[{"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."}],"date_updated":"2024-10-09T21:01:38Z","title":"Continuous and discrete radius functions on Voronoi tessellations and Delaunay mosaics","author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890"},{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera Di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","last_name":"Cultrera Di Montesano","first_name":"Sebastiano"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","first_name":"Morteza"}],"external_id":{"isi":["000752175300002"]},"date_created":"2022-02-20T23:01:34Z","corr_author":"1","date_published":"2022-04-01T00:00:00Z","file_date_updated":"2022-08-02T06:07:55Z","publication":"Discrete and Computational Geometry","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","ddc":["510"],"citation":{"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>.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Discrete and Computational Geometry 67 (2022) 811–842.","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.","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>","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>"},"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","_id":"10773","day":"01","department":[{"_id":"HeEd"}],"intvolume":"        67","scopus_import":"1","article_type":"original","isi":1,"license":"https://creativecommons.org/licenses/by/4.0/","month":"04","has_accepted_license":"1","page":"811-842","doi":"10.1007/s00454-022-00371-2","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"file":[{"date_created":"2022-08-02T06:07:55Z","relation":"main_file","file_size":2518111,"content_type":"application/pdf","checksum":"9383d3b70561bacee905e335dc922680","file_name":"2022_DiscreteCompGeometry_Biswas.pdf","date_updated":"2022-08-02T06:07:55Z","file_id":"11718","access_level":"open_access","success":1,"creator":"dernst"}],"oa":1,"year":"2022","status":"public","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"volume":67,"type":"journal_article","acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria)."},{"volume":68,"publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"status":"public","acknowledgement":"Research supported by NSF Award DMS-1953990.","type":"journal_article","month":"06","arxiv":1,"isi":1,"oa":1,"year":"2022","language":[{"iso":"eng"}],"page":"3823-3828","related_material":{"record":[{"relation":"earlier_version","id":"11145","status":"public"}]},"issue":"6","doi":"10.1109/TIT.2022.3148779","citation":{"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>.","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>","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>","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>.","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.","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."},"quality_controlled":"1","publisher":"IEEE","article_type":"original","scopus_import":"1","department":[{"_id":"MaKw"}],"intvolume":"        68","day":"01","article_processing_charge":"No","oa_version":"Preprint","_id":"10775","title":"List-decodability with large radius for Reed-Solomon codes","author":[{"full_name":"Ferber, Asaf","last_name":"Ferber","first_name":"Asaf"},{"last_name":"Kwan","first_name":"Matthew Alan","orcid":"0000-0002-4003-7567","full_name":"Kwan, Matthew Alan","id":"5fca0887-a1db-11eb-95d1-ca9d5e0453b3"},{"last_name":"Sauermann","first_name":"Lisa","full_name":"Sauermann, Lisa"}],"date_created":"2022-02-20T23:01:34Z","external_id":{"arxiv":["2012.10584"],"isi":["000799622500022"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2012.10584"}],"date_updated":"2025-07-10T11:50:08Z","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."}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"IEEE Transactions on Information Theory","date_published":"2022-06-01T00:00:00Z","corr_author":"1"},{"day":"01","article_processing_charge":"No","oa_version":"Preprint","_id":"10776","article_type":"original","scopus_import":"1","department":[{"_id":"UlWa"}],"intvolume":"        68","publisher":"Springer Nature","quality_controlled":"1","citation":{"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>","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>","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>.","ista":"Patakova Z, Tancer M, Wagner U. 2022. Barycentric cuts through a convex body. Discrete and Computational Geometry. 68, 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.","short":"Z. Patakova, M. Tancer, U. Wagner, Discrete and Computational Geometry 68 (2022) 1133–1154.","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>."},"date_published":"2022-12-01T00:00:00Z","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Discrete and Computational Geometry","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2003.13536"}],"date_updated":"2023-08-02T14:38:58Z","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"}],"author":[{"full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","last_name":"Patakova","orcid":"0000-0002-3975-1683"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin"},{"orcid":"0000-0002-1494-0568","first_name":"Uli","last_name":"Wagner","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"title":"Barycentric cuts through a convex body","date_created":"2022-02-20T23:01:35Z","external_id":{"arxiv":["2003.13536"],"isi":["000750681500001"]},"type":"journal_article","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.","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"status":"public","volume":68,"page":"1133-1154","doi":"10.1007/s00454-021-00364-7","oa":1,"year":"2022","language":[{"iso":"eng"}],"arxiv":1,"isi":1,"month":"12"},{"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.","department":[{"_id":"TiBr"}],"day":"22","article_processing_charge":"No","oa_version":"Preprint","type":"preprint","_id":"10788","citation":{"ieee":"F. A. Wilsch, “Integral points of bounded height on a certain toric variety,” <i>arXiv</i>. .","short":"F.A. Wilsch, ArXiv (n.d.).","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>.","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>.","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>","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>"},"keyword":["Integral point","toric variety","Manin's conjecture"],"status":"public","publication_status":"submitted","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","publication":"arXiv","language":[{"iso":"eng"}],"date_published":"2022-02-22T00:00:00Z","corr_author":"1","doi":"10.48550/arXiv.2202.10909","article_number":"2202.10909","month":"02","project":[{"call_identifier":"FWF","name":"New frontiers of the Manin conjecture","grant_number":"P32428","_id":"26AEDAB2-B435-11E9-9278-68D0E5697425"}],"title":"Integral points of bounded height on a certain toric variety","author":[{"id":"560601DA-8D36-11E9-A136-7AC1E5697425","full_name":"Wilsch, Florian Alexander","orcid":"0000-0001-7302-8256","last_name":"Wilsch","first_name":"Florian Alexander"}],"external_id":{"arxiv":["2202.10909"]},"date_created":"2022-02-23T09:04:43Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2202.10909"}],"arxiv":1,"date_updated":"2025-04-15T07:39:01Z","abstract":[{"lang":"eng","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."