[{"file_date_updated":"2021-04-26T09:33:44Z","file":[{"file_id":"9328","file_size":802586232,"date_updated":"2021-04-16T14:15:12Z","date_created":"2021-04-16T14:15:12Z","success":1,"access_level":"open_access","checksum":"0324cb519273371708743f3282e7c081","creator":"gsperl","file_name":"MADYPG_extra_data.zip","content_type":"application/zip","relation":"main_file"},{"file_id":"9353","file_size":64962865,"date_updated":"2021-04-26T09:33:44Z","date_created":"2021-04-26T09:33:44Z","access_level":"open_access","checksum":"4c224551adf852b136ec21a4e13f0c1b","creator":"pub-gitlab-bot","content_type":"application/gzip","relation":"main_file","file_name":"MADYPG.zip"}],"ddc":["005"],"license":"https://opensource.org/licenses/MIT","type":"software","citation":{"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>.","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>","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>","short":"G. Sperl, R. Narain, C. Wojtan, (2021).","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>.","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>.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021."},"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"}],"date_published":"2021-05-01T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_for_analysis_in","id":"9818"}]},"date_created":"2021-04-16T14:26:19Z","title":"Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data)","gitlab_url":"https://git.ist.ac.at/gsperl/MADYPG","doi":"10.15479/AT:ISTA:9327","year":"2021","oa":1,"tmp":{"short":"MIT","name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT"},"_id":"9327","has_accepted_license":"1","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","gitlab_commit_id":"6a77e7e22769230ae5f5edaa090fb4b828e57573","date_updated":"2026-06-18T19:57:47Z","publisher":"IST Austria","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"author":[{"full_name":"Sperl, Georg","first_name":"Georg","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","last_name":"Sperl"},{"last_name":"Narain","first_name":"Rahul","full_name":"Narain, Rahul"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan"}],"month":"05"},{"oa_version":"Published Version","date_created":"2021-04-18T22:01:39Z","publication_status":"published","article_processing_charge":"Yes (via OA deal)","title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","issue":"6","article_type":"original","file_date_updated":"2021-04-19T08:30:22Z","pmid":1,"file":[{"file_size":6924738,"file_id":"9339","date_updated":"2021-04-19T08:30:22Z","checksum":"2a5800d91b96d08b525e17319dcd5e44","access_level":"open_access","date_created":"2021-04-19T08:30:22Z","success":1,"content_type":"application/pdf","file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","relation":"main_file","creator":"dernst"}],"external_id":{"isi":["000661088500005"],"pmid":["33711356"]},"abstract":[{"lang":"eng","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."}],"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"Elsevier","isi":1,"project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020"},{"name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312","call_identifier":"FWF","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Zhang, Xiaomin","last_name":"Zhang","first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"}],"oa":1,"scopus_import":"1","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","has_accepted_license":"1","article_number":"109125","date_published":"2021-03-09T00:00:00Z","day":"09","doi":"10.1016/j.jneumeth.2021.109125","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       357","publication":"Journal of Neuroscience Methods","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.","ddc":["570"],"volume":357,"citation":{"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.","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).","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>","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>.","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>.","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."},"type":"journal_article","ec_funded":1,"publication_identifier":{"issn":["0165-0270"],"eissn":["1872-678X"]},"month":"03","acknowledged_ssus":[{"_id":"SSU"}],"year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9329","date_updated":"2025-06-12T06:39:15Z"},{"project":[{"call_identifier":"H2020","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Schöpf, Clemens L.","last_name":"Schöpf","first_name":"Clemens L."},{"full_name":"Ablinger, Cornelia","last_name":"Ablinger","first_name":"Cornelia"},{"last_name":"Geisler","first_name":"Stefanie M.","full_name":"Geisler, Stefanie M."},{"full_name":"Stanika, Ruslan I.","last_name":"Stanika","first_name":"Ruslan I."},{"full_name":"Campiglio, Marta","last_name":"Campiglio","first_name":"Marta"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"last_name":"Nimmervoll","first_name":"Benedikt","full_name":"Nimmervoll, Benedikt"},{"full_name":"Schlick, Bettina","last_name":"Schlick","first_name":"Bettina"},{"full_name":"Brockhaus, Johannes","last_name":"Brockhaus","first_name":"Johannes"},{"full_name":"Missler, Markus","last_name":"Missler","first_name":"Markus"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Obermair, Gerald J.","last_name":"Obermair","first_name":"Gerald J."