[{"day":"18","publisher":"Frontiers","_id":"10536","pmid":1,"ddc":["610"],"publication":"Frontiers in Oncology","title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms","article_type":"original","volume":11,"quality_controlled":"1","abstract":[{"text":"TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner.","lang":"eng"}],"date_created":"2021-12-12T23:01:27Z","intvolume":"        11","year":"2021","date_published":"2021-11-18T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2021-12-13T13:32:37Z","scopus_import":"1","language":[{"iso":"eng"}],"article_number":"765151","has_accepted_license":"1","citation":{"ama":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. <i>Frontiers in Oncology</i>. 2021;11. doi:<a href=\"https://doi.org/10.3389/fonc.2021.765151\">10.3389/fonc.2021.765151</a>","apa":"Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., &#38; Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. <i>Frontiers in Oncology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fonc.2021.765151\">https://doi.org/10.3389/fonc.2021.765151</a>","chicago":"Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” <i>Frontiers in Oncology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fonc.2021.765151\">https://doi.org/10.3389/fonc.2021.765151</a>.","ista":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151.","ieee":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” <i>Frontiers in Oncology</i>, vol. 11. Frontiers, 2021.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","mla":"Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” <i>Frontiers in Oncology</i>, vol. 11, 765151, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fonc.2021.765151\">10.3389/fonc.2021.765151</a>."},"publication_identifier":{"eissn":["2234-943X"]},"external_id":{"pmid":["34868988"],"isi":["000726603400001"]},"file":[{"file_id":"10539","access_level":"open_access","success":1,"date_created":"2021-12-13T13:32:37Z","creator":"alisjak","content_type":"application/pdf","file_name":"2021_Frontiers_Stefanescu.pdf","date_updated":"2021-12-13T13:32:37Z","relation":"main_file","checksum":"56cbac80e6891ce750511a30161b7792","file_size":9245199}],"acknowledgement":"The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","oa_version":"Published Version","type":"journal_article","doi":"10.3389/fonc.2021.765151","publication_status":"published","status":"public","isi":1,"department":[{"_id":"DaSi"}],"date_updated":"2023-08-17T06:20:32Z","article_processing_charge":"No","author":[{"first_name":"Cristina","full_name":"Stefanescu, Cristina","last_name":"Stefanescu"},{"first_name":"Merel","last_name":"Van Gogh","full_name":"Van Gogh, Merel"},{"last_name":"Roblek","full_name":"Roblek, Marko","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389"},{"last_name":"Heikenwalder","full_name":"Heikenwalder, Mathias","first_name":"Mathias"},{"full_name":"Borsig, Lubor","last_name":"Borsig","first_name":"Lubor"}]},{"abstract":[{"lang":"eng","text":"We derive optimal-order homogenization rates for random nonlinear elliptic PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely, for a random monotone operator on \\mathbb {R}^d with stationary law (that is spatially homogeneous statistics) and fast decay of correlations on scales larger than the microscale \\varepsilon >0, we establish homogenization error estimates of the order \\varepsilon in case d\\geqq 3, and of the order \\varepsilon |\\log \\varepsilon |^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have been limited to a small algebraic rate of convergence \\varepsilon ^\\delta . We also establish error estimates for the approximation of the homogenized operator by the method of representative volumes of the order (L/\\varepsilon )^{-d/2} for a representative volume of size L. Our results also hold in the case of systems for which a (small-scale) C^{1,\\alpha } regularity theory is available."}],"date_created":"2021-12-16T12:12:33Z","intvolume":"       242","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2021-06-30T00:00:00Z","year":"2021","issue":"1","ddc":["530"],"_id":"10549","publisher":"Springer Nature","arxiv":1,"day":"30","volume":242,"article_type":"original","title":"Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"publication":"Archive for Rational Mechanics and Analysis","isi":1,"status":"public","publication_status":"published","doi":"10.1007/s00205-021-01686-9","type":"journal_article","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","full_name":"Fischer, Julian L","last_name":"Fischer"},{"last_name":"Neukamm","full_name":"Neukamm, Stefan","first_name":"Stefan"}],"date_updated":"2023-08-17T06:23:21Z","department":[{"_id":"JuFi"}],"citation":{"mla":"Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 242, no. 1, Springer Nature, 2021, pp. 343–452, doi:<a href=\"https://doi.org/10.1007/s00205-021-01686-9\">10.1007/s00205-021-01686-9</a>.","short":"J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452.","ieee":"J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 242, no. 1. Springer Nature, pp. 343–452, 2021.","ista":"Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 242(1), 343–452.","chicago":"Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00205-021-01686-9\">https://doi.org/10.1007/s00205-021-01686-9</a>.","apa":"Fischer, J. L., &#38; Neukamm, S. (2021). Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-021-01686-9\">https://doi.org/10.1007/s00205-021-01686-9</a>","ama":"Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. <i>Archive for Rational Mechanics and Analysis</i>. 2021;242(1):343-452. doi:<a href=\"https://doi.org/10.1007/s00205-021-01686-9\">10.1007/s00205-021-01686-9</a>"},"has_accepted_license":"1","language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-12-16T14:58:08Z","month":"06","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 405009441.","page":"343-452","file":[{"creator":"cchlebak","content_type":"application/pdf","file_id":"10558","access_level":"open_access","success":1,"date_created":"2021-12-16T14:58:08Z","relation":"main_file","checksum":"cc830b739aed83ca2e32c4e0ce266a4c","file_size":1640121,"date_updated":"2021-12-16T14:58:08Z","file_name":"2021_ArchRatMechAnalysis_Fischer.pdf"}],"external_id":{"isi":["000668431200001"],"arxiv":["1908.02273"]},"publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]}},{"date_published":"2021-01-01T00:00:00Z","issue":"1","year":"2021","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2001.00497"}],"intvolume":"        33","date_created":"2020-04-26T22:00:45Z","abstract":[{"lang":"eng","text":"We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein."}],"quality_controlled":"1","publication":"Reviews in Mathematical Physics","volume":33,"title":"The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime","article_type":"original","ec_funded":1,"_id":"7685","day":"01","arxiv":1,"publisher":"World Scientific Publishing","date_updated":"2025-05-14T10:49:57Z","department":[{"_id":"RoSe"}],"author":[{"last_name":"Boccato","full_name":"Boccato, Chiara","first_name":"Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","doi":"10.1142/S0129055X20600065","publication_status":"published","oa_version":"Preprint","type":"journal_article","isi":1,"status":"public","external_id":{"arxiv":["2001.00497"],"isi":["000613313200007"]},"publication_identifier":{"issn":["0129-055X"]},"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"article_number":"2060006","citation":{"ama":"Boccato C. The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. <i>Reviews in Mathematical Physics</i>. 2021;33(1). doi:<a href=\"https://doi.org/10.1142/S0129055X20600065\">10.1142/S0129055X20600065</a>","apa":"Boccato, C. (2021). The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X20600065\">https://doi.org/10.1142/S0129055X20600065</a>","chicago":"Boccato, Chiara. “The Excitation Spectrum of the Bose Gas in the Gross-Pitaevskii Regime.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2021. <a href=\"https://doi.org/10.1142/S0129055X20600065\">https://doi.org/10.1142/S0129055X20600065</a>.","ieee":"C. Boccato, “The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1. World Scientific Publishing, 2021.","ista":"Boccato C. 2021. The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime. Reviews in Mathematical Physics. 33(1), 2060006.","short":"C. Boccato, Reviews in Mathematical Physics 33 (2021).","mla":"Boccato, Chiara. “The Excitation Spectrum of the Bose Gas in the Gross-Pitaevskii Regime.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1, 2060006, World Scientific Publishing, 2021, doi:<a href=\"https://doi.org/10.1142/S0129055X20600065\">10.1142/S0129055X20600065</a>."},"language":[{"iso":"eng"}]},{"volume":33,"article_type":"original","title":"Bosonic collective excitations in Fermi gases","ec_funded":1,"publication":"Reviews in Mathematical Physics","_id":"7900","day":"01","arxiv":1,"publisher":"World Scientific Publishing","oa":1,"date_published":"2021-01-01T00:00:00Z","issue":"1","year":"2021","main_file_link":[{"url":"https://arxiv.org/abs/1910.08190","open_access":"1"}],"abstract":[{"lang":"eng","text":"Hartree–Fock theory has been justified as a mean-field approximation for fermionic systems. However, it suffers from some defects in predicting physical properties, making necessary a theory of quantum correlations. Recently, bosonization of many-body correlations has been rigorously justified as an upper bound on the correlation energy at high density with weak interactions. We review the bosonic approximation, deriving an effective Hamiltonian. We then show that for systems with Coulomb interaction this effective theory predicts collective excitations (plasmons) in accordance with the random phase approximation of Bohm and Pines, and with experimental observation."}],"date_created":"2020-05-28T16:47:55Z","intvolume":"        33","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","external_id":{"arxiv":["1910.08190"],"isi":["000613313200010"]},"publication_identifier":{"issn":["0129-055X"],"eissn":["1793-6659"]},"article_number":"2060009","citation":{"mla":"Benedikter, Niels P. “Bosonic Collective Excitations in Fermi Gases.” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1, 2060009, World Scientific Publishing, 2021, doi:<a href=\"https://doi.org/10.1142/s0129055x20600090\">10.1142/s0129055x20600090</a>.","ista":"Benedikter NP. 2021. Bosonic collective excitations in Fermi gases. Reviews in Mathematical Physics. 