}]},{"publisher":"Research Square","status":"public","publication_identifier":{"eissn":["2693-5015"]},"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>","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>","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>.","ieee":"Z. Schaaf <i>et al.</i>, “WDFY3 cell autonomously controls neuronal migration.” Research Square.","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>.","short":"Z. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K. Zarbalis, (n.d.)."},"article_processing_charge":"No","oa_version":"Preprint","_id":"10792","type":"preprint","day":"16","department":[{"_id":"SiHi"}],"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."}],"main_file_link":[{"url":"https://doi.org/10.21203/rs.3.rs-1316167/v1","open_access":"1"}],"date_updated":"2023-10-17T13:06:52Z","author":[{"full_name":"Schaaf, Zachary","first_name":"Zachary","last_name":"Schaaf"},{"first_name":"Lyvin","last_name":"Tat","full_name":"Tat, Lyvin"},{"full_name":"Cannizzaro, Noemi","first_name":"Noemi","last_name":"Cannizzaro"},{"first_name":"Ralph","last_name":"Green","full_name":"Green, Ralph"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"full_name":"Zarbalis, K","first_name":"K","last_name":"Zarbalis"}],"title":"WDFY3 cell autonomously controls neuronal migration","date_created":"2022-02-25T07:53:26Z","external_id":{"pmid":["PPR454733"]},"month":"02","page":"30","doi":"10.21203/rs.3.rs-1316167/v1","date_published":"2022-02-16T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"pmid":1,"publication_status":"submitted","oa":1,"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"arxiv":1,"isi":1,"month":"02","page":"220-247","doi":"10.1214/21-AIHP1163","issue":"1","language":[{"iso":"eng"}],"oa":1,"year":"2022","ec_funded":1,"status":"public","publication_identifier":{"issn":["0246-0203"]},"volume":58,"type":"journal_article","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.","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"}],"main_file_link":[{"url":"https://arxiv.org/abs/2007.08272","open_access":"1"}],"date_updated":"2025-04-14T07:43:48Z","author":[{"first_name":"Simone","last_name":"Floreani","full_name":"Floreani, Simone"},{"full_name":"Redig, Frank","first_name":"Frank","last_name":"Redig"},{"last_name":"Sau","first_name":"Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico"}],"title":"Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations","external_id":{"arxiv":["2007.08272"],"isi":["000752489300010"]},"date_created":"2022-02-27T23:01:50Z","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"date_published":"2022-02-01T00:00:00Z","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","citation":{"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>","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>","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>.","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.","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.","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>."},"article_processing_charge":"No","oa_version":"Preprint","_id":"10797","day":"01","department":[{"_id":"JaMa"}],"intvolume":"        58","article_type":"original","scopus_import":"1"},{"publication":"Nature Reviews Microbiology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","pmid":1,"date_published":"2022-08-01T00:00:00Z","date_created":"2022-03-04T04:33:49Z","external_id":{"isi":["000763891900001"],"pmid":["35241807"]},"title":"The physiology and genetics of bacterial responses to antibiotic combinations","author":[{"id":"68E56E44-62B0-11EA-B963-444F3DDC885E","full_name":"Römhild, Roderich","orcid":"0000-0001-9480-5261","last_name":"Römhild","first_name":"Roderich"},{"first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"},{"first_name":"Dan I.","last_name":"Andersson","full_name":"Andersson, Dan I."}],"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."}],"date_updated":"2023-08-02T14:41:44Z","intvolume":"        20","department":[{"_id":"CaGu"}],"scopus_import":"1","article_type":"review","_id":"10812","oa_version":"None","article_processing_charge":"No","day":"01","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.","short":"R. Römhild, M.T. Bollenbach, D.I. Andersson, Nature Reviews Microbiology 20 (2022) 478–490.","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>.","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.","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>","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>","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>."},"quality_controlled":"1","publisher":"Springer Nature","language":[{"iso":"eng"}],"year":"2022","doi":"10.1038/s41579-022-00700-5","page":"478-490","month":"08","isi":1,"acknowledgement":"The authors thank B. Kavčič and H. Schulenburg for constructive feedback on the manuscript.","type":"journal_article","keyword":["General Immunology and Microbiology","Microbiology","Infectious Diseases"],"volume":20,"status":"public","publication_identifier":{"eissn":["1740-1534"],"issn":["1740-1526"]}},{"isi":1,"month":"03","doi":"10.1038/s41929-022-00752-z","page":"193-201","related_material":{"record":[{"id":"9978","status":"public","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"year":"2022","oa":1,"status":"public","publication_identifier":{"issn":["2520-1158"]},"keyword":["Process Chemistry and Technology","Biochemistry","Bioengineering","Catalysis"],"volume":5,"type":"journal_article","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.","abstract":[{"lang":"eng","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."}],"date_updated":"2024-10-09T21:01:46Z","main_file_link":[{"url":"https://doi.org/10.21203/rs.3.rs-750965/v1","open_access":"1"}],"date_created":"2022-03-04T07:50:10Z","external_id":{"isi":["000763879400001"]},"title":"Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries","author":[{"last_name":"Cao","first_name":"Deqing","full_name":"Cao, Deqing"},{"full_name":"Shen, Xiaoxiao","last_name":"Shen","first_name":"Xiaoxiao"},{"last_name":"Wang","first_name":"Aiping","full_name":"Wang, Aiping"},{"full_name":"Yu, Fengjiao","last_name":"Yu","first_name":"Fengjiao"},{"full_name":"Wu, Yuping","first_name":"Yuping","last_name":"Wu"},{"full_name":"Shi, Siqi","first_name":"Siqi","last_name":"Shi"},{"orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Yuhui","last_name":"Chen","full_name":"Chen, Yuhui"}],"corr_author":"1","date_published":"2022-03-03T00:00:00Z","publication":"Nature Catalysis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Springer Nature","citation":{"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>.","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>","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.","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>.","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Nature Catalysis 5 (2022) 193–201.","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."