[{"doi":"10.1098/rsta.2022.0112","citation":{"apa":"Wang, B., Mellibovsky, F., Ayats López, R., Deguchi, K., &#38; Meseguer, A. (2023). Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. <i>Philosophical Transactions of the Royal Society A</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsta.2022.0112\">https://doi.org/10.1098/rsta.2022.0112</a>","chicago":"Wang, B., F. Mellibovsky, Roger Ayats López, K. Deguchi, and A. Meseguer. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” <i>Philosophical Transactions of the Royal Society A</i>. The Royal Society, 2023. <a href=\"https://doi.org/10.1098/rsta.2022.0112\">https://doi.org/10.1098/rsta.2022.0112</a>.","short":"B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, A. Meseguer, Philosophical Transactions of the Royal Society A 381 (2023).","ista":"Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. 2023. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 381(2246), 0112.","ieee":"B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, and A. Meseguer, “Mean structure of the supercritical turbulent spiral in Taylor–Couette flow,” <i>Philosophical Transactions of the Royal Society A</i>, vol. 381, no. 2246. The Royal Society, 2023.","mla":"Wang, B., et al. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” <i>Philosophical Transactions of the Royal Society A</i>, vol. 381, no. 2246, 0112, The Royal Society, 2023, doi:<a href=\"https://doi.org/10.1098/rsta.2022.0112\">10.1098/rsta.2022.0112</a>.","ama":"Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. <i>Philosophical Transactions of the Royal Society A</i>. 2023;381(2246). doi:<a href=\"https://doi.org/10.1098/rsta.2022.0112\">10.1098/rsta.2022.0112</a>"},"quality_controlled":"1","acknowledgement":"K.D.’s research was supported by Australian Research Council Discovery Early Career Researcher Award (DE170100171). B.W., R.A., F.M. and A.M. research was supported by the Spanish Ministerio de Economía y Competitividad (grant nos. FIS2016-77849-R and FIS2017-85794-P) and Ministerio de Ciencia e Innovación (grant no. PID2020-114043GB-I00) and the Generalitat de Catalunya (grant no. 2017-SGR-785). B.W.’s research was also supported by the Chinese Scholarship Council (grant CSC no. 201806440152). F.M. is a Serra-Húnter Fellow.","year":"2023","publication_identifier":{"eissn":["1471-2962"],"issn":["1364-503X"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","pmid":1,"intvolume":"       381","license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"pmid":["36907214"]},"oa":1,"ddc":["530"],"keyword":["General Physics and Astronomy","General Engineering","General Mathematics"],"abstract":[{"lang":"eng","text":"The large-scale laminar/turbulent spiral patterns that appear in the linearly unstable regime of counter-rotating Taylor–Couette flow are investigated from a statistical perspective by means of direct numerical simulation. Unlike the vast majority of previous numerical studies, we analyse the flow in periodic parallelogram-annular domains, following a coordinate change that aligns one of the parallelogram sides with the spiral pattern. The domain size, shape and spatial resolution have been varied and the results compared with those in a sufficiently large computational orthogonal domain with natural axial and azimuthal periodicity. We find that a minimal parallelogram of the right tilt significantly reduces the computational cost without notably compromising the statistical properties of the supercritical turbulent spiral. Its mean structure, obtained from extremely long time integrations in a co-rotating reference frame using the method of slices, bears remarkable similarity with the turbulent stripes observed in plane Couette flow, the centrifugal instability playing only a secondary role."}],"file":[{"file_id":"14763","date_created":"2024-01-09T09:13:53Z","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2023_PhilTransactionsA_Wang_accepted.pdf","relation":"main_file","file_size":6421086,"checksum":"1978d126c0ce2f47c22ac20107cc0106","creator":"dernst","date_updated":"2024-01-09T09:13:53Z"}],"oa_version":"Submitted Version","date_created":"2024-01-08T13:11:45Z","issue":"2246","_id":"14754","type":"journal_article","article_processing_charge":"No","publication":"Philosophical Transactions of the Royal Society A","file_date_updated":"2024-01-09T09:13:53Z","author":[{"last_name":"Wang","first_name":"B.","full_name":"Wang, B."},{"full_name":"Mellibovsky, F.","first_name":"F.","last_name":"Mellibovsky"},{"full_name":"Ayats López, Roger","orcid":"0000-0001-6572-0621","first_name":"Roger","id":"ab77522d-073b-11ed-8aff-e71b39258362","last_name":"Ayats López"},{"full_name":"Deguchi, K.","last_name":"Deguchi","first_name":"K."},{"last_name":"Meseguer","first_name":"A.","full_name":"Meseguer, A."}],"department":[{"_id":"BjHo"}],"day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Mean structure of the supercritical turbulent spiral in Taylor–Couette flow","volume":381,"article_number":"0112","status":"public","scopus_import":"1","date_published":"2023-05-01T00:00:00Z","month":"05","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"The Royal Society","date_updated":"2024-01-09T09:15:29Z"},{"year":"2023","publication_identifier":{"eissn":["1875-8576"],"issn":["0921-7134"]},"language":[{"iso":"eng"}],"intvolume":"       131","arxiv":1,"quality_controlled":"1","citation":{"ama":"Moser M. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. <i>Asymptotic Analysis</i>. 2023;131(3-4):297-383. doi:<a href=\"https://doi.org/10.3233/asy-221775\">10.3233/asy-221775</a>","mla":"Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” <i>Asymptotic Analysis</i>, vol. 131, no. 3–4, IOS Press, 2023, pp. 297–383, doi:<a href=\"https://doi.org/10.3233/asy-221775\">10.3233/asy-221775</a>.","ista":"Moser M. 2023. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 131(3–4), 297–383.","ieee":"M. Moser, “Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result,” <i>Asymptotic Analysis</i>, vol. 131, no. 3–4. IOS Press, pp. 297–383, 2023.","short":"M. Moser, Asymptotic Analysis 131 (2023) 297–383.","chicago":"Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” <i>Asymptotic Analysis</i>. IOS Press, 2023. <a href=\"https://doi.org/10.3233/asy-221775\">https://doi.org/10.3233/asy-221775</a>.","apa":"Moser, M. (2023). Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. <i>Asymptotic Analysis</i>. IOS Press. <a href=\"https://doi.org/10.3233/asy-221775\">https://doi.org/10.3233/asy-221775</a>"},"doi":"10.3233/asy-221775","acknowledgement":"The author gratefully acknowledges support through DFG, GRK 1692 “Curvature,\r\nCycles and Cohomology” during parts of the work.","abstract":[{"lang":"eng","text":"We consider the sharp interface limit for the scalar-valued and vector-valued Allen–Cahn equation with homogeneous Neumann boundary condition in a bounded smooth domain Ω of arbitrary dimension N ⩾ 2 in the situation when a two-phase diffuse interface has developed and intersects the boundary ∂ Ω. The limit problem is mean curvature flow with 90°-contact angle and we show convergence in strong norms for well-prepared initial data as long as a smooth solution to the limit problem exists. To this end we assume that the limit problem has a smooth solution on [ 0 , T ] for some time T &gt; 0. Based on the latter we construct suitable curvilinear coordinates and set up an asymptotic expansion for the scalar-valued and the vector-valued Allen–Cahn equation. In order to estimate the difference of the exact and approximate solutions with a Gronwall-type argument, a spectral estimate for the linearized Allen–Cahn operator in both cases is required. The latter will be shown in a separate paper, cf. (Moser (2021))."}],"keyword":["General Mathematics"],"oa":1,"page":"297-383","external_id":{"arxiv":["2105.07100"]},"day":"02","volume":131,"title":"Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result","status":"public","date_created":"2024-01-08T13:13:28Z","oa_version":"Preprint","publication":"Asymptotic Analysis","_id":"14755","issue":"3-4","type":"journal_article","article_processing_charge":"No","author":[{"full_name":"Moser, Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","first_name":"Maximilian","last_name":"Moser"}],"department":[{"_id":"JuFi"}],"article_type":"original","date_published":"2023-02-02T00:00:00Z","month":"02","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-09T09:22:16Z","publisher":"IOS Press","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.07100","open_access":"1"}],"scopus_import":"1"},{"publisher":"European Mathematical Society","date_updated":"2024-01-09T09:27:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"10","date_published":"2023-10-16T00:00:00Z","article_type":"original","scopus_import":"1","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Fully extended r-spin TQFTs","volume":14,"day":"16","department":[{"_id":"MiLe"}],"author":[{"last_name":"Carqueville","first_name":"Nils","full_name":"Carqueville, Nils"},{"first_name":"Lorant","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","last_name":"Szegedy","orcid":"0000-0003-2834-5054","full_name":"Szegedy, Lorant"}],"_id":"14756","article_processing_charge":"Yes","issue":"3","type":"journal_article","publication":"Quantum Topology","file_date_updated":"2024-01-09T09:25:34Z","oa_version":"Published Version","date_created":"2024-01-08T13:14:48Z","file":[{"file_size":707344,"checksum":"b0590aff6e7ec89cc149ba94d459d3a3","creator":"dernst","date_updated":"2024-01-09T09:25:34Z","file_id":"14764","date_created":"2024-01-09T09:25:34Z","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2023_QuantumTopol_Carqueville.pdf","relation":"main_file"}],"ddc":["530"],"oa":1,"keyword":["Geometry and Topology","Mathematical Physics"],"abstract":[{"lang":"eng","text":"We prove the r-spin cobordism hypothesis in the setting of (weak) 2-categories for every positive integer r: the 2-groupoid of 2-dimensional fully extended r-spin TQFTs with given target is equivalent to the homotopy fixed points of an induced Spin 2r -action. In particular, such TQFTs are classified by fully dualisable objects together with a trivialisation of the rth power of their Serre automorphisms. For r=1, we recover the oriented case (on which our proof builds), while ordinary spin structures correspond to r=2.