33(1), 2060009.","ieee":"N. P. Benedikter, “Bosonic collective excitations in Fermi gases,” <i>Reviews in Mathematical Physics</i>, vol. 33, no. 1. World Scientific Publishing, 2021.","short":"N.P. Benedikter, Reviews in Mathematical Physics 33 (2021).","ama":"Benedikter NP. Bosonic collective excitations in Fermi gases. <i>Reviews in Mathematical Physics</i>. 2021;33(1). doi:<a href=\"https://doi.org/10.1142/s0129055x20600090\">10.1142/s0129055x20600090</a>","chicago":"Benedikter, Niels P. “Bosonic Collective Excitations in Fermi Gases.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2021. <a href=\"https://doi.org/10.1142/s0129055x20600090\">https://doi.org/10.1142/s0129055x20600090</a>.","apa":"Benedikter, N. P. (2021). Bosonic collective excitations in Fermi gases. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/s0129055x20600090\">https://doi.org/10.1142/s0129055x20600090</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"694227"}],"article_processing_charge":"No","author":[{"full_name":"Benedikter, Niels P","last_name":"Benedikter","orcid":"0000-0002-1071-6091","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P"}],"date_updated":"2025-05-14T10:49:46Z","department":[{"_id":"RoSe"}],"isi":1,"status":"public","doi":"10.1142/s0129055x20600090","publication_status":"published","oa_version":"Preprint","type":"journal_article"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"05","publication_identifier":{"issn":["0020-9910"],"eissn":["1432-1297"]},"acknowledgement":"We thank Christian Hainzl for helpful discussions and a referee for very careful reading of the paper and many helpful suggestions. NB and RS were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 694227). Part of the research of NB was conducted on the RZD18 Nice–Milan–Vienna–Moscow. NB thanks Elliott H. Lieb and Peter Otte for explanations about the Luttinger model. PTN has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP acknowledges financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, grant agreement No. 802901). BS gratefully acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC-AdG CLaQS (grant agreement No. 834782). All authors acknowledge support for workshop participation from Mathematisches Forschungsinstitut Oberwolfach (Leibniz Association). NB, PTN, BS, and RS acknowledge support for workshop participation from Fondation des Treilles.","page":"885-979","file":[{"file_name":"2021_InventMath_Benedikter.pdf","date_updated":"2022-05-16T12:23:40Z","relation":"main_file","checksum":"f38c79dfd828cdc7f49a34b37b83d376","file_size":1089319,"file_id":"11386","success":1,"access_level":"open_access","date_created":"2022-05-16T12:23:40Z","creator":"dernst","content_type":"application/pdf"}],"external_id":{"arxiv":["2005.08933"],"isi":["000646573600001"]},"language":[{"iso":"eng"}],"citation":{"mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas.” <i>Inventiones Mathematicae</i>, vol. 225, Springer, 2021, pp. 885–979, doi:<a href=\"https://doi.org/10.1007/s00222-021-01041-5\">10.1007/s00222-021-01041-5</a>.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Correlation energy of a weakly interacting Fermi gas. Inventiones Mathematicae. 225, 885–979.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas,” <i>Inventiones Mathematicae</i>, vol. 225. Springer, pp. 885–979, 2021.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Inventiones Mathematicae 225 (2021) 885–979.","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas.” <i>Inventiones Mathematicae</i>. Springer, 2021. <a href=\"https://doi.org/10.1007/s00222-021-01041-5\">https://doi.org/10.1007/s00222-021-01041-5</a>.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., &#38; Seiringer, R. (2021). Correlation energy of a weakly interacting Fermi gas. <i>Inventiones Mathematicae</i>. Springer. <a href=\"https://doi.org/10.1007/s00222-021-01041-5\">https://doi.org/10.1007/s00222-021-01041-5</a>","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas. <i>Inventiones Mathematicae</i>. 2021;225:885-979. doi:<a href=\"https://doi.org/10.1007/s00222-021-01041-5\">10.1007/s00222-021-01041-5</a>"},"has_accepted_license":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"file_date_updated":"2022-05-16T12:23:40Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1071-6091","last_name":"Benedikter","full_name":"Benedikter, Niels P"},{"first_name":"Phan Thành","full_name":"Nam, Phan Thành","last_name":"Nam"},{"first_name":"Marcello","full_name":"Porta, Marcello","last_name":"Porta"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"department":[{"_id":"RoSe"}],"date_updated":"2025-04-14T07:27:00Z","status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1007/s00222-021-01041-5","ec_funded":1,"article_type":"original","title":"Correlation energy of a weakly interacting Fermi gas","volume":225,"publication":"Inventiones Mathematicae","ddc":["510"],"arxiv":1,"publisher":"Springer","day":"03","_id":"7901","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2021","date_published":"2021-05-03T00:00:00Z","quality_controlled":"1","intvolume":"       225","abstract":[{"lang":"eng","text":"We derive rigorously the leading order of the correlation energy of a Fermi gas in a scaling regime of high density and weak interaction. The result verifies the prediction of the random-phase approximation. Our proof refines the method of collective bosonization in three dimensions. We approximately diagonalize an effective Hamiltonian describing approximately bosonic collective excitations around the Hartree–Fock state, while showing that gapless and non-collective excitations have only a negligible effect on the ground state energy."}],"date_created":"2020-05-28T16:48:20Z"},{"isi":1,"status":"public","doi":"10.1007/s00454-020-00206-y","publication_status":"published","oa_version":"Published Version","type":"journal_article","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Brown, Adam","last_name":"Brown","id":"70B7FDF6-608D-11E9-9333-8535E6697425","first_name":"Adam"},{"full_name":"Wang, Bei","last_name":"Wang","first_name":"Bei"}],"date_updated":"2025-04-15T06:53:15Z","department":[{"_id":"HeEd"}],"has_accepted_license":"1","citation":{"ama":"Brown A, Wang B. Sheaf-theoretic stratification learning from geometric and topological perspectives. <i>Discrete and Computational Geometry</i>. 2021;65:1166-1198. doi:<a href=\"https://doi.org/10.1007/s00454-020-00206-y\">10.1007/s00454-020-00206-y</a>","chicago":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00206-y\">https://doi.org/10.1007/s00454-020-00206-y</a>.","apa":"Brown, A., &#38; Wang, B. (2021). Sheaf-theoretic stratification learning from geometric and topological perspectives. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00206-y\">https://doi.org/10.1007/s00454-020-00206-y</a>","mla":"Brown, Adam, and Bei Wang. “Sheaf-Theoretic Stratification Learning from Geometric and Topological Perspectives.” <i>Discrete and Computational Geometry</i>, vol. 65, Springer Nature, 2021, pp. 1166–98, doi:<a href=\"https://doi.org/10.1007/s00454-020-00206-y\">10.1007/s00454-020-00206-y</a>.","ieee":"A. Brown and B. Wang, “Sheaf-theoretic stratification learning from geometric and topological perspectives,” <i>Discrete and Computational Geometry</i>, vol. 65. Springer Nature, pp. 1166–1198, 2021.","short":"A. Brown, B. Wang, Discrete and Computational Geometry 65 (2021) 1166–1198.","ista":"Brown A, Wang B. 2021. Sheaf-theoretic stratification learning from geometric and topological perspectives. Discrete and Computational Geometry. 65, 1166–1198."},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"file_date_updated":"2020-11-25T09:06:41Z","corr_author":"1","month":"06","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000536324700001"],"arxiv":["1712.07734"]},"file":[{"content_type":"application/pdf","creator":"dernst","access_level":"open_access","success":1,"date_created":"2020-11-25T09:06:41Z","file_id":"8803","file_size":1013730,"relation":"main_file","checksum":"487a84ea5841b75f04f66d7ebd71b67e","file_name":"2020_DiscreteCompGeometry_Brown.pdf","date_updated":"2020-11-25T09:06:41Z"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was partially supported by NSF IIS-1513616 and NSF ABI-1661375. The authors would like to thank the anonymous referees for their insightful comments.","page":"1166-1198","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"abstract":[{"lang":"eng","text":"We investigate a sheaf-theoretic interpretation of stratification learning from geometric and topological perspectives. Our main result is the construction of stratification learning algorithms framed in terms of a sheaf on a partially ordered set with the Alexandroff topology. We prove that the resulting decomposition is the unique minimal stratification for which the strata are homogeneous and the given sheaf is constructible. In particular, when we choose to work with the local homology sheaf, our algorithm gives an alternative to the local homology transfer algorithm given in Bendich et al. (Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, pp. 1355–1370, ACM, New York, 2012), and the cohomology stratification algorithm given in Nanda (Found. Comput. Math. 20(2), 195–222, 2020). Additionally, we give examples of stratifications based on the geometric techniques of Breiding et al. (Rev. Mat. Complut. 31(3), 545–593, 2018), illustrating how the sheaf-theoretic approach can be used to study stratifications from both topological and geometric perspectives. This approach also points toward future applications of sheaf theory in the study of topological data analysis by illustrating the utility of the language of sheaf theory in generalizing existing algorithms."