},"quality_controlled":"1","_id":"10813","oa_version":"Preprint","article_processing_charge":"No","day":"03","intvolume":"         5","department":[{"_id":"StFr"}],"scopus_import":"1","article_type":"original"},{"issue":"1","doi":"10.1002/glia.24101","page":"173-195","has_accepted_license":"1","file":[{"success":1,"creator":"dernst","access_level":"open_access","file_id":"10819","content_type":"application/pdf","file_size":5340294,"checksum":"f10a897290e66c0a062e04ba91db6c17","file_name":"2021_Glia_Basilico.pdf","date_updated":"2022-03-04T08:55:27Z","relation":"main_file","date_created":"2022-03-04T08:55:27Z"}],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png"},"year":"2022","oa":1,"isi":1,"month":"01","license":"https://creativecommons.org/licenses/by-nc/4.0/","type":"journal_article","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.","status":"public","publication_identifier":{"issn":["0894-1491"],"eissn":["1098-1136"]},"keyword":["Cellular and Molecular Neuroscience","Neurology"],"volume":70,"corr_author":"1","date_published":"2022-01-01T00:00:00Z","file_date_updated":"2022-03-04T08:55:27Z","publication":"Glia","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"publication_status":"published","abstract":[{"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.","lang":"eng"}],"date_updated":"2024-10-09T21:04:02Z","external_id":{"pmid":["34661306"],"isi":["000708025800001"]},"date_created":"2022-03-04T08:53:37Z","title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","author":[{"full_name":"Basilico, Bernadette","id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","first_name":"Bernadette","last_name":"Basilico"},{"full_name":"Ferrucci, Laura","first_name":"Laura","last_name":"Ferrucci"},{"first_name":"Patrizia","last_name":"Ratano","full_name":"Ratano, Patrizia"},{"full_name":"Golia, Maria T.","last_name":"Golia","first_name":"Maria T."},{"full_name":"Grimaldi, Alfonso","first_name":"Alfonso","last_name":"Grimaldi"},{"last_name":"Rosito","first_name":"Maria","full_name":"Rosito, Maria"},{"last_name":"Ferretti","first_name":"Valentina","full_name":"Ferretti, Valentina"},{"first_name":"Ingrid","last_name":"Reverte","full_name":"Reverte, Ingrid"},{"last_name":"Sanchini","first_name":"Caterina","full_name":"Sanchini, Caterina"},{"full_name":"Marrone, Maria C.","last_name":"Marrone","first_name":"Maria C."},{"full_name":"Giubettini, Maria","first_name":"Maria","last_name":"Giubettini"},{"last_name":"De Turris","first_name":"Valeria","full_name":"De Turris, Valeria"},{"first_name":"Debora","last_name":"Salerno","full_name":"Salerno, Debora"},{"full_name":"Garofalo, Stefano","last_name":"Garofalo","first_name":"Stefano"},{"full_name":"St‐Pierre, Marie‐Kim","first_name":"Marie‐Kim","last_name":"St‐Pierre"},{"full_name":"Carrier, Micael","last_name":"Carrier","first_name":"Micael"},{"full_name":"Renzi, Massimiliano","last_name":"Renzi","first_name":"Massimiliano"},{"full_name":"Pagani, Francesca","last_name":"Pagani","first_name":"Francesca"},{"full_name":"Modi, Brijesh","last_name":"Modi","first_name":"Brijesh"},{"full_name":"Raspa, Marcello","last_name":"Raspa","first_name":"Marcello"},{"full_name":"Scavizzi, Ferdinando","first_name":"Ferdinando","last_name":"Scavizzi"},{"last_name":"Gross","first_name":"Cornelius T.","full_name":"Gross, Cornelius T."},{"full_name":"Marinelli, Silvia","first_name":"Silvia","last_name":"Marinelli"},{"first_name":"Marie‐Ève","last_name":"Tremblay","full_name":"Tremblay, Marie‐Ève"},{"full_name":"Caprioli, Daniele","last_name":"Caprioli","first_name":"Daniele"},{"last_name":"Maggi","first_name":"Laura","full_name":"Maggi, Laura"},{"first_name":"Cristina","last_name":"Limatola","full_name":"Limatola, Cristina"},{"last_name":"Di Angelantonio","first_name":"Silvia","full_name":"Di Angelantonio, Silvia"},{"full_name":"Ragozzino, Davide","last_name":"Ragozzino","first_name":"Davide"}],"_id":"10818","article_processing_charge":"No","oa_version":"Published Version","day":"01","intvolume":"        70","department":[{"_id":"GaNo"}],"scopus_import":"1","article_type":"original","publisher":"Wiley","ddc":["570"],"citation":{"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.","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.","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>.","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>","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>."},"quality_controlled":"1"},{"citation":{"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>, 38:587–98. 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>.","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: <i>IUTAM Laminar-Turbulent Transition</i>. Vol 38. 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>","apa":"Liu, J., Marensi, E., &#38; Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In <i>IUTAM Laminar-Turbulent Transition</i> (Vol. 38, pp. 587–598). London, United Kingdom: 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>","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>, London, United Kingdom, 2022, vol. 38, pp. 587–598.","short":"J. Liu, E. Marensi, X. Wu, in:, IUTAM Laminar-Turbulent Transition, Springer Nature, 2022, pp. 587–598.","mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” <i>IUTAM Laminar-Turbulent Transition</i>, 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>.","ista":"Liu J, Marensi E, Wu X. 2022. Effects of streaky structures on the instability of supersonic boundary layers. IUTAM Laminar-Turbulent Transition. IUTAM Symposium, IUTAM, vol. 38, 587–598."