text":"Nous considérons des processus d’exclusion partielle, et des processus d’inclusion sur un graphe général en contact avec des réservoirs. Nous autorisons la présence de inhomogenéités sur les arrêts ainsi que sur les sommets du graph. Nous généralisons les “dualités classiques” dans ce contexte et nous démontrons des nouvelles dualités orthogonales. À partir des dualités classiques, nous démontrons l’unicité de l’état stationnaire non-équilibre, ainsi que des inégalités de corrélation. À partir des dualités orthogonales nous démontrons des propriétés universelles des fonctions de corrélation à n points dans l’état stationnaire non-équilibre pour des systèmes avec deux paramètres de réservoirs inégaux, comme par exemple une chaîne avec des réservoirs à droite et à gauche.","lang":"fre"}],"intvolume":"        58","article_type":"original","date_created":"2022-02-27T23:01:50Z","volume":58,"oa_version":"Preprint","title":"Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations","author":[{"last_name":"Floreani","full_name":"Floreani, Simone","first_name":"Simone"},{"full_name":"Redig, Frank","last_name":"Redig","first_name":"Frank"},{"first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico","last_name":"Sau"}],"day":"01","scopus_import":"1"},{"oa":1,"language":[{"iso":"eng"}],"citation":{"short":"N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute of Science and Technology Austria, 2022.","ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:10799\">10.15479/at:ista:10799</a>","mla":"Konstantinov, Nikola H. <i>Robustness and Fairness in Machine Learning</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:10799\">10.15479/at:ista:10799</a>.","apa":"Konstantinov, N. H. (2022). <i>Robustness and fairness in machine learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10799\">https://doi.org/10.15479/at:ista:10799</a>","ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","chicago":"Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:10799\">https://doi.org/10.15479/at:ista:10799</a>."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"month":"03","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"file":[{"relation":"main_file","checksum":"626bc523ae8822d20e635d0e2d95182e","success":1,"file_name":"thesis.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"10823","file_size":4204905,"date_created":"2022-03-06T11:42:54Z","date_updated":"2022-03-06T11:42:54Z","creator":"nkonstan"},{"file_id":"10824","date_updated":"2022-03-10T12:11:48Z","creator":"nkonstan","date_created":"2022-03-06T11:42:57Z","file_size":22841103,"checksum":"e2ca2b88350ac8ea1515b948885cbcb1","relation":"source_file","access_level":"closed","content_type":"application/x-zip-compressed","file_name":"thesis.zip"}],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the\r\nsake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range\r\nof training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the\r\ndata they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting."}],"publication_status":"published","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-015-2"]},"file_date_updated":"2022-03-10T12:11:48Z","author":[{"last_name":"Konstantinov","full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola H"}],"day":"08","oa_version":"Published Version","title":"Robustness and fairness in machine learning","date_created":"2022-02-28T13:03:49Z","degree_awarded":"PhD","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"status":"public","ec_funded":1,"date_published":"2022-03-08T00:00:00Z","year":"2022","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8724"},{"status":"public","relation":"part_of_dissertation","id":"10803"},{"status":"public","relation":"part_of_dissertation","id":"10802"},{"status":"public","relation":"part_of_dissertation","id":"6590"}]},"keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"page":"176","ddc":["000"],"doi":"10.15479/at:ista:10799","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","date_updated":"2023-10-17T12:31:54Z","_id":"10799","type":"dissertation"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Addressing fairness concerns about machine learning models is a crucial step towards their long-term adoption in real-world automated systems. While many approaches have been developed for training fair models from data, little is known about the robustness of these methods to data corruption. In this work we consider fairness-aware learning under worst-case data manipulations. We show that an adversary can in some situations force any learner to return an overly biased classifier, regardless of the sample size and with or without degrading\r\naccuracy, and that the strength of the excess bias increases for learning problems with underrepresented protected groups in the data. We also prove that our hardness results are tight up to constant factors. To this end, we study two natural learning algorithms that optimize for both accuracy and fairness and show that these algorithms enjoy guarantees that are order-optimal in terms of the corruption ratio and the protected groups frequencies in the large data\r\nlimit."