\r\nTo construct examples, we explicitly describe Spin 2r​-homotopy fixed points in the equivariant completion of any symmetric monoidal 2-category. We also show that every object in a 2-category of Landau–Ginzburg models gives rise to fully extended spin TQFTs and that half of these do not factor through the oriented bordism 2-category."}],"page":"467-532","intvolume":"        14","has_accepted_license":"1","publication_identifier":{"issn":["1663-487X"]},"language":[{"iso":"eng"}],"year":"2023","acknowledgement":"N.C. is supported by the DFG Heisenberg Programme.\r\nWe are grateful to Tobias Dyckerhoff, Lukas Müller, Ingo Runkel, and Christopher Schommer-Pries for helpful discussions.","citation":{"ama":"Carqueville N, Szegedy L. Fully extended r-spin TQFTs. <i>Quantum Topology</i>. 2023;14(3):467-532. doi:<a href=\"https://doi.org/10.4171/qt/193\">10.4171/qt/193</a>","apa":"Carqueville, N., &#38; Szegedy, L. (2023). Fully extended r-spin TQFTs. <i>Quantum Topology</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/qt/193\">https://doi.org/10.4171/qt/193</a>","chicago":"Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” <i>Quantum Topology</i>. European Mathematical Society, 2023. <a href=\"https://doi.org/10.4171/qt/193\">https://doi.org/10.4171/qt/193</a>.","short":"N. Carqueville, L. Szegedy, Quantum Topology 14 (2023) 467–532.","ieee":"N. Carqueville and L. Szegedy, “Fully extended r-spin TQFTs,” <i>Quantum Topology</i>, vol. 14, no. 3. European Mathematical Society, pp. 467–532, 2023.","ista":"Carqueville N, Szegedy L. 2023. Fully extended r-spin TQFTs. Quantum Topology. 14(3), 467–532.","mla":"Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” <i>Quantum Topology</i>, vol. 14, no. 3, European Mathematical Society, 2023, pp. 467–532, doi:<a href=\"https://doi.org/10.4171/qt/193\">10.4171/qt/193</a>."},"doi":"10.4171/qt/193","quality_controlled":"1"},{"scopus_import":"1","date_published":"2023-07-16T00:00:00Z","month":"07","date_updated":"2024-02-27T07:39:51Z","publisher":"Springer Nature","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-09T10:01:07Z","publication":"35th International Conference on Computer Aided Verification","article_processing_charge":"Yes (in subscription journal)","_id":"14758","type":"conference","date_created":"2024-01-08T13:18:00Z","oa_version":"Published Version","project":[{"grant_number":"101020093","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software"}],"department":[{"_id":"ToHe"}],"author":[{"full_name":"Majumdar, Rupak","last_name":"Majumdar","first_name":"Rupak"},{"full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475","last_name":"Mallik","first_name":"Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"},{"full_name":"Rychlicki, Mateusz","last_name":"Rychlicki","first_name":"Mateusz"},{"first_name":"Anne-Kathrin","last_name":"Schmuck","full_name":"Schmuck, Anne-Kathrin"},{"full_name":"Soudjani, Sadegh","last_name":"Soudjani","first_name":"Sadegh"}],"day":"16","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties","volume":13966,"alternative_title":["LNCS"],"page":"3-15","file":[{"date_created":"2024-01-09T10:01:07Z","access_level":"open_access","file_id":"14765","file_name":"2023_LNCSCAV_Majumdar.pdf","relation":"main_file","success":1,"content_type":"application/pdf","creator":"dernst","checksum":"1a361d83db0244fd32c03b544c294b5a","file_size":405147,"date_updated":"2024-01-09T10:01:07Z"}],"abstract":[{"text":"We present a flexible and efficient toolchain to symbolically solve (standard) Rabin games, fair-adversarial Rabin games, and 2 1/2 license type-player Rabin games. To our best knowledge, our tools are the first ones to be able to solve these problems. Furthermore, using these flexible game solvers as a back-end, we implemented a tool for computing correct-by-construction controllers for stochastic dynamical systems under LTL specifications. Our implementations use the recent theoretical result that all of these games can be solved using the same symbolic fixpoint algorithm but utilizing different, domain specific calculations of the involved predecessor operators. The main feature of our toolchain is the utilization of two programming abstractions: one to separate the symbolic fixpoint computations from the predecessor calculations, and another one to allow the integration of different BDD libraries as back-ends. In particular, we employ a multi-threaded execution of the fixpoint algorithm by using the multi-threaded BDD library Sylvan, which leads to enormous computational savings.","lang":"eng"}],"ddc":["000"],"oa":1,"ec_funded":1,"quality_controlled":"1","citation":{"short":"R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, in:, 35th International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 3–15.","chicago":"Majumdar, Rupak, Kaushik Mallik, Mateusz Rychlicki, Anne-Kathrin Schmuck, and Sadegh Soudjani. “A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties.” In <i>35th International Conference on Computer Aided Verification</i>, 13966:3–15. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_1\">https://doi.org/10.1007/978-3-031-37709-9_1</a>.","apa":"Majumdar, R., Mallik, K., Rychlicki, M., Schmuck, A.-K., &#38; Soudjani, S. (2023). A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. In <i>35th International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 3–15). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_1\">https://doi.org/10.1007/978-3-031-37709-9_1</a>","mla":"Majumdar, Rupak, et al. “A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties.” <i>35th International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 3–15, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_1\">10.1007/978-3-031-37709-9_1</a>.","ista":"Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. 2023. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. 35th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 3–15.","ieee":"R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, and S. Soudjani, “A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties,” in <i>35th International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 3–15.","ama":"Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. In: <i>35th International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:3-15. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_1\">10.1007/978-3-031-37709-9_1</a>"},"doi":"10.1007/978-3-031-37709-9_1","acknowledgement":"Authors ordered alphabetically. R. Majumdar and A.-K. Schmuck are partially supported by DFG project 389792660 TRR 248-CPEC. A.-K. Schmuck is additionally funded through DFG project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093. M. Rychlicki is supported by the EPSRC project EP/V00252X/1. S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802, and ERC 101089047.","conference":{"end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France","name":"CAV: Computer Aided Verification"},"related_material":{"record":[{"id":"14994","status":"public","relation":"research_data"}]},"publication_identifier":{"eisbn":["9783031377099"],"isbn":["9783031377082"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"year":"2023","intvolume":"     13966","has_accepted_license":"1"},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.11591","open_access":"1"}],"scopus_import":"1","month":"01","date_published":"2023-01-01T00:00:00Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Optica Publishing Group","date_updated":"2024-01-09T10:10:34Z","oa_version":"Preprint","date_created":"2024-01-08T13:19:14Z","article_processing_charge":"No","_id":"14759","type":"journal_article","issue":"1","publication":"Applied Optics","author":[{"orcid":"0000-0002-5869-1604","full_name":"Wald, Sebastian","id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","last_name":"Wald"},{"orcid":"0000-0002-4947-8924","full_name":"Diorico, Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","first_name":"Fritz R","last_name":"Diorico"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur"}],"department":[{"_id":"OnHo"}],"day":"01","volume":62,"title":"Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone","status":"public","page":"1-7","external_id":{"arxiv":["2208.11591"]},"oa":1,"keyword":["Atomic and Molecular Physics","and Optics","Engineering (miscellaneous)","Electrical and Electronic Engineering"],"abstract":[{"lang":"eng","text":"Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method."