[{"publisher":"Springer Nature","type":"journal_article","article_type":"original","pmid":1,"ddc":["516"],"year":"2021","date_published":"2021-03-31T00:00:00Z","status":"public","date_created":"2021-04-11T22:01:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000635460400001"],"pmid":["34720303"]},"date_updated":"2025-06-12T06:36:54Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"187"}]},"department":[{"_id":"HeEd"}],"oa_version":"Published Version","file_date_updated":"2021-12-01T10:56:53Z","file":[{"relation":"main_file","date_created":"2021-12-01T10:56:53Z","content_type":"application/pdf","success":1,"access_level":"open_access","date_updated":"2021-12-01T10:56:53Z","checksum":"59b4e1e827e494209bcb4aae22e1d347","file_name":"2021_DisCompGeo_Edelsbrunner_Osang.pdf","file_size":677704,"file_id":"10394","creator":"cchlebak"}],"_id":"9317","doi":"10.1007/s00454-021-00281-9","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"month":"03","scopus_import":"1","volume":65,"language":[{"iso":"eng"}],"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","last_name":"Osang","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116"}],"citation":{"chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00454-021-00281-9\">https://doi.org/10.1007/s00454-021-00281-9</a>.","ista":"Edelsbrunner H, Osang GF. 2021. The multi-cover persistence of Euclidean balls. Discrete and Computational Geometry. 65, 1296–1313.","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2021). The multi-cover persistence of Euclidean balls. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-021-00281-9\">https://doi.org/10.1007/s00454-021-00281-9</a>","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. <i>Discrete and Computational Geometry</i>. 2021;65:1296–1313. doi:<a href=\"https://doi.org/10.1007/s00454-021-00281-9\">10.1007/s00454-021-00281-9</a>","short":"H. Edelsbrunner, G.F. Osang, Discrete and Computational Geometry 65 (2021) 1296–1313.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “The Multi-Cover Persistence of Euclidean Balls.” <i>Discrete and Computational Geometry</i>, vol. 65, Springer Nature, 2021, pp. 1296–1313, doi:<a href=\"https://doi.org/10.1007/s00454-021-00281-9\">10.1007/s00454-021-00281-9</a>.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” <i>Discrete and Computational Geometry</i>, vol. 65. Springer Nature, pp. 1296–1313, 2021."},"article_processing_charge":"Yes (via OA deal)","isi":1,"page":"1296–1313","oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha), and by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF)\r\nOpen Access funding provided by the Institute of Science and Technology (IST Austria).","day":"31","quality_controlled":"1","intvolume":"        65","abstract":[{"text":"Given a locally finite X⊆Rd and a radius r≥0, the k-fold cover of X and r consists of all points in Rd that have k or more points of X within distance r. We consider two filtrations—one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k—and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in Rd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module of Delaunay mosaics that is isomorphic to the persistence module of the multi-covers.","lang":"eng"}],"publication":"Discrete and Computational Geometry","publication_status":"published","corr_author":"1","title":"The multi-cover persistence of Euclidean balls","has_accepted_license":"1","ec_funded":1},{"external_id":{"isi":["000634006900001"]},"date_updated":"2026-04-02T14:02:29Z","department":[{"_id":"RoSe"}],"file_date_updated":"2021-04-12T07:15:58Z","oa_version":"Published Version","file":[{"relation":"main_file","content_type":"application/pdf","success":1,"date_created":"2021-04-12T07:15:58Z","checksum":"17a3e6786d1e930cf0c14a880a6d7e92","date_updated":"2021-04-12T07:15:58Z","access_level":"open_access","creator":"dernst","file_id":"9319","file_name":"2021_ForumMath_Bossmann.pdf","file_size":883851}],"_id":"9318","article_number":"e28","doi":"10.1017/fms.2021.22","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","type":"journal_article","publisher":"Cambridge University Press","ddc":["510"],"year":"2021","status":"public","date_published":"2021-03-26T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2021-04-11T22:01:15Z","day":"26","quality_controlled":"1","publication":"Forum of Mathematics, Sigma","abstract":[{"lang":"eng","text":"We consider a system of N bosons in the mean-field scaling regime for a class of interactions including the repulsive Coulomb potential. We derive an asymptotic expansion of the low-energy eigenstates and the corresponding energies, which provides corrections to Bogoliubov theory to any order in 1/N."}],"intvolume":"         9","has_accepted_license":"1","publication_status":"published","title":"Asymptotic expansion of low-energy excitations for weakly interacting bosons","ec_funded":1,"publication_identifier":{"eissn":["2050-5094"]},"volume":9,"month":"03","scopus_import":"1","author":[{"last_name":"Bossmann","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea","orcid":"0000-0002-6854-1343","full_name":"Bossmann, Lea"},{"last_name":"Petrat","first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P"},{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"Yes (via OA deal)","isi":1,"citation":{"ista":"Bossmann L, Petrat SP, Seiringer R. 2021. Asymptotic expansion of low-energy excitations for weakly interacting bosons. Forum of Mathematics, Sigma. 9, e28.","chicago":"Bossmann, Lea, Sören P Petrat, and Robert Seiringer. “Asymptotic Expansion of Low-Energy Excitations for Weakly Interacting Bosons.” <i>Forum of Mathematics, Sigma</i>. Cambridge University Press, 2021. <a href=\"https://doi.org/10.1017/fms.2021.22\">https://doi.org/10.1017/fms.2021.22</a>.","ama":"Bossmann L, Petrat SP, Seiringer R. Asymptotic expansion of low-energy excitations for weakly interacting bosons. <i>Forum of Mathematics, Sigma</i>. 2021;9. doi:<a href=\"https://doi.org/10.1017/fms.2021.22\">10.1017/fms.2021.22</a>","apa":"Bossmann, L., Petrat, S. P., &#38; Seiringer, R. (2021). Asymptotic expansion of low-energy excitations for weakly interacting bosons. <i>Forum of Mathematics, Sigma</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/fms.2021.22\">https://doi.org/10.1017/fms.2021.22</a>","short":"L. Bossmann, S.P. Petrat, R. Seiringer, Forum of Mathematics, Sigma 9 (2021).","mla":"Bossmann, Lea, et al. “Asymptotic Expansion of Low-Energy Excitations for Weakly Interacting Bosons.” <i>Forum of Mathematics, Sigma</i>, vol. 9, e28, Cambridge University Press, 2021, doi:<a href=\"https://doi.org/10.1017/fms.2021.22\">10.1017/fms.2021.22</a>.","ieee":"L. Bossmann, S. P. Petrat, and R. Seiringer, “Asymptotic expansion of low-energy excitations for weakly interacting bosons,” <i>Forum of Mathematics, Sigma</i>, vol. 9. Cambridge University Press, 2021."},"oa":1,"acknowledgement":"The first author gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411. The third author was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227)."},{"publisher":"Institute of Science and Technology Austria","type":"research_data","month":"04","year":"2021","ddc":["530"],"date_published":"2021-04-14T00:00:00Z","article_processing_charge":"No","contributor":[{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Jirovec","contributor_type":"project_member"}],"citation":{"mla":"Jirovec, Daniel. <i>Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9323\">10.15479/AT:ISTA:9323</a>.","ieee":"D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’” Institute of Science and Technology Austria, 2021.","short":"D. Jirovec, (2021).","ista":"Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9323\">10.15479/AT:ISTA:9323</a>.","chicago":"Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit Planar Ge.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9323\">https://doi.org/10.15479/AT:ISTA:9323</a>.","ama":"Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9323\">10.15479/AT:ISTA:9323</a>","apa":"Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar Ge.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9323\">https://doi.org/10.15479/AT:ISTA:9323</a>"},"status":"public","author":[{"last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"}],"date_created":"2021-04-14T09:50:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"status":"public","id":"8909","relation":"used_in_publication"}]},"date_updated":"2025-06-12T06:57:18Z","day":"14","department":[{"_id":"GradSch"},{"_id":"GeKa"}],"_id":"9323","file":[{"creator":"djirovec","file_size":221832287,"file_name":"DataRepositorySTqubit.zip","file_id":"9324","checksum":"c569d2a2ce1694445cdbca19cf8ae023","access_level":"open_access","date_updated":"2021-04-14T09:48:47Z","date_created":"2021-04-14T09:48:47Z","success":1,"content_type":"application/x-zip-compressed","relation":"main_file"},{"creator":"djirovec","file_id":"9325","file_size":4323,"file_name":"ReadMe","checksum":"845bdf87430718ad6aff47eda7b5fc92","date_updated":"2021-04-14T09:49:30Z","access_level":"open_access","success":1,"content_type":"application/octet-stream","date_created":"2021-04-14T09:49:30Z","relation":"main_file"}],"title":"Research data for \"A singlet-triplet hole spin qubit planar Ge\"","has_accepted_license":"1","oa_version":"Published Version","abstract":[{"text":"This .zip File contains the data for figures presented in the main text and supplementary material of \"A singlet triplet hole spin qubit in planar Ge\" by D. Jirovec, et. al. The measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python.","lang":"eng"}],"file_date_updated":"2021-04-14T09:49:30Z","doi":"10.15479/AT:ISTA:9323","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"}},{"doi":"10.15479/AT:ISTA:9327","tmp":{"name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT","short":"MIT"},"gitlab_url":"https://git.ist.ac.at/gsperl/MADYPG","file_date_updated":"2021-04-26T09:33:44Z","abstract":[{"lang":"eng","text":"This archive contains the missing sweater mesh animations and displacement models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode Repository: https://git.ist.ac.at/gsperl/MADYPG"}],"has_accepted_license":"1","_id":"9327","file":[{"checksum":"0324cb519273371708743f3282e7c081","date_updated":"2021-04-16T14:15:12Z","access_level":"open_access","creator":"gsperl","file_id":"9328","file_name":"MADYPG_extra_data.zip","file_size":802586232,"relation":"main_file","content_type":"application/zip","success":1,"date_created":"2021-04-16T14:15:12Z"},{"creator":"pub-gitlab-bot","file_name":"MADYPG.zip","file_size":64962865,"file_id":"9353","checksum":"4c224551adf852b136ec21a4e13f0c1b","access_level":"open_access","date_updated":"2021-04-26T09:33:44Z","date_created":"2021-04-26T09:33:44Z","content_type":"application/gzip","relation":"main_file"}],"title":"Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"date_updated":"2026-06-18T19:57:47Z","related_material":{"record":[{"status":"public","id":"9818","relation":"used_for_analysis_in"}]},"gitlab_commit_id":"6a77e7e22769230ae5f5edaa090fb4b828e57573","oa":1,"date_created":"2021-04-16T14:26:19Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"id":"4DD40360-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Sperl","full_name":"Sperl, Georg"},{"full_name":"Narain, Rahul","last_name":"Narain","first_name":"Rahul"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan"}],"status":"public","citation":{"short":"G. Sperl, R. Narain, C. Wojtan, (2021).","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9327\">https://doi.org/10.15479/AT:ISTA:9327</a>.","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data), IST Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9327\">10.15479/AT:ISTA:9327</a>.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9327\">10.15479/AT:ISTA:9327</a>","apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2021). Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9327\">https://doi.org/10.15479/AT:ISTA:9327</a>","mla":"Sperl, Georg, et al. <i>Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)</i>. IST Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9327\">10.15479/AT:ISTA:9327</a>.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021."},"date_published":"2021-05-01T00:00:00Z","ddc":["005"],"year":"2021","month":"05","license":"https://opensource.org/licenses/MIT","type":"software","publisher":"IST Austria"},{"file_date_updated":"2021-04-19T08:30:22Z","oa_version":"Published Version","file":[{"success":1,"content_type":"application/pdf","date_created":"2021-04-19T08:30:22Z","relation":"main_file","file_id":"9339","file_size":6924738,"file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","creator":"dernst","date_updated":"2021-04-19T08:30:22Z","access_level":"open_access","checksum":"2a5800d91b96d08b525e17319dcd5e44"}],"_id":"9329","article_number":"109125","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"doi":"10.1016/j.jneumeth.2021.109125","external_id":{"isi":["000661088500005"],"pmid":["33711356"]},"date_updated":"2025-06-12T06:39:15Z","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"status":"public","date_published":"2021-03-09T00:00:00Z","date_created":"2021-04-18T22:01:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","type":"journal_article","publisher":"Elsevier","ddc":["570"],"issue":"6","pmid":1,"acknowledged_ssus":[{"_id":"SSU"}],"year":"2021","publication":"Journal of Neuroscience Methods","intvolume":"       357","abstract":[{"text":"Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.\r\nNew method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.\r\nResults: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.\r\nComparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.\r\nConclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity.","lang":"eng"}],"has_accepted_license":"1","publication_status":"published","title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","ec_funded":1,"day":"09","quality_controlled":"1","author":[{"full_name":"Zhang, Xiaomin","last_name":"Zhang","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","last_name":"Schlögl"},{"orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"project":[{"grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"Synaptic communication in neuronal microcircuits","call_identifier":"FWF","grant_number":"Z00312"}],"language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","isi":1,"citation":{"ieee":"X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo,” <i>Journal of Neuroscience Methods</i>, vol. 357, no. 6. Elsevier, 2021.","mla":"Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” <i>Journal of Neuroscience Methods</i>, vol. 357, no. 6, 109125, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jneumeth.2021.109125\">10.1016/j.jneumeth.2021.109125</a>.","ista":"Zhang X, Schlögl A, Vandael DH, Jonas PM. 2021. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. 357(6), 109125.","chicago":"Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” <i>Journal of Neuroscience Methods</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jneumeth.2021.109125\">https://doi.org/10.1016/j.jneumeth.2021.109125</a>.","ama":"Zhang X, Schlögl A, Vandael DH, Jonas PM. MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. <i>Journal of Neuroscience Methods</i>. 2021;357(6). doi:<a href=\"https://doi.org/10.1016/j.jneumeth.2021.109125\">10.1016/j.jneumeth.2021.109125</a>","apa":"Zhang, X., Schlögl, A., Vandael, D. H., &#38; Jonas, P. M. (2021). MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. <i>Journal of Neuroscience Methods</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jneumeth.2021.109125\">https://doi.org/10.1016/j.jneumeth.2021.109125</a>","short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021)."},"oa":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari, Christoph Lampert, and Federico Stella for critically reading previous manuscript versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help with applying the Bayesian detection method to our data. We also thank Florian Marr for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support.","publication_identifier":{"issn":["0165-0270"],"eissn":["1872-678X"]},"volume":357,"scopus_import":"1","month":"03"},{"status":"public","date_published":"2021-04-06T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-04-18T22:01:40Z","article_type":"original","type":"journal_article","publisher":"National Academy of Sciences","ddc":["570"],"acknowledged_ssus":[{"_id":"EM-Fac"}],"pmid":1,"issue":"14","year":"2021","file_date_updated":"2021-04-19T10:10:56Z","oa_version":"Published Version","_id":"9330","file":[{"creator":"dernst","file_name":"2021_PNAS_Schoepf.pdf","file_size":2603911,"file_id":"9340","checksum":"dd014f68ae9d7d8d8fc4139a24e04506","access_level":"open_access","date_updated":"2021-04-19T10:10:56Z","date_created":"2021-04-19T10:10:56Z","success":1,"content_type":"application/pdf","relation":"main_file"}],"doi":"10.1073/pnas.1920827118","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"pmid":["33782113"],"isi":["000637398300002"]},"date_updated":"2025-06-12T06:56:21Z","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"author":[{"full_name":"Schöpf, Clemens L.","first_name":"Clemens L.","last_name":"Schöpf"},{"first_name":"Cornelia","last_name":"Ablinger","full_name":"Ablinger, Cornelia"},{"full_name":"Geisler, Stefanie M.","first_name":"Stefanie M.","last_name":"Geisler"},{"full_name":"Stanika, Ruslan I.","last_name":"Stanika","first_name":"Ruslan I."},{"first_name":"Marta","last_name":"Campiglio","full_name":"Campiglio, Marta"},{"last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"full_name":"Nimmervoll, Benedikt","first_name":"Benedikt","last_name":"Nimmervoll"},{"first_name":"Bettina","last_name":"Schlick","full_name":"Schlick, Bettina"},{"first_name":"Johannes","last_name":"Brockhaus","full_name":"Brockhaus, Johannes"},{"last_name":"Missler","first_name":"Markus","full_name":"Missler, Markus"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gerald J.","last_name":"Obermair","full_name":"Obermair, Gerald J."}],"project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"mla":"Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 14, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.1920827118\">10.1073/pnas.1920827118</a>.","ieee":"C. L. Schöpf <i>et al.</i>, “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 14. National Academy of Sciences, 2021.","short":"C.L. Schöpf, C. Ablinger, S.M. Geisler, R.I. Stanika, M. Campiglio, W. Kaufmann, B. Nimmervoll, B. Schlick, J. Brockhaus, M. Missler, R. Shigemoto, G.J. Obermair, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ama":"Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(14). doi:<a href=\"https://doi.org/10.1073/pnas.1920827118\">10.1073/pnas.1920827118</a>","apa":"Schöpf, C. L., Ablinger, C., Geisler, S. M., Stanika, R. I., Campiglio, M., Kaufmann, W., … Obermair, G. J. (2021). Presynaptic α2δ subunits are key organizers of glutamatergic synapses. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1920827118\">https://doi.org/10.1073/pnas.1920827118</a>","chicago":"Schöpf, Clemens L., Cornelia Ablinger, Stefanie M. Geisler, Ruslan I. Stanika, Marta Campiglio, Walter Kaufmann, Benedikt Nimmervoll, et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.1920827118\">https://doi.org/10.1073/pnas.1920827118</a>.","ista":"Schöpf CL, Ablinger C, Geisler SM, Stanika RI, Campiglio M, Kaufmann W, Nimmervoll B, Schlick B, Brockhaus J, Missler M, Shigemoto R, Obermair GJ. 2021. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. Proceedings of the National Academy of Sciences of the United States of America. 118(14)."},"isi":1,"oa":1,"acknowledgement":"We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A.","publication_identifier":{"eissn":["1091-6490"]},"volume":118,"scopus_import":"1","month":"04","publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":"       118","abstract":[{"text":"In nerve cells the genes encoding for α2δ subunits of voltage-gated calcium channels have been linked to synaptic functions and neurological disease. Here we show that α2δ subunits are essential for the formation and organization of glutamatergic synapses. Using a cellular α2δ subunit triple-knockout/knockdown model, we demonstrate a failure in presynaptic differentiation evidenced by defective presynaptic calcium channel clustering and calcium influx, smaller presynaptic active zones, and a strongly reduced accumulation of presynaptic vesicle-associated proteins (synapsin and vGLUT). The presynaptic defect is associated with the downscaling of postsynaptic AMPA receptors and the postsynaptic density. The role of α2δ isoforms as synaptic organizers is highly redundant, as each individual α2δ isoform can rescue presynaptic calcium channel trafficking and expression of synaptic proteins. Moreover, α2δ-2 and α2δ-3 with mutated metal ion-dependent adhesion sites can fully rescue presynaptic synapsin expression but only partially calcium channel trafficking, suggesting that the regulatory role of α2δ subunits is independent from its role as a calcium channel subunit. Our findings influence the current view on excitatory synapse formation. First, our study suggests that postsynaptic differentiation is secondary to presynaptic differentiation. Second, the dependence of presynaptic differentiation on α2δ implicates α2δ subunits as potential nucleation points for the organization of synapses. Finally, our results suggest that α2δ subunits act as transsynaptic organizers of glutamatergic synapses, thereby aligning the synaptic active zone with the postsynaptic density.","lang":"eng"}],"has_accepted_license":"1","title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","publication_status":"published","ec_funded":1,"day":"06","quality_controlled":"1"},{"publisher":"MDPI","article_type":"original","type":"journal_article","year":"2021","issue":"8","pmid":1,"ddc":["570"],"date_published":"2021-04-08T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-04-18T22:01:41Z","date_updated":"2025-06-12T06:39:41Z","external_id":{"isi":["000644394800001"],"pmid":["33917959"]},"department":[{"_id":"EvBe"}],"article_number":"3862","_id":"9332","file":[{"file_id":"9342","file_name":"2021_JourMolecularScience_Oetvoes.pdf","file_size":2769717,"creator":"dernst","date_updated":"2021-04-19T10:54:55Z","access_level":"open_access","checksum":"26ada2531ad1f9c01a1664de0431f1fe","success":1,"content_type":"application/pdf","date_created":"2021-04-19T10:54:55Z","relation":"main_file"}],"oa_version":"Published Version","file_date_updated":"2021-04-19T10:54:55Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.3390/ijms22083862","publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"scopus_import":"1","month":"04","volume":22,"isi":1,"article_processing_charge":"No","citation":{"mla":"Ötvös, Krisztina, et al. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 8, 3862, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22083862\">10.3390/ijms22083862</a>.","ieee":"K. Ötvös <i>et al.</i>, “Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 8. MDPI, 2021.","short":"K. Ötvös, P. Miskolczi, P. Marhavý, A. Cruz-Ramírez, E. Benková, S. Robert, L. Bakó, International Journal of Molecular Sciences 22 (2021).","chicago":"Ötvös, Krisztina, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva Benková, Stéphanie Robert, and László Bakó. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22083862\">https://doi.org/10.3390/ijms22083862</a>.","ista":"Ötvös K, Miskolczi P, Marhavý P, Cruz-Ramírez A, Benková E, Robert S, Bakó L. 2021. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. 22(8), 3862.","ama":"Ötvös K, Miskolczi P, Marhavý P, et al. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. <i>International Journal of Molecular Sciences</i>. 2021;22(8). doi:<a href=\"https://doi.org/10.3390/ijms22083862\">10.3390/ijms22083862</a>","apa":"Ötvös, K., Miskolczi, P., Marhavý, P., Cruz-Ramírez, A., Benková, E., Robert, S., &#38; Bakó, L. (2021). Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22083862\">https://doi.org/10.3390/ijms22083862</a>"},"language":[{"iso":"eng"}],"author":[{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös"},{"first_name":"Pál","last_name":"Miskolczi","full_name":"Miskolczi, Pál"},{"last_name":"Marhavý","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","full_name":"Marhavý, Peter"},{"full_name":"Cruz-Ramírez, Alfredo","first_name":"Alfredo","last_name":"Cruz-Ramírez"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"full_name":"Bakó, László","first_name":"László","last_name":"Bakó"}],"acknowledgement":"This research was supported by a postdoctoral fellowship of the Carl Tryggers Foundation (to K.Ö.) and by grants from Vetenskapsrådet (Nr.: 621-2004-2921 to L.B.) and VINNOVA (to L.B. and S.R.).\r\nWe thank Frederic Berger, Hidehiro Fukaki, Malcolm Bennett, Claudia Köhler, Jiri Friml for providing pRBR1::RBR1-RFP, ssl2-1, slr-1, pPKL::PKL-GFP seeds and the DR5 expressing vector, respectively. Authors are grateful to Hayashi Kenichiro for providing the auxinol compound and to Rishi Bhalerao for stimulating discussions. The technical help of Adeline Rigal and Thomas Vain with the auxinol experiments is much appreciated.","oa":1,"quality_controlled":"1","day":"08","title":"Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis","publication_status":"published","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner."}],"intvolume":"        22","publication":"International Journal of Molecular Sciences"},{"publication":"Letters in Mathematical Physics","abstract":[{"text":"We revise a previous result about the Fröhlich dynamics in the strong coupling limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα, where φ0 is the electron ground state of the Pekar energy functional and ξα the associated coherent state of the phonons, can be approximated by a global phase for times small compared to α2. In the present note we prove that a similar approximation holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons that is generated by an operator proportional to α−2 and quadratic in creation and annihilation operators. Our result implies that the electron ground state remains close to its initial state for times of order α2, while the phonon fluctuations around the coherent state ξα can be described by a time-dependent Bogoliubov transformation.","lang":"eng"}],"intvolume":"       111","has_accepted_license":"1","publication_status":"published","title":"A note on the Fröhlich dynamics in the strong coupling limit","day":"05","quality_controlled":"1","oa":1,"acknowledgement":"I thank Marcel Griesemer for many interesting discussions about the Fröhlich polaron and also for valuable comments on this manuscript. Helpful discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged. This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems. Open Access funding enabled and organized by Projekt DEAL.","author":[{"full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","last_name":"Mitrouskas"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"chicago":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-021-01380-7\">https://doi.org/10.1007/s11005-021-01380-7</a>.","ista":"Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45.","ama":"Mitrouskas DJ. A note on the Fröhlich dynamics in the strong coupling limit. <i>Letters in Mathematical Physics</i>. 2021;111. doi:<a href=\"https://doi.org/10.1007/s11005-021-01380-7\">10.1007/s11005-021-01380-7</a>","apa":"Mitrouskas, D. J. (2021). A note on the Fröhlich dynamics in the strong coupling limit. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-021-01380-7\">https://doi.org/10.1007/s11005-021-01380-7</a>","short":"D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021).","ieee":"D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling limit,” <i>Letters in Mathematical Physics</i>, vol. 111. Springer Nature, 2021.","mla":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” <i>Letters in Mathematical Physics</i>, vol. 111, 45, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-021-01380-7\">10.1007/s11005-021-01380-7</a>."