}],"intvolume":"        65","date_created":"2020-05-30T10:26:04Z","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2021-06-01T00:00:00Z","year":"2021","ddc":["510"],"_id":"7905","day":"01","publisher":"Springer Nature","arxiv":1,"volume":65,"article_type":"original","title":"Sheaf-theoretic stratification learning from geometric and topological perspectives","publication":"Discrete and Computational Geometry"},{"publication_status":"published","doi":"10.1007/s11590-020-01603-1","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","date_updated":"2024-11-04T13:52:35Z","department":[{"_id":"VlKo"}],"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Shehu, Yekini","last_name":"Shehu","first_name":"Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gibali, Aviv","last_name":"Gibali","first_name":"Aviv"}],"scopus_import":"1","corr_author":"1","file_date_updated":"2024-03-07T14:58:51Z","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"citation":{"mla":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” <i>Optimization Letters</i>, vol. 15, Springer Nature, 2021, pp. 2109–26, doi:<a href=\"https://doi.org/10.1007/s11590-020-01603-1\">10.1007/s11590-020-01603-1</a>.","ieee":"Y. Shehu and A. Gibali, “New inertial relaxed method for solving split feasibilities,” <i>Optimization Letters</i>, vol. 15. Springer Nature, pp. 2109–2126, 2021.","short":"Y. Shehu, A. Gibali, Optimization Letters 15 (2021) 2109–2126.","ista":"Shehu Y, Gibali A. 2021. New inertial relaxed method for solving split feasibilities. Optimization Letters. 15, 2109–2126.","chicago":"Shehu, Yekini, and Aviv Gibali. “New Inertial Relaxed Method for Solving Split Feasibilities.” <i>Optimization Letters</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11590-020-01603-1\">https://doi.org/10.1007/s11590-020-01603-1</a>.","apa":"Shehu, Y., &#38; Gibali, A. (2021). New inertial relaxed method for solving split feasibilities. <i>Optimization Letters</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11590-020-01603-1\">https://doi.org/10.1007/s11590-020-01603-1</a>","ama":"Shehu Y, Gibali A. New inertial relaxed method for solving split feasibilities. <i>Optimization Letters</i>. 2021;15:2109-2126. doi:<a href=\"https://doi.org/10.1007/s11590-020-01603-1\">10.1007/s11590-020-01603-1</a>"},"has_accepted_license":"1","language":[{"iso":"eng"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are grateful to the referees for their insightful comments which have improved the earlier version of the manuscript greatly. The first author has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","page":"2109-2126","file":[{"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","success":1,"date_created":"2024-03-07T14:58:51Z","file_id":"15089","file_size":2148882,"relation":"main_file","checksum":"63c5f31cd04626152a19f97a2476281b","file_name":"2021_OptimizationLetters_Shehu.pdf","date_updated":"2024-03-07T14:58:51Z"}],"external_id":{"isi":["000537342300001"]},"publication_identifier":{"eissn":["1862-4480"],"issn":["1862-4472"]},"month":"09","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In this paper, we introduce a relaxed CQ method with alternated inertial step for solving split feasibility problems. We give convergence of the sequence generated by our method under some suitable assumptions. Some numerical implementations from sparse signal and image deblurring are reported to show the efficiency of our method."}],"intvolume":"        15","date_created":"2020-06-04T11:28:33Z","quality_controlled":"1","date_published":"2021-09-01T00:00:00Z","year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"_id":"7925","publisher":"Springer Nature","day":"01","ddc":["510"],"publication":"Optimization Letters","volume":15,"ec_funded":1,"article_type":"original","title":"New inertial relaxed method for solving split feasibilities"},{"external_id":{"isi":["000556444600001"],"arxiv":["1903.05956"]},"related_material":{"record":[{"id":"6933","status":"public","relation":"earlier_version"}]},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). We thank Mohsen Ghaffari, Michael Elkin and Merav Parter for fruitful discussions. This project has received funding from the European Union’s Horizon 2020 Research And Innovation Program under Grant Agreement No. 755839.","page":"463-487","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"12","scopus_import":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"corr_author":"1","citation":{"ama":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. Fast approximate shortest paths in the congested clique. <i>Distributed Computing</i>. 2021;34:463-487. doi:<a href=\"https://doi.org/10.1007/s00446-020-00380-5\">10.1007/s00446-020-00380-5</a>","apa":"Censor-Hillel, K., Dory, M., Korhonen, J., &#38; Leitersdorf, D. (2021). Fast approximate shortest paths in the congested clique. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-020-00380-5\">https://doi.org/10.1007/s00446-020-00380-5</a>","chicago":"Censor-Hillel, Keren, Michal Dory, Janne Korhonen, and Dean Leitersdorf. “Fast Approximate Shortest Paths in the Congested Clique.” <i>Distributed Computing</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00446-020-00380-5\">https://doi.org/10.1007/s00446-020-00380-5</a>.","short":"K. Censor-Hillel, M. Dory, J. Korhonen, D. Leitersdorf, Distributed Computing 34 (2021) 463–487.","ista":"Censor-Hillel K, Dory M, Korhonen J, Leitersdorf D. 2021. Fast approximate shortest paths in the congested clique. Distributed Computing. 34, 463–487.","ieee":"K. Censor-Hillel, M. Dory, J. Korhonen, and D. Leitersdorf, “Fast approximate shortest paths in the congested clique,” <i>Distributed Computing</i>, vol. 34. Springer Nature, pp. 463–487, 2021.","mla":"Censor-Hillel, Keren, et al. “Fast Approximate Shortest Paths in the Congested Clique.” <i>Distributed Computing</i>, vol. 34, Springer Nature, 2021, pp. 463–87, doi:<a href=\"https://doi.org/10.1007/s00446-020-00380-5\">10.1007/s00446-020-00380-5</a>."},"language":[{"iso":"eng"}],"date_updated":"2025-04-15T06:53:15Z","department":[{"_id":"DaAl"}],"author":[{"last_name":"Censor-Hillel","full_name":"Censor-Hillel, Keren","first_name":"Keren"},{"first_name":"Michal","last_name":"Dory","full_name":"Dory, Michal"},{"full_name":"Korhonen, Janne","last_name":"Korhonen","id":"C5402D42-15BC-11E9-A202-CA2BE6697425","first_name":"Janne"},{"first_name":"Dean","full_name":"Leitersdorf, Dean","last_name":"Leitersdorf"}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s00446-020-00380-5","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","publication":"Distributed Computing","volume":34,"article_type":"original","title":"Fast approximate shortest paths in the congested clique","_id":"7939","day":"01","arxiv":1,"publisher":"Springer Nature","date_published":"2021-12-01T00:00:00Z","year":"2021","oa":1,"main_file_link":[{"url":"https://doi.org/10.1007/s00446-020-00380-5","open_access":"1"}],"date_created":"2020-06-07T22:00:54Z","abstract":[{"text":"We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:\r\n    A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.\r\n    A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.\r\n\r\nOur main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds. ","lang":"eng"}],"intvolume":"        34","quality_controlled":"1"},{"scopus_import":"1","corr_author":"1","citation":{"chicago":"Truckenbrodt, Sven M, and Silvio O. Rizzoli. “Simple Multi-Color Super-Resolution by X10 Microscopy.” In <i>Methods in Cell Biology</i>, 161:33–56. Elsevier, 2021. <a href=\"https://doi.org/10.1016/bs.mcb.2020.04.016\">https://doi.org/10.1016/bs.mcb.2020.04.016</a>.","apa":"Truckenbrodt, S. M., &#38; Rizzoli, S. O. (2021). Simple multi-color super-resolution by X10 microscopy. In <i>Methods in Cell Biology</i> (Vol. 161, pp. 33–56). Elsevier. <a href=\"https://doi.org/10.1016/bs.mcb.2020.04.016\">https://doi.org/10.1016/bs.mcb.2020.04.016</a>","ama":"Truckenbrodt SM, Rizzoli SO. Simple multi-color super-resolution by X10 microscopy. In: <i>Methods in Cell Biology</i>. Vol 161. Elsevier; 2021:33-56. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.04.016\">10.1016/bs.mcb.2020.04.016</a>","mla":"Truckenbrodt, Sven M., and Silvio O. Rizzoli. “Simple Multi-Color Super-Resolution by X10 Microscopy.” <i>Methods in Cell Biology</i>, vol. 161, Elsevier, 2021, pp. 33–56, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.04.016\">10.1016/bs.mcb.2020.04.016</a>.","ieee":"S. M. Truckenbrodt and S. O. Rizzoli, “Simple multi-color super-resolution by X10 microscopy,” in <i>Methods in Cell Biology</i>, vol. 161, Elsevier, 2021, pp. 33–56.","ista":"Truckenbrodt SM, Rizzoli SO. 2021.Simple multi-color super-resolution by X10 microscopy. In: Methods in Cell Biology. vol. 161, 33–56.","short":"S.M. Truckenbrodt, S.O. Rizzoli, in:, Methods in Cell Biology, Elsevier, 2021, pp. 33–56."},"language":[{"iso":"eng"}],"external_id":{"pmid":["33478696"]},"page":"33-56","publication_identifier":{"isbn":["978012820807-6"],"issn":["0091-679X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","doi":"10.1016/bs.mcb.2020.04.016","publication_status":"published","oa_version":"None","type":"book_chapter","status":"public","date_updated":"2024-10-09T20:59:36Z","department":[{"_id":"JoDa"}],"article_processing_charge":"No","author":[{"first_name":"Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","full_name":"Truckenbrodt, Sven M","last_name":"Truckenbrodt"},{"first_name":"Silvio O.","last_name":"Rizzoli","full_name":"Rizzoli, Silvio O."}],"_id":"7941","day":"01","publisher":"Elsevier","pmid":1,"publication":"Methods in Cell Biology","volume":161,"title":"Simple multi-color super-resolution by X10 microscopy","abstract":[{"lang":"eng","text":"Expansion microscopy is a recently developed super-resolution imaging technique, which provides an alternative to optics-based methods such as deterministic approaches (e.g. STED) or stochastic approaches (e.g. PALM/STORM). The idea behind expansion microscopy is to embed the biological sample in a swellable gel, and then to expand it isotropically, thereby increasing the distance between the fluorophores. This approach breaks the diffraction barrier by simply separating the emission point-spread-functions of the fluorophores. The resolution attainable in expansion microscopy is thus directly dependent on the separation that can be achieved, i.e. on the expansion factor. The original implementation of the technique achieved an expansion factor of fourfold, for a resolution of 70–80 nm. The subsequently developed X10 method achieves an expansion factor of 10-fold, for a resolution of 25–30 nm. This technique can be implemented with minimal technical requirements on any standard fluorescence microscope, and is more easily applied for multi-color imaging than either deterministic or stochastic super-resolution approaches. This renders X10 expansion microscopy a highly promising tool for new biological discoveries, as discussed here, and as demonstrated by several recent applications."