}],"citation":{"chicago":"Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” <i>Applied Optics</i>. Optica Publishing Group, 2023. <a href=\"https://doi.org/10.1364/ao.474118\">https://doi.org/10.1364/ao.474118</a>.","short":"S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7.","apa":"Wald, S., Diorico, F. R., &#38; Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. <i>Applied Optics</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/ao.474118\">https://doi.org/10.1364/ao.474118</a>","mla":"Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” <i>Applied Optics</i>, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:<a href=\"https://doi.org/10.1364/ao.474118\">10.1364/ao.474118</a>.","ieee":"S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” <i>Applied Optics</i>, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023.","ista":"Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7.","ama":"Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. <i>Applied Optics</i>. 2023;62(1):1-7. doi:<a href=\"https://doi.org/10.1364/ao.474118\">10.1364/ao.474118</a>"},"doi":"10.1364/ao.474118","quality_controlled":"1","acknowledgement":"We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript.","year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2155-3165"],"issn":["1559-128X"]},"arxiv":1,"intvolume":"        62"},{"day":"22","status":"public","title":"Deterministic clustering in high dimensional spaces: Sketches and approximation","article_processing_charge":"No","_id":"14768","type":"conference","publication":"2023 IEEE 64th Annual Symposium on Foundations of Computer Science","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564"}],"date_created":"2024-01-09T16:20:09Z","oa_version":"Preprint","department":[{"_id":"MoHe"}],"author":[{"full_name":"Cohen-Addad, Vincent","first_name":"Vincent","last_name":"Cohen-Addad"},{"full_name":"Saulpic, David","last_name":"Saulpic","first_name":"David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964"},{"full_name":"Schwiegelshohn, Chris","last_name":"Schwiegelshohn","first_name":"Chris"}],"month":"12","date_published":"2023-12-22T00:00:00Z","publisher":"IEEE","date_updated":"2024-01-16T07:28:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.04076"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9798350318944"]},"year":"2023","arxiv":1,"doi":"10.1109/focs57990.2023.00066","citation":{"ama":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. Deterministic clustering in high dimensional spaces: Sketches and approximation. In: <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i>. IEEE; 2023:1105-1130. doi:<a href=\"https://doi.org/10.1109/focs57990.2023.00066\">10.1109/focs57990.2023.00066</a>","mla":"Cohen-Addad, Vincent, et al. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i>, IEEE, 2023, pp. 1105–30, doi:<a href=\"https://doi.org/10.1109/focs57990.2023.00066\">10.1109/focs57990.2023.00066</a>.","ista":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. 2023. Deterministic clustering in high dimensional spaces: Sketches and approximation. 2023 IEEE 64th Annual Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science, 1105–1130.","ieee":"V. Cohen-Addad, D. Saulpic, and C. Schwiegelshohn, “Deterministic clustering in high dimensional spaces: Sketches and approximation,” in <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i>, Santa Cruz, CA, United States, 2023, pp. 1105–1130.","chicago":"Cohen-Addad, Vincent, David Saulpic, and Chris Schwiegelshohn. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” In <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i>, 1105–30. IEEE, 2023. <a href=\"https://doi.org/10.1109/focs57990.2023.00066\">https://doi.org/10.1109/focs57990.2023.00066</a>.","short":"V. Cohen-Addad, D. Saulpic, C. Schwiegelshohn, in:, 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–1130.","apa":"Cohen-Addad, V., Saulpic, D., &#38; Schwiegelshohn, C. (2023). Deterministic clustering in high dimensional spaces: Sketches and approximation. In <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i> (pp. 1105–1130). Santa Cruz, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/focs57990.2023.00066\">https://doi.org/10.1109/focs57990.2023.00066</a>"},"quality_controlled":"1","ec_funded":1,"conference":{"location":"Santa Cruz, CA, United States","start_date":"2023-11-06","end_date":"2023-11-09","name":"FOCS: Symposium on Foundations of Computer Science"},"acknowledgement":"D. Sauplic has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413, and Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)”.\r\nC. Schwiegelshohn acknowledges the support of the Independent Research Fund Denmark (DFF) under a Sapere Aude Research Leader grant No 1051-00106B.","oa":1,"abstract":[{"text":"In all state-of-the-art sketching and coreset techniques for clustering, as well as in the best known fixed-parameter tractable approximation algorithms, randomness plays a key role. For the classic k-median and k-means problems, there are no known deterministic dimensionality reduction procedure or coreset construction that avoid an exponential dependency on the input dimension d, the precision parameter $\\varepsilon^{-1}$ or k. Furthermore, there is no coreset construction that succeeds with probability $1-1/n$ and whose size does not depend on the number of input points, n. This has led researchers in the area to ask what is the power of randomness for clustering sketches [Feldman WIREs Data Mining Knowl. Discov’20].Similarly, the best approximation ratio achievable deterministically without a complexity exponential in the dimension are $1+\\sqrt{2}$ for k-median [Cohen-Addad, Esfandiari, Mirrokni, Narayanan, STOC’22] and 6.12903 for k-means [Grandoni, Ostrovsky, Rabani, Schulman, Venkat, Inf. Process. Lett.’22]. Those are the best results, even when allowing a complexity FPT in the number of clusters k: this stands in sharp contrast with the $(1+\\varepsilon)$-approximation achievable in that case, when allowing randomization.In this paper, we provide deterministic sketches constructions for clustering, whose size bounds are close to the best-known randomized ones. We show how to compute a dimension reduction onto $\\varepsilon^{-O(1)} \\log k$ dimensions in time $k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$, and how to build a coreset of size $O\\left(k^{2} \\log ^{3} k \\varepsilon^{-O(1)}\\right)$ in time $2^{\\varepsilon^{O(1)} k \\log ^{3} k}+k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$. In the case where k is small, this answers an open question of [Feldman WIDM’20] and [Munteanu and Schwiegelshohn, Künstliche Intell. ’18] on whether it is possible to efficiently compute coresets deterministically.We also construct a deterministic algorithm for computing $(1+$ $\\varepsilon)$-approximation to k-median and k-means in high dimensional Euclidean spaces in time $2^{k^{2} \\log ^{3} k / \\varepsilon^{O(1)}}$ poly $(n d)$, close to the best randomized complexity of $2^{(k / \\varepsilon)^{O(1)}}$ nd (see [Kumar, Sabharwal, Sen, JACM 10] and [Bhattacharya, Jaiswal, Kumar, TCS’18]).Furthermore, our new insights on sketches also yield a randomized coreset construction that uses uniform sampling, that immediately improves over the recent results of [Braverman et al. FOCS ’22] by a factor k.","lang":"eng"}],"external_id":{"arxiv":["2310.04076"]},"page":"1105-1130"},{"external_id":{"arxiv":["2304.12622"],"isi":["001062531308068"]},"isi":1,"page":"24364-24373","oa":1,"abstract":[{"text":"Pruning—that is, setting a significant subset of the parameters of a neural network to zero—is one of the most popular methods of model compression. Yet, several recent works have raised the issue that pruning may induce or exacerbate bias in the output of the compressed model. Despite existing evidence for this phenomenon, the relationship between neural network pruning and induced bias is not well-understood. In this work, we systematically investigate and characterize this phenomenon in Convolutional Neural Networks for computer vision. First, we show that it is in fact possible to obtain highly-sparse models, e.g. with less than 10% remaining weights, which do not decrease in accuracy nor substantially increase in bias when compared to dense models. At the same time, we also find that, at higher sparsities, pruned models exhibit higher uncertainty in their outputs, as well as increased correlations, which we directly link to increased bias. We propose easy-to-use criteria which, based only on the uncompressed model, establish whether bias will increase with pruning, and identify the samples most susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias.","lang":"eng"}],"doi":"10.1109/cvpr52729.2023.02334","citation":{"mla":"Iofinova, Eugenia B., et al. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2023, pp. 24364–73, doi:<a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">10.1109/cvpr52729.2023.02334</a>.","ieee":"E. B. Iofinova, E.