},"isi":1,"volume":111,"month":"04","scopus_import":"1","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"doi":"10.1007/s11005-021-01380-7","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2021-04-19T10:40:01Z","oa_version":"Published Version","article_number":"45","_id":"9333","file":[{"date_updated":"2021-04-19T10:40:01Z","access_level":"open_access","checksum":"be56c0845a43c0c5c772ee0b5053f7d7","file_id":"9341","file_name":"2021_LettersMathPhysics_Mitrouskas.pdf","file_size":438084,"creator":"dernst","relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2021-04-19T10:40:01Z"}],"department":[{"_id":"RoSe"}],"external_id":{"isi":["000637359300002"]},"date_updated":"2026-04-02T13:58:00Z","date_created":"2021-04-18T22:01:41Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_published":"2021-04-05T00:00:00Z","ddc":["510"],"year":"2021","article_type":"original","type":"journal_article","publisher":"Springer Nature"},{"day":"02","quality_controlled":"1","abstract":[{"lang":"eng","text":"Polaritons with directional in-plane propagation and ultralow losses in van der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale. However, these polaritons present a crucial limitation: their directional propagation is intrinsically determined by the crystal structure of the host material, imposing forbidden directions of propagation. Here, we demonstrate that directional polaritons (in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide) can be directed along forbidden directions by inducing an optical topological transition, which emerges when the slab is placed on a substrate with a given negative permittivity (4H–silicon carbide). By visualizing the transition in real space, we observe exotic polaritonic states between mutually orthogonal hyperbolic regimes, which unveil the topological origin of the transition: a gap opening in the dispersion. This work provides insights into optical topological transitions in vdW crystals, which introduce a route to direct light at the nanoscale."}],"intvolume":"         7","publication":"Science Advances","publication_status":"published","title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","has_accepted_license":"1","month":"04","scopus_import":"1","volume":7,"publication_identifier":{"eissn":["2375-2548"]},"oa":1,"acknowledgement":"G.Á.-P. and J.T.-G. acknowledge support through the Severo Ochoa Program from the government of the Principality of Asturias (grant nos. PA20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). K.V.V. and V.S.V. acknowledge the Ministry of Science and Higher Education of the Russian Federation (no. 0714-2020-0002). J. M.-S. acknowledges financial support through the Ramón y Cajal Program from the government of Spain and FSE (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT201788358-C3-3-R), and the Basque Department of Education (PIBA-2020-1-0014). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA. ","language":[{"iso":"eng"}],"author":[{"last_name":"Duan","first_name":"J.","full_name":"Duan, J."},{"full_name":"Álvarez-Pérez, G.","last_name":"Álvarez-Pérez","first_name":"G."},{"full_name":"Voronin, K. V.","first_name":"K. V.","last_name":"Voronin"},{"full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez"},{"last_name":"Taboada-Gutiérrez","first_name":"J.","full_name":"Taboada-Gutiérrez, J."},{"first_name":"V. S.","last_name":"Volkov","full_name":"Volkov, V. S."},{"last_name":"Martín-Sánchez","first_name":"J.","full_name":"Martín-Sánchez, J."},{"last_name":"Nikitin","first_name":"A. Y.","full_name":"Nikitin, A. Y."},{"full_name":"Alonso-González, P.","first_name":"P.","last_name":"Alonso-González"}],"isi":1,"citation":{"ieee":"J. Duan <i>et al.</i>, “Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition,” <i>Science Advances</i>, vol. 7, no. 14. AAAS, 2021.","mla":"Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” <i>Science Advances</i>, vol. 7, no. 14, eabf2690, AAAS, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abf2690\">10.1126/sciadv.abf2690</a>.","short":"J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez, V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","chicago":"Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez, V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” <i>Science Advances</i>. AAAS, 2021. <a href=\"https://doi.org/10.1126/sciadv.abf2690\">https://doi.org/10.1126/sciadv.abf2690</a>.","ista":"Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 7(14), eabf2690.","apa":"Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez, J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abf2690\">https://doi.org/10.1126/sciadv.abf2690</a>","ama":"Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. <i>Science Advances</i>. 2021;7(14). doi:<a href=\"https://doi.org/10.1126/sciadv.abf2690\">10.1126/sciadv.abf2690</a>"},"article_processing_charge":"No","department":[{"_id":"NanoFab"}],"external_id":{"isi":["000636455600027"],"pmid":["33811076"]},"date_updated":"2026-04-02T13:58:21Z","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"doi":"10.1126/sciadv.abf2690","oa_version":"Published Version","file_date_updated":"2021-04-19T11:17:29Z","file":[{"content_type":"application/pdf","success":1,"date_created":"2021-04-19T11:17:29Z","relation":"main_file","file_id":"9343","file_size":717489,"file_name":"2021_ScienceAdv_Duan.pdf","creator":"dernst","date_updated":"2021-04-19T11:17:29Z","access_level":"open_access","checksum":"4b383d4a1d484a71bbc64ecf401bbdbb"}],"_id":"9334","article_number":"eabf2690","pmid":1,"issue":"14","ddc":["530"],"year":"2021","publisher":"AAAS","article_type":"original","type":"journal_article","date_created":"2021-04-18T22:01:42Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-04-02T00:00:00Z","status":"public"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-04-18T22:01:42Z","date_published":"2021-01-01T00:00:00Z","status":"public","year":"2021","issue":"1","publisher":"Society for Industrial and Applied Mathematics","type":"journal_article","article_type":"original","doi":"10.1137/19M1300017","_id":"9335","oa_version":"Preprint","department":[{"_id":"JuFi"}],"date_updated":"2023-08-08T13:10:40Z","external_id":{"arxiv":["1911.04185"],"isi":["000625044600003"]},"acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”.","arxiv":1,"oa":1,"isi":1,"article_processing_charge":"No","citation":{"mla":"Fischer, Julian L., and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 1, Society for Industrial and Applied Mathematics, 2021, pp. 60–87, doi:<a href=\"https://doi.org/10.1137/19M1300017\">10.1137/19M1300017</a>.","ieee":"J. L. Fischer and D. Matthes, “The waiting time phenomenon in spatially discretized porous medium and thin film equations,” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 1. Society for Industrial and Applied Mathematics, pp. 60–87, 2021.","apa":"Fischer, J. L., &#38; Matthes, D. (2021). The waiting time phenomenon in spatially discretized porous medium and thin film equations. <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/19M1300017\">https://doi.org/10.1137/19M1300017</a>","ama":"Fischer JL, Matthes D. The waiting time phenomenon in spatially discretized porous medium and thin film equations. <i>SIAM Journal on Numerical Analysis</i>. 2021;59(1):60-87. doi:<a href=\"https://doi.org/10.1137/19M1300017\">10.1137/19M1300017</a>","chicago":"Fischer, Julian L, and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics, 2021. <a href=\"https://doi.org/10.1137/19M1300017\">https://doi.org/10.1137/19M1300017</a>.","ista":"Fischer JL, Matthes D. 2021. The waiting time phenomenon in spatially discretized porous medium and thin film equations. SIAM Journal on Numerical Analysis. 59(1), 60–87.","short":"J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 60–87."},"page":"60-87","language":[{"iso":"eng"}],"author":[{"last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"},{"last_name":"Matthes","first_name":"Daniel","full_name":"Matthes, Daniel"}],"month":"01","scopus_import":"1","volume":59,"publication_identifier":{"issn":["0036-1429"]},"title":"The waiting time phenomenon in spatially discretized porous medium and thin film equations","publication_status":"published","intvolume":"        59","abstract":[{"text":"Various degenerate diffusion equations exhibit a waiting time phenomenon: depending on the “flatness” of the compactly supported initial datum at the boundary of the support, the support of the solution may not expand for a certain amount of time. We show that this phenomenon is captured by particular Lagrangian discretizations of the porous medium and the thin film equations, and we obtain sufficient criteria for the occurrence of waiting times that are consistent with the known ones for the original PDEs. For the spatially discrete solution, the waiting time phenomenon refers to a deviation of the edge of support from its original position by a quantity comparable to the mesh width, over a mesh-independent time interval. Our proof is based on estimates on the fluid velocity in Lagrangian coordinates. Combining weighted entropy estimates with an iteration technique à la Stampacchia leads to upper bounds on free boundary propagation. Numerical simulations show that the phenomenon is already clearly visible for relatively coarse discretizations.","lang":"eng"}],"publication":"SIAM Journal on Numerical Analysis","main_file_link":[{"url":"https://arxiv.org/abs/1911.04185","open_access":"1"}],"quality_controlled":"1","day":"01"},{"oa_version":"Preprint","article_number":"109029","_id":"9348","doi":"10.1016/j.jfa.2021.109029","external_id":{"isi":["000644702800005"],"arxiv":["1911.03187"]},"date_updated":"2023-08-08T13:15:11Z","department":[{"_id":"RoSe"}],"status":"public","date_published":"2021-04-07T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-04-25T22:01:29Z","article_type":"original","type":"journal_article","publisher":"Elsevier","issue":"3","year":"2021","publication":"Journal of Functional Analysis","abstract":[{"lang":"eng","text":"We consider the stochastic quantization of a quartic double-well energy functional in the semiclassical regime and derive optimal asymptotics for the exponentially small splitting of the ground state energy. Our result provides an infinite-dimensional version of some sharp tunneling estimates known in finite dimensions for semiclassical Witten Laplacians in degree zero. From a stochastic point of view it proves that the L2 spectral gap of the stochastic one-dimensional Allen-Cahn equation in finite volume satisfies a Kramers-type formula in the limit of vanishing noise. We work with finite-dimensional lattice approximations and establish semiclassical estimates which are uniform in the dimension. Our key estimate shows that the constant separating the two exponentially small eigenvalues from the rest of the spectrum can be taken independently of the dimension."