}],"intvolume":"        23","has_accepted_license":"1","file_date_updated":"2022-07-12T15:08:28Z","publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"publication_status":"published","oa_version":"Published Version","title":"Fairness-aware PAC learning from corrupted data","day":"01","scopus_import":"1","author":[{"full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","first_name":"Nikola H"},{"first_name":"Christoph","orcid":"0000-0002-4561-241X","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert"}],"date_created":"2022-02-28T14:05:42Z","article_type":"original","volume":23,"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"N. H. Konstantinov and C. Lampert, “Fairness-aware PAC learning from corrupted data,” <i>Journal of Machine Learning Research</i>, vol. 23. ML Research Press, pp. 1–60, 2022.","short":"N.H. Konstantinov, C. Lampert, Journal of Machine Learning Research 23 (2022) 1–60.","ama":"Konstantinov NH, Lampert C. Fairness-aware PAC learning from corrupted data. <i>Journal of Machine Learning Research</i>. 2022;23:1-60.","apa":"Konstantinov, N. H., &#38; Lampert, C. (2022). Fairness-aware PAC learning from corrupted data. <i>Journal of Machine Learning Research</i>. ML Research Press.","mla":"Konstantinov, Nikola H., and Christoph Lampert. “Fairness-Aware PAC Learning from Corrupted Data.” <i>Journal of Machine Learning Research</i>, vol. 23, ML Research Press, 2022, pp. 1–60.","ista":"Konstantinov NH, Lampert C. 2022. Fairness-aware PAC learning from corrupted data. Journal of Machine Learning Research. 23, 1–60.","chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Fairness-Aware PAC Learning from Corrupted Data.” <i>Journal of Machine Learning Research</i>. ML Research Press, 2022."},"month":"05","arxiv":1,"file":[{"file_id":"11570","date_created":"2022-07-12T15:08:28Z","file_size":551862,"creator":"kschuh","date_updated":"2022-07-12T15:08:28Z","relation":"main_file","checksum":"9cac897b54a0ddf3a553a2c33e88cfda","file_name":"2022_JournalMachineLearningResearch_Konstantinov.pdf","success":1,"content_type":"application/pdf","access_level":"open_access"}],"department":[{"_id":"ChLa"}],"ddc":["004"],"page":"1-60","quality_controlled":"1","publisher":"ML Research Press","article_processing_charge":"No","type":"journal_article","_id":"10802","date_updated":"2023-09-26T10:44:37Z","status":"public","publication":"Journal of Machine Learning Research","acknowledgement":"The authors thank Eugenia Iofinova and Bernd Prach for providing feedback on early versions of this paper. This publication was made possible by an ETH AI Center postdoctoral fellowship to Nikola Konstantinov.","date_published":"2022-05-01T00:00:00Z","related_material":{"record":[{"id":"10799","status":"public","relation":"dissertation_contains"},{"id":"13241","status":"public","relation":"shorter_version"}]},"external_id":{"arxiv":["2102.06004"]},"year":"2022","keyword":["Fairness","robustness","data poisoning","trustworthy machine learning","PAC learning"]},{"doi":"10.1038/s41579-022-00700-5","article_processing_charge":"No","publisher":"Springer Nature","date_updated":"2023-08-02T14:41:44Z","_id":"10812","type":"journal_article","page":"478-490","quality_controlled":"1","isi":1,"year":"2022","external_id":{"pmid":["35241807"],"isi":["000763891900001"]},"keyword":["General Immunology and Microbiology","Microbiology","Infectious Diseases"],"publication":"Nature Reviews Microbiology","status":"public","pmid":1,"date_published":"2022-08-01T00:00:00Z","acknowledgement":"The authors thank B. Kavčič and H. Schulenburg for constructive feedback on the manuscript.","author":[{"orcid":"0000-0001-9480-5261","first_name":"Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","full_name":"Römhild, Roderich","last_name":"Römhild"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"},{"first_name":"Dan I.","full_name":"Andersson, Dan I.","last_name":"Andersson"}],"scopus_import":"1","day":"01","title":"The physiology and genetics of bacterial responses to antibiotic combinations","oa_version":"None","volume":20,"article_type":"review","date_created":"2022-03-04T04:33:49Z","intvolume":"        20","abstract":[{"lang":"eng","text":"Several promising strategies based on combining or cycling different antibiotics have been proposed to increase efficacy and counteract resistance evolution, but we still lack a deep understanding of the physiological responses and genetic mechanisms that underlie antibiotic interactions and the clinical applicability of these strategies. In antibiotic-exposed bacteria, the combined effects of physiological stress responses and emerging resistance mutations (occurring at different time scales) generate complex and often unpredictable dynamics. In this Review, we present our current understanding of bacterial cell physiology and genetics of responses to antibiotics. We emphasize recently discovered mechanisms of synergistic and antagonistic drug interactions, hysteresis in temporal interactions between antibiotics that arise from microbial physiology and interactions between antibiotics and resistance mutations that can cause collateral sensitivity or cross-resistance. We discuss possible connections between the different phenomena and indicate relevant research directions. A better and more unified understanding of drug and genetic interactions is likely to advance antibiotic therapy."