}],"date_created":"2020-06-07T22:00:55Z","intvolume":"       161","quality_controlled":"1","date_published":"2021-01-01T00:00:00Z","year":"2021"},{"date_created":"2020-08-03T14:29:57Z","intvolume":"        22","abstract":[{"text":"This paper aims to obtain a strong convergence result for a Douglas–Rachford splitting method with inertial extrapolation step for finding a zero of the sum of two set-valued maximal monotone operators without any further assumption of uniform monotonicity on any of the involved maximal monotone operators. Furthermore, our proposed method is easy to implement and the inertial factor in our proposed method is a natural choice. Our method of proof is of independent interest. Finally, some numerical implementations are given to confirm the theoretical analysis.","lang":"eng"}],"quality_controlled":"1","date_published":"2021-02-25T00:00:00Z","year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"_id":"8196","publisher":"Springer Nature","day":"25","ddc":["510"],"publication":"Optimization and Engineering","volume":22,"ec_funded":1,"title":"New strong convergence method for the sum of two maximal monotone operators","article_type":"original","publication_status":"published","doi":"10.1007/s11081-020-09544-5","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","date_updated":"2024-11-04T13:52:38Z","department":[{"_id":"VlKo"}],"article_processing_charge":"Yes (via OA deal)","author":[{"first_name":"Yekini","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","last_name":"Shehu","full_name":"Shehu, Yekini"},{"full_name":"Dong, Qiao-Li","last_name":"Dong","first_name":"Qiao-Li"},{"last_name":"Liu","full_name":"Liu, Lu-Lu","first_name":"Lu-Lu"},{"full_name":"Yao, Jen-Chih","last_name":"Yao","first_name":"Jen-Chih"}],"scopus_import":"1","corr_author":"1","file_date_updated":"2020-08-03T15:24:39Z","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"citation":{"apa":"Shehu, Y., Dong, Q.-L., Liu, L.-L., &#38; Yao, J.-C. (2021). New strong convergence method for the sum of two maximal monotone operators. <i>Optimization and Engineering</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11081-020-09544-5\">https://doi.org/10.1007/s11081-020-09544-5</a>","chicago":"Shehu, Yekini, Qiao-Li Dong, Lu-Lu Liu, and Jen-Chih Yao. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” <i>Optimization and Engineering</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11081-020-09544-5\">https://doi.org/10.1007/s11081-020-09544-5</a>.","ama":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. New strong convergence method for the sum of two maximal monotone operators. <i>Optimization and Engineering</i>. 2021;22:2627-2653. doi:<a href=\"https://doi.org/10.1007/s11081-020-09544-5\">10.1007/s11081-020-09544-5</a>","short":"Y. Shehu, Q.-L. Dong, L.-L. Liu, J.-C. Yao, Optimization and Engineering 22 (2021) 2627–2653.","ieee":"Y. Shehu, Q.-L. Dong, L.-L. Liu, and J.-C. Yao, “New strong convergence method for the sum of two maximal monotone operators,” <i>Optimization and Engineering</i>, vol. 22. Springer Nature, pp. 2627–2653, 2021.","ista":"Shehu Y, Dong Q-L, Liu L-L, Yao J-C. 2021. New strong convergence method for the sum of two maximal monotone operators. Optimization and Engineering. 22, 2627–2653.","mla":"Shehu, Yekini, et al. “New Strong Convergence Method for the Sum of Two Maximal Monotone Operators.” <i>Optimization and Engineering</i>, vol. 22, Springer Nature, 2021, pp. 2627–53, doi:<a href=\"https://doi.org/10.1007/s11081-020-09544-5\">10.1007/s11081-020-09544-5</a>."},"has_accepted_license":"1","language":[{"iso":"eng"}],"page":"2627-2653","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The project of Yekini Shehu has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Program (FP7—2007–2013) (Grant Agreement No. 616160). The authors are grateful to the anonymous referees and the handling Editor for their comments and suggestions which have improved the earlier version of the manuscript greatly.","file":[{"date_updated":"2020-08-03T15:24:39Z","file_name":"2020_OptimizationEngineering_Shehu.pdf","file_size":2137860,"relation":"main_file","date_created":"2020-08-03T15:24:39Z","success":1,"access_level":"open_access","file_id":"8197","creator":"dernst","content_type":"application/pdf"}],"external_id":{"isi":["000559345400001"]},"publication_identifier":{"issn":["1389-4420"],"eissn":["1573-2924"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"02"},{"_id":"8248","day":"01","publisher":"Springer Nature","ddc":["510"],"publication":"Discrete and Computational Geometry","volume":66,"title":"Local conditions for triangulating submanifolds of Euclidean space","article_type":"original","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-020-00233-9"}],"abstract":[{"lang":"eng","text":"We consider the following setting: suppose that we are given a manifold M in Rd with positive reach. Moreover assume that we have an embedded simplical complex A without boundary, whose vertex set lies on the manifold, is sufficiently dense and such that all simplices in A have sufficient quality. We prove that if, locally, interiors of the projection of the simplices onto the tangent space do not intersect, then A is a triangulation of the manifold, that is, they are homeomorphic."}],"intvolume":"        66","date_created":"2020-08-11T07:11:51Z","quality_controlled":"1","date_published":"2021-09-01T00:00:00Z","year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"scopus_import":"1","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"corr_author":"1","has_accepted_license":"1","citation":{"mla":"Boissonnat, Jean-Daniel, et al. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” <i>Discrete and Computational Geometry</i>, vol. 66, Springer Nature, 2021, pp. 666–86, doi:<a href=\"https://doi.org/10.1007/s00454-020-00233-9\">10.1007/s00454-020-00233-9</a>.","short":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, M. Wintraecken, Discrete and Computational Geometry 66 (2021) 666–686.","ista":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. 2021. Local conditions for triangulating submanifolds of Euclidean space. Discrete and Computational Geometry. 66, 666–686.","ieee":"J.-D. Boissonnat, R. Dyer, A. Ghosh, A. Lieutier, and M. Wintraecken, “Local conditions for triangulating submanifolds of Euclidean space,” <i>Discrete and Computational Geometry</i>, vol. 66. Springer Nature, pp. 666–686, 2021.","ama":"Boissonnat J-D, Dyer R, Ghosh A, Lieutier A, Wintraecken M. Local conditions for triangulating submanifolds of Euclidean space. <i>Discrete and Computational Geometry</i>. 2021;66:666-686. doi:<a href=\"https://doi.org/10.1007/s00454-020-00233-9\">10.1007/s00454-020-00233-9</a>","chicago":"Boissonnat, Jean-Daniel, Ramsay Dyer, Arijit Ghosh, Andre Lieutier, and Mathijs Wintraecken. “Local Conditions for Triangulating Submanifolds of Euclidean Space.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00233-9\">https://doi.org/10.1007/s00454-020-00233-9</a>.","apa":"Boissonnat, J.-D., Dyer, R., Ghosh, A., Lieutier, A., &#38; Wintraecken, M. (2021). Local conditions for triangulating submanifolds of Euclidean space. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00233-9\">https://doi.org/10.1007/s00454-020-00233-9</a>"},"language":[{"iso":"eng"}],"external_id":{"isi":["000558119300001"]},"acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria). Arijit Ghosh is supported by the Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India.\r\nThis work has been funded by the European Research Council under the European Union’s ERC Grant Agreement number 339025 GUDHI (Algorithmic Foundations of Geometric Understanding in Higher Dimensions). The third author is supported by Ramanujan Fellowship (No. SB/S2/RJN-064/2015), India. The fifth author also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","page":"666-686","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"09","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/s00454-020-00233-9","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","date_updated":"2025-04-14T07:44:05Z","department":[{"_id":"HeEd"}],"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Boissonnat","full_name":"Boissonnat, Jean-Daniel","first_name":"Jean-Daniel"},{"first_name":"Ramsay","last_name":"Dyer","full_name":"Dyer, Ramsay"},{"full_name":"Ghosh, Arijit","last_name":"Ghosh","first_name":"Arijit"},{"first_name":"Andre","full_name":"Lieutier, Andre","last_name":"Lieutier"},{"full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220"}]},{"ec_funded":1,"title":"The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks","article_type":"original","volume":33,"publication":"Neural Computation","pmid":1,"ddc":["000","570"],"publisher":"MIT Press","day":"01","_id":"8253","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2021","issue":"4","date_published":"2021-03-01T00:00:00Z","quality_controlled":"1","date_created":"2020-08-12T12:08:24Z","intvolume":"        33","abstract":[{"text":"Brains process information in spiking neural networks. Their intricate connections shape the diverse functions these networks perform. In comparison, the functional capabilities of models of spiking networks are still rudimentary. This shortcoming is mainly due to the lack of insight and practical algorithms to construct the necessary connectivity. Any such algorithm typically attempts to build networks by iteratively reducing the error compared to a desired output. But assigning credit to hidden units in multi-layered spiking networks has remained challenging due to the non-differentiable nonlinearity of spikes. To avoid this issue, one can employ surrogate gradients to discover the required connectivity in spiking network models. However, the choice of a surrogate is not unique, raising the question of how its implementation influences the effectiveness of the method. Here, we use numerical simulations to systematically study how essential design parameters of surrogate gradients impact learning performance on a range of classification problems. We show that surrogate gradient learning is robust to different shapes of underlying surrogate derivatives, but the choice of the derivative’s scale can substantially affect learning performance. When we combine surrogate gradients with a suitable activity regularization technique, robust information processing can be achieved in spiking networks even at the sparse activity limit. Our study provides a systematic account of the remarkable robustness of surrogate gradient learning and serves as a practical guide to model functional spiking neural networks.","lang":"eng"}],"month":"03","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1530-888X"],"issn":["0899-7667"]},"page":"899-925","acknowledgement":"F.Z. was supported by the Wellcome Trust (110124/Z/15/Z) and the Novartis Research Foundation. T.P.V. was supported by a Wellcome Trust Sir Henry Dale Research fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and an ERC Consolidator Grant SYNAPSEEK.","file":[{"creator":"dernst","content_type":"application/pdf","file_id":"11131","date_created":"2022-04-08T06:05:39Z","success":1,"access_level":"open_access","checksum":"eac5a51c24c8989ae7cf9ae32ec3bc95","relation":"main_file","file_size":1611614,"date_updated":"2022-04-08T06:05:39Z","file_name":"2021_NeuralComputation_Zenke.pdf"}],"external_id":{"pmid":["33513328"],"isi":["000663433900003"]},"language":[{"iso":"eng"}],"citation":{"ama":"Zenke F, Vogels TP. The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. <i>Neural Computation</i>. 