-A. Peste, and D.-A. Alistarh, “Bias in pruned vision models: In-depth analysis and countermeasures,” in <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Vancouver, BC, Canada, 2023, pp. 24364–24373.","ista":"Iofinova EB, Peste E-A, Alistarh D-A. 2023. Bias in pruned vision models: In-depth analysis and countermeasures. 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24364–24373.","chicago":"Iofinova, Eugenia B, Elena-Alexandra Peste, and Dan-Adrian Alistarh. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” In <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 24364–73. IEEE, 2023. <a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">https://doi.org/10.1109/cvpr52729.2023.02334</a>.","short":"E.B. Iofinova, E.-A. Peste, D.-A. Alistarh, in:, 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–24373.","apa":"Iofinova, E. B., Peste, E.-A., &#38; Alistarh, D.-A. (2023). Bias in pruned vision models: In-depth analysis and countermeasures. In <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 24364–24373). Vancouver, BC, Canada: IEEE. <a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">https://doi.org/10.1109/cvpr52729.2023.02334</a>","ama":"Iofinova EB, Peste E-A, Alistarh D-A. Bias in pruned vision models: In-depth analysis and countermeasures. In: <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2023:24364-24373. doi:<a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">10.1109/cvpr52729.2023.02334</a>"},"ec_funded":1,"quality_controlled":"1","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2023-06-24","start_date":"2023-06-17","location":"Vancouver, BC, Canada"},"acknowledgement":"The authors would like to sincerely thank Sara Hooker for her feedback during the development of this work. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. AP and DA acknowledge generous ERC support, via Starting Grant 805223 ScaleML.","related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/pruned-vision-model-bias"}]},"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9798350301298"],"eissn":["2575-7075"]},"year":"2023","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.12622"}],"month":"08","date_published":"2023-08-22T00:00:00Z","publisher":"IEEE","date_updated":"2024-01-10T08:59:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","_id":"14771","type":"conference","article_processing_charge":"No","publication":"2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition","project":[{"_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","name":"Vienna Graduate School on Computational Optimization","grant_number":" W1260-N35"},{"name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020"}],"oa_version":"Preprint","date_created":"2024-01-10T08:42:40Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"author":[{"first_name":"Eugenia B","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","last_name":"Iofinova","orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B"},{"last_name":"Peste","first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"}],"day":"22","status":"public","title":"Bias in pruned vision models: In-depth analysis and countermeasures"},{"article_number":"110146","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Maximal Lp-regularity and H∞-calculus for block operator matrices and applications","volume":285,"day":"01","department":[{"_id":"JuFi"}],"author":[{"orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio","last_name":"Agresti","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio"},{"last_name":"Hussein","first_name":"Amru","full_name":"Hussein, Amru"}],"_id":"14772","issue":"11","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-01-10T11:23:57Z","publication":"Journal of Functional Analysis","oa_version":"Published Version","date_created":"2024-01-10T09:15:18Z","publisher":"Elsevier","date_updated":"2024-01-10T11:24:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2023-12-01T00:00:00Z","month":"12","article_type":"original","scopus_import":"1","arxiv":1,"intvolume":"       285","has_accepted_license":"1","publication_identifier":{"issn":["0022-1236"]},"language":[{"iso":"eng"}],"year":"2023","acknowledgement":"We would like to thank Tim Binz, Emiel Lorist and Mark Veraar for valuable discussions. We also thank the anonymous referees for their helpful comments and suggestions, and for the very accurate reading of the manuscript.\r\nThe first author has been supported partially by the Nachwuchsring – Network for the promotion of young scientists – at TU Kaiserslautern. Both authors have been supported by MathApp – Mathematics Applied to Real-World Problems - part of the Research Initiative of the Federal State of Rhineland-Palatinate, Germany.","citation":{"short":"A. Agresti, A. Hussein, Journal of Functional Analysis 285 (2023).","chicago":"Agresti, Antonio, and Amru Hussein. “Maximal Lp-Regularity and H∞-Calculus for Block Operator Matrices and Applications.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.110146\">https://doi.org/10.1016/j.jfa.2023.110146</a>.","apa":"Agresti, A., &#38; Hussein, A. (2023). Maximal Lp-regularity and H∞-calculus for block operator matrices and applications. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.110146\">https://doi.org/10.1016/j.jfa.2023.110146</a>","mla":"Agresti, Antonio, and Amru Hussein. “Maximal Lp-Regularity and H∞-Calculus for Block Operator Matrices and Applications.” <i>Journal of Functional Analysis</i>, vol. 285, no. 11, 110146, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110146\">10.1016/j.jfa.2023.110146</a>.","ieee":"A. Agresti and A. Hussein, “Maximal Lp-regularity and H∞-calculus for block operator matrices and applications,” <i>Journal of Functional Analysis</i>, vol. 285, no. 11. Elsevier, 2023.","ista":"Agresti A, Hussein A. 2023. Maximal Lp-regularity and H∞-calculus for block operator matrices and applications. Journal of Functional Analysis. 285(11), 110146.","ama":"Agresti A, Hussein A. Maximal Lp-regularity and H∞-calculus for block operator matrices and applications. <i>Journal of Functional Analysis</i>. 2023;285(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110146\">10.1016/j.jfa.2023.110146</a>"},"doi":"10.1016/j.jfa.2023.110146","quality_controlled":"1","file":[{"relation":"main_file","file_name":"2023_JourFunctionalAnalysis_Agresti.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2024-01-10T11:23:57Z","file_id":"14789","date_updated":"2024-01-10T11:23:57Z","creator":"dernst","file_size":1120592,"checksum":"eda98ca2aa73da91bd074baed34c2b3c"}],"oa":1,"ddc":["510"],"keyword":["Analysis"],"abstract":[{"text":"Many coupled evolution equations can be described via 2×2-block operator matrices of the form A=[ \r\nA\tB\r\nC\tD\r\n ] in a product space X=X1×X2 with possibly unbounded entries. Here, the case of diagonally dominant block operator matrices is considered, that is, the case where the full operator A can be seen as a relatively bounded perturbation of its diagonal part with D(A)=D(A)×D(D) though with possibly large relative bound. For such operators the properties of sectoriality, R-sectoriality and the boundedness of the H∞-calculus are studied, and for these properties perturbation results for possibly large but structured perturbations are derived. Thereby, the time dependent parabolic problem associated with A can be analyzed in maximal Lpt\r\n-regularity spaces, and this is applied to a wide range of problems such as different theories for liquid crystals, an artificial Stokes system, strongly damped wave and plate equations, and a Keller-Segel model.","lang":"eng"}],"external_id":{"isi":["001081809000001"],"arxiv":["2108.01962"]},"isi":1},{"oa":1,"abstract":[{"text":"Through a combination of idealized simulations and real-world data, researchers are uncovering how internal feedbacks and large-scale motions influence cloud dynamics.","lang":"eng"}],"keyword":["General Physics and Astronomy"],"isi":1,"external_id":{"isi":["000984516100007"]},"intvolume":"        76","year":"2023","publication_identifier":{"issn":["0031-9228"],"eissn":["1945-0699"]},"language":[{"iso":"eng"}],"citation":{"ama":"Muller CJ, Abramian S. The cloud dynamics of convective storm systems. <i>Physics Today</i>. 2023;76(5). doi:<a href=\"https://doi.org/10.1063/pt.3.5234\">10.1063/pt.3.5234</a>","mla":"Muller, Caroline J., and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” <i>Physics Today</i>, vol. 76, no. 5, 28, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/pt.3.5234\">10.1063/pt.3.5234</a>.","ista":"Muller CJ, Abramian S. 2023. The cloud dynamics of convective storm systems. Physics Today. 