},"quality_controlled":"1","publisher":"Springer Nature","scopus_import":"1","intvolume":"        38","alternative_title":["IUTAM"],"department":[{"_id":"BjHo"}],"day":"01","_id":"10820","article_processing_charge":"No","oa_version":"None","external_id":{"isi":["000709087600051"]},"date_created":"2022-03-04T09:14:34Z","author":[{"full_name":"Liu, Jianxin","first_name":"Jianxin","last_name":"Liu"},{"full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E","last_name":"Marensi","first_name":"Elena","orcid":"0000-0001-7173-4923"},{"full_name":"Wu, Xuesong","last_name":"Wu","first_name":"Xuesong"}],"title":"Effects of streaky structures on the instability of supersonic boundary layers","date_updated":"2025-05-20T06:08:26Z","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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publication":"IUTAM Laminar-Turbulent Transition","OA_type":"closed access","date_published":"2022-01-01T00:00:00Z","volume":38,"publication_identifier":{"eissn":["1875-3493"],"eisbn":["9783030679026"],"issn":["1875-3507"],"isbn":["9783030679019"]},"status":"public","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).","type":"conference","month":"01","isi":1,"year":"2022","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-67902-6_51","conference":{"name":"IUTAM Symposium","end_date":"2019-09-06","location":"London, United Kingdom","start_date":"2019-09-02"},"page":"587-598"},{"department":[{"_id":"GaTk"}],"day":"04","_id":"10821","article_processing_charge":"No","oa_version":"Preprint","citation":{"apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (n.d.). 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>","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. doi:<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, n.d. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>.","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis L, Shriki O. 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>.","ieee":"F. Lombardi <i>et al.</i>, “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 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 (n.d.)."},"publisher":"Cold Spring Harbor Laboratory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"draft","publication":"bioRxiv","date_published":"2022-03-04T00:00:00Z","corr_author":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"date_created":"2022-03-04T22:20:59Z","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi"},{"full_name":"Herrmann, Hans J.","first_name":"Hans J.","last_name":"Herrmann"},{"last_name":"Parrino","first_name":"Liborio","full_name":"Parrino, Liborio"},{"full_name":"Plenz, Dietmar","first_name":"Dietmar","last_name":"Plenz"},{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano","first_name":"Anna Elisabetta"},{"first_name":"Lucilla","last_name":"de Arcangelis","full_name":"de Arcangelis, Lucilla"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"}],"date_updated":"2025-04-15T06:55:02Z","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.03.482657","open_access":"1"}],"abstract":[{"lang":"eng","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."}],"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.","type":"preprint","OA_place":"repository","status":"public","ec_funded":1,"year":"2022","oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/2022.03.03.482657","page":"25","related_material":{"record":[{"relation":"later_version","id":"14402","status":"public"}]},"month":"03"},{"oa_version":"Published Version","article_processing_charge":"No","_id":"10825","day":"22","department":[{"_id":"EdHa"}],"intvolume":"       185","article_type":"original","scopus_import":"1","publisher":"Cell Press","ddc":["570"],"citation":{"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>.","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>","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>","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.","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>.","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.","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."},"quality_controlled":"1","date_published":"2022-02-22T00:00:00Z","publication":"Cell","file_date_updated":"2022-03-07T07:55:23Z","pmid":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"date_updated":"2025-07-10T11:50:00Z","author":[{"full_name":"Yanagida, Ayaka","first_name":"Ayaka","last_name":"Yanagida"},{"full_name":"Corujo-Simon, Elena","first_name":"Elena","last_name":"Corujo-Simon"},{"first_name":"Christopher K.","last_name":"Revell","full_name":"Revell, Christopher K."},{"last_name":"Sahu","first_name":"Preeti","full_name":"Sahu, Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"full_name":"Stirparo, Giuliano G.","first_name":"Giuliano G.","last_name":"Stirparo"},{"full_name":"Aspalter, Irene M.","last_name":"Aspalter","first_name":"Irene M."},{"full_name":"Winkel, Alex K.","first_name":"Alex K.","last_name":"Winkel"},{"full_name":"Peters, Ruby","first_name":"Ruby","last_name":"Peters"},{"first_name":"Henry","last_name":"De Belly","full_name":"De Belly, Henry"},{"full_name":"Cassani, Davide A.D.","last_name":"Cassani","first_name":"Davide A.D."},{"last_name":"Achouri","first_name":"Sarra","full_name":"Achouri, Sarra"},{"full_name":"Blumenfeld, Raphael","last_name":"Blumenfeld","first_name":"Raphael"},{"full_name":"Franze, Kristian","last_name":"Franze","first_name":"Kristian"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"last_name":"Paluch","first_name":"Ewa K.","full_name":"Paluch, Ewa K."},{"full_name":"Nichols, Jennifer","last_name":"Nichols","first_name":"Jennifer"},{"full_name":"Chalut, Kevin J.","first_name":"Kevin J.","last_name":"Chalut"}],"title":"Cell surface fluctuations regulate early embryonic lineage sorting","external_id":{"isi":["000796293700007"],"pmid":["35196500"]},"date_created":"2022-03-06T23:01:52Z","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"type":"journal_article","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.","ec_funded":1,"status":"public","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"volume":185,"has_accepted_license":"1","page":"777-793.e20","doi":"10.1016/j.cell.2022.01.022","issue":"5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2022-03-07T07:55:23Z","relation":"main_file","date_updated":"2022-03-07T07:55:23Z","file_name":"2022_Cell_Yanagida.pdf","file_size":8478995,"checksum":"ae305060e8031297771b89dae9e36a29","content_type":"application/pdf","file_id":"10831","access_level":"open_access","creator":"dernst","success":1}],"language":[{"iso":"eng"}],"oa":1,"year":"2022","isi":1,"month":"02"},{"citation":{"ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford University Press, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford University Press, pp. 2150–2173, 2022.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>."