}],"isi":1,"department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publisher":"National Academy of Sciences","status":"public","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1","issue":"14","article_processing_charge":"No","title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","publication_status":"published","oa_version":"Published Version","date_created":"2021-04-18T22:01:40Z","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"}],"external_id":{"isi":["000637398300002"],"pmid":["33782113"]},"pmid":1,"file":[{"checksum":"dd014f68ae9d7d8d8fc4139a24e04506","access_level":"open_access","date_created":"2021-04-19T10:10:56Z","success":1,"file_name":"2021_PNAS_Schoepf.pdf","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":2603911,"file_id":"9340","date_updated":"2021-04-19T10:10:56Z"}],"article_type":"original","file_date_updated":"2021-04-19T10:10:56Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"04","publication_identifier":{"eissn":["1091-6490"]},"ec_funded":1,"date_updated":"2025-06-12T06:56:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9330","year":"2021","doi":"10.1073/pnas.1920827118","day":"06","date_published":"2021-04-06T00:00:00Z","citation":{"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>","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).","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.","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>.","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>.","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>"},"type":"journal_article","ddc":["570"],"volume":118,"intvolume":"       118","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":"Proceedings of the National Academy of Sciences of the United States of America","language":[{"iso":"eng"}],"quality_controlled":"1"},{"oa_version":"Published Version","date_created":"2021-04-18T22:01:41Z","publication_status":"published","article_processing_charge":"No","title":"Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis","issue":"8","article_type":"original","file_date_updated":"2021-04-19T10:54:55Z","pmid":1,"file":[{"content_type":"application/pdf","file_name":"2021_JourMolecularScience_Oetvoes.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","date_created":"2021-04-19T10:54:55Z","success":1,"checksum":"26ada2531ad1f9c01a1664de0431f1fe","date_updated":"2021-04-19T10:54:55Z","file_id":"9342","file_size":2769717}],"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."}],"external_id":{"isi":["000644394800001"],"pmid":["33917959"]},"publisher":"MDPI","department":[{"_id":"EvBe"}],"isi":1,"author":[{"full_name":"Ötvös, Krisztina","orcid":"0000-0002-5503-4983","last_name":"Ötvös","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina"},{"last_name":"Miskolczi","first_name":"Pál","full_name":"Miskolczi, Pál"},{"orcid":"0000-0001-5227-5741","full_name":"Marhavý, Peter","last_name":"Marhavý","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"full_name":"Cruz-Ramírez, Alfredo","last_name":"Cruz-Ramírez","first_name":"Alfredo"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"full_name":"Bakó, László","last_name":"Bakó","first_name":"László"}],"oa":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","has_accepted_license":"1","article_number":"3862","date_published":"2021-04-08T00:00:00Z","day":"08","doi":"10.3390/ijms22083862","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        22","publication":"International Journal of Molecular Sciences","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.","ddc":["570"],"volume":22,"citation":{"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.","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>","short":"K. Ötvös, P. Miskolczi, P. Marhavý, A. Cruz-Ramírez, E. Benková, S. Robert, L. Bakó, International Journal of Molecular Sciences 22 (2021).","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>","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>.","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>.","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."},"type":"journal_article","publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"month":"04","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9332","date_updated":"2025-06-12T06:39:41Z"},{"title":"A note on the Fröhlich dynamics in the strong coupling limit","article_processing_charge":"No","date_created":"2021-04-18T22:01:41Z","publication_status":"published","oa_version":"Published Version","file_date_updated":"2021-04-19T10:40:01Z","article_type":"original","external_id":{"isi":["000637359300002"]},"abstract":[{"lang":"eng","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."}],"file":[{"date_updated":"2021-04-19T10:40:01Z","file_size":438084,"file_id":"9341","creator":"dernst","file_name":"2021_LettersMathPhysics_Mitrouskas.pdf","content_type":"application/pdf","relation":"main_file","checksum":"be56c0845a43c0c5c772ee0b5053f7d7","date_created":"2021-04-19T10:40:01Z","success":1,"access_level":"open_access"}],"isi":1,"department":[{"_id":"RoSe"}],"publisher":"Springer Nature","author":[{"last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes","full_name":"Mitrouskas, David Johannes"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"status":"public","has_accepted_license":"1","day":"05","date_published":"2021-04-05T00:00:00Z","article_number":"45","doi":"10.1007/s11005-021-01380-7","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.","publication":"Letters in Mathematical Physics","intvolume":"       111","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","citation":{"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.","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>","short":"D.J. Mitrouskas, Letters in Mathematical Physics 111 (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>.","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>.","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>","ista":"Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45."},"volume":111,"ddc":["510"],"publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"month":"04","year":"2021","date_updated":"2026-04-02T13:58:00Z","_id":"9333","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"citation":{"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).","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>","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>.","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>.","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.","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>"},"type":"journal_article","volume":7,"ddc":["530"],"publication":"Science Advances","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. ","intvolume":"         7","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abf2690","day":"02","article_number":"eabf2690","date_published":"2021-04-02T00:00:00Z","date_updated":"2026-04-02T13:58:21Z","_id":"9334","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2021","month":"04","publication_identifier":{"eissn":["2375-2548"]},"external_id":{"isi":["000636455600027"],"pmid":["33811076"]},"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."