[{"isi":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","external_id":{"isi":["000661088500005"]},"ddc":["570"],"oa":1,"abstract":[{"text":"Background: To understand information coding in single neurons, it is necessary to analyze subthreshold synaptic events, action potentials (APs), and their interrelation in different behavioral states. However, detecting excitatory postsynaptic potentials (EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and variable time course of synaptic events.\r\nNew method: We developed a method for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure), which combines concepts of supervised machine learning and optimal Wiener filtering. Experts were asked to manually score short epochs of data. The algorithm was trained to obtain the optimal filter coefficients of a Wiener filter and the optimal detection threshold. Scored and unscored data were then processed with the optimal filter, and events were detected as peaks above threshold.\r\nResults: We challenged MOD with EPSP traces in vivo in mice during spatial navigation and EPSC traces in vitro in slices under conditions of enhanced transmitter release. The area under the curve (AUC) of the receiver operating characteristics (ROC) curve was, on average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection accuracy and efficiency.\r\nComparison with existing methods: When benchmarked using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution, and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but showed comparable (template-fit, deconvolution) or higher (Bayesian) computational efficacy.\r\nConclusions: MOD may become an important new tool for large-scale, real-time analysis of synaptic activity.","lang":"eng"}],"file":[{"file_size":6924738,"checksum":"2a5800d91b96d08b525e17319dcd5e44","creator":"dernst","date_updated":"2021-04-19T08:30:22Z","file_id":"9339","date_created":"2021-04-19T08:30:22Z","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","relation":"main_file"}],"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.","citation":{"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>.","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.","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.","short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021).","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>.","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>"},"doi":"10.1016/j.jneumeth.2021.109125","ec_funded":1,"quality_controlled":"1","has_accepted_license":"1","intvolume":"       357","year":"2021","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0165-0270"],"eissn":["1872-678X"]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Elsevier","date_updated":"2023-08-07T14:36:14Z","month":"03","date_published":"2021-03-09T00:00:00Z","article_type":"original","acknowledged_ssus":[{"_id":"SSU"}],"author":[{"first_name":"Xiaomin","id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100"},{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","last_name":"Vandael","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"project":[{"grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"oa_version":"Published Version","date_created":"2021-04-18T22:01:39Z","_id":"9329","issue":"6","type":"journal_article","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Neuroscience Methods","file_date_updated":"2021-04-19T08:30:22Z","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","volume":357,"article_number":"109125","status":"public","day":"09"},{"day":"06","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":118,"title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","status":"public","project":[{"_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","grant_number":"694539","call_identifier":"H2020"}],"date_created":"2021-04-18T22:01:40Z","oa_version":"Published Version","_id":"9330","article_processing_charge":"No","type":"journal_article","issue":"14","publication":"PNAS","file_date_updated":"2021-04-19T10:10:56Z","acknowledged_ssus":[{"_id":"EM-Fac"}],"author":[{"full_name":"Schöpf, Clemens L.","first_name":"Clemens L.","last_name":"Schöpf"},{"last_name":"Ablinger","first_name":"Cornelia","full_name":"Ablinger, Cornelia"},{"full_name":"Geisler, Stefanie M.","last_name":"Geisler","first_name":"Stefanie M."