},"quality_controlled":"1","acknowledged_ssus":[{"_id":"EM-Fac"}],"publisher":"Oxford University Press","article_type":"original","scopus_import":"1","intvolume":"        34","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"day":"01","_id":"10841","article_processing_charge":"No","oa_version":"Preprint","project":[{"call_identifier":"FWF","grant_number":"I03630","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"date_created":"2022-03-08T13:47:51Z","author":[{"full_name":"Dahhan, DA","last_name":"Dahhan","first_name":"DA"},{"last_name":"Reynolds","first_name":"GD","full_name":"Reynolds, GD"},{"full_name":"Cárdenas, JJ","first_name":"JJ","last_name":"Cárdenas"},{"last_name":"Eeckhout","first_name":"D","full_name":"Eeckhout, D"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson"},{"full_name":"Yperman, K","first_name":"K","last_name":"Yperman"},{"first_name":"Walter","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"first_name":"N","last_name":"Vang","full_name":"Vang, N"},{"first_name":"X","last_name":"Yan","full_name":"Yan, X"},{"first_name":"I","last_name":"Hwang","full_name":"Hwang, I"},{"full_name":"Heese, A","last_name":"Heese","first_name":"A"},{"last_name":"De Jaeger","first_name":"G","full_name":"De Jaeger, G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"D","last_name":"Van Damme","full_name":"Van Damme, D"},{"last_name":"Pan","first_name":"J","full_name":"Pan, J"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"}],"title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","date_updated":"2025-05-14T11:06:15Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2021.09.16.460678"}],"abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_status":"published","publication":"Plant Cell","date_published":"2022-06-01T00:00:00Z","volume":34,"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"status":"public","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","type":"journal_article","month":"06","isi":1,"year":"2022","oa":1,"language":[{"iso":"eng"}],"issue":"6","doi":"10.1093/plcell/koac071","page":"2150-2173"},{"quality_controlled":"1","citation":{"apa":"Köse, S., &#38; Özbudak, F. (2022). Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>","ama":"Köse S, Özbudak F. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. 2022;14(4):933-948. doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>","chicago":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>.","ista":"Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 14(4), 933–948.","ieee":"S. Köse and F. Özbudak, “Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes,” <i>Cryptography and Communications</i>, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022.","mla":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>, vol. 14, no. 4, Springer Nature, 2022, pp. 933–48, doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>.","short":"S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948."},"publisher":"Springer Nature","article_type":"original","scopus_import":"1","department":[{"_id":"GradSch"}],"intvolume":"        14","day":"01","article_processing_charge":"No","oa_version":"None","_id":"10842","author":[{"first_name":"Seyda","last_name":"Köse","full_name":"Köse, Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"},{"full_name":"Özbudak, Ferruh","first_name":"Ferruh","last_name":"Özbudak"}],"title":"Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes","external_id":{"isi":["000766422000002"]},"date_created":"2022-03-10T12:16:19Z","date_updated":"2023-09-05T15:35:55Z","abstract":[{"lang":"eng","text":"We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory."}],"publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Cryptography and Communications","date_published":"2022-07-01T00:00:00Z","volume":14,"keyword":["Applied Mathematics","Computational Theory and Mathematics","Computer Networks and Communications"],"publication_identifier":{"issn":["1936-2447"],"eissn":["1936-2455"]},"status":"public","acknowledgement":"The authors would like to thank Prof. Dr. Minjia Shi for bringing [13, Conjecture 3.5] to our attention. We would also like to thank the associate editor and anonymous reviewers for their valuable comments and suggestions which improved and clarified the manuscript.","type":"journal_article","month":"07","isi":1,"year":"2022","language":[{"iso":"eng"}],"page":"933-948","doi":"10.1007/s12095-022-00557-8","issue":"4"},{"day":"19","article_processing_charge":"No","oa_version":"Published Version","_id":"10846","scopus_import":"1","article_type":"original","department":[{"_id":"MaDe"}],"intvolume":"        18","publisher":"Taylor & Francis","quality_controlled":"1","citation":{"short":"M. Artan, J. Sohn, C. Lee, S.Y. Park, S.J.V. Lee, Autophagy 18 (2022) 1208–1210.","mla":"Artan, Murat, et al. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>, vol. 18, no. 5, Taylor &#38; Francis, 2022, pp. 1208–10, doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>.","ieee":"M. Artan, J. Sohn, C. Lee, S. Y. Park, and S. J. V. Lee, “MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications,” <i>Autophagy</i>, vol. 18, no. 5. Taylor &#38; Francis, pp. 1208–1210, 2022.","ista":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. 2022. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. Autophagy. 18(5), 1208–1210.","chicago":"Artan, Murat, Jooyeon Sohn, Cheolju Lee, Seung Yeol Park, and Seung Jae V. Lee. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>.","apa":"Artan, M., Sohn, J., Lee, C., Park, S. Y., &#38; Lee, S. J. V. (2022). MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>","ama":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. 2022;18(5):1208-1210. doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>"},"date_published":"2022-02-19T00:00:00Z","publication_status":"published","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Autophagy","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2022.2039523"}],"date_updated":"2023-10-03T10:54:54Z","abstract":[{"lang":"eng","text":"The Golgi apparatus regulates the process of modification and subcellular localization of macromolecules, including proteins and lipids. Aberrant protein sorting caused by defects in the Golgi leads to various diseases in mammals. However, the role of the Golgi apparatus in organismal longevity remained largely unknown. By employing a quantitative proteomic approach, we demonstrated that MON-2, an evolutionarily conserved Arf-GEF protein implicated in Golgi-to-endosome trafficking, promotes longevity via upregulating macroautophagy/autophagy in C. elegans. Our data using cultured mammalian cells indicate that MON2 translocates from the Golgi to the endosome under starvation conditions, subsequently increasing autophagic flux by binding LGG-1/GABARAPL2. Thus, Golgi-to-endosome trafficking appears to be an evolutionarily conserved process for the upregulation of autophagy, which contributes to organismal longevity."}],"title":"MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications","author":[{"orcid":"0000-0001-8945-6992","last_name":"Artan","first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425","full_name":"Artan, Murat"},{"first_name":"Jooyeon","last_name":"Sohn","full_name":"Sohn, Jooyeon"},{"full_name":"Lee, Cheolju","first_name":"Cheolju","last_name":"Lee"},{"full_name":"Park, Seung Yeol","first_name":"Seung Yeol","last_name":"Park"},{"first_name":"Seung Jae V.","last_name":"Lee","full_name":"Lee, Seung Jae V."