}],"file":[{"date_created":"2021-04-19T11:17:29Z","success":1,"access_level":"open_access","checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_name":"2021_ScienceAdv_Duan.pdf","file_id":"9343","file_size":717489,"date_updated":"2021-04-19T11:17:29Z"}],"pmid":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2021-04-19T11:17:29Z","article_type":"original","issue":"14","article_processing_charge":"No","title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","oa_version":"Published Version","date_created":"2021-04-18T22:01:42Z","publication_status":"published","status":"public","has_accepted_license":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"scopus_import":"1","oa":1,"author":[{"full_name":"Duan, J.","last_name":"Duan","first_name":"J."},{"last_name":"Álvarez-Pérez","first_name":"G.","full_name":"Álvarez-Pérez, G."},{"full_name":"Voronin, K. V.","first_name":"K. V.","last_name":"Voronin"},{"last_name":"Prieto Gonzalez","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357"},{"last_name":"Taboada-Gutiérrez","first_name":"J.","full_name":"Taboada-Gutiérrez, J."},{"first_name":"V. S.","last_name":"Volkov","full_name":"Volkov, V. S."},{"first_name":"J.","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, J."},{"full_name":"Nikitin, A. Y.","last_name":"Nikitin","first_name":"A. Y."},{"full_name":"Alonso-González, P.","first_name":"P.","last_name":"Alonso-González"}],"isi":1,"publisher":"AAAS","department":[{"_id":"NanoFab"}]},{"article_processing_charge":"No","title":"The waiting time phenomenon in spatially discretized porous medium and thin film equations","arxiv":1,"publication_status":"published","oa_version":"Preprint","date_created":"2021-04-18T22:01:42Z","issue":"1","article_type":"original","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"}],"external_id":{"isi":["000625044600003"],"arxiv":["1911.04185"]},"page":"60-87","isi":1,"department":[{"_id":"JuFi"}],"publisher":"Society for Industrial and Applied Mathematics","author":[{"last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"},{"last_name":"Matthes","first_name":"Daniel","full_name":"Matthes, Daniel"}],"oa":1,"scopus_import":"1","status":"public","day":"01","date_published":"2021-01-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.04185"}],"doi":"10.1137/19M1300017","intvolume":"        59","acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”.","publication":"SIAM Journal on Numerical Analysis","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"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.","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>","short":"J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 60–87.","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>","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>.","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>.","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."},"volume":59,"publication_identifier":{"issn":["0036-1429"]},"month":"01","year":"2021","date_updated":"2023-08-08T13:10:40Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9335"},{"scopus_import":"1","oa":1,"status":"public","isi":1,"publisher":"Elsevier","department":[{"_id":"RoSe"}],"author":[{"first_name":"Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","last_name":"Brooks","orcid":"0000-0002-6249-0928","full_name":"Brooks, Morris"},{"last_name":"Di Gesù","first_name":"Giacomo","full_name":"Di Gesù, Giacomo"}],"article_type":"original","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."}],"external_id":{"arxiv":["1911.03187"],"isi":["000644702800005"]},"arxiv":1,"article_processing_charge":"No","title":"Sharp tunneling estimates for a double-well model in infinite dimension","date_created":"2021-04-25T22:01:29Z","publication_status":"published","oa_version":"Preprint","issue":"3","year":"2021","date_updated":"2023-08-08T13:15:11Z","_id":"9348","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"month":"04","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":"Journal of Functional Analysis","intvolume":"       281","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","citation":{"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.","short":"M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021).","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>","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>.","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>.","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>","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."},"volume":281,"day":"07","main_file_link":[{"url":"https://arxiv.org/abs/1911.03187","open_access":"1"}],"article_number":"109029","date_published":"2021-04-07T00:00:00Z","doi":"10.1016/j.jfa.2021.109029"},{"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).","publication":"Biophysical Journal","intvolume":"       120","quality_controlled":"1","language":[{"iso":"eng"}],"citation":{"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.","short":"F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal 120 (2021) 4182–4192.","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>.","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>.","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>","ista":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together: when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192."