76(5), 28.","ieee":"C. J. Muller and S. Abramian, “The cloud dynamics of convective storm systems,” <i>Physics Today</i>, vol. 76, no. 5. AIP Publishing, 2023.","short":"C.J. Muller, S. Abramian, Physics Today 76 (2023).","chicago":"Muller, Caroline J, and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” <i>Physics Today</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/pt.3.5234\">https://doi.org/10.1063/pt.3.5234</a>.","apa":"Muller, C. J., &#38; Abramian, S. (2023). The cloud dynamics of convective storm systems. <i>Physics Today</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/pt.3.5234\">https://doi.org/10.1063/pt.3.5234</a>"},"doi":"10.1063/pt.3.5234","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"AIP Publishing","date_updated":"2024-01-10T12:38:02Z","date_published":"2023-05-01T00:00:00Z","month":"05","article_type":"original","main_file_link":[{"open_access":"1","url":"https://www.lmd.ens.fr/muller/Pubs/2023-MullerAbramianPhysToday.pdf"}],"volume":76,"title":"The cloud dynamics of convective storm systems","article_number":"28","status":"public","day":"01","author":[{"full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller"},{"last_name":"Abramian","first_name":"Sophie","full_name":"Abramian, Sophie"}],"department":[{"_id":"CaMu"}],"date_created":"2024-01-10T09:18:04Z","oa_version":"Published Version","type":"journal_article","_id":"14773","issue":"5","article_processing_charge":"No","publication":"Physics Today"},{"abstract":[{"lang":"eng","text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential."}],"keyword":["Developmental Biology","Molecular Biology"],"ddc":["570"],"oa":1,"file":[{"success":1,"content_type":"application/pdf","relation":"main_file","file_name":"2023_Development_Harish.pdf","file_id":"14790","date_created":"2024-01-10T12:41:13Z","access_level":"open_access","date_updated":"2024-01-10T12:41:13Z","file_size":12836306,"checksum":"2d6f52dc33260a9b2352b8f28374ba5f","creator":"dernst"}],"isi":1,"external_id":{"pmid":["37665167"],"isi":["001097449100002"]},"year":"2023","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"       150","pmid":1,"quality_controlled":"1","citation":{"ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. 2023;150(19). doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>","mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>, vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>.","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.","ieee":"R. K. Harish <i>et al.</i>, “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” <i>Development</i>, vol. 150, no. 19. The Company of Biologists, 2023.","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>.","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>"},"doi":"10.1242/dev.201559","acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","article_type":"original","month":"10","date_published":"2023-10-01T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-10T12:45:25Z","publisher":"The Company of Biologists","day":"01","volume":150,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","status":"public","article_number":"dev201559","date_created":"2024-01-10T09:18:54Z","oa_version":"Published Version","publication":"Development","file_date_updated":"2024-01-10T12:41:13Z","type":"journal_article","_id":"14774","article_processing_charge":"Yes (via OA deal)","issue":"19","author":[{"full_name":"Harish, Rohit K","last_name":"Harish","first_name":"Rohit K","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d"},{"first_name":"Mansi","last_name":"Gupta","full_name":"Gupta, Mansi"},{"full_name":"Zöller, Daniela","first_name":"Daniela","last_name":"Zöller"},{"last_name":"Hartmann","first_name":"Hella","full_name":"Hartmann, Hella"},{"full_name":"Gheisari, Ali","last_name":"Gheisari","first_name":"Ali"},{"full_name":"Machate, Anja","first_name":"Anja","last_name":"Machate"},{"first_name":"Stefan","last_name":"Hans","full_name":"Hans, Stefan"},{"full_name":"Brand, Michael","last_name":"Brand","first_name":"Michael"}],"department":[{"_id":"AnKi"}]},{"date_updated":"2024-01-10T13:31:46Z","publisher":"Institute of Mathematical Statistics","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","month":"02","date_published":"2023-02-01T00:00:00Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2108.02728"}],"status":"public","volume":33,"title":"Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices","day":"01","department":[{"_id":"LaEr"}],"author":[{"full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin"},{"orcid":"0000-0003-1559-1205","full_name":"Xu, Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","first_name":"Yuanyuan","last_name":"Xu"}],"publication":"The Annals of Applied Probability","_id":"14775","issue":"1","type":"journal_article","article_processing_charge":"No","oa_version":"Preprint","date_created":"2024-01-10T09:23:31Z","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","call_identifier":"H2020"}],"keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"abstract":[{"lang":"eng","text":"We establish a quantitative version of the Tracy–Widom law for the largest eigenvalue of high-dimensional sample covariance matrices. To be precise, we show that the fluctuations of the largest eigenvalue of a sample covariance matrix X∗X converge to its Tracy–Widom limit at a rate nearly N−1/3, where X is an M×N random matrix whose entries are independent real or complex random variables, assuming that both M and N tend to infinity at a constant rate. This result improves the previous estimate N−2/9 obtained by Wang (2019). Our proof relies on a Green function comparison method (Adv. Math. 229 (2012) 1435–1515) using iterative cumulant expansions, the local laws for the Green function and asymptotic properties of the correlation kernel of the white Wishart ensemble."}],"oa":1,"external_id":{"isi":["000946432400021"],"arxiv":["2108.02728"]},"page":"677-725","isi":1,"arxiv":1,"intvolume":"        33","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1050-5164"]},"year":"2023","acknowledgement":"K. Schnelli was supported by the Swedish Research Council Grants VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Y. Xu was supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced Grant “RMTBeyond” No. 101020331.","quality_controlled":"1","ec_funded":1,"doi":"10.1214/22-aap1826","citation":{"mla":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” <i>The Annals of Applied Probability</i>, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 677–725, doi:<a href=\"https://doi.org/10.1214/22-aap1826\">10.1214/22-aap1826</a>.","ieee":"K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices,” <i>The Annals of Applied Probability</i>, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 677–725, 2023.","ista":"Schnelli K, Xu Y. 2023. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. 33(1), 677–725.","short":"K. Schnelli, Y. Xu, The Annals of Applied Probability 33 (2023) 677–725.","chicago":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/22-aap1826\">https://doi.org/10.1214/22-aap1826</a>.","apa":"Schnelli, K., &#38; Xu, Y. (2023). Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/22-aap1826\">https://doi.org/10.1214/22-aap1826</a>","ama":"Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. <i>The Annals of Applied Probability</i>. 2023;33(1):677-725. doi:<a href=\"https://doi.org/10.1214/22-aap1826\">10.1214/22-aap1826</a>"}},{"citation":{"ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. 2023;24(22). doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., &#38; Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023).","chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>.","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","ieee":"A. Teplova <i>et al.</i>, “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22. MDPI, 2023.","mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22, 16527, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>."},"doi":"10.3390/ijms242216527","quality_controlled":"1","acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","year":"2023","publication_identifier":{"issn":["1422-0067"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","pmid":1,"intvolume":"        24","isi":1,"external_id":{"pmid":["38003717"],"isi":["001113792600001"]},"ddc":["580"],"oa":1,"abstract":[{"lang":"eng","text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident."}],"keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"file":[{"creator":"dernst","file_size":2637784,"checksum":"4df7d206ba022b7f54eff1f0aec1659a","date_updated":"2024-01-10T13:39:42Z","date_created":"2024-01-10T13:39:42Z","access_level":"open_access","file_id":"14791","file_name":"2023_IJMS_Teplova.pdf","relation":"main_file","content_type":"application/pdf","success":1}],"oa_version":"Published Version","date_created":"2024-01-10T09:24:35Z","_id":"14776","article_processing_charge":"Yes","type":"journal_article","issue":"22","file_date_updated":"2024-01-10T13:39:42Z","publication":"International Journal of Molecular Sciences","author":[{"full_name":"Teplova, Anastasiia","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6","last_name":"Teplova"},{"first_name":"Artemii A.","last_name":"Pigidanov","full_name":"Pigidanov, Artemii A."},{"last_name":"Serebryakova","first_name":"Marina V.","full_name":"Serebryakova, Marina V."},{"first_name":"Sergei A.","last_name":"Golyshev","full_name":"Golyshev, Sergei A."},{"last_name":"Galiullina","first_name":"Raisa A.","full_name":"Galiullina, Raisa A."},{"last_name":"Chichkova","first_name":"Nina V.","full_name":"Chichkova, Nina V."},{"full_name":"Vartapetian, Andrey B.","last_name":"Vartapetian","first_name":"Andrey B."