2021;33(4):899-925. doi:<a href=\"https://doi.org/10.1162/neco_a_01367\">10.1162/neco_a_01367</a>","apa":"Zenke, F., &#38; Vogels, T. P. (2021). The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. <i>Neural Computation</i>. MIT Press. <a href=\"https://doi.org/10.1162/neco_a_01367\">https://doi.org/10.1162/neco_a_01367</a>","chicago":"Zenke, Friedemann, and Tim P Vogels. “The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks.” <i>Neural Computation</i>. MIT Press, 2021. <a href=\"https://doi.org/10.1162/neco_a_01367\">https://doi.org/10.1162/neco_a_01367</a>.","ista":"Zenke F, Vogels TP. 2021. The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. Neural Computation. 33(4), 899–925.","short":"F. Zenke, T.P. Vogels, Neural Computation 33 (2021) 899–925.","ieee":"F. Zenke and T. P. Vogels, “The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks,” <i>Neural Computation</i>, vol. 33, no. 4. MIT Press, pp. 899–925, 2021.","mla":"Zenke, Friedemann, and Tim P. Vogels. “The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks.” <i>Neural Computation</i>, vol. 33, no. 4, MIT Press, 2021, pp. 899–925, doi:<a href=\"https://doi.org/10.1162/neco_a_01367\">10.1162/neco_a_01367</a>."},"has_accepted_license":"1","corr_author":"1","project":[{"grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234"},{"name":"What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks.","_id":"c084a126-5a5b-11eb-8a69-d75314a70a87","grant_number":"214316/Z/18/Z"}],"file_date_updated":"2022-04-08T06:05:39Z","scopus_import":"1","article_processing_charge":"No","author":[{"orcid":"0000-0003-1883-644X","first_name":"Friedemann","last_name":"Zenke","full_name":"Zenke, Friedemann"},{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P","last_name":"Vogels"}],"department":[{"_id":"TiVo"}],"date_updated":"2025-04-14T09:44:14Z","status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.1162/neco_a_01367"},{"date_updated":"2025-04-14T07:48:36Z","department":[{"_id":"HeEd"}],"article_processing_charge":"No","author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"first_name":"Alexander I.","full_name":"Bobenko, Alexander I.","last_name":"Bobenko"},{"full_name":"Schief, Wolfgang K.","last_name":"Schief","first_name":"Wolfgang K."},{"full_name":"Techter, Jan","last_name":"Techter","first_name":"Jan"}],"doi":"10.1007/s00454-020-00240-w","publication_status":"published","oa_version":"Preprint","type":"journal_article","isi":1,"status":"public","external_id":{"isi":["000564488500002"],"arxiv":["1908.00856"]},"acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”. W.K.S. was also supported by the Australian Research Council (DP1401000851). A.V.A. was also supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha).","page":"938-976","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","scopus_import":"1","project":[{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183"}],"citation":{"ama":"Akopyan A, Bobenko AI, Schief WK, Techter J. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. <i>Discrete and Computational Geometry</i>. 2021;66:938-976. doi:<a href=\"https://doi.org/10.1007/s00454-020-00240-w\">10.1007/s00454-020-00240-w</a>","chicago":"Akopyan, Arseniy, Alexander I. Bobenko, Wolfgang K. Schief, and Jan Techter. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-020-00240-w\">https://doi.org/10.1007/s00454-020-00240-w</a>.","apa":"Akopyan, A., Bobenko, A. I., Schief, W. K., &#38; Techter, J. (2021). On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00240-w\">https://doi.org/10.1007/s00454-020-00240-w</a>","mla":"Akopyan, Arseniy, et al. “On Mutually Diagonal Nets on (Confocal) Quadrics and 3-Dimensional Webs.” <i>Discrete and Computational Geometry</i>, vol. 66, Springer Nature, 2021, pp. 938–76, doi:<a href=\"https://doi.org/10.1007/s00454-020-00240-w\">10.1007/s00454-020-00240-w</a>.","ieee":"A. Akopyan, A. I. Bobenko, W. K. Schief, and J. Techter, “On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs,” <i>Discrete and Computational Geometry</i>, vol. 66. Springer Nature, pp. 938–976, 2021.","ista":"Akopyan A, Bobenko AI, Schief WK, Techter J. 2021. On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs. Discrete and Computational Geometry. 66, 938–976.","short":"A. Akopyan, A.I. Bobenko, W.K. Schief, J. Techter, Discrete and Computational Geometry 66 (2021) 938–976."},"language":[{"iso":"eng"}],"date_published":"2021-10-01T00:00:00Z","year":"2021","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1908.00856","open_access":"1"}],"abstract":[{"lang":"eng","text":"Canonical parametrisations of classical confocal coordinate systems are introduced and exploited to construct non-planar analogues of incircular (IC) nets on individual quadrics and systems of confocal quadrics. Intimate connections with classical deformations of quadrics that are isometric along asymptotic lines and circular cross-sections of quadrics are revealed. The existence of octahedral webs of surfaces of Blaschke type generated by asymptotic and characteristic lines that are diagonally related to lines of curvature is proved theoretically and established constructively. Appropriate samplings (grids) of these webs lead to three-dimensional extensions of non-planar IC nets. Three-dimensional octahedral grids composed of planes and spatially extending (checkerboard) IC-nets are shown to arise in connection with systems of confocal quadrics in Minkowski space. In this context, the Laguerre geometric notion of conical octahedral grids of planes is introduced. The latter generalise the octahedral grids derived from systems of confocal quadrics in Minkowski space. An explicit construction of conical octahedral grids is presented. The results are accompanied by various illustrations which are based on the explicit formulae provided by the theory."}],"date_created":"2020-09-06T22:01:13Z","intvolume":"        66","quality_controlled":"1","publication":"Discrete and Computational Geometry","volume":66,"article_type":"original","title":"On mutually diagonal nets on (confocal) quadrics and 3-dimensional webs","ec_funded":1,"_id":"8338","day":"01","arxiv":1,"publisher":"Springer Nature"},{"citation":{"mla":"Pitrik, József, and Daniel Virosztek. “A Divergence Center Interpretation of General Symmetric Kubo-Ando Means, and Related Weighted Multivariate Operator Means.” <i>Linear Algebra and Its Applications</i>, vol. 609, Elsevier, 2021, pp. 203–17, doi:<a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">10.1016/j.laa.2020.09.007</a>.","short":"J. Pitrik, D. Virosztek, Linear Algebra and Its Applications 609 (2021) 203–217.","ista":"Pitrik J, Virosztek D. 2021. A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. Linear Algebra and its Applications. 609, 203–217.","ieee":"J. Pitrik and D. Virosztek, “A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means,” <i>Linear Algebra and its Applications</i>, vol. 609. Elsevier, pp. 203–217, 2021.","chicago":"Pitrik, József, and Daniel Virosztek. “A Divergence Center Interpretation of General Symmetric Kubo-Ando Means, and Related Weighted Multivariate Operator Means.” <i>Linear Algebra and Its Applications</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">https://doi.org/10.1016/j.laa.2020.09.007</a>.","apa":"Pitrik, J., &#38; Virosztek, D. (2021). A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. <i>Linear Algebra and Its Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">https://doi.org/10.1016/j.laa.2020.09.007</a>","ama":"Pitrik J, Virosztek D. A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means. <i>Linear Algebra and its Applications</i>. 2021;609:203-217. doi:<a href=\"https://doi.org/10.1016/j.laa.2020.09.007\">10.1016/j.laa.2020.09.007</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"_id":"26A455A6-B435-11E9-9278-68D0E5697425","name":"Geometric study of Wasserstein spaces and free probability","call_identifier":"H2020","grant_number":"846294"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"01","external_id":{"isi":["000581730500011"],"arxiv":["2002.11678"]},"page":"203-217","acknowledgement":"The authors are grateful to Milán Mosonyi for fruitful discussions on the topic, and to the anonymous referee for his/her comments and suggestions.