},"type":"journal_article","volume":120,"ddc":["570"],"day":"05","main_file_link":[{"open_access":"1","url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view"}],"date_published":"2021-10-05T00:00:00Z","doi":"10.1016/j.bpj.2021.03.025","year":"2021","date_updated":"2026-06-18T19:47:51Z","_id":"9350","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"month":"10","article_type":"original","page":"4182-4192","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"}],"external_id":{"isi":["000704646900006"],"pmid":["33794149"]},"pmid":1,"title":"Holding it together: when cadherin meets cadherin","article_processing_charge":"No","publication_status":"published","oa_version":"Published Version","date_created":"2021-04-25T22:01:30Z","related_material":{"record":[{"id":"12368","status":"public","relation":"dissertation_contains"}]},"scopus_import":"1","oa":1,"status":"public","isi":1,"publisher":"Biophysical Society","department":[{"_id":"CaHe"}],"author":[{"orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","last_name":"Arslan"},{"full_name":"Eckert, Julia","first_name":"Julia","last_name":"Eckert"},{"full_name":"Schmidt, Thomas","first_name":"Thomas","last_name":"Schmidt"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"corr_author":"1"},{"publication_identifier":{"issn":["1424-0637"]},"ec_funded":1,"month":"04","year":"2021","date_updated":"2025-06-12T06:39:59Z","_id":"9351","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","date_published":"2021-04-08T00:00:00Z","doi":"10.1007/s00023-021-01044-1","publication":"Annales Henri Poincare","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).","intvolume":"        22","quality_controlled":"1","language":[{"iso":"eng"}],"citation":{"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>.","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>.","short":"K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22 (2021) 2595–2618.","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>","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.","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>"},"type":"journal_article","volume":22,"ddc":["530"],"isi":1,"publisher":"Springer Nature","department":[{"_id":"RoSe"}],"author":[{"first_name":"Kay","last_name":"Kirkpatrick","full_name":"Kirkpatrick, Kay"},{"last_name":"Rademacher","first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466"},{"full_name":"Schlein, Benjamin","last_name":"Schlein","first_name":"Benjamin"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"has_accepted_license":"1","status":"public","arxiv":1,"article_processing_charge":"Yes (via OA deal)","title":"A large deviation principle in many-body quantum dynamics","publication_status":"published","oa_version":"Published Version","date_created":"2021-04-25T22:01:30Z","file_date_updated":"2021-10-15T11:15:40Z","article_type":"original","page":"2595-2618","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. "}],"external_id":{"isi":["000638022600001"],"arxiv":["2010.13754"],"pmid":["34776771"]},"file":[{"creator":"cchlebak","file_name":"2021_Annales_Kirkpatrick.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2021-10-15T11:15:40Z","success":1,"access_level":"open_access","checksum":"1a0fb963f2f415ba470881a794f20eb6","date_updated":"2021-10-15T11:15:40Z","file_id":"10143","file_size":522669}],"pmid":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9352","date_updated":"2023-08-08T13:13:37Z","year":"2021","month":"03","publication_identifier":{"issn":["0036-1429"]},"volume":59,"citation":{"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>.","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>.","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>","short":"J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis 59 (2021) 660–674.","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.","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.","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>"},"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        59","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.","publication":"SIAM Journal on Numerical Analysis","doi":"10.1137/19M1308992","date_published":"2021-03-09T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.11646"}],"day":"09","status":"public","oa":1,"scopus_import":"1","author":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dietmar","last_name":"Gallistl","full_name":"Gallistl, Dietmar"},{"last_name":"Peterseim","first_name":"Dietmar","full_name":"Peterseim, Dietmar"}],"publisher":"Society for Industrial and Applied Mathematics","department":[{"_id":"JuFi"}],"isi":1,"abstract":[{"lang":"eng","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."}],"external_id":{"isi":["000646030400003"],"arxiv":["1912.11646"]},"page":"660-674","article_type":"original","issue":"2","oa_version":"Preprint","publication_status":"published","date_created":"2021-04-25T22:01:31Z","article_processing_charge":"No","title":"A priori error analysis of a numerical stochastic homogenization method","arxiv":1},{"ec_funded":1,"publication_identifier":{"issn":["1364-0380"]},"month":"04","year":"2021","_id":"9359","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-04-14T09:09:36Z","date_published":"2021-04-27T00:00:00Z","day":"27","doi":"10.2140/gt.2021.25.813","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Geometry & Topology","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.","intvolume":"        25","volume":25,"ddc":["514","516","512"],"type":"journal_article","citation":{"short":"Q.P. Ho, Geometry &#38; Topology 25 (2021) 813–912.","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>.","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.","ista":"Ho QP. 2021. Homological stability and densities of generalized configuration spaces. Geometry &#38; Topology. 