}],"intvolume":"       281","title":"Sharp tunneling estimates for a double-well model in infinite dimension","publication_status":"published","day":"07","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1911.03187","open_access":"1"}],"author":[{"id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","first_name":"Morris","last_name":"Brooks","full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928"},{"full_name":"Di Gesù, Giacomo","first_name":"Giacomo","last_name":"Di Gesù"}],"language":[{"iso":"eng"}],"citation":{"ama":"Brooks M, Di Gesù G. Sharp tunneling estimates for a double-well model in infinite dimension. <i>Journal of Functional Analysis</i>. 2021;281(3). doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">10.1016/j.jfa.2021.109029</a>","apa":"Brooks, M., &#38; Di Gesù, G. (2021). Sharp tunneling estimates for a double-well model in infinite dimension. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">https://doi.org/10.1016/j.jfa.2021.109029</a>","chicago":"Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well Model in Infinite Dimension.” <i>Journal of Functional Analysis</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">https://doi.org/10.1016/j.jfa.2021.109029</a>.","ista":"Brooks M, Di Gesù G. 2021. Sharp tunneling estimates for a double-well model in infinite dimension. Journal of Functional Analysis. 281(3), 109029.","short":"M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021).","ieee":"M. Brooks and G. Di Gesù, “Sharp tunneling estimates for a double-well model in infinite dimension,” <i>Journal of Functional Analysis</i>, vol. 281, no. 3. Elsevier, 2021.","mla":"Brooks, Morris, and Giacomo Di Gesù. “Sharp Tunneling Estimates for a Double-Well Model in Infinite Dimension.” <i>Journal of Functional Analysis</i>, vol. 281, no. 3, 109029, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">10.1016/j.jfa.2021.109029</a>."},"isi":1,"article_processing_charge":"No","oa":1,"arxiv":1,"acknowledgement":"GDG gratefully acknowledges the financial support of HIM Bonn in the framework of the 2019 Junior Trimester Programs “Kinetic Theory” and “Randomness, PDEs and Nonlinear Fluctuations” and the hospitality at the University of Rome La Sapienza during his frequent visits.","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"volume":281,"scopus_import":"1","month":"04"},{"department":[{"_id":"CaHe"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12368"}]},"date_updated":"2026-06-18T19:47:51Z","external_id":{"isi":["000704646900006"],"pmid":["33794149"]},"doi":"10.1016/j.bpj.2021.03.025","_id":"9350","oa_version":"Published Version","year":"2021","ddc":["570"],"pmid":1,"article_type":"original","type":"journal_article","publisher":"Biophysical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-04-25T22:01:30Z","status":"public","date_published":"2021-10-05T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view"}],"quality_controlled":"1","day":"05","corr_author":"1","publication_status":"published","title":"Holding it together: when cadherin meets cadherin","publication":"Biophysical Journal","intvolume":"       120","abstract":[{"text":"Intercellular adhesion is the key to multicellularity, and its malfunction plays an important role in various developmental and disease-related processes. Although it has been intensively studied by both biologists and physicists, a commonly accepted definition of cell-cell adhesion is still being debated. Cell-cell adhesion has been described at the molecular scale as a function of adhesion receptors controlling binding affinity, at the cellular scale as resistance to detachment forces or modulation of surface tension, and at the tissue scale as a regulator of cellular rearrangements and morphogenesis. In this review, we aim to summarize and discuss recent advances in the molecular, cellular, and theoretical description of cell-cell adhesion, ranging from biomimetic models to the complexity of cells and tissues in an organismal context. In particular, we will focus on cadherin-mediated cell-cell adhesion and the role of adhesion signaling and mechanosensation therein, two processes central for understanding the biological and physical basis of cell-cell adhesion.","lang":"eng"}],"volume":120,"scopus_import":"1","month":"10","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"acknowledgement":"T.S. acknowledges funding by the research program “The Active Matter Physics of Collective Metastasis,” which is financed by the Dutch Research Council (NWO).","oa":1,"page":"4182-4192","article_processing_charge":"No","isi":1,"citation":{"short":"F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal 120 (2021) 4182–4192.","chicago":"Arslan, Feyza N, Julia Eckert, Thomas Schmidt, and Carl-Philipp J Heisenberg. “Holding It Together: When Cadherin Meets Cadherin.” <i>Biophysical Journal</i>. Biophysical Society, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2021.03.025\">https://doi.org/10.1016/j.bpj.2021.03.025</a>.","ista":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together: when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192.","apa":"Arslan, F. N., Eckert, J., Schmidt, T., &#38; Heisenberg, C.-P. J. (2021). Holding it together: when cadherin meets cadherin. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2021.03.025\">https://doi.org/10.1016/j.bpj.2021.03.025</a>","ama":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. Holding it together: when cadherin meets cadherin. <i>Biophysical Journal</i>. 2021;120:4182-4192. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.03.025\">10.1016/j.bpj.2021.03.025</a>","mla":"Arslan, Feyza N., et al. “Holding It Together: When Cadherin Meets Cadherin.” <i>Biophysical Journal</i>, vol. 120, Biophysical Society, 2021, pp. 4182–92, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.03.025\">10.1016/j.bpj.2021.03.025</a>.","ieee":"F. N. Arslan, J. Eckert, T. Schmidt, and C.-P. J. Heisenberg, “Holding it together: when cadherin meets cadherin,” <i>Biophysical Journal</i>, vol. 120. Biophysical Society, pp. 4182–4192, 2021."},"author":[{"full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","last_name":"Arslan"},{"full_name":"Eckert, Julia","last_name":"Eckert","first_name":"Julia"},{"first_name":"Thomas","last_name":"Schmidt","full_name":"Schmidt, Thomas"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}],"language":[{"iso":"eng"}]},{"date_created":"2021-04-25T22:01:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-04-08T00:00:00Z","status":"public","year":"2021","pmid":1,"ddc":["530"],"publisher":"Springer Nature","type":"journal_article","article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1007/s00023-021-01044-1","file":[{"file_id":"10143","file_size":522669,"file_name":"2021_Annales_Kirkpatrick.pdf","creator":"cchlebak","date_updated":"2021-10-15T11:15:40Z","access_level":"open_access","checksum":"1a0fb963f2f415ba470881a794f20eb6","content_type":"application/pdf","success":1,"date_created":"2021-10-15T11:15:40Z","relation":"main_file"}],"_id":"9351","oa_version":"Published Version","file_date_updated":"2021-10-15T11:15:40Z","department":[{"_id":"RoSe"}],"date_updated":"2025-06-12T06:39:59Z","external_id":{"pmid":["34776771"],"arxiv":["2010.13754"],"isi":["000638022600001"]},"acknowledgement":"The authors gratefully acknowledge Gérard Ben Arous for suggesting this kind of result. K.L.K. was partially supported by NSF CAREER Award DMS-125479 and a Simons Sabbatical Fellowship. S.R. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. B. S. gratefully acknowledges partial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose–Einstein condensates” and from the European Research Council through the ERC-AdG CLaQS. Funding Open access funding provided by Institute of Science and Technology (IST Austria).","arxiv":1,"oa":1,"article_processing_charge":"Yes (via OA deal)","citation":{"mla":"Kirkpatrick, Kay, et al. “A Large Deviation Principle in Many-Body Quantum Dynamics.” <i>Annales Henri Poincare</i>, vol. 22, Springer Nature, 2021, pp. 2595–618, doi:<a href=\"https://doi.org/10.1007/s00023-021-01044-1\">10.1007/s00023-021-01044-1</a>.","ieee":"K. Kirkpatrick, S. A. E. Rademacher, and B. Schlein, “A large deviation principle in many-body quantum dynamics,” <i>Annales Henri Poincare</i>, vol. 22. Springer Nature, pp. 2595–2618, 2021.","ista":"Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618.","chicago":"Kirkpatrick, Kay, Simone Anna Elvira Rademacher, and Benjamin Schlein. “A Large Deviation Principle in Many-Body Quantum Dynamics.” <i>Annales Henri Poincare</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00023-021-01044-1\">https://doi.org/10.1007/s00023-021-01044-1</a>.","ama":"Kirkpatrick K, Rademacher SAE, Schlein B. A large deviation principle in many-body quantum dynamics. <i>Annales Henri Poincare</i>. 2021;22:2595-2618. doi:<a href=\"https://doi.org/10.1007/s00023-021-01044-1\">10.1007/s00023-021-01044-1</a>","apa":"Kirkpatrick, K., Rademacher, S. A. E., &#38; Schlein, B. (2021). A large deviation principle in many-body quantum dynamics. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01044-1\">https://doi.org/10.1007/s00023-021-01044-1</a>","short":"K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22 (2021) 2595–2618."},"isi":1,"page":"2595-2618","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Kirkpatrick, Kay","last_name":"Kirkpatrick","first_name":"Kay"},{"full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","last_name":"Rademacher"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}],"scopus_import":"1","month":"04","volume":22,"publication_identifier":{"issn":["1424-0637"]},"ec_funded":1,"title":"A large deviation principle in many-body quantum dynamics","publication_status":"published","has_accepted_license":"1","intvolume":"        22","abstract":[{"lang":"eng","text":"We consider the many-body quantum evolution of a factorized initial data, in the mean-field regime. We show that fluctuations around the limiting Hartree dynamics satisfy large deviation estimates that are consistent with central limit theorems that have been established in the last years. "}],"publication":"Annales Henri Poincare","quality_controlled":"1","day":"08"},{"abstract":[{"text":"This paper provides an a priori error analysis of a localized orthogonal decomposition method for the numerical stochastic homogenization of a model random diffusion problem. If the uniformly elliptic and bounded random coefficient field of the model problem is stationary and satisfies a quantitative decorrelation assumption in the form of the spectral gap inequality, then the expected $L^2$ error of the method can be estimated, up to logarithmic factors, by $H+(\\varepsilon/H)^{d/2}$, $\\varepsilon$ being the small correlation length of the random coefficient and $H$ the width of the coarse finite element mesh that determines the spatial resolution. The proof bridges recent results of numerical homogenization and quantitative stochastic homogenization.","lang":"eng"}],"intvolume":"        59","publication":"SIAM Journal on Numerical Analysis","title":"A priori error analysis of a numerical stochastic homogenization method","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.11646"}],"day":"09","quality_controlled":"1","oa":1,"acknowledgement":"This work was initiated while the authors enjoyed the kind hospitality of the Hausdorff Institute for Mathematics in Bonn during the trimester program Multiscale Problems: Algorithms, Numerical Analysis, and Computation. D. Peterseim would like to acknowledge the kind hospitality of the Erwin Schrödinger International Institute  for  Mathematics and Physics  (ESI), where parts of this research were developed under the frame of the thematic program Numerical Analysis of Complex PDE Models in the Sciences.","arxiv":1,"language":[{"iso":"eng"}],"author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer"},{"full_name":"Gallistl, Dietmar","last_name":"Gallistl","first_name":"Dietmar"},{"first_name":"Dietmar","last_name":"Peterseim","full_name":"Peterseim, Dietmar"}],"isi":1,"article_processing_charge":"No","citation":{"ama":"Fischer JL, Gallistl D, Peterseim D. A priori error analysis of a numerical stochastic homogenization method. <i>SIAM Journal on Numerical Analysis</i>. 2021;59(2):660-674. doi:<a href=\"https://doi.org/10.1137/19M1308992\">10.1137/19M1308992</a>","apa":"Fischer, J. L., Gallistl, D., &#38; Peterseim, D. (2021). A priori error analysis of a numerical stochastic homogenization method. <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/19M1308992\">https://doi.org/10.1137/19M1308992</a>","chicago":"Fischer, Julian L, Dietmar Gallistl, and Dietmar Peterseim. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics, 2021. <a href=\"https://doi.org/10.1137/19M1308992\">https://doi.org/10.1137/19M1308992</a>.","ista":"Fischer JL, Gallistl D, Peterseim D. 2021. A priori error analysis of a numerical stochastic homogenization method. SIAM Journal on Numerical Analysis. 59(2), 660–674.","short":"J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis 59 (2021) 660–674.","mla":"Fischer, Julian L., et al. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 2, Society for Industrial and Applied Mathematics, 2021, pp. 660–74, doi:<a href=\"https://doi.org/10.1137/19M1308992\">10.1137/19M1308992</a>.","ieee":"J. L. Fischer, D. Gallistl, and D. Peterseim, “A priori error analysis of a numerical stochastic homogenization method,” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 2. Society for Industrial and Applied Mathematics, pp. 660–674, 2021."},"page":"660-674","month":"03","scopus_import":"1","volume":59,"publication_identifier":{"issn":["0036-1429"]},"doi":"10.1137/19M1308992","oa_version":"Preprint","_id":"9352","department":[{"_id":"JuFi"}],"external_id":{"isi":["000646030400003"],"arxiv":["1912.11646"]},"date_updated":"2023-08-08T13:13:37Z","date_created":"2021-04-25T22:01:31Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-03-09T00:00:00Z","status":"public","issue":"2","year":"2021","publisher":"Society for Industrial and Applied Mathematics","article_type":"original","type":"journal_article"},{"quality_controlled":"1","day":"27","publication_status":"published","corr_author":"1","title":"Homological stability and densities of generalized configuration spaces","has_accepted_license":"1","intvolume":"        25","abstract":[{"lang":"eng","text":"We prove that the factorization homologies of a scheme with coefficients in truncated polynomial algebras compute the cohomologies of its generalized configuration spaces. Using Koszul duality between commutative algebras and Lie algebras, we obtain new expressions for the cohomologies of the latter. As a consequence, we obtain a uniform and conceptual approach for treating homological stability, homological densities, and arithmetic densities of generalized configuration spaces. Our results categorify, generalize, and in fact provide a conceptual understanding of the coincidences appearing in the work of Farb--Wolfson--Wood. Our computation of the stable homological densities also yields rational homotopy types, answering a question posed by Vakil--Wood. Our approach hinges on the study of homological stability of cohomological Chevalley complexes, which is of independent interest.\r\n"}],"publication":"Geometry & Topology","ec_funded":1,"publication_identifier":{"issn":["1364-0380"]},"month":"04","scopus_import":"1","volume":25,"isi":1,"citation":{"short":"Q.P. Ho, Geometry &#38; Topology 25 (2021) 813–912.","apa":"Ho, Q. P. (2021). Homological stability and densities of generalized configuration spaces. <i>Geometry &#38; Topology</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/gt.2021.25.813\">https://doi.org/10.2140/gt.2021.25.813</a>","ama":"Ho QP. Homological stability and densities of generalized configuration spaces. <i>Geometry &#38; Topology</i>. 2021;25(2):813-912. doi:<a href=\"https://doi.org/10.2140/gt.2021.25.813\">10.2140/gt.2021.25.813</a>","chicago":"Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” <i>Geometry &#38; Topology</i>. Mathematical Sciences Publishers, 2021. <a href=\"https://doi.org/10.2140/gt.2021.25.813\">https://doi.org/10.2140/gt.2021.25.813</a>.","ista":"Ho QP. 2021. Homological stability and densities of generalized configuration spaces. Geometry &#38; Topology. 25(2), 813–912.","mla":"Ho, Quoc P. “Homological Stability and Densities of Generalized Configuration Spaces.” <i>Geometry &#38; Topology</i>, vol. 25, no. 2, Mathematical Sciences Publishers, 2021, pp. 813–912, doi:<a href=\"https://doi.org/10.2140/gt.2021.25.813\">10.2140/gt.2021.25.813</a>.","ieee":"Q. P. Ho, “Homological stability and densities of generalized configuration spaces,” <i>Geometry &#38; Topology</i>, vol. 25, no. 2. Mathematical Sciences Publishers, pp. 813–912, 2021."},"article_processing_charge":"No","page":"813-912","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593"},{"name":"Algebro-Geometric Applications of Factorization Homology","call_identifier":"FWF","_id":"26B96266-B435-11E9-9278-68D0E5697425","grant_number":"M02751"}],"language":[{"iso":"eng"}],"author":[{"id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Quoc P","last_name":"Ho","full_name":"Ho, Quoc P","orcid":"0000-0001-6889-1418"}],"acknowledgement":"This paper owes an obvious intellectual debt to the illuminating treatments of factorization homology by J.\r\nFrancis, D. Gaitsgory, and J. Lurie in [GL,G1, FG]. The author would like to thank B. Farb and J. Wolfson for\r\nbringing the question of explaining coincidences in homological densities to his attention. Moreover, the author\r\nthanks J. Wolfson for many helpful conversations on the subject, O. Randal-Williams for many comments which\r\ngreatly help improve the exposition, and G. C. Drummond-Cole for many useful conversations on L∞-algebras.\r\nFinally, the author is grateful to the anonymous referee for carefully reading the manuscript and for providing\r\nnumerous comments which greatly helped improve the clarity and precision of the exposition.