\r\nJ. Pitrik was supported by the Hungarian Academy of Sciences Lendület-Momentum Grant for Quantum Information Theory, No. 96 141, and by Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K119442, no. K124152, and no. KH129601. D. Virosztek was supported by the ISTFELLOW program of the Institute of Science and Technology Austria (project code IC1027FELL01), by the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National Research, Development and Innovation Office (NKFIH) via grants no. K124152, and no. KH129601.","publication_identifier":{"issn":["0024-3795"]},"isi":1,"status":"public","doi":"10.1016/j.laa.2020.09.007","publication_status":"published","oa_version":"Preprint","type":"journal_article","author":[{"last_name":"Pitrik","full_name":"Pitrik, József","first_name":"József"},{"first_name":"Daniel","orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek","full_name":"Virosztek, Daniel"}],"article_processing_charge":"No","date_updated":"2025-04-14T07:50:40Z","department":[{"_id":"LaEr"}],"_id":"8373","day":"15","arxiv":1,"publisher":"Elsevier","volume":609,"title":"A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means","article_type":"original","ec_funded":1,"publication":"Linear Algebra and its Applications","keyword":["Kubo-Ando mean","weighted multivariate mean","barycenter"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.11678"}],"abstract":[{"text":"It is well known that special Kubo-Ando operator means admit divergence center interpretations, moreover, they are also mean squared error estimators for certain metrics on positive definite operators. In this paper we give a divergence center interpretation for every symmetric Kubo-Ando mean. This characterization of the symmetric means naturally leads to a definition of weighted and multivariate versions of a large class of symmetric Kubo-Ando means. We study elementary properties of these weighted multivariate means, and note in particular that in the special case of the geometric mean we recover the weighted A#H-mean introduced by Kim, Lawson, and Lim.","lang":"eng"}],"date_created":"2020-09-11T08:35:50Z","intvolume":"       609","quality_controlled":"1","oa":1,"date_published":"2021-01-15T00:00:00Z","year":"2021"},{"day":"30","publisher":"Springer Nature","_id":"8429","pmid":1,"ddc":["610"],"publication":"Nature Communications","title":"Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits","article_type":"original","volume":12,"quality_controlled":"1","date_created":"2020-09-17T10:52:38Z","abstract":[{"text":"We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only ≤10% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32–44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having ≥95% probability of contributing ≥0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data.","lang":"eng"}],"intvolume":"        12","issue":"1","year":"2021","date_published":"2021-11-30T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2021-12-06T07:47:11Z","scopus_import":"1","language":[{"iso":"eng"}],"article_number":"6972","has_accepted_license":"1","citation":{"chicago":"Patxot, Marion, Daniel Trejo Banos, Athanasios Kousathanas, Etienne J Orliac, Sven E Ojavee, Gerhard Moser, Julia Sidorenko, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-27258-9\">https://doi.org/10.1038/s41467-021-27258-9</a>.","apa":"Patxot, M., Trejo Banos, D., Kousathanas, A., Orliac, E. J., Ojavee, S. E., Moser, G., … Robinson, M. R. (2021). Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-27258-9\">https://doi.org/10.1038/s41467-021-27258-9</a>","ama":"Patxot M, Trejo Banos D, Kousathanas A, et al. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-27258-9\">10.1038/s41467-021-27258-9</a>","mla":"Patxot, Marion, et al. “Probabilistic Inference of the Genetic Architecture Underlying Functional Enrichment of Complex Traits.” <i>Nature Communications</i>, vol. 12, no. 1, 6972, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-27258-9\">10.1038/s41467-021-27258-9</a>.","ieee":"M. Patxot <i>et al.</i>, “Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ista":"Patxot M, Trejo Banos D, Kousathanas A, Orliac EJ, Ojavee SE, Moser G, Sidorenko J, Kutalik Z, Magi R, Visscher PM, Ronnegard L, Robinson MR. 2021. Probabilistic inference of the genetic architecture underlying functional enrichment of complex traits. Nature Communications. 12(1), 6972.","short":"M. Patxot, D. Trejo Banos, A. Kousathanas, E.J. Orliac, S.E. Ojavee, G. Moser, J. Sidorenko, Z. Kutalik, R. Magi, P.M. Visscher, L. Ronnegard, M.R. Robinson, Nature Communications 12 (2021)."},"publication_identifier":{"eissn":["2041-1723"]},"external_id":{"pmid":["34848700"],"isi":["000724450600023"]},"acknowledgement":"This project was funded by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by core funding from the Institute of Science and Technology Austria. We would like to thank the participants of the cohort studies, and the Ecole Polytechnique Federal Lausanne (EPFL) SCITAS for their excellent compute resources, their generosity with their time and the kindness of their support. P.M.V. acknowledges funding from the Australian National Health and Medical Research Council (1113400) and the Australian Research Council (FL180100072). L.R. acknowledges funding from the Kjell & Märta Beijer Foundation (Stockholm, Sweden). We also would like to acknowledge Simone Rubinacci, Oliver Delanau, Alexander Terenin, Eleonora Porcu, and Mike Goddard for their useful comments and suggestions.","related_material":{"record":[{"status":"public","relation":"research_data","id":"13063"}]},"file":[{"file_id":"10419","date_created":"2021-12-06T07:47:11Z","success":1,"access_level":"open_access","creator":"cchlebak","content_type":"application/pdf","file_name":"2021_NatComm_Paxtot.pdf","date_updated":"2021-12-06T07:47:11Z","checksum":"384681be17aff902c149a48f52d13d4f","relation":"main_file","file_size":6519771}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","oa_version":"Published Version","type":"journal_article","doi":"10.1038/s41467-021-27258-9","publication_status":"published","status":"public","isi":1,"department":[{"_id":"MaRo"}],"date_updated":"2025-06-12T06:54:52Z","article_processing_charge":"No","author":[{"first_name":"Marion","last_name":"Patxot","full_name":"Patxot, Marion"},{"last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel","first_name":"Daniel"},{"first_name":"Athanasios","last_name":"Kousathanas","full_name":"Kousathanas, Athanasios"},{"last_name":"Orliac","full_name":"Orliac, Etienne J","first_name":"Etienne J"},{"first_name":"Sven E","last_name":"Ojavee","full_name":"Ojavee, Sven E"},{"first_name":"Gerhard","full_name":"Moser, Gerhard","last_name":"Moser"},{"first_name":"Julia","full_name":"Sidorenko, Julia","last_name":"Sidorenko"},{"first_name":"Zoltan","full_name":"Kutalik, Zoltan","last_name":"Kutalik"},{"last_name":"Magi","full_name":"Magi, Reedik","first_name":"Reedik"},{"full_name":"Visscher, Peter M","last_name":"Visscher","first_name":"Peter M"},{"last_name":"Ronnegard","full_name":"Ronnegard, Lars","first_name":"Lars"},{"last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","first_name":"Matthew Richard"}]},{"isi":1,"status":"public","publication_status":"published","doi":"10.1016/j.neuron.2020.11.028","type":"journal_article","oa_version":"Preprint","author":[{"first_name":"Yukari H.","full_name":"Takeo, Yukari H.","last_name":"Takeo"},{"last_name":"Shuster","full_name":"Shuster, S. Andrew","first_name":"S. Andrew"},{"first_name":"Linnie","last_name":"Jiang","full_name":"Jiang, Linnie"},{"last_name":"Hu","full_name":"Hu, Miley","first_name":"Miley"},{"first_name":"David J.","full_name":"Luginbuhl, David J.","last_name":"Luginbuhl"},{"first_name":"Thomas","full_name":"Rülicke, Thomas","last_name":"Rülicke"},{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"first_name":"Mark J.","full_name":"Wagner, Mark J.","last_name":"Wagner"},{"first_name":"Surya","last_name":"Ganguli","full_name":"Ganguli, Surya"},{"last_name":"Luo","full_name":"Luo, Liqun","first_name":"Liqun"}],"article_processing_charge":"No","date_updated":"2025-09-10T09:58:28Z","department":[{"_id":"SiHi"}],"citation":{"mla":"Takeo, Yukari H., et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” <i>Neuron</i>, vol. 109, no. 4, Elsevier, 2021, p. P629–644.E8, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">10.1016/j.neuron.2020.11.028</a>.","ista":"Takeo YH, Shuster SA, Jiang L, Hu M, Luginbuhl DJ, Rülicke T, Contreras X, Hippenmeyer S, Wagner MJ, Ganguli S, Luo L. 2021. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. Neuron. 109(4), P629–644.E8.","short":"Y.H. Takeo, S.A. Shuster, L. Jiang, M. Hu, D.J. Luginbuhl, T. Rülicke, X. Contreras, S. Hippenmeyer, M.J. Wagner, S. Ganguli, L. Luo, Neuron 109 (2021) P629–644.E8.","ieee":"Y. H. Takeo <i>et al.</i>, “GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells,” <i>Neuron</i>, vol. 109, no. 4. Elsevier, p. P629–644.E8, 2021.","ama":"Takeo YH, Shuster SA, Jiang L, et al. GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. <i>Neuron</i>. 2021;109(4):P629-644.E8. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">10.1016/j.neuron.2020.11.028</a>","chicago":"Takeo, Yukari H., S. Andrew Shuster, Linnie Jiang, Miley Hu, David J. Luginbuhl, Thomas Rülicke, Ximena Contreras, et al. “GluD2- and Cbln1-Mediated Competitive Synaptogenesis Shapes the Dendritic Arbors of Cerebellar Purkinje Cells.” <i>Neuron</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">https://doi.org/10.1016/j.neuron.2020.11.028</a>.","apa":"Takeo, Y. H., Shuster, S. A., Jiang, L., Hu, M., Luginbuhl, D. J., Rülicke, T., … Luo, L. (2021). GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.11.028\">https://doi.org/10.1016/j.neuron.2020.11.028</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"month":"02","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank M. Mishina for GluD2fl frozen embryos, T.C. Südhof and J.I. Morgan for Cbln1fl mice, L. Anderson for help in generating the MADM alleles, W. Joo for a previously unpublished construct, M. Yuzaki, K. Shen, J. Ding, and members of the Luo lab, including J.M. Kebschull, H. Li, J. Li, T. Li, C.M. McLaughlin, D. Pederick, J. Ren, D.C. Wang and C. Xu for discussions and critiques of the manuscript, and M. Yuzaki for supporting Y.H.T. during the final phase of this project. Y.H.T. was supported by a JSPS fellowship; S.A.S. was supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; L.J. is supported by a Stanford Graduate Fellowship and an NSF Predoctoral Fellowship; M.J.W. is supported by a Burroughs Wellcome Fund CASI Award. This work was supported by an NIH grant (R01-NS050538) to L.L.; the European Research Council (ERC) under the European Union's Horizon 2020 research and innovations programme (No. 725780 LinPro) to S.H.; and Simons and James S. McDonnell Foundations and an NSF CAREER award to S.G.; L.L. is an HHMI investigator.","page":"P629-644.E8","external_id":{"isi":["000632657400006"],"pmid":["33352118"]},"publication_identifier":{"eissn":["1097-4199"]},"date_created":"2020-09-21T11:59:47Z","intvolume":"       109","abstract":[{"lang":"eng","text":"The synaptotrophic hypothesis posits that synapse formation stabilizes dendritic branches, yet this hypothesis has not been causally tested in vivo in the mammalian brain. Presynaptic ligand cerebellin-1 (Cbln1) and postsynaptic receptor GluD2 mediate synaptogenesis between granule cells and Purkinje cells in the molecular layer of the cerebellar cortex. Here we show that sparse but not global knockout of GluD2 causes under-elaboration of Purkinje cell dendrites in the deep molecular layer and overelaboration in the superficial molecular layer. Developmental, overexpression, structure-function, and genetic epistasis analyses indicate that dendrite morphogenesis defects result from competitive synaptogenesis in a Cbln1/GluD2-dependent manner. A generative model of dendritic growth based on competitive synaptogenesis largely recapitulates GluD2 sparse and global knockout phenotypes. Our results support the synaptotrophic hypothesis at initial stages of dendrite development, suggest a second mode in which cumulative synapse formation inhibits further dendrite growth, and highlight the importance of competition in dendrite morphogenesis."