},{"first_name":"Ruslan I.","last_name":"Stanika","full_name":"Stanika, Ruslan I."},{"last_name":"Campiglio","first_name":"Marta","full_name":"Campiglio, Marta"},{"orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann"},{"first_name":"Benedikt","last_name":"Nimmervoll","full_name":"Nimmervoll, Benedikt"},{"full_name":"Schlick, Bettina","first_name":"Bettina","last_name":"Schlick"},{"full_name":"Brockhaus, Johannes","last_name":"Brockhaus","first_name":"Johannes"},{"first_name":"Markus","last_name":"Missler","full_name":"Missler, Markus"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto"},{"last_name":"Obermair","first_name":"Gerald J.","full_name":"Obermair, Gerald J."}],"department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"date_published":"2021-04-06T00:00:00Z","month":"04","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"National Academy of Sciences","date_updated":"2023-08-08T13:08:47Z","scopus_import":"1","year":"2021","publication_identifier":{"eissn":["1091-6490"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","intvolume":"       118","citation":{"ama":"Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. <i>PNAS</i>. 2021;118(14). 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>PNAS</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, PNAS 118 (2021).","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>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1920827118\">https://doi.org/10.1073/pnas.1920827118</a>","mla":"Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” <i>PNAS</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>.","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. PNAS. 118(14).","ieee":"C. L. Schöpf <i>et al.</i>, “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” <i>PNAS</i>, vol. 118, no. 14. National Academy of Sciences, 2021."},"doi":"10.1073/pnas.1920827118","ec_funded":1,"quality_controlled":"1","acknowledgement":"We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A.","ddc":["570"],"oa":1,"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"}],"file":[{"success":1,"content_type":"application/pdf","file_name":"2021_PNAS_Schoepf.pdf","relation":"main_file","file_id":"9340","date_created":"2021-04-19T10:10:56Z","access_level":"open_access","date_updated":"2021-04-19T10:10:56Z","file_size":2603911,"checksum":"dd014f68ae9d7d8d8fc4139a24e04506","creator":"dernst"}],"isi":1,"external_id":{"isi":["000637398300002"]}},{"day":"07","status":"public","article_number":"140501","title":"Improving cold-atom sensors with quantum entanglement: Prospects and challenges","volume":118,"publication":"Applied Physics Letters","_id":"9331","article_processing_charge":"No","type":"journal_article","issue":"14","date_created":"2021-04-18T22:01:40Z","oa_version":"Preprint","department":[{"_id":"OnHo"}],"author":[{"last_name":"Szigeti","first_name":"Stuart S.","full_name":"Szigeti, Stuart S."},{"full_name":"Hosten, Onur","orcid":"0000-0002-2031-204X","first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten"},{"full_name":"Haine, Simon A.","first_name":"Simon A.","last_name":"Haine"}],"article_type":"original","date_published":"2021-04-07T00:00:00Z","month":"04","date_updated":"2023-08-07T14:36:42Z","publisher":"AIP Publishing","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/2010.09168","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00036951"]},"year":"2021","intvolume":"       118","arxiv":1,"quality_controlled":"1","citation":{"apa":"Szigeti, S. S., Hosten, O., &#38; Haine, S. A. (2021). Improving cold-atom sensors with quantum entanglement: Prospects and challenges. <i>Applied Physics Letters</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0050235\">https://doi.org/10.1063/5.0050235</a>","short":"S.S. Szigeti, O. Hosten, S.A. Haine, Applied Physics Letters 118 (2021).","chicago":"Szigeti, Stuart S., Onur Hosten, and Simon A. Haine. “Improving Cold-Atom Sensors with Quantum Entanglement: Prospects and Challenges.” <i>Applied Physics Letters</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0050235\">https://doi.org/10.1063/5.0050235</a>.","ieee":"S. S. Szigeti, O. Hosten, and S. A. Haine, “Improving cold-atom sensors with quantum entanglement: Prospects and challenges,” <i>Applied Physics Letters</i>, vol. 118, no. 14. AIP Publishing, 2021.","ista":"Szigeti SS, Hosten O, Haine SA. 2021. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. Applied Physics Letters. 118(14), 140501.","mla":"Szigeti, Stuart S., et al. “Improving Cold-Atom Sensors with Quantum Entanglement: Prospects and Challenges.” <i>Applied Physics Letters</i>, vol. 118, no. 14, 140501, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0050235\">10.1063/5.0050235</a>.","ama":"Szigeti SS, Hosten O, Haine SA. Improving cold-atom sensors with quantum entanglement: Prospects and challenges. <i>Applied Physics Letters</i>. 2021;118(14). doi:<a href=\"https://doi.org/10.1063/5.0050235\">10.1063/5.0050235</a>"},"doi":"10.1063/5.0050235","acknowledgement":"We acknowledge fruitful discussions with John Close, Chris Freier, Kyle Hardman, Joseph Hope, and Paul Wigley, and insightful suggestions made by Franck Pereira dos Santos on behalf of the Atom Interferometry and Inertial Sensors team at SYRTE. S.S.S. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA), Project No. DE200100495. O.H. was supported by IST Austria.","abstract":[{"lang":"eng","text":"Quantum entanglement has been generated and verified in cold-atom experiments and used to make atom-interferometric measurements below the shot-noise limit. However, current state-of-the-art cold-atom devices exploit separable (i.e., unentangled) atomic states. This perspective piece asks the question: can entanglement usefully improve cold-atom sensors, in the sense that it gives new sensing capabilities unachievable with current state-of-the-art devices? We briefly review the state-of-the-art in precision cold-atom sensing, focusing on clocks and inertial sensors, identifying the potential benefits entanglement could bring to these devices, and the challenges that need to be overcome to realize these benefits. We survey demonstrated methods of generating metrologically useful entanglement in cold-atom systems, note their relative strengths and weaknesses, and assess their prospects for near-to-medium term quantum-enhanced cold-atom sensing."}],"oa":1,"external_id":{"isi":["000637702100001"],"arxiv":["2010.09168"]},"isi":1},{"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"MDPI","date_updated":"2023-08-08T13:09:58Z","month":"04","date_published":"2021-04-08T00:00:00Z","article_type":"original","author":[{"orcid":"0000-0002-5503-4983","full_name":"Ötvös, Krisztina","id":"29B901B0-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztina","last_name":"Ötvös"},{"last_name":"Miskolczi","first_name":"Pál","full_name":"Miskolczi, Pál"},{"last_name":"Marhavý","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","orcid":"0000-0001-5227-5741","full_name":"Marhavý, Peter"},{"full_name":"Cruz-Ramírez, Alfredo","first_name":"Alfredo","last_name":"Cruz-Ramírez"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"full_name":"Bakó, László","first_name":"László","last_name":"Bakó"}],"department":[{"_id":"EvBe"}],"date_created":"2021-04-18T22:01:41Z","oa_version":"Published Version","issue":"8","_id":"9332","type":"journal_article","article_processing_charge":"No","file_date_updated":"2021-04-19T10:54:55Z","publication":"International Journal of Molecular Sciences","volume":22,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis","article_number":"3862","status":"public","day":"08","isi":1,"external_id":{"isi":["000644394800001"]},"oa":1,"ddc":["570"],"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."}],"file":[{"relation":"main_file","file_name":"2021_JourMolecularScience_Oetvoes.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2021-04-19T10:54:55Z","file_id":"9342","date_updated":"2021-04-19T10:54:55Z","creator":"dernst","checksum":"26ada2531ad1f9c01a1664de0431f1fe","file_size":2769717}],"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.","citation":{"ama":"Ötvös K, Miskolczi P, Marhavý P, et al. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. <i>International Journal of Molecular Sciences</i>. 2021;22(8). doi:<a href=\"https://doi.org/10.3390/ijms22083862\">10.3390/ijms22083862</a>","apa":"Ötvös, K., Miskolczi, P., Marhavý, P., Cruz-Ramírez, A., Benková, E., Robert, S., &#38; Bakó, L. (2021). Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22083862\">https://doi.org/10.3390/ijms22083862</a>","short":"K. Ötvös, P. Miskolczi, P. Marhavý, A. Cruz-Ramírez, E. Benková, S. Robert, L. Bakó, International Journal of Molecular Sciences 22 (2021).","chicago":"Ötvös, Krisztina, Pál Miskolczi, Peter Marhavý, Alfredo Cruz-Ramírez, Eva Benková, Stéphanie Robert, and László Bakó. “Pickle Recruits Retinoblastoma Related 1 to Control Lateral Root Formation in Arabidopsis.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22083862\">https://doi.org/10.3390/ijms22083862</a>.","ista":"Ötvös K, Miskolczi P, Marhavý P, Cruz-Ramírez A, Benková E, Robert S, Bakó L. 2021. Pickle recruits retinoblastoma related 1 to control lateral root formation in arabidopsis. International Journal of Molecular Sciences. 22(8), 3862.","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.","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>."},"doi":"10.3390/ijms22083862","quality_controlled":"1","has_accepted_license":"1","intvolume":"        22","year":"2021","publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"language":[{"iso":"eng"}]},{"scopus_import":"1","article_type":"original","month":"04","date_published":"2021-04-05T00:00:00Z","date_updated":"2023-08-08T13:09:28Z","publisher":"Springer Nature","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-04-19T10:40:01Z","publication":"Letters in Mathematical Physics","article_processing_charge":"No","_id":"9333","type":"journal_article","date_created":"2021-04-18T22:01:41Z","oa_version":"Published Version","department":[{"_id":"RoSe"}],"author":[{"last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes"}],"day":"05","status":"public","article_number":"45","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":111,"title":"A note on the Fröhlich dynamics in the strong coupling limit","external_id":{"isi":["000637359300002"]},"isi":1,"file":[{"content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2021_LettersMathPhysics_Mitrouskas.pdf","file_id":"9341","date_created":"2021-04-19T10:40:01Z","access_level":"open_access","date_updated":"2021-04-19T10:40:01Z","checksum":"be56c0845a43c0c5c772ee0b5053f7d7","file_size":438084,"creator":"dernst"}],"abstract":[{"text":"We revise a previous result about the Fröhlich dynamics in the strong coupling limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα, where φ0 is the electron ground state of the Pekar energy functional and ξα the associated coherent state of the phonons, can be approximated by a global phase for times small compared to α2. In the present note we prove that a similar approximation holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons that is generated by an operator proportional to α−2 and quadratic in creation and annihilation operators. Our result implies that the electron ground state remains close to its initial state for times of order α2, while the phonon fluctuations around the coherent state ξα can be described by a time-dependent Bogoliubov transformation.","lang":"eng"}],"ddc":["510"],"oa":1,"quality_controlled":"1","doi":"10.1007/s11005-021-01380-7","citation":{"short":"D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021).","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>","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>.","ista":"Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45.","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>"},"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_identifier":{"eissn":["15730530"],"issn":["03779017"]},"language":[{"iso":"eng"}],"year":"2021","intvolume":"       111","has_accepted_license":"1"},{"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","volume":7,"status":"public","article_number":"eabf2690","day":"02","author":[{"full_name":"Duan, J.","first_name":"J.","last_name":"Duan"},{"first_name":"G.","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, G."},{"last_name":"Voronin","first_name":"K. V.","full_name":"Voronin, K. V."},{"full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez"},{"last_name":"Taboada-Gutiérrez","first_name":"J.","full_name":"Taboada-Gutiérrez, J."},{"first_name":"V. S.","last_name":"Volkov","full_name":"Volkov, V. S."},{"last_name":"Martín-Sánchez","first_name":"J.","full_name":"Martín-Sánchez, J."},{"last_name":"Nikitin","first_name":"A. Y.","full_name":"Nikitin, A. Y."