}],"publication_identifier":{"issn":["1740-1526"],"eissn":["1740-1534"]},"publication_status":"published","month":"08","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"citation":{"ista":"Römhild R, Bollenbach MT, Andersson DI. 2022. The physiology and genetics of bacterial responses to antibiotic combinations. Nature Reviews Microbiology. 20, 478–490.","chicago":"Römhild, Roderich, Mark Tobias Bollenbach, and Dan I. Andersson. “The Physiology and Genetics of Bacterial Responses to Antibiotic Combinations.” <i>Nature Reviews Microbiology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41579-022-00700-5\">https://doi.org/10.1038/s41579-022-00700-5</a>.","apa":"Römhild, R., Bollenbach, M. T., &#38; Andersson, D. I. (2022). The physiology and genetics of bacterial responses to antibiotic combinations. <i>Nature Reviews Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41579-022-00700-5\">https://doi.org/10.1038/s41579-022-00700-5</a>","mla":"Römhild, Roderich, et al. “The Physiology and Genetics of Bacterial Responses to Antibiotic Combinations.” <i>Nature Reviews Microbiology</i>, vol. 20, Springer Nature, 2022, pp. 478–90, doi:<a href=\"https://doi.org/10.1038/s41579-022-00700-5\">10.1038/s41579-022-00700-5</a>.","ama":"Römhild R, Bollenbach MT, Andersson DI. The physiology and genetics of bacterial responses to antibiotic combinations. <i>Nature Reviews Microbiology</i>. 2022;20:478-490. doi:<a href=\"https://doi.org/10.1038/s41579-022-00700-5\">10.1038/s41579-022-00700-5</a>","ieee":"R. Römhild, M. T. Bollenbach, and D. I. Andersson, “The physiology and genetics of bacterial responses to antibiotic combinations,” <i>Nature Reviews Microbiology</i>, vol. 20. Springer Nature, pp. 478–490, 2022.","short":"R. Römhild, M.T. Bollenbach, D.I. Andersson, Nature Reviews Microbiology 20 (2022) 478–490."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"status":"public","publication":"Nature Catalysis","acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (grant nos. 51773092, 21975124, 11874254, 51802187 and U2030206). It was further supported by Fujian science & technology innovation laboratory for energy devices of China (21C-LAB), Key Research Project of Zhejiang Laboratory (grant no. 2021PE0AC02) and the Cultivation Program for the Excellent Doctoral Dissertation of Nanjing Tech University. S.A.F. is indebted to IST Austria for support.","date_published":"2022-03-03T00:00:00Z","year":"2022","isi":1,"external_id":{"isi":["000763879400001"]},"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9978"}]},"keyword":["Process Chemistry and Technology","Biochemistry","Bioengineering","Catalysis"],"page":"193-201","main_file_link":[{"open_access":"1","url":"https://doi.org/10.21203/rs.3.rs-750965/v1"}],"quality_controlled":"1","doi":"10.1038/s41929-022-00752-z","article_processing_charge":"No","publisher":"Springer Nature","date_updated":"2023-10-17T13:06:28Z","_id":"10813","type":"journal_article","oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. 2022. Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. Nature Catalysis. 5, 193–201.","chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Threshold Potentials for Fast Kinetics during Mediated Redox Catalysis of Insulators in Li–O2 and Li–S Batteries.” <i>Nature Catalysis</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41929-022-00752-z\">https://doi.org/10.1038/s41929-022-00752-z</a>.","mla":"Cao, Deqing, et al. “Threshold Potentials for Fast Kinetics during Mediated Redox Catalysis of Insulators in Li–O2 and Li–S Batteries.” <i>Nature Catalysis</i>, vol. 5, Springer Nature, 2022, pp. 193–201, doi:<a href=\"https://doi.org/10.1038/s41929-022-00752-z\">10.1038/s41929-022-00752-z</a>.","apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (2022). Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. <i>Nature Catalysis</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41929-022-00752-z\">https://doi.org/10.1038/s41929-022-00752-z</a>","ama":"Cao D, Shen X, Wang A, et al. Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. <i>Nature Catalysis</i>. 2022;5:193-201. doi:<a href=\"https://doi.org/10.1038/s41929-022-00752-z\">10.1038/s41929-022-00752-z</a>","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Nature Catalysis 5 (2022) 193–201.","ieee":"D. Cao <i>et al.</i>, “Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries,” <i>Nature Catalysis</i>, vol. 5. Springer Nature, pp. 193–201, 2022."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"03","department":[{"_id":"StFr"}],"abstract":[{"text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li–S and Li–O2 batteries by shuttling electrons or holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics but with the lowest possible overpotential. However, the dependence of kinetics and overpotential is unclear, which hinders informed improvement. Here, we find that when the redox potentials of mediators are tuned via, for example, Li+ concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediator and electrolyte. The acceleration originates from the overpotentials required to activate fast Li+/e− extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids therefore requires careful consideration of the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.","lang":"eng"}],"intvolume":"         