}],"department":[{"_id":"JiFr"}],"day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","volume":24,"article_number":"16527","status":"public","month":"11","date_published":"2023-11-01T00:00:00Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"MDPI","date_updated":"2024-01-10T13:41:10Z"},{"publisher":"AIP Publishing","date_updated":"2024-01-10T13:49:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2023-12-01T00:00:00Z","month":"12","article_type":"original","department":[{"_id":"MaIb"}],"author":[{"full_name":"Sato, Kosuke","last_name":"Sato","first_name":"Kosuke"},{"last_name":"Singh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","first_name":"Saurabh","full_name":"Singh, Saurabh","orcid":"0000-0003-2209-5269"},{"full_name":"Yamazaki, Itsuki","first_name":"Itsuki","last_name":"Yamazaki"},{"full_name":"Hirata, Keisuke","last_name":"Hirata","first_name":"Keisuke"},{"first_name":"Artoni Kevin R.","last_name":"Ang","full_name":"Ang, Artoni Kevin R."},{"last_name":"Matsunami","first_name":"Masaharu","full_name":"Matsunami, Masaharu"},{"last_name":"Takeuchi","first_name":"Tsunehiro","full_name":"Takeuchi, Tsunehiro"}],"_id":"14777","article_processing_charge":"Yes","issue":"12","type":"journal_article","publication":"AIP Advances","file_date_updated":"2024-01-10T13:47:31Z","date_created":"2024-01-10T09:26:08Z","oa_version":"Published Version","article_number":"125206","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":13,"title":"Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag","day":"01","external_id":{"isi":["001114917200005"]},"isi":1,"file":[{"date_updated":"2024-01-10T13:47:31Z","creator":"dernst","file_size":9676071,"checksum":"a7098388b8ff822b47f5ddd37ed3bdbc","file_name":"2023_AIPAdvances_Sato.pdf","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2024-01-10T13:47:31Z","file_id":"14792"}],"ddc":["540"],"oa":1,"abstract":[{"lang":"eng","text":"The effects of the partial V-substitution for Ag on the thermoelectric (TE) properties are investigated for a flexible semiconducting compound Ag2S0.55Se0.45. Density functional theory calculations predict that such a partial V-substitution constructively modifies the electronic structure near the bottom of the conduction band to improve the TE performance. The synthesized Ag1.97V0.03S0.55Se0.45 is found to possess a TE dimensionless figure-of-merit (ZT) of 0.71 at 350 K with maintaining its flexible nature. This ZT value is relatively high in comparison with those reported for flexible TE materials below 360 K. The increase in the ZT value is caused by the enhanced absolute value of the Seebeck coefficient with less significant variation in electrical resistivity. The high ZT value with the flexible nature naturally allows us to employ the Ag1.97V0.03S0.55Se0.45 as a component of flexible TE generators."}],"keyword":["General Physics and Astronomy"],"acknowledgement":"This work received financial support partially from Japan Science and Technology Agency (JST) CREST Grant No. JPMJCR18I2, Japan. The powder-XRD experiments were conducted at BL5S2 of Aichi Synchrotron Radiation Center, Aichi Science & Technology Foundation, Aichi, Japan (Proposal No. 202301057).","citation":{"short":"K. Sato, S. Singh, I. Yamazaki, K. Hirata, A.K.R. Ang, M. Matsunami, T. Takeuchi, AIP Advances 13 (2023).","chicago":"Sato, Kosuke, Saurabh Singh, Itsuki Yamazaki, Keisuke Hirata, Artoni Kevin R. Ang, Masaharu Matsunami, and Tsunehiro Takeuchi. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” <i>AIP Advances</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0171888\">https://doi.org/10.1063/5.0171888</a>.","apa":"Sato, K., Singh, S., Yamazaki, I., Hirata, K., Ang, A. K. R., Matsunami, M., &#38; Takeuchi, T. (2023). Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. <i>AIP Advances</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0171888\">https://doi.org/10.1063/5.0171888</a>","mla":"Sato, Kosuke, et al. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” <i>AIP Advances</i>, vol. 13, no. 12, 125206, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0171888\">10.1063/5.0171888</a>.","ista":"Sato K, Singh S, Yamazaki I, Hirata K, Ang AKR, Matsunami M, Takeuchi T. 2023. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. 13(12), 125206.","ieee":"K. Sato <i>et al.</i>, “Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag,” <i>AIP Advances</i>, vol. 13, no. 12. AIP Publishing, 2023.","ama":"Sato K, Singh S, Yamazaki I, et al. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. <i>AIP Advances</i>. 2023;13(12). doi:<a href=\"https://doi.org/10.1063/5.0171888\">10.1063/5.0171888</a>"},"doi":"10.1063/5.0171888","quality_controlled":"1","intvolume":"        13","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2158-3226"]},"year":"2023"},{"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kafshdar Goharshady, Ehsan","first_name":"Ehsan","last_name":"Kafshdar Goharshady"},{"last_name":"Novotný","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr"},{"full_name":"Zárevúcky, Jiří","last_name":"Zárevúcky","first_name":"Jiří"},{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic"}],"department":[{"_id":"KrCh"}],"date_created":"2024-01-10T09:27:43Z","oa_version":"Published Version","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"file_date_updated":"2024-01-16T08:11:24Z","publication":"Formal Aspects of Computing","article_processing_charge":"Yes (via OA deal)","_id":"14778","type":"journal_article","issue":"2","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":35,"title":"On lexicographic proof rules for probabilistic termination","status":"public","article_number":"11","day":"23","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-14T09:10:10Z","publisher":"Association for Computing Machinery","article_type":"original","date_published":"2023-06-23T00:00:00Z","month":"06","related_material":{"record":[{"status":"public","id":"10414","relation":"earlier_version"}]},"acknowledgement":"This research was partially supported by the ERC CoG (grant no. 863818; ForM-SMArt), the Czech Science Foundation (grant no. GA21-24711S), and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","ec_funded":1,"quality_controlled":"1","citation":{"ama":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. <i>Formal Aspects of Computing</i>. 2023;35(2). doi:<a href=\"https://doi.org/10.1145/3585391\">10.1145/3585391</a>","apa":"Chatterjee, K., Kafshdar Goharshady, E., Novotný, P., Zárevúcky, J., &#38; Zikelic, D. (2023). On lexicographic proof rules for probabilistic termination. <i>Formal Aspects of Computing</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3585391\">https://doi.org/10.1145/3585391</a>","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” <i>Formal Aspects of Computing</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3585391\">https://doi.org/10.1145/3585391</a>.","short":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, Formal Aspects of Computing 35 (2023).","ista":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. 2023. On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. 35(2), 11.","ieee":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” <i>Formal Aspects of Computing</i>, vol. 35, no. 2. Association for Computing Machinery, 2023.","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” <i>Formal Aspects of Computing</i>, vol. 35, no. 2, 11, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3585391\">10.1145/3585391</a>."},"doi":"10.1145/3585391","has_accepted_license":"1","arxiv":1,"intvolume":"        35","year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1433-299X"],"issn":["0934-5043"]},"external_id":{"arxiv":["2108.02188"]},"keyword":["Theoretical Computer Science","Software"],"abstract":[{"text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in a LexRSM not existing even for simple terminating programs. Our contributions are twofold. First, we introduce a generalization of LexRSMs that allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.","lang":"eng"}],"ddc":["000"],"oa":1,"file":[{"date_updated":"2024-01-16T08:11:24Z","creator":"dernst","file_size":502522,"checksum":"3bb133eeb27ec01649a9a36445d952d9","file_name":"2023_FormalAspectsComputing_Chatterjee.pdf","relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2024-01-16T08:11:24Z","access_level":"open_access","file_id":"14804"}]},{"article_type":"original","month":"06","date_published":"2023-06-16T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-16T08:42:36Z","publisher":"American Geophysical Union","oa_version":"Published Version","date_created":"2024-01-10T09:28:34Z","file_date_updated":"2024-01-16T08:35:02Z","publication":"Geophysical Research Letters","article_processing_charge":"No","_id":"14779","type":"journal_article","issue":"11","author":[{"first_name":"Thomas E.","last_name":"Shaw","full_name":"Shaw, Thomas E."