},{"last_name":"Alonso-González","first_name":"P.","full_name":"Alonso-González, P."}],"department":[{"_id":"NanoFab"}],"oa_version":"Published Version","date_created":"2021-04-18T22:01:42Z","file_date_updated":"2021-04-19T11:17:29Z","publication":"Science Advances","_id":"9334","issue":"14","type":"journal_article","article_processing_charge":"No","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-08T13:11:31Z","publisher":"AAAS","article_type":"original","date_published":"2021-04-02T00:00:00Z","month":"04","scopus_import":"1","has_accepted_license":"1","intvolume":"         7","pmid":1,"year":"2021","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["23752548"]},"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. ","quality_controlled":"1","doi":"10.1126/sciadv.abf2690","citation":{"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>","short":"J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez, V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","chicago":"Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez, V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” <i>Science Advances</i>. AAAS, 2021. <a href=\"https://doi.org/10.1126/sciadv.abf2690\">https://doi.org/10.1126/sciadv.abf2690</a>.","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.","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>.","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>"},"abstract":[{"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.","lang":"eng"}],"ddc":["530"],"oa":1,"file":[{"file_size":717489,"checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","creator":"dernst","date_updated":"2021-04-19T11:17:29Z","file_id":"9343","access_level":"open_access","date_created":"2021-04-19T11:17:29Z","success":1,"content_type":"application/pdf","relation":"main_file","file_name":"2021_ScienceAdv_Duan.pdf"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","isi":1,"external_id":{"isi":["000636455600027"],"pmid":["33811076"]}},{"title":"The waiting time phenomenon in spatially discretized porous medium and thin film equations","volume":59,"status":"public","day":"01","author":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"},{"last_name":"Matthes","first_name":"Daniel","full_name":"Matthes, Daniel"}],"department":[{"_id":"JuFi"}],"date_created":"2021-04-18T22:01:42Z","oa_version":"Preprint","article_processing_charge":"No","_id":"9335","type":"journal_article","issue":"1","publication":"SIAM Journal on Numerical Analysis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","date_updated":"2023-08-08T13:10:40Z","month":"01","date_published":"2021-01-01T00:00:00Z","article_type":"original","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.04185"}],"intvolume":"        59","arxiv":1,"year":"2021","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0036-1429"]},"acknowledgement":"This research was supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics”.","doi":"10.1137/19M1300017","citation":{"ama":"Fischer JL, Matthes D. The waiting time phenomenon in spatially discretized porous medium and thin film equations. <i>SIAM Journal on Numerical Analysis</i>. 2021;59(1):60-87. doi:<a href=\"https://doi.org/10.1137/19M1300017\">10.1137/19M1300017</a>","chicago":"Fischer, Julian L, and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics, 2021. <a href=\"https://doi.org/10.1137/19M1300017\">https://doi.org/10.1137/19M1300017</a>.","short":"J.L. Fischer, D. Matthes, SIAM Journal on Numerical Analysis 59 (2021) 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>","mla":"Fischer, Julian L., and Daniel Matthes. “The Waiting Time Phenomenon in Spatially Discretized Porous Medium and Thin Film Equations.” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 1, Society for Industrial and Applied Mathematics, 2021, pp. 60–87, doi:<a href=\"https://doi.org/10.1137/19M1300017\">10.1137/19M1300017</a>.","ieee":"J. L. Fischer and D. Matthes, “The waiting time phenomenon in spatially discretized porous medium and thin film equations,” <i>SIAM Journal on Numerical Analysis</i>, vol. 59, no. 1. Society for Industrial and Applied Mathematics, pp. 60–87, 2021.","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."