5","publication_identifier":{"issn":["2520-1158"]},"publication_status":"published","author":[{"full_name":"Cao, Deqing","last_name":"Cao","first_name":"Deqing"},{"last_name":"Shen","full_name":"Shen, Xiaoxiao","first_name":"Xiaoxiao"},{"first_name":"Aiping","full_name":"Wang, Aiping","last_name":"Wang"},{"last_name":"Yu","full_name":"Yu, Fengjiao","first_name":"Fengjiao"},{"last_name":"Wu","full_name":"Wu, Yuping","first_name":"Yuping"},{"first_name":"Siqi","full_name":"Shi, Siqi","last_name":"Shi"},{"first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander"},{"first_name":"Yuhui","last_name":"Chen","full_name":"Chen, Yuhui"}],"day":"03","scopus_import":"1","title":"Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries","oa_version":"Preprint","volume":5,"article_type":"original","date_created":"2022-03-04T07:50:10Z"},{"quality_controlled":"1","ddc":["570"],"page":"173-195","type":"journal_article","_id":"10818","date_updated":"2023-09-05T16:01:23Z","publisher":"Wiley","article_processing_charge":"No","doi":"10.1002/glia.24101","date_published":"2022-01-01T00:00:00Z","acknowledgement":"The work was supported by a grant from MIUR (PRIN 2017HPTFFC_003) to Davide Ragozzino and in part by funds to Silvia Di Angelantonio (CrestOptics-IIT JointLab for Advanced Microscopy) and Daniele Caprioli (Istituto Pasteur-Fondazione Cenci Bolognetti). Bernadette Basilico, and Laura Ferrucci were supported by the PhD program in Clinical-Experimental Neuroscience and Psychiatry, Sapienza University, Rome; Caterina Sanchini was supported by the PhD program in Life Science, Sapienza University, Rome and by the Italian Institute of Technology, Rome. The authors thank Alessandro Felici, Claudia Valeri, Arsenio Armagno, and Senthilkumar Deivasigamani for help with animal husbandry and transgenic colonies management. They also wish to thank Piotr Bregestovski and Michal Schwartz for helpful discussions and criticism. PLX5622 was provided under Materials Transfer Agreement by Plexxikon Inc. (Berkeley, CA). Open Access Funding provided by Universita degli Studi di Roma La Sapienza within the CRUI-CARE Agreement.","pmid":1,"status":"public","publication":"Glia","keyword":["Cellular and Molecular Neuroscience","Neurology"],"external_id":{"pmid":["34661306"],"isi":["000708025800001"]},"isi":1,"year":"2022","file_date_updated":"2022-03-04T08:55:27Z","publication_status":"published","publication_identifier":{"eissn":["1098-1136"],"issn":["0894-1491"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","intvolume":"        70","abstract":[{"lang":"eng","text":"Microglia cells are active players in regulating synaptic development and plasticity in the brain. However, how they influence the normal functioning of synapses is largely unknown. In this study, we characterized the effects of pharmacological microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1 synapses of adult wild type mice. Following microglial depletion, we observed a reduction of spontaneous and evoked glutamatergic activity associated with a decrease of dendritic spine density. We also observed the appearance of immature synaptic features and higher levels of plasticity. Microglia depleted mice showed a deficit in the acquisition of the Novel Object Recognition task. These events were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably, microglia repopulation after PLX5622 withdrawal was associated with the recovery of hippocampal synapses and learning functions. Altogether, these data demonstrate that microglia contribute to normal synaptic functioning in the adult brain and that their removal induces reversible changes in organization and activity of glutamatergic synapses."}],"has_accepted_license":"1","date_created":"2022-03-04T08:53:37Z","article_type":"original","volume":70,"title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","oa_version":"Published Version","day":"01","scopus_import":"1","author":[{"last_name":"Basilico","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","full_name":"Basilico, Bernadette","first_name":"Bernadette","orcid":"0000-0003-1843-3173"},{"full_name":"Ferrucci, Laura","last_name":"Ferrucci","first_name":"Laura"},{"full_name":"Ratano, Patrizia","last_name":"Ratano","first_name":"Patrizia"},{"last_name":"Golia","full_name":"Golia, Maria T.","first_name":"Maria T."},{"first_name":"Alfonso","last_name":"Grimaldi","full_name":"Grimaldi, Alfonso"},{"full_name":"Rosito, Maria","last_name":"Rosito","first_name":"Maria"},{"last_name":"Ferretti","full_name":"Ferretti, Valentina","first_name":"Valentina"},{"full_name":"Reverte, Ingrid","last_name":"Reverte","first_name":"Ingrid"},{"first_name":"Caterina","full_name":"Sanchini, Caterina","last_name":"Sanchini"},{"first_name":"Maria C.","last_name":"Marrone","full_name":"Marrone, Maria C."},{"first_name":"Maria","last_name":"Giubettini","full_name":"Giubettini, Maria"},{"full_name":"De Turris, Valeria","last_name":"De Turris","first_name":"Valeria"},{"full_name":"Salerno, Debora","last_name":"Salerno","first_name":"Debora"},{"full_name":"Garofalo, Stefano","last_name":"Garofalo","first_name":"Stefano"},{"full_name":"St‐Pierre, Marie‐Kim","last_name":"St‐Pierre","first_name":"Marie‐Kim"},{"last_name":"Carrier","full_name":"Carrier, Micael","first_name":"Micael"},{"first_name":"Massimiliano","full_name":"Renzi, Massimiliano","last_name":"Renzi"},{"full_name":"Pagani, Francesca","last_name":"Pagani","first_name":"Francesca"},{"last_name":"Modi","full_name":"Modi, Brijesh","first_name":"Brijesh"},{"first_name":"Marcello","full_name":"Raspa, Marcello","last_name":"Raspa"},{"first_name":"Ferdinando","full_name":"Scavizzi, Ferdinando","last_name":"Scavizzi"},{"full_name":"Gross, Cornelius T.","last_name":"Gross","first_name":"Cornelius T."