},{"full_name":"Buri, Pascal","first_name":"Pascal","last_name":"Buri"},{"first_name":"Michael","last_name":"McCarthy","full_name":"McCarthy, Michael"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"full_name":"Ayala, Álvaro","last_name":"Ayala","first_name":"Álvaro"},{"full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti"}],"department":[{"_id":"FrPe"}],"day":"16","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":50,"title":"The decaying near‐surface boundary layer of a retreating alpine glacier","status":"public","article_number":"e2023GL103043","isi":1,"external_id":{"isi":["000999436400001"]},"keyword":["General Earth and Planetary Sciences","Geophysics"],"abstract":[{"text":"The presence of a developed boundary layer decouples a glacier's response from ambient conditions, suggesting that sensitivity to climate change is increased by glacier retreat. To test this hypothesis, we explore six years of distributed meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding with notable frontal retreat, an observed switch from down‐glacier katabatic to up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic winds, sensible heat fluxes on the glacier are increasingly determined by the conditions occurring outside the boundary layer of the glacier, sealing the glacier's demise as the climate continues to warm and experience an increased frequency of extreme summers.","lang":"eng"}],"oa":1,"ddc":["550"],"file":[{"date_updated":"2024-01-16T08:35:02Z","creator":"dernst","file_size":2529327,"checksum":"391a3005c95340a0ae129ce4fbdf2bae","relation":"main_file","file_name":"2023_GeophysicalResearchLetter_Shaw.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","date_created":"2024-01-16T08:35:02Z","file_id":"14805"}],"quality_controlled":"1","doi":"10.1029/2023gl103043","citation":{"apa":"Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., Ayala, Á., &#38; Pellicciotti, F. (2023). The decaying near‐surface boundary layer of a retreating alpine glacier. <i>Geophysical Research Letters</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2023gl103043\">https://doi.org/10.1029/2023gl103043</a>","short":"T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical Research Letters 50 (2023).","chicago":"Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, Álvaro Ayala, and Francesca Pellicciotti. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” <i>Geophysical Research Letters</i>. American Geophysical Union, 2023. <a href=\"https://doi.org/10.1029/2023gl103043\">https://doi.org/10.1029/2023gl103043</a>.","ieee":"T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, Á. Ayala, and F. Pellicciotti, “The decaying near‐surface boundary layer of a retreating alpine glacier,” <i>Geophysical Research Letters</i>, vol. 50, no. 11. American Geophysical Union, 2023.","ista":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. 2023. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 50(11), e2023GL103043.","mla":"Shaw, Thomas E., et al. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” <i>Geophysical Research Letters</i>, vol. 50, no. 11, e2023GL103043, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2023gl103043\">10.1029/2023gl103043</a>.","ama":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. The decaying near‐surface boundary layer of a retreating alpine glacier. <i>Geophysical Research Letters</i>. 2023;50(11). doi:<a href=\"https://doi.org/10.1029/2023gl103043\">10.1029/2023gl103043</a>"},"acknowledgement":"This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie Actions Grant 101026058. The authors acknowl-edge the dedicated collection of field data by many parties since 2001, including those acknowledged for the cited works on Arolla Glacier. The authors would like to thank Fabienne Meier, Alice Zaugg, Raphael Willi, Maria Grundmann, and Marta Corrà for assistance in the field for the summers of 2021 and 2022. Off-glacier data provided by Grand Dixence SA (Arolla) and MeteoSwiss are kindly acknowledged. Simone Fatichi is thanked for the provision and support in the use of the Tethys-Chloris model. We thank Editor Mathieu Morlighem and two anonymous reviewers whose comments have helped to improve the quality of the manuscript.","year":"2023","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"        50"},{"has_accepted_license":"1","arxiv":1,"intvolume":"       163","year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0304-4149"],"eissn":["1879-209X"]},"acknowledgement":"The authors would like to thank the editor, the associated editor and two anonymous referees for their many critical suggestions which have significantly improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee for many helpful discussions. The first author also wants to thank Hari Bercovici for many useful comments. The first author is partially supported by National Science Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","doi":"10.1016/j.spa.2023.05.009","citation":{"ama":"Ding X, Ji HC. Spiked multiplicative random matrices and principal components. <i>Stochastic Processes and their Applications</i>. 2023;163:25-60. doi:<a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">10.1016/j.spa.2023.05.009</a>","chicago":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” <i>Stochastic Processes and Their Applications</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">https://doi.org/10.1016/j.spa.2023.05.009</a>.","short":"X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023) 25–60.","apa":"Ding, X., &#38; Ji, H. C. (2023). Spiked multiplicative random matrices and principal components. <i>Stochastic Processes and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">https://doi.org/10.1016/j.spa.2023.05.009</a>","mla":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” <i>Stochastic Processes and Their Applications</i>, vol. 163, Elsevier, 2023, pp. 25–60, doi:<a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">10.1016/j.spa.2023.05.009</a>.","ieee":"X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal components,” <i>Stochastic Processes and their Applications</i>, vol. 163. Elsevier, pp. 25–60, 2023.","ista":"Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 163, 25–60."},"ec_funded":1,"quality_controlled":"1","ddc":["510"],"oa":1,"abstract":[{"lang":"eng","text":"In this paper, we study the eigenvalues and eigenvectors of the spiked invariant multiplicative models when the randomness is from Haar matrices. We establish the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩ for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence rates. Moreover, we prove that the non-outlier eigenvalues stick with those of the unspiked matrices and the non-outlier eigenvectors are delocalized. The results also hold near the so-called BBP transition and for degenerate spikes. On one hand, our results can be regarded as a refinement of the counterparts of [12] under additional regularity conditions. On the other hand, they can be viewed as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar random matrix."}],"keyword":["Applied Mathematics","Modeling and Simulation","Statistics and Probability"],"file":[{"date_updated":"2024-01-16T08:47:31Z","checksum":"46a708b0cd5569a73d0f3d6c3e0a44dc","file_size":1870349,"creator":"dernst","content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2023_StochasticProcAppl_Ding.pdf","file_id":"14806","access_level":"open_access","date_created":"2024-01-16T08:47:31Z"}],"isi":1,"page":"25-60","external_id":{"arxiv":["2302.13502"],"isi":["001113615900001"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":163,"title":"Spiked multiplicative random matrices and principal components","status":"public","day":"01","author":[{"full_name":"Ding, Xiucai","first_name":"Xiucai","last_name":"Ding"},{"full_name":"Ji, Hong Chang","last_name":"Ji","id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d","first_name":"Hong Chang"}],"department":[{"_id":"LaEr"}],"project":[{"call_identifier":"H2020","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"oa_version":"Published Version","date_created":"2024-01-10T09:29:25Z","_id":"14780","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","publication":"Stochastic Processes and their Applications","file_date_updated":"2024-01-16T08:47:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Elsevier","date_updated":"2024-01-16T08:49:51Z","month":"09","date_published":"2023-09-01T00:00:00Z","article_type":"original"},{"quality_controlled":"1","doi":"10.1016/j.devcel.2023.06.009","citation":{"ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>.","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","ieee":"K. J. Westerich <i>et al.</i>, “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” <i>Developmental Cell</i>, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>."