},"quality_controlled":"1","oa":1,"abstract":[{"lang":"eng","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."}],"isi":1,"page":"60-87","external_id":{"isi":["000625044600003"],"arxiv":["1911.04185"]}},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/febs.15823"}],"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-08T13:12:55Z","publisher":"Wiley","article_type":"original","date_published":"2021-04-05T00:00:00Z","month":"04","author":[{"full_name":"Sarabipour, Sarvenaz","first_name":"Sarvenaz","last_name":"Sarabipour"},{"full_name":"Hainer, Sarah J.","last_name":"Hainer","first_name":"Sarah J."},{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","last_name":"Arslan","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N"},{"full_name":"De Winde, Charlotte M.","first_name":"Charlotte M.","last_name":"De Winde"},{"full_name":"Furlong, Emily","first_name":"Emily","last_name":"Furlong"},{"full_name":"Bielczyk, Natalia","first_name":"Natalia","last_name":"Bielczyk"},{"first_name":"Nafisa M.","last_name":"Jadavji","full_name":"Jadavji, Nafisa M."},{"last_name":"Shah","first_name":"Aparna P.","full_name":"Shah, Aparna P."},{"first_name":"Sejal","last_name":"Davla","full_name":"Davla, Sejal"}],"department":[{"_id":"CaHe"}],"oa_version":"Published Version","date_created":"2021-04-18T22:01:43Z","publication":"FEBS Journal","_id":"9336","type":"journal_article","article_processing_charge":"No","title":"Building and sustaining mentor interactions as a mentee","status":"public","day":"05","isi":1,"alternative_title":["Words of Advice"],"external_id":{"pmid":["33818917"],"isi":["000636678800001"]},"abstract":[{"text":"Mentorship is experience and/or knowledge‐based guidance. Mentors support, sponsor and advocate for mentees. Having one or more mentors when you seek advice can significantly influence and improve your research endeavours, well‐being and career development. Positive mentee–mentor relationships are vital for maintaining work–life balance and success in careers. Early‐career researchers (ECRs), in particular, can benefit from mentorship to navigate challenges in academic and nonacademic life and careers. Yet, strategies for selecting mentors and maintaining interactions with them are often underdiscussed within research environments. In this Words of Advice, we provide recommendations for ECRs to seek and manage mentorship interactions. Our article draws from our experiences as ECRs and published work, to provide suggestions for mentees to proactively promote beneficial mentorship interactions. The recommended practices highlight the importance of identifying mentorship needs, planning and selecting multiple and diverse mentors, setting goals, and maintaining constructive, and mutually beneficial working relationships with mentors.","lang":"eng"}],"oa":1,"acknowledgement":"The authors thank Nicholas Asby of the University of Chicago for valuable comments on an earlier version of this work. A.P.S. was partially supported by the NARSAD Young Investigator Grant 27705. S.J.H was supported by the National Institutes of Health grant R35GM133732.","quality_controlled":"1","citation":{"ama":"Sarabipour S, Hainer SJ, Arslan FN, et al. Building and sustaining mentor interactions as a mentee. <i>FEBS Journal</i>. 2021. doi:<a href=\"https://doi.org/10.1111/febs.15823\">10.1111/febs.15823</a>","ista":"Sarabipour S, Hainer SJ, Arslan FN, De Winde CM, Furlong E, Bielczyk N, Jadavji NM, Shah AP, Davla S. 2021. Building and sustaining mentor interactions as a mentee. FEBS Journal.","ieee":"S. Sarabipour <i>et al.</i>, “Building and sustaining mentor interactions as a mentee,” <i>FEBS Journal</i>. Wiley, 2021.","mla":"Sarabipour, Sarvenaz, et al. “Building and Sustaining Mentor Interactions as a Mentee.” <i>FEBS Journal</i>, Wiley, 2021, doi:<a href=\"https://doi.org/10.1111/febs.15823\">10.1111/febs.15823</a>.","apa":"Sarabipour, S., Hainer, S. J., Arslan, F. N., De Winde, C. M., Furlong, E., Bielczyk, N., … Davla, S. (2021). Building and sustaining mentor interactions as a mentee. <i>FEBS Journal</i>. Wiley. <a href=\"https://doi.org/10.1111/febs.15823\">https://doi.org/10.1111/febs.15823</a>","short":"S. Sarabipour, S.J. Hainer, F.N. Arslan, C.M. De Winde, E. Furlong, N. Bielczyk, N.M. Jadavji, A.P. Shah, S. Davla, FEBS Journal (2021).","chicago":"Sarabipour, Sarvenaz, Sarah J. Hainer, Feyza N Arslan, Charlotte M. De Winde, Emily Furlong, Natalia Bielczyk, Nafisa M. Jadavji, Aparna P. Shah, and Sejal Davla. “Building and Sustaining Mentor Interactions as a Mentee.” <i>FEBS Journal</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/febs.15823\">https://doi.org/10.1111/febs.15823</a>."