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.06.14.151258"}],"quality_controlled":"1","oa":1,"date_published":"2021-02-17T00:00:00Z","year":"2021","issue":"4","pmid":1,"_id":"8544","publisher":"Elsevier","day":"17","volume":109,"ec_funded":1,"article_type":"original","title":"GluD2- and Cbln1-mediated competitive synaptogenesis shapes the dendritic arbors of cerebellar Purkinje cells","publication":"Neuron"},{"pmid":1,"ddc":["580"],"day":"01","publisher":"Wiley","_id":"8582","title":"Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana","article_type":"original","ec_funded":1,"volume":229,"publication":"New Phytologist","quality_controlled":"1","date_created":"2020-09-28T08:59:28Z","abstract":[{"lang":"eng","text":"Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.\r\nHere, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.\r\nPharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.\r\nThis study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems."}],"intvolume":"       229","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"1","year":"2021","date_published":"2021-01-01T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"ieee":"H. Li <i>et al.</i>, “Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 229, no. 1. Wiley, pp. 351–369, 2021.","short":"H. Li, D. von Wangenheim, X. Zhang, S. Tan, N. Darwish-Miranda, S. Naramoto, K.T. Wabnik, R. de Rycke, W. Kaufmann, D.J. Gütl, R. Tejos, P. Grones, M. Ke, X. Chen, J. Dettmer, J. Friml, New Phytologist 229 (2021) 351–369.","ista":"Li H, von Wangenheim D, Zhang X, Tan S, Darwish-Miranda N, Naramoto S, Wabnik KT, de Rycke R, Kaufmann W, Gütl DJ, Tejos R, Grones P, Ke M, Chen X, Dettmer J, Friml J. 2021. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. New Phytologist. 229(1), 351–369.","mla":"Li, Hongjiang, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 229, no. 1, Wiley, 2021, pp. 351–69, doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>.","ama":"Li H, von Wangenheim D, Zhang X, et al. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. 2021;229(1):351-369. doi:<a href=\"https://doi.org/10.1111/nph.16887\">10.1111/nph.16887</a>","apa":"Li, H., von Wangenheim, D., Zhang, X., Tan, S., Darwish-Miranda, N., Naramoto, S., … Friml, J. (2021). Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>","chicago":"Li, Hongjiang, Daniel von Wangenheim, Xixi Zhang, Shutang Tan, Nasser Darwish-Miranda, Satoshi Naramoto, Krzysztof T Wabnik, et al. “Cellular Requirements for PIN Polar Cargo Clustering in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.16887\">https://doi.org/10.1111/nph.16887</a>."},"file_date_updated":"2021-02-04T09:44:17Z","project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"external_id":{"pmid":["32810889"],"isi":["000570187900001"]},"acknowledged_ssus":[{"_id":"Bio"}],"page":"351-369","file":[{"creator":"dernst","content_type":"application/pdf","date_created":"2021-02-04T09:44:17Z","success":1,"access_level":"open_access","file_id":"9084","file_size":4061962,"checksum":"b45621607b4cab97eeb1605ab58e896e","relation":"main_file","date_updated":"2021-02-04T09:44:17Z","file_name":"2021_NewPhytologist_Li.pdf"}],"acknowledgement":"We thank Dr Ingo Heilmann (Martin‐Luther‐University Halle‐Wittenberg) for the XVE>>PIP5K1‐YFP line, Dr Brad Day (Michigan State University) for the ndr1‐1 mutant and the complementation lines, and Dr Patricia C. Zambryski (University of California, Berkeley) for the 35S::P30‐GFP line, the Bioimaging team (IST Austria) for assistance with imaging, group members for discussions, Martine De Cock for help in preparing the manuscript and Nataliia Gnyliukh for critical reading and revision of the manuscript. This project received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No. 742985) and Comisión Nacional de Investigación Científica y Tecnológica (Project CONICYT‐PAI 82130047). DvW received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007‐2013) under REA grant agreement no. 291734.","status":"public","isi":1,"oa_version":"Published Version","type":"journal_article","doi":"10.1111/nph.16887","publication_status":"published","article_processing_charge":"Yes (via OA deal)","author":[{"orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang","last_name":"Li","full_name":"Li, Hongjiang"},{"full_name":"von Wangenheim, Daniel","last_name":"von Wangenheim","first_name":"Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Xixi","last_name":"Zhang","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi"},{"full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0471-8285","first_name":"Shutang"},{"last_name":"Darwish-Miranda","full_name":"Darwish-Miranda, Nasser","first_name":"Nasser","id":"39CD9926-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8821-8236"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560","first_name":"Krzysztof T","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T"},{"last_name":"de Rycke","full_name":"de Rycke, Riet","first_name":"Riet"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315"},{"first_name":"Daniel J","id":"381929CE-F248-11E8-B48F-1D18A9856A87","last_name":"Gütl","full_name":"Gütl, Daniel J"},{"first_name":"Ricardo","full_name":"Tejos, Ricardo","last_name":"Tejos"},{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter","last_name":"Grones"},{"full_name":"Ke, Meiyu","last_name":"Ke","first_name":"Meiyu"},{"first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Xu"},{"full_name":"Dettmer, Jan","last_name":"Dettmer","first_name":"Jan"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"EvBe"}],"date_updated":"2025-06-12T06:32:24Z"},{"abstract":[{"text":"We consider the Fröhlich polaron model in the strong coupling limit. It is well‐known that to leading order the ground state energy is given by the (classical) Pekar energy. In this work, we establish the subleading correction, describing quantum fluctuation about the classical limit. Our proof applies to a model of a confined polaron, where both the electron and the polarization field are restricted to a set of finite volume, with linear size determined by the natural length scale of the Pekar problem.","lang":"eng"}],"date_created":"2020-10-04T22:01:37Z","intvolume":"        74","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2021-03-01T00:00:00Z","issue":"3","year":"2021","ddc":["510"],"_id":"8603","day":"01","publisher":"Wiley","volume":74,"article_type":"original","title":"Quantum corrections to the Pekar asymptotics of a strongly coupled polaron","ec_funded":1,"publication":"Communications on Pure and Applied Mathematics","isi":1,"status":"public","doi":"10.1002/cpa.21944","publication_status":"published","oa_version":"Published Version","type":"journal_article","author":[{"first_name":"Rupert","last_name":"Frank","full_name":"Frank, Rupert"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","date_updated":"2025-07-10T11:57:12Z","department":[{"_id":"RoSe"}],"has_accepted_license":"1","citation":{"chicago":"Frank, Rupert, and Robert Seiringer. “Quantum Corrections to the Pekar Asymptotics of a Strongly Coupled Polaron.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/cpa.21944\">https://doi.org/10.1002/cpa.21944</a>.","apa":"Frank, R., &#38; Seiringer, R. (2021). Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21944\">https://doi.org/10.1002/cpa.21944</a>","ama":"Frank R, Seiringer R. Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. <i>Communications on Pure and Applied Mathematics</i>. 2021;74(3):544-588. doi:<a href=\"https://doi.org/10.1002/cpa.21944\">10.1002/cpa.21944</a>","mla":"Frank, Rupert, and Robert Seiringer. “Quantum Corrections to the Pekar Asymptotics of a Strongly Coupled Polaron.” <i>Communications on Pure and Applied Mathematics</i>, vol. 74, no. 3, Wiley, 2021, pp. 544–88, doi:<a href=\"https://doi.org/10.1002/cpa.21944\">10.1002/cpa.21944</a>.","short":"R. Frank, R. Seiringer, Communications on Pure and Applied Mathematics 74 (2021) 544–588.","ieee":"R. Frank and R. Seiringer, “Quantum corrections to the Pekar asymptotics of a strongly coupled polaron,” <i>Communications on Pure and Applied Mathematics</i>, vol. 74, no. 3. Wiley, pp. 544–588, 2021.","ista":"Frank R, Seiringer R. 2021. Quantum corrections to the Pekar asymptotics of a strongly coupled polaron. Communications on Pure and Applied Mathematics. 74(3), 544–588."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-03-11T10:03:30Z","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","external_id":{"isi":["000572991500001"]},"page":"544-588","file":[{"file_id":"9236","date_created":"2021-03-11T10:03:30Z","access_level":"open_access","success":1,"content_type":"application/pdf","creator":"dernst","file_name":"2021_CommPureApplMath_Frank.pdf","date_updated":"2021-03-11T10:03:30Z","checksum":"5f665ffa6e6dd958aec5c3040cbcfa84","relation":"main_file","file_size":334987}],"acknowledgement":"Partial support through National Science Foundation GrantDMS-1363432 (R.L.F.) and the European Research Council (ERC) under the Euro-pean Union’s Horizon 2020 research and innovation programme (grant agreementNo 694227; R.S.), is acknowledged. Open access funding enabled and organizedby Projekt DEAL.","publication_identifier":{"eissn":["1097-0312"],"issn":["0010-3640"]}},{"scopus_import":"1","file_date_updated":"2021-04-12T12:29:07Z","has_accepted_license":"1","citation":{"ama":"He P, Zhang Y, Li H, et al. GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. <i>Plant Biotechnology Journal</i>. 