},{"first_name":"Silvia","full_name":"Marinelli, Silvia","last_name":"Marinelli"},{"full_name":"Tremblay, Marie‐Ève","last_name":"Tremblay","first_name":"Marie‐Ève"},{"first_name":"Daniele","full_name":"Caprioli, Daniele","last_name":"Caprioli"},{"first_name":"Laura","last_name":"Maggi","full_name":"Maggi, Laura"},{"first_name":"Cristina","full_name":"Limatola, Cristina","last_name":"Limatola"},{"first_name":"Silvia","last_name":"Di Angelantonio","full_name":"Di Angelantonio, Silvia"},{"first_name":"Davide","last_name":"Ragozzino","full_name":"Ragozzino, Davide"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"B. Basilico <i>et al.</i>, “Microglia control glutamatergic synapses in the adult mouse hippocampus,” <i>Glia</i>, vol. 70, no. 1. Wiley, pp. 173–195, 2022.","short":"B. Basilico, L. Ferrucci, P. Ratano, M.T. Golia, A. Grimaldi, M. Rosito, V. Ferretti, I. Reverte, C. Sanchini, M.C. Marrone, M. Giubettini, V. De Turris, D. Salerno, S. Garofalo, M. St‐Pierre, M. Carrier, M. Renzi, F. Pagani, B. Modi, M. Raspa, F. Scavizzi, C.T. Gross, S. Marinelli, M. Tremblay, D. Caprioli, L. Maggi, C. Limatola, S. Di Angelantonio, D. Ragozzino, Glia 70 (2022) 173–195.","ama":"Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. 2022;70(1):173-195. doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>","apa":"Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito, M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. Wiley. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>","mla":"Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>, vol. 70, no. 1, Wiley, 2022, pp. 173–95, doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>.","chicago":"Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia, Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>.","ista":"Basilico B, Ferrucci L, Ratano P, Golia MT, Grimaldi A, Rosito M, Ferretti V, Reverte I, Sanchini C, Marrone MC, Giubettini M, De Turris V, Salerno D, Garofalo S, St‐Pierre M, Carrier M, Renzi M, Pagani F, Modi B, Raspa M, Scavizzi F, Gross CT, Marinelli S, Tremblay M, Caprioli D, Maggi L, Limatola C, Di Angelantonio S, Ragozzino D. 2022. Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. 70(1), 173–195."},"issue":"1","language":[{"iso":"eng"}],"oa":1,"file":[{"checksum":"f10a897290e66c0a062e04ba91db6c17","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2021_Glia_Basilico.pdf","success":1,"file_id":"10819","date_updated":"2022-03-04T08:55:27Z","creator":"dernst","date_created":"2022-03-04T08:55:27Z","file_size":5340294}],"department":[{"_id":"GaNo"}],"month":"01"},{"status":"public","publication":"IUTAM Laminar-Turbulent Transition","acknowledgement":"The work is supported by the National Key Research and Development Program of China (No. 2016YFA0401200), the National Natural Science Foundation of China (Grant Nos. 91952202 and 11402167).","date_published":"2022-01-01T00:00:00Z","conference":{"location":"London, United Kingdom","name":"IUTAM Symposium","start_date":"2019-09-02","end_date":"2019-09-06"},"isi":1,"year":"2022","external_id":{"isi":["000709087600051"]},"page":"587-598","quality_controlled":"1","article_processing_charge":"No","doi":"10.1007/978-3-030-67902-6_51","publisher":"Springer Nature","editor":[{"first_name":"Spencer","last_name":"Sherwin","full_name":"Sherwin, Spencer"},{"first_name":"Peter","full_name":"Schmid, Peter","last_name":"Schmid"},{"first_name":"Xuesong","last_name":"Wu","full_name":"Wu, Xuesong"}],"_id":"10820","edition":"1","date_updated":"2023-08-03T12:54:59Z","series_title":"IUTAM Bookseries","type":"book_chapter","language":[{"iso":"eng"}],"citation":{"ista":"Liu J, Marensi E, Wu X. 2022.Effects of streaky structures on the instability of supersonic boundary layers. In: IUTAM Laminar-Turbulent Transition. vol. 38, 587–598.","chicago":"Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” In <i>IUTAM Laminar-Turbulent Transition</i>, edited by Spencer Sherwin, Peter Schmid, and Xuesong Wu, 1st ed., 38:587–98. IUTAM Bookseries. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>.","apa":"Liu, J., Marensi, E., &#38; Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In S. Sherwin, P. Schmid, &#38; X. Wu (Eds.), <i>IUTAM Laminar-Turbulent Transition</i> (1st ed., Vol. 38, pp. 587–598). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>","mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” <i>IUTAM Laminar-Turbulent Transition</i>, edited by Spencer Sherwin et al., 1st ed., vol. 38, Springer Nature, 2022, pp. 587–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>.","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: Sherwin S, Schmid P, Wu X, eds. <i>IUTAM Laminar-Turbulent Transition</i>. Vol 38. 1st ed. IUTAM Bookseries. Cham: Springer Nature; 2022:587-598. doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>","ieee":"J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability of supersonic boundary layers,” in <i>IUTAM Laminar-Turbulent Transition</i>, 1st ed., vol. 38, S. Sherwin, P. Schmid, and X. Wu, Eds. Cham: Springer Nature, 2022, pp. 587–598.","short":"J. Liu, E. Marensi, X. Wu, in:, S. Sherwin, P. Schmid, X. Wu (Eds.), IUTAM Laminar-Turbulent Transition, 1st ed., Springer Nature, Cham, 2022, pp. 587–598."