},"acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1534-5807"]},"year":"2023","intvolume":"        58","pmid":1,"external_id":{"pmid":["37463577"]},"page":"1578-1592.e5","abstract":[{"text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency.","lang":"eng"}],"keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"oa":1,"publication":"Developmental Cell","_id":"14781","issue":"17","article_processing_charge":"No","type":"journal_article","date_created":"2024-01-10T09:41:21Z","oa_version":"Preprint","department":[{"_id":"Bio"}],"author":[{"full_name":"Westerich, Kim Joana","last_name":"Westerich","first_name":"Kim Joana"},{"first_name":"Katsiaryna","last_name":"Tarbashevich","full_name":"Tarbashevich, Katsiaryna"},{"full_name":"Schick, Jan","last_name":"Schick","first_name":"Jan"},{"first_name":"Antra","last_name":"Gupta","full_name":"Gupta, Antra"},{"full_name":"Zhu, Mingzhao","last_name":"Zhu","first_name":"Mingzhao"},{"last_name":"Hull","first_name":"Kenneth","full_name":"Hull, Kenneth"},{"last_name":"Romo","first_name":"Daniel","full_name":"Romo, Daniel"},{"first_name":"Dagmar","last_name":"Zeuschner","full_name":"Zeuschner, Dagmar"},{"first_name":"Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi","full_name":"Goudarzi, Mohammad"},{"full_name":"Gross-Thebing, Theresa","last_name":"Gross-Thebing","first_name":"Theresa"},{"full_name":"Raz, Erez","last_name":"Raz","first_name":"Erez"}],"day":"11","status":"public","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","volume":58,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"article_type":"original","date_published":"2023-09-11T00:00:00Z","month":"09","date_updated":"2024-01-16T08:56:36Z","publisher":"Elsevier","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2023-06-06T00:00:00Z","month":"06","article_type":"original","publisher":"Elsevier","date_updated":"2024-01-16T09:20:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","_id":"14782","type":"journal_article","issue":"11","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2024-01-16T09:09:29Z","publication":"Biophysical Journal","date_created":"2024-01-10T09:45:48Z","oa_version":"Published Version","department":[{"_id":"AnSa"}],"author":[{"full_name":"Baldauf, Lucia","last_name":"Baldauf","first_name":"Lucia"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F","last_name":"Frey","full_name":"Frey, Felix F"},{"full_name":"Arribas Perez, Marcos","last_name":"Arribas Perez","first_name":"Marcos"},{"first_name":"Timon","last_name":"Idema","full_name":"Idema, Timon"},{"full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H.","last_name":"Koenderink"}],"day":"06","status":"public","title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"volume":122,"external_id":{"isi":["001016792600001"],"pmid":["36806830"]},"isi":1,"page":"2311-2324","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"date_created":"2024-01-16T09:09:29Z","access_level":"open_access","file_id":"14807","file_name":"2023_BiophysicalJournal_Baldauf.pdf","relation":"main_file","success":1,"content_type":"application/pdf","creator":"dernst","checksum":"70566e54cd95ea6df340909ad44c5cd5","file_size":3285810,"date_updated":"2024-01-16T09:09:29Z"}],"ddc":["570"],"oa":1,"abstract":[{"text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration.","lang":"eng"}],"keyword":["Biophysics"],"citation":{"chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>.","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., &#38; Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>.","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” <i>Biophysical Journal</i>, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. 2023;122(11):2311-2324. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>"},"doi":"10.1016/j.bpj.2023.02.018","quality_controlled":"1","acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","related_material":{"link":[{"url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing","relation":"software"}]},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0006-3495"]},"year":"2023","pmid":1,"intvolume":"       122","has_accepted_license":"1"},{"article_type":"original","date_published":"2023-03-01T00:00:00Z","month":"03","date_updated":"2023-10-04T09:19:12Z","publisher":"Springer Nature","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","day":"01","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":58,"title":"Ergodic decomposition of Dirichlet forms via direct integrals and applications","file_date_updated":"2023-10-04T09:18:59Z","publication":"Potential Analysis","_id":"10145","article_processing_charge":"Yes (via OA deal)","type":"journal_article","oa_version":"Published Version","date_created":"2021-10-17T22:01:17Z","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020"}],"department":[{"_id":"JaMa"}],"author":[{"full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo"}],"file":[{"access_level":"open_access","date_created":"2023-10-04T09:18:59Z","file_id":"14387","file_name":"2023_PotentialAnalysis_DelloSchiavo.pdf","relation":"main_file","success":1,"content_type":"application/pdf","creator":"dernst","file_size":806391,"checksum":"625526482be300ca7281c91c30d41725","date_updated":"2023-10-04T09:18:59Z"}],"abstract":[{"lang":"eng","text":"We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique."}],"ddc":["510"],"oa":1,"external_id":{"arxiv":["2003.01366"],"isi":["000704213400001"]},"isi":1,"page":"573-615","publication_identifier":{"eissn":["1572-929X"],"issn":["0926-2601"]},"language":[{"iso":"eng"}],"year":"2023","arxiv":1,"intvolume":"        58","has_accepted_license":"1","ec_funded":1,"quality_controlled":"1","doi":"10.1007/s11118-021-09951-y","citation":{"ama":"Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals and applications. <i>Potential Analysis</i>. 2023;58:573-615. doi:<a href=\"https://doi.org/10.1007/s11118-021-09951-y\">10.1007/s11118-021-09951-y</a>","ista":"Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 58, 573–615.","ieee":"L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals and applications,” <i>Potential Analysis</i>, vol. 58. Springer Nature, pp. 573–615, 2023.","mla":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” <i>Potential Analysis</i>, vol. 58, Springer Nature, 2023, pp. 573–615, doi:<a href=\"https://doi.org/10.1007/s11118-021-09951-y\">10.1007/s11118-021-09951-y</a>.","apa":"Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct integrals and applications. <i>Potential Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11118-021-09951-y\">https://doi.org/10.1007/s11118-021-09951-y</a>","short":"L. Dello Schiavo, Potential Analysis 58 (2023) 573–615.","chicago":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” <i>Potential Analysis</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11118-021-09951-y\">https://doi.org/10.1007/s11118-021-09951-y</a>."},"acknowledgement":"The author is grateful to Professors Sergio Albeverio and Andreas Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the present work, and for respectively pointing out the references [1, 13], and [3, 20]. Finally, he is especially grateful to an anonymous Reviewer for their very careful reading and their suggestions which improved the readability of the paper."},{"abstract":[{"text":"We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods.","lang":"eng"}],"ddc":["510"],"oa":1,"file":[{"date_updated":"2023-08-14T11:51:04Z","creator":"dernst","file_size":1635193,"checksum":"f83dcaecdbd3ace862c4ed97a20e8501","file_name":"2023_StochPartialDiffEquations_Clozeau.pdf","relation":"main_file","content_type":"application/pdf","success":1,"date_created":"2023-08-14T11:51:04Z","access_level":"open_access","file_id":"14052"}],"page":"1254–1378","isi":1,"external_id":{"isi":["000799715600001"],"arxiv":["2102.07452"]},"year":"2023","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2194-0401"]},"has_accepted_license":"1","arxiv":1,"intvolume":"        11","quality_controlled":"1","citation":{"ieee":"N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields,” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>, vol. 11. Springer Nature, pp. 1254–1378, 2023.","ista":"Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 11, 1254–1378.","mla":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization  for Correlated Coefficient Fields.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>, vol. 11, Springer Nature, 2023, pp. 1254–1378, doi:<a href=\"https://doi.org/10.1007/s40072-022-00254-w\">10.1007/s40072-022-00254-w</a>.","apa":"Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40072-022-00254-w\">https://doi.org/10.1007/s40072-022-00254-w</a>","short":"N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378.","chicago":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization  for Correlated Coefficient Fields.” <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s40072-022-00254-w\">https://doi.org/10.1007/s40072-022-00254-w</a>.","ama":"Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields. <i>Stochastics and Partial Differential Equations: Analysis and Computations</i>. 2023;11:1254–1378. doi:<a href=\"https://doi.org/10.1007/s40072-022-00254-w\">10.1007/s40072-022-00254-w</a>"},"doi":"10.1007/s40072-022-00254-w","acknowledgement":"I would like to thank my advisor Antoine Gloria for suggesting this problem to me, as well for many interesting discussions and suggestions.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","article_type":"original","date_published":"2023-09-01T00:00:00Z","month":"09","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-14T11:51:47Z","publisher":"Springer Nature","scopus_import":"1","day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":11,"title":"Optimal decay of the parabolic semigroup in stochastic homogenization  for correlated coefficient fields","status":"public","oa_version":"Published Version","date_created":"2021-10-23T10:50:22Z","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","file_date_updated":"2023-08-14T11:51:04Z","_id":"10173","type":"journal_article","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Clozeau","first_name":"Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas"}],"department":[{"_id":"JuFi"}]}]