25(2), 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>"},"department":[{"_id":"TaHa"}],"publisher":"Mathematical Sciences Publishers","isi":1,"corr_author":"1","author":[{"id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Quoc P","last_name":"Ho","orcid":"0000-0001-6889-1418","full_name":"Ho, Quoc P"}],"project":[{"call_identifier":"FP7","grant_number":"320593","name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425"},{"_id":"26B96266-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02751","name":"Algebro-Geometric Applications of Factorization Homology"}],"scopus_import":"1","oa":1,"has_accepted_license":"1","status":"public","date_created":"2021-05-02T06:59:33Z","publication_status":"published","oa_version":"Submitted Version","arxiv":1,"article_processing_charge":"No","title":"Homological stability and densities of generalized configuration spaces","issue":"2","keyword":["Generalized configuration spaces","homological stability","homological densities","chiral algebras","chiral homology","factorization algebras","Koszul duality","Ran space"],"file_date_updated":"2021-05-03T06:54:06Z","article_type":"original","file":[{"date_updated":"2021-05-03T06:54:06Z","file_id":"9366","file_size":479268,"content_type":"application/pdf","relation":"main_file","file_name":"densities.pdf","creator":"qho","access_level":"open_access","date_created":"2021-05-03T06:54:06Z","success":1,"checksum":"643a8d2d6f06f0888dcd7503f55d0920"}],"page":"813-912","abstract":[{"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","lang":"eng"}],"external_id":{"arxiv":["1802.07948"],"isi":["000682738600005"]}},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"9361","date_updated":"2026-04-02T13:58:38Z","year":"2021","month":"04","publication_identifier":{"eissn":["2379-5042"]},"ddc":["570"],"volume":6,"citation":{"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>.","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>.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","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>","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.","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>"},"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"         6","publication":"mSphere","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","doi":"10.1128/mSphere.01024-20","article_number":"e01024-20","date_published":"2021-04-14T00:00:00Z","day":"14","has_accepted_license":"1","status":"public","oa":1,"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Gast","first_name":"Matthieu","full_name":"Gast, Matthieu"},{"first_name":"Nicole P.","last_name":"Kadzioch","full_name":"Kadzioch, Nicole P."},{"full_name":"Milius, Doreen","last_name":"Milius","first_name":"Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Origgi","first_name":"Francesco","full_name":"Origgi, Francesco"},{"full_name":"Plattet, Philippe","last_name":"Plattet","first_name":"Philippe"}],"department":[{"_id":"Bio"}],"publisher":"American Society for Microbiology","isi":1,"pmid":1,"file":[{"date_updated":"2021-05-04T12:41:38Z","file_size":3379349,"file_id":"9370","file_name":"2021_mSphere_Gast.pdf","relation":"main_file","content_type":"application/pdf","creator":"kschuh","checksum":"310748d140c8838335c1314431095898","access_level":"open_access","success":1,"date_created":"2021-05-04T12:41:38Z"}],"external_id":{"isi":["000663823400025"],"pmid":["33853875"]},"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"}],"file_date_updated":"2021-05-04T12:41:38Z","issue":"2","publication_status":"published","oa_version":"Published Version","date_created":"2021-05-02T22:01:28Z","article_processing_charge":"No","title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein"},{"article_processing_charge":"No","title":"Inferring the function performed by a recurrent neural network","oa_version":"Published Version","date_created":"2021-05-02T22:01:28Z","publication_status":"published","issue":"4","file_date_updated":"2021-05-04T13:22:19Z","article_type":"original","external_id":{"isi":["000641474900072"],"pmid":["33857170"]},"abstract":[{"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.","lang":"eng"}],"file":[{"checksum":"c52da133850307d2031f552d998f00e8","access_level":"open_access","date_created":"2021-05-04T13:22:19Z","success":1,"file_name":"2021_pone_Chalk.pdf","content_type":"application/pdf","relation":"main_file","creator":"kschuh","file_size":2768282,"file_id":"9371","date_updated":"2021-05-04T13:22:19Z"}],"pmid":1,"isi":1,"publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"author":[{"first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","last_name":"Chalk","full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","oa":1,"has_accepted_license":"1","status":"public","day":"15","date_published":"2021-04-15T00:00:00Z","article_number":"e0248940","doi":"10.1371/journal.pone.0248940","acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","publication":"PLoS ONE","intvolume":"        16","quality_controlled":"1","language":[{"iso":"eng"}],"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.","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>","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>.","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>.","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>","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940."},"type":"journal_article","volume":16,"ddc":["570"],"publication_identifier":{"eissn":["1932-6203"]},"month":"04","year":"2021","date_updated":"2026-04-02T13:58:56Z","_id":"9362","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"citation":{"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>","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.","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.","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>","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.","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>.","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>."},"type":"journal_article","ddc":["570"],"volume":17,"intvolume":"        17","publication":"PLoS genetics","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.","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1371/journal.pgen.1009479","day":"01","date_published":"2021-04-01T00:00:00Z","date_updated":"2026-04-02T14:07:10Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"9363","year":"2021","month":"04","publication_identifier":{"eissn":["1553-7404"]},"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."