},"place":"Cham","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"01","department":[{"_id":"BjHo"}],"abstract":[{"text":"Streaky structures in the boundary layers are often generated by surface roughness elements and/or free-stream turbulence, and are known to have significant effects on boundary-layer instability. In this paper, we investigate the impact of two forms of streaks on the instability of supersonic boundary layers. The first concerns the streaks generated by an array of spanwise periodic and streamwise elongated surface roughness elements, and our interest is how these streaks influence the lower-branch viscous first modes, whose characteristic wavelength and frequency are on the classical triple-deck scales. By adapting the triple-deck theory in the incompressible regime to the supersonic one, we first derived a simplified system which allows for efficient calculation of the streaks. The asymptotic analysis simplifies a bi-global eigenvalue problem to a one-dimensional problem in the spanwise direction, showing that the instability is controlled at leading order solely by the spanwise-dependent wall shear. In the fundamental configuration, the streaks stabilize first modes at low frequencies but destabilize the high-frequency ones. In the subharmonic configuration, the streaks generally destabilize the first mode across the entire frequency band. Importantly, the spanwise even modes are of radiating nature, i.e. they emit acoustic waves spontaneously to the far field. Streaks of the second form are generated by low-frequency vortical disturbances representing free-stream turbulence. They alter the flow in the entire layer and their effects on instability are investigated by solving the inviscid bi-global eigenvalue problem. Different from the incompressible case, a multitude of compressible instability modes exists, of which the dominant mode is an inviscid instability associated with the spanwise shear. In addition, there exists a separate branch of instability modes that have smaller growth rates but are spontaneously radiating.","lang":"eng"}],"intvolume":"        38","publication_status":"published","publication_identifier":{"issn":["1875-3507"],"isbn":["9783030679019"],"eissn":["1875-3493"],"eisbn":["9783030679026"]},"scopus_import":"1","day":"01","author":[{"first_name":"Jianxin","full_name":"Liu, Jianxin","last_name":"Liu"},{"id":"0BE7553A-1004-11EA-B805-18983DDC885E","full_name":"Marensi, Elena","last_name":"Marensi","first_name":"Elena"},{"first_name":"Xuesong","full_name":"Wu, Xuesong","last_name":"Wu"}],"title":"Effects of streaky structures on the instability of supersonic boundary layers","oa_version":"None","volume":38,"date_created":"2022-03-04T09:14:34Z"},{"publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","doi":"10.1101/2022.03.03.482657","author":[{"last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","orcid":"0000-0003-2623-5249"},{"first_name":"Hans J.","full_name":"Herrmann, Hans J.","last_name":"Herrmann"},{"last_name":"Parrino","full_name":"Parrino, Liborio","first_name":"Liborio"},{"first_name":"Dietmar","full_name":"Plenz, Dietmar","last_name":"Plenz"},{"first_name":"Silvia","full_name":"Scarpetta, Silvia","last_name":"Scarpetta"},{"first_name":"Anna Elisabetta","full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano"},{"first_name":"Lucilla","full_name":"de Arcangelis, Lucilla","last_name":"de Arcangelis"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"}],"day":"04","article_processing_charge":"No","type":"preprint","date_created":"2022-03-04T22:20:59Z","date_updated":"2022-03-07T07:28:34Z","_id":"10821","abstract":[{"text":"Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the \"waxing and waning\" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the \"waxing and waning\" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales.","lang":"eng"}],"page":"25","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.03.482657","open_access":"1"}],"month":"03","year":"2022","department":[{"_id":"GaTk"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"}],"status":"public","publication":"bioRxiv","language":[{"iso":"eng"}],"oa":1,"acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and the project E-PASSION of the program VALERE 2019 funded by the University of Campania, Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation, Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.","date_published":"2022-03-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. 2022. doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022).","ieee":"F. Lombardi <i>et al.</i>, “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2022.","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis L, Shriki O. 2022. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2022. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>.","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2022, doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2022). Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>"},"ec_funded":1},{"external_id":{"pmid":["35196500"],"isi":["000796293700007"]},"isi":1,"year":"2022","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"status":"public","publication":"Cell","acknowledgement":"We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M. Merkel for developing and sharing the original version of the 3D Voronoi code. This work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C. and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637 -MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H., and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation (Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","date_published":"2022-02-22T00:00:00Z","pmid":1,"ec_funded":1,"publisher":"Cell Press","doi":"10.1016/j.cell.2022.01.022","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-02T14:43:50Z","_id":"10825","ddc":["570"],"page":"777-793.e20","quality_controlled":"1","month":"02","file":[{"file_size":8478995,"date_created":"2022-03-07T07:55:23Z","creator":"dernst","date_updated":"2022-03-07T07:55:23Z","file_id":"10831","success":1,"file_name":"2022_Cell_Yanagida.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"ae305060e8031297771b89dae9e36a29"}],"department":[{"_id":"EdHa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"5","citation":{"short":"A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter, A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld, K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022) 777–793.e20.","ieee":"A. Yanagida <i>et al.</i>, “Cell surface fluctuations regulate early embryonic lineage sorting,” <i>Cell</i>, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.","ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. 2022;185(5):777-793.e20. doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>","mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>.","apa":"Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>","ista":"Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20.","chicago":"Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>."},"title":"Cell surface fluctuations regulate early embryonic lineage sorting","oa_version":"Published Version","author":[{"first_name":"Ayaka","last_name":"Yanagida","full_name":"Yanagida, Ayaka"},{"first_name":"Elena","last_name":"Corujo-Simon","full_name":"Corujo-Simon, Elena"},{"full_name":"Revell, Christopher K.","last_name":"Revell","first_name":"Christopher K."},{"last_name":"Sahu","full_name":"Sahu, Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","first_name":"Preeti"},{"last_name":"Stirparo","full_name":"Stirparo, Giuliano G.","first_name":"Giuliano G."},{"full_name":"Aspalter, Irene M.","last_name":"Aspalter","first_name":"Irene M."},{"last_name":"Winkel","full_name":"Winkel, Alex K.","first_name":"Alex K."},{"first_name":"Ruby","full_name":"Peters, Ruby","last_name":"Peters"},{"first_name":"Henry","full_name":"De Belly, Henry","last_name":"De Belly"},{"last_name":"Cassani","full_name":"Cassani, Davide A.D.","first_name":"Davide A.D."},{"first_name":"Sarra","full_name":"Achouri, Sarra","last_name":"Achouri"},{"last_name":"Blumenfeld","full_name":"Blumenfeld, Raphael","first_name":"Raphael"},{"full_name":"Franze, Kristian","last_name":"Franze","first_name":"Kristian"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ewa K.","full_name":"Paluch, Ewa K.","last_name":"Paluch"},{"first_name":"Jennifer","full_name":"Nichols, Jennifer","last_name":"Nichols"},{"last_name":"Chalut","full_name":"Chalut, Kevin J.","first_name":"Kevin J."}],"day":"22","scopus_import":"1","article_type":"original","date_created":"2022-03-06T23:01:52Z","volume":185,"intvolume":"       185","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages."}],"has_accepted_license":"1","publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"publication_status":"published","file_date_updated":"2022-03-07T07:55:23Z"},{"year":"2022","isi":1,"external_id":{"pmid":["35201977"],"isi":["000763432300001"]},"project":[{"name":"Molecular mechanisms of neural circuit function","grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"}],"publication":"eLife","status":"public","pmid":1,"date_published":"2022-02-24T00:00:00Z","acknowledgement":"We would like to thank Gemma Chandratillake and Merav Cohen for identifying mutants and José David Moñino Sánchez for his help on neurosecretion assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida) for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp, GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets (KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank the CRUK Cambridge Research Institute Genomics Core for next generation sequencing and the Flow Cytometry Facility at LMB for FACS. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing (SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome Investigator Award (209504/Z/17/Z to MdB).","doi":"10.7554/eLife.68040","article_processing_charge":"No","publisher":"eLife Sciences Publications","date_updated":"2023-08-02T14:42:55Z","_id":"10826","type":"journal_article","ddc":["570"],"quality_controlled":"1","month":"02","department":[{"_id":"MaDe"}],"article_number":"e68040","file":[{"file_id":"10830","file_size":4095591,"date_created":"2022-03-07T07:39:25Z","creator":"dernst","date_updated":"2022-03-07T07:39:25Z","relation":"main_file","checksum":"cc1b9bf866d0f61f965556e0dd03d3ac","success":1,"file_name":"2022_eLife_Valperga.pdf","access_level":"open_access","content_type":"application/pdf"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"apa":"Valperga, G., &#38; de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>","mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>, vol. 11, e68040, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>.","chicago":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>.","ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040.","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","short":"G. Valperga, M. de Bono, ELife 11 (2022).","ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"last_name":"Valperga","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E","full_name":"Valperga, Giulio","first_name":"Giulio"},{"orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"De Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"De Bono, Mario"}],"scopus_import":"1","day":"24","oa_version":"Published Version","title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","volume":11,"article_type":"original","date_created":"2022-03-06T23:01:52Z","has_accepted_license":"1","abstract":[{"text":"Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        11","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"publication_identifier":{"eissn":["2050084X"]},"publication_status":"published","file_date_updated":"2022-03-07T07:39:25Z"},{"doi":"10.1063/5.0079844","article_processing_charge":"No","publisher":"AIP Publishing","date_updated":"2023-08-02T14:45:46Z","_id":"10827","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/2111.12968","open_access":"1"}],"quality_controlled":"1","year":"2022","isi":1,"external_id":{"arxiv":["2111.12968"],"isi":["000796704500014"]},"status":"public","publication":"The Journal of chemical physics","date_published":"2022-02-16T00:00:00Z","acknowledgement":"J.G.L. and B.C. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by the EPSRC Tier-2 capital (Grant No. EP/P020259/1).","author":[{"full_name":"Lee, Jacob G.","last_name":"Lee","first_name":"Jacob G."},{"first_name":"Chris J.","last_name":"Pickard","full_name":"Pickard, Chris J."},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","orcid":"0000-0002-3584-9632"}],"day":"16","scopus_import":"1","oa_version":"Preprint","title":"High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential","volume":156,"article_type":"original","date_created":"2022-03-06T23:01:53Z","abstract":[{"text":"Titanium dioxide has been extensively studied in the rutile or anatase phase, while its high-pressure phases are less well-understood, despite that many are thought to have interesting optical, mechanical, and electrochemical properties. First-principles methods, such as density functional theory (DFT), are often used to compute the enthalpies of TiO2 phases at 0 K, but they are expensive and, thus, impractical for long time scale and large system-size simulations at finite temperatures. On the other hand, cheap empirical potentials fail to capture the relative stabilities of various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure phases of TiO2, we design an empirical model as a baseline and then train a machine learning potential based on the difference between the DFT data and the empirical model. This so-called Δ-learning potential contains long-range electrostatic interactions and predicts the 0 K enthalpies of stable TiO2 phases that are in good agreement with DFT. We construct a pressure–temperature phase diagram of TiO2 in the range 0 < P < 70 GPa and 100 < T < 1500 K. We then simulate dynamic phase transition processes by compressing anatase at different temperatures. At 300 K, we predominantly observe an anatase-to-baddeleyite transformation at about 20 GPa via a martensitic two-step mechanism with a highly ordered and collective atomic motion. At 2000 K, anatase can transform into cotunnite around 45–55 GPa in a thermally activated and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The pressures computed for these transitions show good agreement with experiments. Our results shed light on how to synthesize and stabilize high-pressure TiO2 phases, and our method is generally applicable to other functional materials with multiple polymorphs.","lang":"eng"}],"intvolume":"       156","publication_status":"published","publication_identifier":{"eissn":["10897690"]},"month":"02","arxiv":1,"department":[{"_id":"BiCh"}],"article_number":"074106","oa":1,"language":[{"iso":"eng"}],"issue":"7","citation":{"apa":"Lee, J. G., Pickard, C. J., &#38; Cheng, B. (2022). High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>","mla":"Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 7, 074106, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>.","chicago":"Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>.","ista":"Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7), 074106.","ieee":"J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential,” <i>The Journal of chemical physics</i>, vol. 156, no. 7. AIP Publishing, 2022.","short":"J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).","ama":"Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of chemical physics</i>. 2022;156(7). doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"}]