\r\nThis work is supported by the Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 of\r\nthe European Research Council and the Lise Meitner fellowship “Algebro-Geometric Applications of Factorization\r\nHomology,” Austrian Science Fund (FWF): M 2751.","arxiv":1,"oa":1,"date_updated":"2025-04-14T09:09:36Z","external_id":{"isi":["000682738600005"],"arxiv":["1802.07948"]},"department":[{"_id":"TaHa"}],"file":[{"date_created":"2021-05-03T06:54:06Z","success":1,"content_type":"application/pdf","relation":"main_file","file_size":479268,"file_name":"densities.pdf","file_id":"9366","creator":"qho","access_level":"open_access","date_updated":"2021-05-03T06:54:06Z","checksum":"643a8d2d6f06f0888dcd7503f55d0920"}],"_id":"9359","oa_version":"Submitted Version","file_date_updated":"2021-05-03T06:54:06Z","doi":"10.2140/gt.2021.25.813","publisher":"Mathematical Sciences Publishers","article_type":"original","type":"journal_article","year":"2021","issue":"2","ddc":["514","516","512"],"date_published":"2021-04-27T00:00:00Z","status":"public","keyword":["Generalized configuration spaces","homological stability","homological densities","chiral algebras","chiral homology","factorization algebras","Koszul duality","Ran space"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-05-02T06:59:33Z"},{"quality_controlled":"1","day":"14","publication_status":"published","title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","has_accepted_license":"1","abstract":[{"text":"The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM.","lang":"eng"}],"intvolume":"         6","publication":"mSphere","scopus_import":"1","month":"04","volume":6,"publication_identifier":{"eissn":["2379-5042"]},"acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","oa":1,"citation":{"ieee":"M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein,” <i>mSphere</i>, vol. 6, no. 2. American Society for Microbiology, 2021.","mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>.","chicago":"Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>. American Society for Microbiology, 2021. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>.","ista":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 6(2), e01024-20.","apa":"Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., &#38; Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>MSphere</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>","ama":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>mSphere</i>. 2021;6(2). doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021)."},"isi":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"author":[{"full_name":"Gast, Matthieu","first_name":"Matthieu","last_name":"Gast"},{"first_name":"Nicole P.","last_name":"Kadzioch","full_name":"Kadzioch, Nicole P."},{"full_name":"Milius, Doreen","first_name":"Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87","last_name":"Milius"},{"first_name":"Francesco","last_name":"Origgi","full_name":"Origgi, Francesco"},{"full_name":"Plattet, Philippe","last_name":"Plattet","first_name":"Philippe"}],"department":[{"_id":"Bio"}],"date_updated":"2026-04-02T13:58:38Z","external_id":{"pmid":["33853875"],"isi":["000663823400025"]},"doi":"10.1128/mSphere.01024-20","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file":[{"checksum":"310748d140c8838335c1314431095898","date_updated":"2021-05-04T12:41:38Z","access_level":"open_access","creator":"kschuh","file_id":"9370","file_name":"2021_mSphere_Gast.pdf","file_size":3379349,"relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2021-05-04T12:41:38Z"}],"_id":"9361","article_number":"e01024-20","oa_version":"Published Version","file_date_updated":"2021-05-04T12:41:38Z","year":"2021","pmid":1,"issue":"2","ddc":["570"],"publisher":"American Society for Microbiology","type":"journal_article","date_created":"2021-05-02T22:01:28Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-04-14T00:00:00Z","status":"public"},{"oa":1,"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","language":[{"iso":"eng"}],"author":[{"last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J"},{"last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"}],"isi":1,"article_processing_charge":"No","citation":{"ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” <i>PLoS ONE</i>, vol. 16, no. 4. Public Library of Science, 2021.","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. 2021;16(4). doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>","apa":"Chalk, M. J., Tkačik, G., &#38; Marre, O. (2021). Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>.","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940."},"month":"04","scopus_import":"1","volume":16,"publication_identifier":{"eissn":["1932-6203"]},"intvolume":"        16","abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"publication":"PLoS ONE","title":"Inferring the function performed by a recurrent neural network","publication_status":"published","has_accepted_license":"1","day":"15","quality_controlled":"1","date_created":"2021-05-02T22:01:28Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-04-15T00:00:00Z","status":"public","pmid":1,"issue":"4","ddc":["570"],"year":"2021","publisher":"Public Library of Science","type":"journal_article","article_type":"original","doi":"10.1371/journal.pone.0248940","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","file_date_updated":"2021-05-04T13:22:19Z","article_number":"e0248940","_id":"9362","file":[{"date_created":"2021-05-04T13:22:19Z","success":1,"content_type":"application/pdf","relation":"main_file","creator":"kschuh","file_name":"2021_pone_Chalk.pdf","file_size":2768282,"file_id":"9371","checksum":"c52da133850307d2031f552d998f00e8","access_level":"open_access","date_updated":"2021-05-04T13:22:19Z"}],"department":[{"_id":"GaTk"}],"external_id":{"isi":["000641474900072"],"pmid":["33857170"]},"date_updated":"2026-04-02T13:58:56Z"},{"ddc":["570"],"pmid":1,"issue":"4","year":"2021","type":"journal_article","publisher":"Public Library of Science","date_created":"2021-05-02T22:01:29Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_published":"2021-04-01T00:00:00Z","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"external_id":{"pmid":["33857132"],"isi":["000640606700001"]},"date_updated":"2026-04-02T14:07:10Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1371/journal.pgen.1009479","file_date_updated":"2021-05-04T09:05:27Z","oa_version":"Published Version","file":[{"relation":"main_file","date_created":"2021-05-04T09:05:27Z","success":1,"content_type":"application/pdf","checksum":"82a74668f863e8dfb22fdd4f845c92ce","access_level":"open_access","date_updated":"2021-05-04T09:05:27Z","creator":"kschuh","file_name":"2021_PLOS_Ingles-Prieto.pdf","file_size":3072764,"file_id":"9369"}],"_id":"9363","volume":17,"scopus_import":"1","month":"04","publication_identifier":{"eissn":["1553-7404"]},"oa":1,"acknowledgement":"We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis.","author":[{"orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro"},{"full_name":"Furthmann, Nikolas","last_name":"Furthmann","first_name":"Nikolas"},{"full_name":"Crossman, Samuel H.","last_name":"Crossman","first_name":"Samuel H."},{"full_name":"Tichy, Alexandra Madelaine","last_name":"Tichy","first_name":"Alexandra Madelaine"},{"last_name":"Hoyer","first_name":"Nina","full_name":"Hoyer, Nina"},{"last_name":"Petersen","first_name":"Meike","full_name":"Petersen, Meike"},{"full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden"},{"full_name":"Bicher, Julia","last_name":"Bicher","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Gschaider-Reichhart","full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738"},{"orcid":"0000-0002-1819-198X","full_name":"György, Attila","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila"},{"last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"first_name":"Peter","last_name":"Soba","full_name":"Soba, Peter"},{"first_name":"Konstanze F.","last_name":"Winklhofer","full_name":"Winklhofer, Konstanze F."},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak"}],"language":[{"iso":"eng"}],"page":"e1009479","citation":{"chicago":"Inglés Prieto, Álvaro, Nikolas Furthmann, Samuel H. Crossman, Alexandra Madelaine Tichy, Nina Hoyer, Meike Petersen, Vanessa Zheden, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” <i>PLoS Genetics</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>.","ista":"Inglés Prieto Á, Furthmann N, Crossman SH, Tichy AM, Hoyer N, Petersen M, Zheden V, Bicher J, Gschaider-Reichhart E, György A, Siekhaus DE, Soba P, Winklhofer KF, Janovjak HL. 2021. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 17(4), e1009479.","ama":"Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS genetics</i>. 2021;17(4):e1009479. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>","apa":"Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N., Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>","short":"Á. Inglés Prieto, N. Furthmann, S.H. Crossman, A.M. Tichy, N. Hoyer, M. Petersen, V. Zheden, J. Bicher, E. Gschaider-Reichhart, A. György, D.E. Siekhaus, P. Soba, K.F. Winklhofer, H.L. Janovjak, PLoS Genetics 17 (2021) e1009479.","ieee":"Á. Inglés Prieto <i>et al.</i>, “Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease,” <i>PLoS genetics</i>, vol. 17, no. 4. Public Library of Science, p. e1009479, 2021.","mla":"Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” <i>PLoS Genetics</i>, vol. 17, no. 4, Public Library of Science, 2021, p. e1009479, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>."