}],"external_id":{"isi":["000640606700001"],"pmid":["33857132"]},"page":"e1009479","pmid":1,"file":[{"date_updated":"2021-05-04T09:05:27Z","file_id":"9369","file_size":3072764,"creator":"kschuh","file_name":"2021_PLOS_Ingles-Prieto.pdf","content_type":"application/pdf","relation":"main_file","date_created":"2021-05-04T09:05:27Z","success":1,"access_level":"open_access","checksum":"82a74668f863e8dfb22fdd4f845c92ce"}],"file_date_updated":"2021-05-04T09:05:27Z","issue":"4","article_processing_charge":"No","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","publication_status":"published","oa_version":"Published Version","date_created":"2021-05-02T22:01:29Z","has_accepted_license":"1","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1","author":[{"first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Furthmann, Nikolas","last_name":"Furthmann","first_name":"Nikolas"},{"full_name":"Crossman, Samuel H.","first_name":"Samuel H.","last_name":"Crossman"},{"full_name":"Tichy, Alexandra Madelaine","first_name":"Alexandra Madelaine","last_name":"Tichy"},{"full_name":"Hoyer, Nina","last_name":"Hoyer","first_name":"Nina"},{"last_name":"Petersen","first_name":"Meike","full_name":"Petersen, Meike"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","last_name":"Zheden","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783"},{"full_name":"Bicher, Julia","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","last_name":"Bicher"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart"},{"orcid":"0000-0002-1819-198X","full_name":"György, Attila","first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","last_name":"Soba","full_name":"Soba, Peter"},{"full_name":"Winklhofer, Konstanze F.","first_name":"Konstanze F.","last_name":"Winklhofer"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"publisher":"Public Library of Science","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}]},{"month":"04","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9368","date_updated":"2026-06-18T19:48:17Z","year":"2021","doi":"10.1093/plphys/kiab199","date_published":"2021-04-30T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plphys/kiab199"}],"day":"30","ddc":["580"],"volume":186,"citation":{"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.","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>.","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>.","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.","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.","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>"},"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       186","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":"Plant Physiology","project":[{"name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis","grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","call_identifier":"FWF"}],"author":[{"full_name":"Kong, W","first_name":"W","last_name":"Kong"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","last_name":"Tan","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhao, Q","last_name":"Zhao","first_name":"Q"},{"first_name":"DL","last_name":"Lin","full_name":"Lin, DL"},{"last_name":"Xu","first_name":"ZH","full_name":"Xu, ZH"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xue, HW","last_name":"Xue","first_name":"HW"}],"publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"isi":1,"status":"public","oa":1,"scopus_import":"1","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"issue":"4","oa_version":"Published Version","publication_status":"published","date_created":"2021-05-03T13:28:20Z","title":"mRNA surveillance complex PELOTA-HBS1 eegulates phosphoinositide-sependent protein kinase1 and plant growth","article_processing_charge":"No","pmid":1,"external_id":{"pmid":["33930167"],"isi":["000703922000025"]},"abstract":[{"lang":"eng","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."}],"page":"2003-2020","article_type":"original"},{"month":"04","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"_id":"9374","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-18T19:48:42Z","year":"2021","doi":"10.1111/evo.14235","main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235","open_access":"1"}],"date_published":"2021-04-19T00:00:00Z","day":"19","volume":75,"ddc":["570"],"citation":{"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>","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.","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>.","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>.","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.","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>"},"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Evolution","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).","intvolume":"        75","author":[{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"full_name":"Servedio, Maria R.","last_name":"Servedio","first_name":"Maria R."},{"full_name":"Smadja, Carole M.","last_name":"Smadja","first_name":"Carole M."},{"last_name":"Bank","first_name":"Claudia","full_name":"Bank, Claudia"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Flaxman, Samuel M.","first_name":"Samuel M.","last_name":"Flaxman"},{"first_name":"Tatiana","last_name":"Giraud","full_name":"Giraud, 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.","first_name":"Martine E.","last_name":"Maan"},{"last_name":"Meier","first_name":"Joana","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."},{"full_name":"Ortiz‐Barrientos, Daniel","last_name":"Ortiz‐Barrientos","first_name":"Daniel"},{"full_name":"Qvarnström, Anna","last_name":"Qvarnström","first_name":"Anna"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","isi":1,"status":"public","scopus_import":"1","oa":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"5","publication_status":"published","date_created":"2021-05-06T04:34:47Z","oa_version":"Published Version","article_processing_charge":"No","title":"Homage to Felsenstein 1981, or why are there so few/many species?","page":"978-988","external_id":{"isi":["000647224000001"]},"abstract":[{"lang":"eng","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."