}],"date_created":"2022-03-13T23:01:47Z","external_id":{"pmid":["35188063"],"isi":["000758859600001"]},"type":"journal_article","acknowledgement":"This work is funded by National Research Foundation of Korea (NRF) grants NRF-2019R1A3B2067745 from the Korean Government (Ministry of Science and Information and Communications Technology (S-J.V.L.). NRF-2017R1A5A1015366 (S.Y.P, S-J.V.L). Korea Institute of Science and Technology (KIST) intramural grant (C.L).","publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"status":"public","volume":18,"page":"1208-1210","issue":"5","doi":"10.1080/15548627.2022.2039523","oa":1,"year":"2022","language":[{"iso":"eng"}],"isi":1,"month":"02"},{"_id":"10863","article_processing_charge":"No","oa_version":"Preprint","day":"17","intvolume":"       105","department":[{"_id":"MaSe"}],"scopus_import":"1","article_type":"letter_note","publisher":"American Physical Society","quality_controlled":"1","citation":{"ama":"Davydova M, Serbyn M, Ishizuka H. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. <i>Physical Review B</i>. 2022;105. doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">10.1103/PhysRevB.105.L121407</a>","apa":"Davydova, M., Serbyn, M., &#38; Ishizuka, H. (2022). Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">https://doi.org/10.1103/PhysRevB.105.L121407</a>","chicago":"Davydova, Margarita, Maksym Serbyn, and Hiroaki Ishizuka. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">https://doi.org/10.1103/PhysRevB.105.L121407</a>.","ista":"Davydova M, Serbyn M, Ishizuka H. 2022. Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials. Physical Review B. 105, L121407.","short":"M. Davydova, M. Serbyn, H. Ishizuka, Physical Review B 105 (2022).","mla":"Davydova, Margarita, et al. “Symmetry-Allowed Nonlinear Orbital Response across the Topological Phase Transition in Centrosymmetric Materials.” <i>Physical Review B</i>, vol. 105, L121407, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevB.105.L121407\">10.1103/PhysRevB.105.L121407</a>.","ieee":"M. Davydova, M. Serbyn, and H. Ishizuka, “Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials,” <i>Physical Review B</i>, vol. 105. American Physical Society, 2022."},"article_number":"L121407","date_published":"2022-03-17T00:00:00Z","publication":"Physical Review B","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","abstract":[{"text":"Nonlinear optical responses are commonly used as a probe for studying the electronic properties of materials. For topological materials, studies thus far focused on photogalvanic electric currents, which are forbidden in centrosymmetric materials because they require broken inversion symmetry. In this Letter, we propose a class of symmetry-allowed responses for inversion-symmetric topological insulators with two doubly degenerate bands. We consider a specific example of such a response, the orbital current, and show that the sign of the response reflects the Z2 topological index, i.e., the orbital current changes sign at the transition between trivial and topological insulator phases. This is illustrated in two models of topological insulators: the Bernevig-Hughes-Zhang model and the 1T′ phase of transition metal dichalcogenides.","lang":"eng"}],"date_updated":"2023-08-03T06:09:56Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2101.08277"}],"external_id":{"arxiv":["2101.08277"],"isi":["000800752500001"]},"date_created":"2022-03-18T10:20:46Z","title":"Symmetry-allowed nonlinear orbital response across the topological phase transition in centrosymmetric materials","author":[{"full_name":"Davydova, Margarita","last_name":"Davydova","first_name":"Margarita"},{"last_name":"Serbyn","first_name":"Maksym","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ishizuka, Hiroaki","last_name":"Ishizuka","first_name":"Hiroaki"}],"type":"journal_article","acknowledgement":"We are grateful to Takahiro Morimoto and Zhanybek Alpichshev for fruitful discussions. MD was supported by Austrian Agency for International Cooperation in Education and Research (OeAD-GmbH) and by the John Seo Fellowship at MIT. HI was supported by JSPS KAKENHI Grant Numbers JP19K14649 and JP18H03676, and by UTokyo Global Activity Support Program for\r\nYoung Researchers.","status":"public","publication_identifier":{"issn":["2469-9969"]},"volume":105,"doi":"10.1103/PhysRevB.105.L121407","language":[{"iso":"eng"}],"year":"2022","oa":1,"isi":1,"arxiv":1,"month":"03"},{"_id":"10887","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","day":"01","intvolume":"       282","department":[{"_id":"UlWa"}],"article_type":"original","scopus_import":"1","publisher":"Elsevier","ddc":["510"],"quality_controlled":"1","citation":{"ama":"Ivanov G, Naszódi M. Functional John ellipsoids. <i>Journal of Functional Analysis</i>. 2022;282(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">10.1016/j.jfa.2022.109441</a>","apa":"Ivanov, G., &#38; Naszódi, M. (2022). Functional John ellipsoids. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">https://doi.org/10.1016/j.jfa.2022.109441</a>","chicago":"Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” <i>Journal of Functional Analysis</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">https://doi.org/10.1016/j.jfa.2022.109441</a>.","ista":"Ivanov G, Naszódi M. 2022. Functional John ellipsoids. Journal of Functional Analysis. 282(11), 109441.","ieee":"G. Ivanov and M. Naszódi, “Functional John ellipsoids,” <i>Journal of Functional Analysis</i>, vol. 282, no. 11. Elsevier, 2022.","short":"G. Ivanov, M. Naszódi, Journal of Functional Analysis 282 (2022).","mla":"Ivanov, Grigory, and Márton Naszódi. “Functional John Ellipsoids.” <i>Journal of Functional Analysis</i>, vol. 282, no. 11, 109441, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jfa.2022.109441\">10.1016/j.jfa.2022.109441</a>."},"article_number":"109441","corr_author":"1","date_published":"2022-06-01T00:00:00Z","file_date_updated":"2022-08-02T10:40:48Z","publication":"Journal of Functional Analysis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","abstract":[{"lang":"eng","text":"We introduce a new way of representing logarithmically concave functions on Rd. It allows us to extend the notion of the largest volume ellipsoid contained in a convex body to the setting of logarithmically concave functions as follows. For every s>0, we define a class of non-negative functions on Rd derived from ellipsoids in Rd+1. For any log-concave function f on Rd , and any fixed s>0, we consider functions belonging to this class, and find the one with the largest integral under the condition that it is pointwise less than or equal to f, and we call it the John s-function of f. After establishing existence and uniqueness, we give a characterization of this function similar to the one given by John in his fundamental theorem. We find that John s-functions converge to characteristic functions of ellipsoids as s tends to zero and to Gaussian densities as s tends to infinity.