2021;19(3):548-562. doi:<a href=\"https://doi.org/10.1111/pbi.13484\">10.1111/pbi.13484</a>","chicago":"He, P, Yuzhou Zhang, H Li, X Fu, H Shang, C Zou, Jiří Friml, and G Xiao. “GhARF16-1 Modulates Leaf Development by Transcriptionally Regulating the GhKNOX2-1 Gene in Cotton.” <i>Plant Biotechnology Journal</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/pbi.13484\">https://doi.org/10.1111/pbi.13484</a>.","apa":"He, P., Zhang, Y., Li, H., Fu, X., Shang, H., Zou, C., … Xiao, G. (2021). GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. <i>Plant Biotechnology Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/pbi.13484\">https://doi.org/10.1111/pbi.13484</a>","mla":"He, P., et al. “GhARF16-1 Modulates Leaf Development by Transcriptionally Regulating the GhKNOX2-1 Gene in Cotton.” <i>Plant Biotechnology Journal</i>, vol. 19, no. 3, Wiley, 2021, pp. 548–62, doi:<a href=\"https://doi.org/10.1111/pbi.13484\">10.1111/pbi.13484</a>.","short":"P. He, Y. Zhang, H. Li, X. Fu, H. Shang, C. Zou, J. Friml, G. Xiao, Plant Biotechnology Journal 19 (2021) 548–562.","ieee":"P. He <i>et al.</i>, “GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton,” <i>Plant Biotechnology Journal</i>, vol. 19, no. 3. Wiley, pp. 548–562, 2021.","ista":"He P, Zhang Y, Li H, Fu X, Shang H, Zou C, Friml J, Xiao G. 2021. GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. Plant Biotechnology Journal. 19(3), 548–562."},"language":[{"iso":"eng"}],"external_id":{"isi":["000577682300001"],"pmid":["32981232"]},"OA_type":"gold","file":[{"file_name":"2021_PlantBiotechJournal_He.pdf","date_updated":"2021-04-12T12:29:07Z","file_size":15691871,"relation":"main_file","checksum":"63845be37fb962586e0c7773f2355970","success":1,"access_level":"open_access","date_created":"2021-04-12T12:29:07Z","file_id":"9321","creator":"dernst","content_type":"application/pdf"}],"acknowledgement":"We are thankful to Professor Yuxian Zhu from Wuhan University for his extremely valuable remarks and helpful comments on the manuscript. This work was supported by the Shaanxi Natural Science Foundation (2019JQ‐062 and 2020JQ‐410), Shaanxi Youth Entrusted Talents Program (20190205), China Postdoctoral Science Foundation (2018M640947, 2020T130394), Shaanxi Postdoctoral Project (2018BSHYDZZ76), Natural Science Basic Research Plan in Shaanxi Province of China (2018JZ3006), Fundamental Research Funds for the Central Universities (GK201903064, GK201901004, GK202002005 and GK202001004), and State Key Laboratory of Cotton Biology Open Fund (CB2020A12).","page":"548-562","publication_identifier":{"issn":["1467-7644"],"eissn":["1467-7652"]},"month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","DOAJ_listed":"1","doi":"10.1111/pbi.13484","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","date_updated":"2025-07-10T11:57:13Z","department":[{"_id":"JiFr"}],"author":[{"full_name":"He, P","last_name":"He","first_name":"P"},{"first_name":"Yuzhou","orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Yuzhou"},{"first_name":"H","full_name":"Li, H","last_name":"Li"},{"last_name":"Fu","full_name":"Fu, X","first_name":"X"},{"full_name":"Shang, H","last_name":"Shang","first_name":"H"},{"first_name":"C","last_name":"Zou","full_name":"Zou, C"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří"},{"first_name":"G","full_name":"Xiao, G","last_name":"Xiao"}],"article_processing_charge":"No","_id":"8606","day":"01","publisher":"Wiley","ddc":["580"],"pmid":1,"publication":"Plant Biotechnology Journal","volume":19,"OA_place":"publisher","title":"GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton","article_type":"original","date_created":"2020-10-05T12:44:33Z","abstract":[{"lang":"eng","text":"The leaf is a crucial organ evolved with remarkable morphological diversity to maximize plant photosynthesis. The leaf shape is a key trait that affects photosynthesis, flowering rates, disease resistance, and yield. Although many genes regulating leaf development have been identified in the past years, the precise regulatory architecture underlying the generation of diverse leaf shapes remains to be elucidated. We used cotton as a reference model to probe the genetic framework underlying divergent leaf forms. Comparative transcriptome analysis revealed that the GhARF16‐1 and GhKNOX2‐1 genes might be potential regulators of leaf shape. We functionally characterized the auxin‐responsive factor ARF16‐1 acting upstream of GhKNOX2‐1 to determine leaf morphology in cotton. The transcription of GhARF16‐1 was significantly higher in lobed‐leaved cotton than in smooth‐leaved cotton. Furthermore, the overexpression of GhARF16‐1 led to the upregulation of GhKNOX2‐1 and resulted in more and deeper serrations in cotton leaves, similar to the leaf shape of cotton plants overexpressing GhKNOX2‐1. We found that GhARF16‐1 specifically bound to the promoter of GhKNOX2‐1 to induce its expression. The heterologous expression of GhARF16‐1 and GhKNOX2‐1 in Arabidopsis led to lobed and curly leaves, and a genetic analysis revealed that GhKNOX2‐1 is epistatic to GhARF16‐1 in Arabidopsis, suggesting that the GhARF16‐1 and GhKNOX2‐1 interaction paradigm also functions to regulate leaf shape in Arabidopsis. To our knowledge, our results uncover a novel mechanism by which auxin, through the key component ARF16‐1 and its downstream‐activated gene KNOX2‐1, determines leaf morphology in eudicots."}],"intvolume":"        19","quality_controlled":"1","date_published":"2021-03-01T00:00:00Z","issue":"3","year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1},{"volume":229,"title":"Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana","article_type":"original","publication":"New Phytologist","ddc":["580"],"pmid":1,"_id":"8608","day":"01","publisher":"Wiley","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2021-01-01T00:00:00Z","issue":"2","year":"2021","intvolume":"       229","abstract":[{"lang":"eng","text":"To adapt to the diverse array of biotic and abiotic cues, plants have evolved sophisticated mechanisms to sense changes in environmental conditions and modulate their growth. Growth-promoting hormones and defence signalling fine tune plant development antagonistically. During host-pathogen interactions, this defence-growth trade-off is mediated by the counteractive effects of the defence hormone salicylic acid (SA) and the growth hormone auxin. Here we revealed an underlying mechanism of SA regulating auxin signalling by constraining the plasma membrane dynamics of PIN2 auxin efflux transporter in Arabidopsis thaliana roots. The lateral diffusion of PIN2 proteins is constrained by SA signalling, during which PIN2 proteins are condensed into hyperclusters depending on REM1.2-mediated nanodomain compartmentalisation. Furthermore, membrane nanodomain compartmentalisation by SA or Remorin (REM) assembly significantly suppressed clathrin-mediated endocytosis. Consequently, SA-induced heterogeneous surface condensation disrupted asymmetric auxin distribution and the resultant gravitropic response. Our results demonstrated a defence-growth trade-off mechanism by which SA signalling crosstalked with auxin transport by concentrating membrane-resident PIN2 into heterogeneous compartments."}],"date_created":"2020-10-05T12:45:36Z","quality_controlled":"1","month":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"pmid":["32901934"],"isi":["000573568000001"]},"acknowledgement":"This work was supported by the National Key Research andDevelopment Programme of China (2017YFA0506100), theNational Natural Science Foundation of China (31870170 and31701168), and the Fok Ying Tung Education Foundation(161027) to XC; NTU startup grant (M4081533) and NIM/01/2016 (NTU, Singapore) to YM. We thank Lei Shi andZhongquan Lin for microscopy assistance.","page":"963-978","file":[{"relation":"main_file","checksum":"d36b6a8c6fafab66264e0d27114dae63","file_size":3674502,"file_name":"2021_NewPhytologist_Ke.pdf","date_updated":"2021-02-04T09:53:16Z","creator":"dernst","content_type":"application/pdf","file_id":"9085","access_level":"open_access","success":1,"date_created":"2021-02-04T09:53:16Z"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"has_accepted_license":"1","citation":{"ama":"Ke M, Ma Z, Wang D, et al. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. <i>New Phytologist</i>. 2021;229(2):963-978. doi:<a href=\"https://doi.org/10.1111/nph.16915\">10.1111/nph.16915</a>","apa":"Ke, M., Ma, Z., Wang, D., Sun, Y., Wen, C., Huang, D., … Chen, X. (2021). Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16915\">https://doi.org/10.1111/nph.16915</a>","chicago":"Ke, M, Z Ma, D Wang, Y Sun, C Wen, D Huang, Z Chen, et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” <i>New Phytologist</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/nph.16915\">https://doi.org/10.1111/nph.16915</a>.","ieee":"M. Ke <i>et al.</i>, “Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana,” <i>New Phytologist</i>, vol. 229, no. 2. Wiley, pp. 963–978, 2021.","ista":"Ke M, Ma Z, Wang D, Sun Y, Wen C, Huang D, Chen Z, Yang L, Tan S, Li R, Friml J, Miao Y, Chen X. 2021. Salicylic acid regulates PIN2 auxin transporter hyper-clustering and root gravitropic growth via Remorin-dependent lipid nanodomain organization in Arabidopsis thaliana. New Phytologist. 229(2), 963–978.","short":"M. Ke, Z. Ma, D. Wang, Y. Sun, C. Wen, D. Huang, Z. Chen, L. Yang, S. Tan, R. Li, J. Friml, Y. Miao, X. Chen, New Phytologist 229 (2021) 963–978.","mla":"Ke, M., et al. “Salicylic Acid Regulates PIN2 Auxin Transporter Hyper-Clustering and Root Gravitropic Growth via Remorin-Dependent Lipid Nanodomain Organization in Arabidopsis Thaliana.” <i>New Phytologist</i>, vol. 229, no. 2, Wiley, 2021, pp. 963–78, doi:<a href=\"https://doi.org/10.1111/nph.16915\">10.1111/nph.16915</a>."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-02-04T09:53:16Z","article_processing_charge":"No","author":[{"first_name":"M","last_name":"Ke","full_name":"Ke, M"},{"first_name":"Z","full_name":"Ma, Z","last_name":"Ma"},{"first_name":"D","full_name":"Wang, D","last_name":"Wang"},{"full_name":"Sun, Y","last_name":"Sun","first_name":"Y"},{"first_name":"C","last_name":"Wen","full_name":"Wen, C"},{"first_name":"D","last_name":"Huang","full_name":"Huang, D"},{"last_name":"Chen","full_name":"Chen, Z","first_name":"Z"},{"first_name":"L","full_name":"Yang, L","last_name":"Yang"},{"first_name":"Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang"},{"first_name":"R","last_name":"Li","full_name":"Li, R"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Miao","full_name":"Miao, Y","first_name":"Y"},{"last_name":"Chen","full_name":"Chen, X","first_name":"X"}],"date_updated":"2023-09-05T16:06:24Z","department":[{"_id":"JiFr"}],"isi":1,"status":"public","doi":"10.1111/nph.16915","publication_status":"published","oa_version":"Published Version","type":"journal_article"}]