}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"article_type":"original"},{"publication_identifier":{"eissn":["0027-8424"]},"month":"06","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9375","date_updated":"2025-05-14T10:58:04Z","date_published":"2021-06-21T00:00:00Z","article_number":"e2015005118","day":"21","doi":"10.1073/pnas.2015005118","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       118","publication":"Proceedings of the National Academy of Sciences of the United States of America","acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).","ddc":["570"],"volume":118,"citation":{"ieee":"J. I. Meier <i>et al.</i>, “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 25. National Academy of Sciences, 2021.","chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” <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.2015005118\">https://doi.org/10.1073/pnas.2015005118</a>.","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 25, e2015005118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2015005118\">10.1073/pnas.2015005118</a>.","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(25). doi:<a href=\"https://doi.org/10.1073/pnas.2015005118\">10.1073/pnas.2015005118</a>","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. <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.2015005118\">https://doi.org/10.1073/pnas.2015005118</a>","ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. Proceedings of the National Academy of Sciences of the United States of America. 118(25), e2015005118."},"type":"journal_article","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"isi":1,"author":[{"full_name":"Meier, Joana I.","first_name":"Joana I.","last_name":"Meier"},{"full_name":"Salazar, Patricio A.","first_name":"Patricio A.","last_name":"Salazar"},{"full_name":"Kučka, Marek","first_name":"Marek","last_name":"Kučka"},{"first_name":"Robert William","last_name":"Davies","full_name":"Davies, Robert William"},{"first_name":"Andreea","last_name":"Dréau","full_name":"Dréau, Andreea"},{"last_name":"Aldás","first_name":"Ismael","full_name":"Aldás, Ismael"},{"full_name":"Power, Olivia Box","last_name":"Power","first_name":"Olivia Box"},{"full_name":"Nadeau, Nicola J.","first_name":"Nicola J.","last_name":"Nadeau"},{"first_name":"Jon R.","last_name":"Bridle","full_name":"Bridle, Jon R."},{"last_name":"Rolian","first_name":"Campbell","full_name":"Rolian, Campbell"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"McMillan, W. Owen","first_name":"W. Owen","last_name":"McMillan"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"}],"oa":1,"scopus_import":"1","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","has_accepted_license":"1","publication_status":"published","oa_version":"Published Version","date_created":"2021-05-07T17:10:21Z","title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","article_processing_charge":"No","issue":"25","article_type":"original","file_date_updated":"2022-03-08T08:18:16Z","pmid":1,"file":[{"content_type":"application/pdf","relation":"main_file","file_name":"2021_PNAS_Meier.pdf","creator":"dernst","access_level":"open_access","success":1,"date_created":"2022-03-08T08:18:16Z","checksum":"cb30c6166b2132ee60d616b31a1a7c29","date_updated":"2022-03-08T08:18:16Z","file_id":"10835","file_size":20592929}],"abstract":[{"text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.","lang":"eng"}],"external_id":{"pmid":["34155138"],"isi":["000671755600001"]}},{"article_type":"original","file_date_updated":"2021-12-17T08:13:51Z","keyword":["multistability","mechanism","computational design","rigidity"],"abstract":[{"lang":"eng","text":"This paper presents a method for designing planar multistable compliant structures. Given a sequence of desired stable states and the corresponding poses of the structure, we identify the topology and geometric realization of a mechanism—consisting of bars and joints—that is able to physically reproduce the desired multistable behavior. In order to solve this problem efficiently, we build on insights from minimally rigid graph theory to identify simple but effective topologies for the mechanism. We then optimize its geometric parameters, such as joint positions and bar lengths, to obtain correct transitions between the given poses. Simultaneously, we ensure adequate stability of each pose based on an effective approximate error metric related to the elastic energy Hessian of the bars in the mechanism. As demonstrated by our results, we obtain functional multistable mechanisms of manageable complexity that can be fabricated using 3D printing. Further, we evaluated the effectiveness of our method on a large number of examples in the simulation and fabricated several physical prototypes."}],"external_id":{"isi":["000752079300003"]},"file":[{"date_updated":"2021-05-08T17:36:59Z","file_size":18926557,"file_id":"9377","creator":"bbickel","relation":"main_file","file_name":"Multistable-authorversion.pdf","content_type":"application/pdf","checksum":"8564b3118457d4c8939a8ef2b1a2f16c","date_created":"2021-05-08T17:36:59Z","access_level":"open_access"},{"file_name":"multistable-video.mp4","relation":"main_file","content_type":"video/mp4","creator":"bbickel","checksum":"3b6e874e30bfa1bfc3ad3498710145a1","access_level":"open_access","date_created":"2021-05-08T17:38:22Z","success":1,"date_updated":"2021-05-08T17:38:22Z","file_size":76542901,"file_id":"9378"},{"description":"This document provides additional results and analyzes the robustness and limitations of our approach.","date_updated":"2021-12-17T08:13:51Z","file_id":"10562","file_size":3367072,"creator":"bbickel","content_type":"application/pdf","relation":"supplementary_material","file_name":"multistable-supplementary material.pdf","date_created":"2021-12-17T08:13:51Z","access_level":"open_access","title":"Supplementary Material for “Computational Design of Planar Multistable Compliant Structures”","checksum":"20dc3bc42e1a912a5b0247c116772098"}],"article_processing_charge":"No","title":"Computational design of planar multistable compliant structures","publication_status":"published","oa_version":"Published