},"isi":1,"article_processing_charge":"No","day":"01","quality_controlled":"1","publication":"PLoS genetics","intvolume":"        17","abstract":[{"lang":"eng","text":"Optogenetics has been harnessed to shed new mechanistic light on current and future therapeutic strategies. This has been to date achieved by the regulation of ion flow and electrical signals in neuronal cells and neural circuits that are known to be affected by disease. In contrast, the optogenetic delivery of trophic biochemical signals, which support cell survival and are implicated in degenerative disorders, has never been demonstrated in an animal model of disease. Here, we reengineered the human and Drosophila melanogaster REarranged during Transfection (hRET and dRET) receptors to be activated by light, creating one-component optogenetic tools termed Opto-hRET and Opto-dRET. Upon blue light stimulation, these receptors robustly induced the MAPK/ERK proliferative signaling pathway in cultured cells. In PINK1B9 flies that exhibit loss of PTEN-induced putative kinase 1 (PINK1), a kinase associated with familial Parkinson’s disease (PD), light activation of Opto-dRET suppressed mitochondrial defects, tissue degeneration and behavioral deficits. In human cells with PINK1 loss-of-function, mitochondrial fragmentation was rescued using Opto-dRET via the PI3K/NF-кB pathway. Our results demonstrate that a light-activated receptor can ameliorate disease hallmarks in a genetic model of PD. The optogenetic delivery of trophic signals is cell type-specific and reversible and thus has the potential to inspire novel strategies towards a spatio-temporal regulation of tissue repair."}],"has_accepted_license":"1","publication_status":"published","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease"},{"intvolume":"       186","abstract":[{"text":"The quality control system for messenger RNA (mRNA) is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3'-Phosphoinositide-Dependent Protein Kinase1 (PDK1), a master regulator that is essential throughout eukaryotic growth and development, we employed a forward genetic approach to screen for suppressors of the loss-of-function T-DNA insertion double mutant pdk1.1 pdk1.2 in Arabidopsis thaliana. Notably, the severe growth attenuation of pdk1.1 pdk1.2 was rescued by sop21 (suppressor of pdk1.1 pdk1.2), which harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast (Saccharomyces cerevisiae) DOM34p, which each form a heterodimeric complex with the GTPase HBS1 (HSP70 SUBFAMILY B SUPPRESSOR1, also called SUPERKILLER PROTEIN7, SKI7), a protein that is responsible for ribosomal rescue and thereby assures the quality and fidelity of mRNA molecules during translation. Genetic analysis further revealed that a dysfunctional PEL1-HBS1 complex failed to degrade the T-DNA-disrupted PDK1 transcripts, which were truncated but functional, and thus rescued the growth and developmental defects of pdk1.1 pdk1.2. Our studies demonstrated the functionality of a homologous PELOTA-HBS1 complex and identified its essential regulatory role in plants, providing insights into the mechanism of mRNA quality control.","lang":"eng"}],"publication":"Plant Physiology","title":"mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth","publication_status":"published","day":"30","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1093/plphys/kiab199","open_access":"1"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"723-2015","name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","_id":"256FEF10-B435-11E9-9278-68D0E5697425"},{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Kong","first_name":"W","full_name":"Kong, W"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"full_name":"Zhao, Q","first_name":"Q","last_name":"Zhao"},{"full_name":"Lin, DL","last_name":"Lin","first_name":"DL"},{"first_name":"ZH","last_name":"Xu","full_name":"Xu, ZH"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"first_name":"HW","last_name":"Xue","full_name":"Xue, HW"}],"isi":1,"citation":{"ieee":"W. Kong <i>et al.</i>, “mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth,” <i>Plant Physiology</i>, vol. 186, no. 4. American Society of Plant Biologists, pp. 2003–2020, 2021.","mla":"Kong, W., et al. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” <i>Plant Physiology</i>, vol. 186, no. 4, American Society of Plant Biologists, 2021, pp. 2003–20, doi:<a href=\"https://doi.org/10.1093/plphys/kiab199\">10.1093/plphys/kiab199</a>.","ista":"Kong W, Tan S, Zhao Q, Lin D, Xu Z, Friml J, Xue H. 2021. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. Plant Physiology. 186(4), 2003–2020.","chicago":"Kong, W, Shutang Tan, Q Zhao, DL Lin, ZH Xu, Jiří Friml, and HW Xue. “MRNA Surveillance Complex PELOTA-HBS1 Eegulates Phosphoinositide-Sependent Protein Kinase1 and Plant Growth.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2021. <a href=\"https://doi.org/10.1093/plphys/kiab199\">https://doi.org/10.1093/plphys/kiab199</a>.","apa":"Kong, W., Tan, S., Zhao, Q., Lin, D., Xu, Z., Friml, J., &#38; Xue, H. (2021). mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1093/plphys/kiab199\">https://doi.org/10.1093/plphys/kiab199</a>","ama":"Kong W, Tan S, Zhao Q, et al. mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth. <i>Plant Physiology</i>. 2021;186(4):2003-2020. doi:<a href=\"https://doi.org/10.1093/plphys/kiab199\">10.1093/plphys/kiab199</a>","short":"W. Kong, S. Tan, Q. Zhao, D. Lin, Z. Xu, J. Friml, H. Xue, Plant Physiology 186 (2021) 2003–2020."},"article_processing_charge":"No","page":"2003-2020","oa":1,"acknowledgement":"We gratefully acknowledge the Arabidopsis Biological Resource Centre (ABRC) for providing T-DNA insertional mutants, and Prof. Remko Offringa for sharing published seeds. We thank Yuchuan Liu (Shanghai OE Biotech Co., Ltd) for help with proteomics data analysis, Xixi Zhang (IST Austria) for providing the pDONR-P4P1r-mCherry plasmid, and Yao Xiao (Technical University of Munich), Alexander Johnson (IST Austria) and Hana Semeradova (IST Austria) for helpful discussions. The study was supported by National Natural Science Foundation of China (NSFC, 31721001, 91954206, to H.-W. X.), “Ten-Thousand Talent Program” (to H.-W. X.) and Collaborative Innovation Center of Crop Stress Biology, Henan Province, and Austrian Science Fund (FWF): I 3630-B25 (to J. F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015).","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"month":"04","scopus_import":"1","volume":186,"oa_version":"Published Version","_id":"9368","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"doi":"10.1093/plphys/kiab199","external_id":{"pmid":["33930167"],"isi":["000703922000025"]},"date_updated":"2026-06-18T19:48:17Z","department":[{"_id":"JiFr"}],"date_published":"2021-04-30T00:00:00Z","status":"public","date_created":"2021-05-03T13:28:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Society of Plant Biologists","article_type":"original","type":"journal_article","issue":"4","pmid":1,"ddc":["580"],"year":"2021"},{"oa":1,"acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","language":[{"iso":"eng"}],"author":[{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"last_name":"Servedio","first_name":"Maria R.","full_name":"Servedio, Maria R."},{"first_name":"Carole M.","last_name":"Smadja","full_name":"Smadja, Carole M."},{"full_name":"Bank, Claudia","first_name":"Claudia","last_name":"Bank"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"Samuel M.","last_name":"Flaxman","full_name":"Flaxman, Samuel M."},{"full_name":"Giraud, Tatiana","last_name":"Giraud","first_name":"Tatiana"},{"full_name":"Hopkins, Robin","first_name":"Robin","last_name":"Hopkins"},{"full_name":"Larson, Erica L.","last_name":"Larson","first_name":"Erica L."},{"full_name":"Maan, Martine E.","last_name":"Maan","first_name":"Martine E."},{"first_name":"Joana","last_name":"Meier","full_name":"Meier, Joana"},{"last_name":"Merrill","first_name":"Richard","full_name":"Merrill, Richard"},{"full_name":"Noor, Mohamed A. F.","last_name":"Noor","first_name":"Mohamed A. F."},{"last_name":"Ortiz‐Barrientos","first_name":"Daniel","full_name":"Ortiz‐Barrientos, Daniel"},{"last_name":"Qvarnström","first_name":"Anna","full_name":"Qvarnström, Anna"}],"isi":1,"citation":{"mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” <i>Evolution</i>, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:<a href=\"https://doi.org/10.1111/evo.14235\">10.1111/evo.14235</a>.","ieee":"R. K. Butlin <i>et al.</i>, “Homage to Felsenstein 1981, or why are there so few/many species?,” <i>Evolution</i>, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” <i>Evolution</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/evo.14235\">https://doi.org/10.1111/evo.14235</a>.","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988.","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14235\">https://doi.org/10.1111/evo.14235</a>","ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? <i>Evolution</i>. 2021;75(5):978-988. doi:<a href=\"https://doi.org/10.1111/evo.14235\">10.1111/evo.14235</a>","short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988."},"article_processing_charge":"No","page":"978-988","scopus_import":"1","month":"04","volume":75,"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"abstract":[{"text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since.","lang":"eng"}],"intvolume":"        75","publication":"Evolution","publication_status":"published","title":"Homage to Felsenstein 1981, or why are there so few/many species?","main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235","open_access":"1"}],"day":"19","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-05-06T04:34:47Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"date_published":"2021-04-19T00:00:00Z","status":"public","issue":"5","ddc":["570"],"year":"2021","publisher":"Wiley","type":"journal_article","article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1111/evo.14235","oa_version":"Published Version","_id":"9374","department":[{"_id":"NiBa"}],"external_id":{"isi":["000647224000001"]},"date_updated":"2026-06-18T19:48:42Z"}]