\r\nAs an application, we prove a quantitative Helly type result: the integral of the pointwise minimum of any family of log-concave functions is at least a constant cd multiple of the integral of the pointwise minimum of a properly chosen subfamily of size 3d+2, where cd depends only on d."}],"date_updated":"2024-10-09T21:01:51Z","external_id":{"isi":["000781371300008"],"arxiv":["2006.09934"]},"date_created":"2022-03-20T23:01:38Z","title":"Functional John ellipsoids","author":[{"first_name":"Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E","full_name":"Ivanov, Grigory"},{"full_name":"Naszódi, Márton","first_name":"Márton","last_name":"Naszódi"}],"type":"journal_article","acknowledgement":"G.I. was supported by the Ministry of Education and Science of the Russian Federation in the framework of MegaGrant no 075-15-2019-1926. M.N. was supported by the National Research, Development and Innovation Fund (NRDI) grants K119670 and KKP-133864 as well as the Bolyai Scholarship of the Hungarian Academy of Sciences and the New National Excellence Programme and the TKP2020-NKA-06 program provided by the NRDI. ","status":"public","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"volume":282,"doi":"10.1016/j.jfa.2022.109441","issue":"11","has_accepted_license":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2022-08-02T10:40:48Z","relation":"main_file","checksum":"1cf185e264e04c87cb1ce67a00db88ab","file_size":734482,"content_type":"application/pdf","date_updated":"2022-08-02T10:40:48Z","file_name":"2022_JourFunctionalAnalysis_Ivanov.pdf","file_id":"11721","access_level":"open_access","success":1,"creator":"dernst"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2022","oa":1,"isi":1,"arxiv":1,"month":"06"},{"date_created":"2022-03-20T23:01:39Z","external_id":{"pmid":["35254915"],"isi":["000771756300008"]},"title":"Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling","author":[{"full_name":"Lu, Qing","last_name":"Lu","first_name":"Qing"},{"full_name":"Zhang, Yonghong","last_name":"Zhang","first_name":"Yonghong"},{"full_name":"Hellner, Joakim","first_name":"Joakim","last_name":"Hellner"},{"last_name":"Giannini","first_name":"Caterina","full_name":"Giannini, Caterina","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4"},{"first_name":"Xiangyu","last_name":"Xu","full_name":"Xu, Xiangyu"},{"last_name":"Pauwels","first_name":"Jarne","full_name":"Pauwels, Jarne"},{"full_name":"Ma, Qian","last_name":"Ma","first_name":"Qian"},{"last_name":"Dejonghe","first_name":"Wim","full_name":"Dejonghe, Wim"},{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"last_name":"Van De Cotte","first_name":"Brigitte","full_name":"Van De Cotte, Brigitte"},{"first_name":"Francis","last_name":"Impens","full_name":"Impens, Francis"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Molina, Daniel Martinez","first_name":"Daniel Martinez","last_name":"Molina"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"}],"abstract":[{"text":"Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling.","lang":"eng"}],"date_updated":"2025-05-14T11:01:45Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","file_date_updated":"2022-03-21T09:19:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_status":"published","article_number":"e2118220119","date_published":"2022-03-07T00:00:00Z","ddc":["580"],"quality_controlled":"1","citation":{"chicago":"Lu, Qing, Yonghong Zhang, Joakim Hellner, Caterina Giannini, Xiangyu Xu, Jarne Pauwels, Qian Ma, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>.","ama":"Lu Q, Zhang Y, Hellner J, et al. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(11). doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>","apa":"Lu, Q., Zhang, Y., Hellner, J., Giannini, C., Xu, X., Pauwels, J., … Russinova, E. (2022). Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2118220119\">https://doi.org/10.1073/pnas.2118220119</a>","ieee":"Q. Lu <i>et al.</i>, “Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11. National Academy of Sciences, 2022.","short":"Q. Lu, Y. Zhang, J. Hellner, C. Giannini, X. Xu, J. Pauwels, Q. Ma, W. Dejonghe, H. Han, B. Van De Cotte, F. Impens, K. Gevaert, I. De Smet, J. Friml, D.M. Molina, E. Russinova, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Lu, Qing, et al. “Proteome-Wide Cellular Thermal Shift Assay Reveals Unexpected Cross-Talk between Brassinosteroid and Auxin Signaling.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 11, e2118220119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2118220119\">10.1073/pnas.2118220119</a>.","ista":"Lu Q, Zhang Y, Hellner J, Giannini C, Xu X, Pauwels J, Ma Q, Dejonghe W, Han H, Van De Cotte B, Impens F, Gevaert K, De Smet I, Friml J, Molina DM, Russinova E. 2022. Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proceedings of the National Academy of Sciences of the United States of America. 119(11), e2118220119."},"publisher":"National Academy of Sciences","intvolume":"       119","department":[{"_id":"JiFr"}],"article_type":"original","scopus_import":"1","_id":"10888","oa_version":"Published Version","article_processing_charge":"No","day":"07","month":"03","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","isi":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2022-03-21T09:19:47Z","relation":"main_file","file_name":"2022_PNAS_Lu.pdf","date_updated":"2022-03-21T09:19:47Z","content_type":"application/pdf","checksum":"83e0fea7919570d0b519b41193342571","file_size":2169534,"file_id":"10910","access_level":"open_access","creator":"dernst","success":1}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"year":"2022","oa":1,"issue":"11","doi":"10.1073/pnas.2118220119","has_accepted_license":"1","volume":119,"status":"public","publication_identifier":{"eissn":["1091-6490"]},"acknowledgement":"We thank Yanhai Yin for providing the anti-BES1 antibody, Johan Winne and Brenda Callebaut for synthesizing bikinin, Yuki Kondo and Hiroo Fukuda for published materials, Tomasz Nodzy\u0003nski for useful advice, and Martine De Cock for help in preparing the manuscript. This\r\nwork was supported by the China Scholarship Council for predoctoral (Q.L. and X.X.) and postdoctoral (Y.Z.) fellowships; the Agency for Innovation by Science and Technology for a predoctoral fellowship (W.D.); the Research Foundation-Flanders, Projects G009018N and G002121N (E.R.); and the VIB TechWatch Fund (E.R.).","type":"journal_article"},{"citation":{"chicago":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>.","apa":"Shigemoto, R. (2022). Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfab048\">https://doi.org/10.1093/jmicro/dfab048</a>","ama":"Shigemoto R. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. <i>Microscopy</i>. 