Version","date_created":"2021-05-08T17:37:08Z","issue":"5","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1","has_accepted_license":"1","status":"public","isi":1,"department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","project":[{"call_identifier":"H2020","name":"Distributed 3D Object Design","grant_number":"642841","_id":"2508E324-B435-11E9-9278-68D0E5697425"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020"}],"author":[{"full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X","last_name":"Zhang","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran"},{"full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","last_name":"Auzinger"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"}],"intvolume":"        40","acknowledgement":"We would like to thank everyone who contributed to this paper, the authors of artworks for all the examples, including @macrovec-tor_official and Wikimedia for the FLAG semaphore, and @pikisuper-star for the FIGURINE. The photos of iconic poses in the teaser were supplied by (from left to right): Mike Hewitt/Olympics Day 8 - Athletics/Gettty Images, Oneinchpunch/Basketball player training on acourt in New york city/Shutterstock, and Andrew Redington/TigerWoods/Getty Images. We also want to express our gratitude to Christian Hafner for insightful discussions, the IST Austria machine shop SSU, all proof-readers, and anonymous reviewers. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska-Curie grant agreement No 642841 (DISTRO), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE).","publication":"ACM Transactions on Graphics","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"ieee":"R. Zhang, T. Auzinger, and B. Bickel, “Computational design of planar multistable compliant structures,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 5. Association for Computing Machinery, 2021.","chicago":"Zhang, Ran, Thomas Auzinger, and Bernd Bickel. “Computational Design of Planar Multistable Compliant Structures.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3453477\">https://doi.org/10.1145/3453477</a>.","mla":"Zhang, Ran, et al. “Computational Design of Planar Multistable Compliant Structures.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 5, 186, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3453477\">10.1145/3453477</a>.","ama":"Zhang R, Auzinger T, Bickel B. Computational design of planar multistable compliant structures. <i>ACM Transactions on Graphics</i>. 2021;40(5). doi:<a href=\"https://doi.org/10.1145/3453477\">10.1145/3453477</a>","short":"R. Zhang, T. Auzinger, B. Bickel, ACM Transactions on Graphics 40 (2021).","apa":"Zhang, R., Auzinger, T., &#38; Bickel, B. (2021). Computational design of planar multistable compliant structures. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3453477\">https://doi.org/10.1145/3453477</a>","ista":"Zhang R, Auzinger T, Bickel B. 2021. Computational design of planar multistable compliant structures. ACM Transactions on Graphics. 40(5), 186."},"ddc":["000"],"volume":40,"day":"08","article_number":"186","date_published":"2021-10-08T00:00:00Z","doi":"10.1145/3453477","year":"2021","date_updated":"2025-03-31T15:58:16Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9376","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"ec_funded":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"month":"10"},{"author":[{"orcid":"0000-0002-8176-4824","full_name":"Bolger-Munro, Madison","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","first_name":"Madison","last_name":"Bolger-Munro"},{"first_name":"Kate","last_name":"Choi","full_name":"Choi, Kate"},{"last_name":"Cheung","first_name":"Faith","full_name":"Cheung, Faith"},{"full_name":"Liu, Yi Tian","last_name":"Liu","first_name":"Yi Tian"},{"full_name":"Dang-Lawson, May","last_name":"Dang-Lawson","first_name":"May"},{"full_name":"Deretic, Nikola","first_name":"Nikola","last_name":"Deretic"},{"last_name":"Keane","first_name":"Connor","full_name":"Keane, Connor"},{"full_name":"Gold, Michael R.","first_name":"Michael R.","last_name":"Gold"}],"isi":1,"publisher":"Frontiers Media","department":[{"_id":"CaHe"}],"status":"public","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"scopus_import":"1","article_processing_charge":"No","title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","date_created":"2021-05-09T22:01:37Z","oa_version":"Published Version","publication_status":"published","external_id":{"isi":["000644419500001"],"pmid":["33928084"]},"abstract":[{"text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens.","lang":"eng"}],"pmid":1,"file":[{"success":1,"date_created":"2021-05-11T15:09:23Z","access_level":"open_access","checksum":"8c8a03575d2f7583f88dc3b658b0976b","creator":"kschuh","content_type":"application/pdf","relation":"main_file","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","file_id":"9386","file_size":4076024,"date_updated":"2021-05-11T15:09:23Z"}],"article_type":"original","file_date_updated":"2021-05-11T15:09:23Z","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"],"month":"04","publication_identifier":{"eissn":["2296-634X"]},"date_updated":"2023-10-18T08:19:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9379","year":"2021","doi":"10.3389/fcell.2021.649433","day":"13","article_number":"649433","date_published":"2021-04-13T00:00:00Z","type":"journal_article","citation":{"ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>. Frontiers Media, 2021. <a href=\"https://doi.org/10.3389/fcell.2021.649433\">https://doi.org/10.3389/fcell.2021.649433</a>.","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9, 649433, Frontiers Media, 2021, doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. <i>Frontiers in Cell and Developmental Biology</i>. 2021;9. doi:<a href=\"https://doi.org/10.3389/fcell.2021.649433\">10.3389/fcell.2021.649433</a>","ieee":"M. Bolger-Munro <i>et al.</i>, “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” <i>Frontiers in Cell and Developmental Biology</i>, vol. 9. Frontiers Media, 2021."},"ddc":["570"],"volume":9,"intvolume":"         9","acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","publication":"Frontiers in Cell and Developmental Biology","language":[{"iso":"eng"}],"quality_controlled":"1"}]