2022;71(Supplement_1):i72-i80. doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>","short":"R. Shigemoto, Microscopy 71 (2022) i72–i80.","mla":"Shigemoto, Ryuichi. “Electron Microscopic Visualization of Single Molecules by Tag-Mediated Metal Particle Labeling.” <i>Microscopy</i>, vol. 71, no. Supplement_1, Oxford University Press, 2022, pp. i72–80, doi:<a href=\"https://doi.org/10.1093/jmicro/dfab048\">10.1093/jmicro/dfab048</a>.","ieee":"R. Shigemoto, “Electron microscopic visualization of single molecules by tag-mediated metal particle labeling,” <i>Microscopy</i>, vol. 71, no. Supplement_1. Oxford University Press, pp. i72–i80, 2022.","ista":"Shigemoto R. 2022. Electron microscopic visualization of single molecules by tag-mediated metal particle labeling. Microscopy. 71(Supplement_1), i72–i80."},"quality_controlled":"1","publisher":"Oxford University Press","intvolume":"        71","department":[{"_id":"RySh"}],"article_type":"original","scopus_import":"1","_id":"10889","oa_version":"Published Version","article_processing_charge":"No","day":"01","external_id":{"isi":["000768384100011"],"pmid":["35275179"]},"date_created":"2022-03-20T23:01:39Z","title":"Electron microscopic visualization of single molecules by tag-mediated metal particle labeling","author":[{"orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"project":[{"name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Genetically encoded tags have introduced extensive lines of application from purification of tagged proteins to their visualization at the single molecular, cellular, histological and whole-body levels. Combined with other rapidly developing technologies such as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, proteomics, super-resolution microscopy and proximity labeling, a large variety of genetically encoded tags have been developed in the last two decades. In this review, I focus on the current status of tag development for electron microscopic (EM) visualization of proteins with metal particle labeling. Compared with conventional immunoelectron microscopy using gold particles, tag-mediated metal particle labeling has several advantages that could potentially improve the sensitivity, spatial and temporal resolution, and applicability to a wide range of proteins of interest (POIs). It may enable researchers to detect single molecules in situ, allowing the quantitative measurement of absolute numbers and exact localization patterns of POI in the ultrastructural context. Thus, genetically encoded tags for EM could revolutionize the field as green fluorescence protein did for light microscopy, although we still have many challenges to overcome before reaching this goal.","lang":"eng"}],"date_updated":"2025-05-14T11:05:40Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/jmicro/dfab048"}],"publication":"Microscopy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"publication_status":"published","corr_author":"1","date_published":"2022-03-01T00:00:00Z","volume":71,"status":"public","ec_funded":1,"publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]},"acknowledgement":"European Research Council Advanced Grant (694539 to R.S.).","type":"journal_article","month":"03","isi":1,"language":[{"iso":"eng"}],"year":"2022","oa":1,"doi":"10.1093/jmicro/dfab048","issue":"Supplement_1","page":"i72-i80"},{"_id":"10891","oa_version":"None","article_processing_charge":"No","day":"22","intvolume":"     13124","department":[{"_id":"ToHe"}],"scopus_import":"1","publisher":"Springer Nature","quality_controlled":"1","citation":{"chicago":"Henzinger, Thomas A. “Quantitative Monitoring of Software.” In <i>Software Verification</i>, 13124:3–6. LNCS. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">https://doi.org/10.1007/978-3-030-95561-8_1</a>.","apa":"Henzinger, T. A. (2022). Quantitative monitoring of software. In <i>Software Verification</i> (Vol. 13124, pp. 3–6). New Haven, CT, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">https://doi.org/10.1007/978-3-030-95561-8_1</a>","ama":"Henzinger TA. Quantitative monitoring of software. In: <i>Software Verification</i>. Vol 13124. LNCS. Springer Nature; 2022:3-6. doi:<a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">10.1007/978-3-030-95561-8_1</a>","ieee":"T. A. Henzinger, “Quantitative monitoring of software,” in <i>Software Verification</i>, New Haven, CT, United States, 2022, vol. 13124, pp. 3–6.","mla":"Henzinger, Thomas A. “Quantitative Monitoring of Software.” <i>Software Verification</i>, vol. 13124, Springer Nature, 2022, pp. 3–6, doi:<a href=\"https://doi.org/10.1007/978-3-030-95561-8_1\">10.1007/978-3-030-95561-8_1</a>.","short":"T.A. Henzinger, in:, Software Verification, Springer Nature, 2022, pp. 3–6.","ista":"Henzinger TA. 2022. Quantitative monitoring of software. Software Verification. NSV: Numerical Software VerificationLNCS vol. 13124, 3–6."},"corr_author":"1","date_published":"2022-02-22T00:00:00Z","publication":"Software Verification","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","abstract":[{"text":"We present a formal framework for the online black-box monitoring of software using monitors with quantitative verdict functions. Quantitative verdict functions have several advantages. First, quantitative monitors can be approximate, i.e., the value of the verdict function does not need to correspond exactly to the value of the property under observation. Second, quantitative monitors can be quantified universally, i.e., for every possible observed behavior, the monitor tries to make the best effort to estimate the value of the property under observation. Third, quantitative monitors can watch boolean as well as quantitative properties, such as average response time. Fourth, quantitative monitors can use non-finite-state resources, such as counters. As a consequence, quantitative monitors can be compared according to how many resources they use (e.g., the number of counters) and how precisely they approximate the property under observation. This allows for a rich spectrum of cost-precision trade-offs in monitoring software.","lang":"eng"}],"date_updated":"2025-04-15T06:25:58Z","date_created":"2022-03-20T23:01:40Z","external_id":{"isi":["000771713200001"]},"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"}],"title":"Quantitative monitoring of software","project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF"}],"type":"conference","series_title":"LNCS","acknowledgement":"The formal framework for quantitative monitoring which is presented in this invited talk was defined jointly with N. Ege Saraç at LICS 2021. This work was supported in part by the Wittgenstein Award Z211-N23 of the Austrian Science Fund.","status":"public","publication_identifier":{"isbn":["9783030955601"],"issn":["0302-9743"],"eissn":["1611-3349"]},"volume":13124,"doi":"10.1007/978-3-030-95561-8_1","conference":{"start_date":"2021-10-18","location":"New Haven, CT, United States","end_date":"2021-10-19","name":"NSV: Numerical Software Verification"},"page":"3-6","language":[{"iso":"eng"}],"year":"2022","isi":1,"month":"02"}]