},"doi":"10.1111/febs.15823","pmid":1,"year":"2021","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1742-464X"],"eissn":["1742-4658"]}},{"status":"public","title":"The density fingerprint of a periodic point set","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":189,"day":"02","department":[{"_id":"HeEd"}],"author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner"},{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","last_name":"Heiss","orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa"},{"full_name":" Kurlin , Vitaliy","last_name":" Kurlin ","first_name":"Vitaliy"},{"last_name":"Smith","first_name":"Philip","full_name":"Smith, Philip"},{"orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","first_name":"Mathijs"}],"article_processing_charge":"No","_id":"9345","type":"conference","publication":"37th International Symposium on Computational Geometry (SoCG 2021)","file_date_updated":"2021-04-22T08:08:14Z","project":[{"call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"Discretization in Geometry and Dynamics","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"},{"name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"}],"oa_version":"Published Version","date_created":"2021-04-22T08:09:58Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2023-02-23T13:55:40Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication_status":"published","month":"06","date_published":"2021-06-02T00:00:00Z","intvolume":"       189","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"]},"year":"2021","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Virtual","end_date":"2021-06-11","start_date":"2021-06-07"},"acknowledgement":"The authors thank Janos Pach for insightful discussions on the topic of thispaper, Morteza Saghafian for finding the one-dimensional counterexample mentioned in Section 5,and Larry Andrews for generously sharing his crystallographic perspective.","doi":"10.4230/LIPIcs.SoCG.2021.32","citation":{"short":"H. Edelsbrunner, T. Heiss, V.  Kurlin , P. Smith, M. Wintraecken, in:, 37th International Symposium on Computational Geometry (SoCG 2021), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, p. 32:1-32:16.","chicago":"Edelsbrunner, Herbert, Teresa Heiss, Vitaliy  Kurlin , Philip Smith, and Mathijs Wintraecken. “The Density Fingerprint of a Periodic Point Set.” In <i>37th International Symposium on Computational Geometry (SoCG 2021)</i>, 189:32:1-32:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.32\">https://doi.org/10.4230/LIPIcs.SoCG.2021.32</a>.","apa":"Edelsbrunner, H., Heiss, T.,  Kurlin , V., Smith, P., &#38; Wintraecken, M. (2021). The density fingerprint of a periodic point set. In <i>37th International Symposium on Computational Geometry (SoCG 2021)</i> (Vol. 189, p. 32:1-32:16). Virtual: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.32\">https://doi.org/10.4230/LIPIcs.SoCG.2021.32</a>","mla":"Edelsbrunner, Herbert, et al. “The Density Fingerprint of a Periodic Point Set.” <i>37th International Symposium on Computational Geometry (SoCG 2021)</i>, vol. 189, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, p. 32:1-32:16, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.32\">10.4230/LIPIcs.SoCG.2021.32</a>.","ieee":"H. Edelsbrunner, T. Heiss, V.  Kurlin , P. Smith, and M. Wintraecken, “The density fingerprint of a periodic point set,” in <i>37th International Symposium on Computational Geometry (SoCG 2021)</i>, Virtual, 2021, vol. 189, p. 32:1-32:16.","ista":"Edelsbrunner H, Heiss T,  Kurlin  V, Smith P, Wintraecken M. 2021. The density fingerprint of a periodic point set. 37th International Symposium on Computational Geometry (SoCG 2021). SoCG: Symposium on Computational Geometry, LIPIcs, vol. 189, 32:1-32:16.","ama":"Edelsbrunner H, Heiss T,  Kurlin  V, Smith P, Wintraecken M. The density fingerprint of a periodic point set. In: <i>37th International Symposium on Computational Geometry (SoCG 2021)</i>. Vol 189. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021:32:1-32:16. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2021.32\">10.4230/LIPIcs.SoCG.2021.32</a>"},"ec_funded":1,"quality_controlled":"1","file":[{"content_type":"application/pdf","success":1,"relation":"main_file","file_name":"df_socg_final_version.pdf","file_id":"9346","date_created":"2021-04-22T08:08:14Z","access_level":"open_access","date_updated":"2021-04-22T08:08:14Z","file_size":3117435,"checksum":"1787baef1523d6d93753b90d0c109a6d","creator":"mwintrae"}],"ddc":["004","516"],"oa":1,"abstract":[{"lang":"eng","text":"Modeling a crystal as a periodic point set, we present a fingerprint consisting of density functionsthat facilitates the efficient search for new materials and material properties. We prove invarianceunder isometries, continuity, and completeness in the generic case, which are necessary featuresfor the reliable comparison of crystals. The proof of continuity integrates methods from discretegeometry and lattice theory, while the proof of generic completeness combines techniques fromgeometry with analysis. The fingerprint has a fast algorithm based on Brillouin zones and relatedinclusion-exclusion formulae. We have implemented the algorithm and describe its application tocrystal structure prediction."}],"page":"32:1-32:16","alternative_title":["LIPIcs"]},{"day":"07","article_number":"109029","status":"public","volume":281,"title":"Sharp tunneling estimates for a double-well model in infinite dimension","article_processing_charge":"No","_id":"9348","type":"journal_article","issue":"3","publication":"Journal of Functional Analysis","oa_version":"Preprint","date_created":"2021-04-25T22:01:29Z","department":[{"_id":"RoSe"}],"author":[{"id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","first_name":"Morris","last_name":"Brooks","full_name":"Brooks, Morris","orcid":"0000-0002-6249-0928"},{"full_name":"Di Gesù, Giacomo","last_name":"Di Gesù","first_name":"Giacomo"}],"date_published":"2021-04-07T00:00:00Z","month":"04","article_type":"original","publisher":"Elsevier","date_updated":"2023-08-08T13:15:11Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1911.03187"}],"scopus_import":"1","publication_identifier":{"eissn":["1096-0783"],"issn":["0022-1236"]},"language":[{"iso":"eng"}],"year":"2021","intvolume":"       281","arxiv":1,"doi":"10.1016/j.jfa.2021.109029","citation":{"ama":"Brooks M, Di Gesù G. Sharp tunneling estimates for a double-well model in infinite dimension. <i>Journal of Functional Analysis</i>. 2021;281(3). doi:<a href=\"https://doi.org/10.1016/j.jfa.2021.109029\">10.1016/j.jfa.2021.109029</a>","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>.","short":"M. Brooks, G. Di Gesù, Journal of Functional Analysis 281 (2021).","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>","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>.","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.","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."},"quality_controlled":"1","acknowledgement":"GDG gratefully acknowledges the financial support of HIM Bonn in the framework of the 2019 Junior Trimester Programs “Kinetic Theory” and “Randomness, PDEs and Nonlinear Fluctuations” and the hospitality at the University of Rome La Sapienza during his frequent visits.","oa":1,"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"]},"isi":1},{"day":"14","status":"public","article_number":"041501","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Roadmap for the multiscale coupling of biochemical and mechanical signals during development","volume":18,"publication":"Physical biology","file_date_updated":"2021-04-27T08:38:35Z","_id":"9349","article_processing_charge":"No","issue":"4","type":"journal_article","date_created":"2021-04-25T22:01:29Z","oa_version":"Published Version","project":[{"call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord"},{"name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425","grant_number":"P31639","call_identifier":"FWF"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020"}],"department":[{"_id":"AnKi"},{"_id":"EdHa"}],"author":[{"last_name":"Lenne","first_name":"Pierre François","full_name":"Lenne, Pierre François"},{"first_name":"Edwin","last_name":"Munro","full_name":"Munro, Edwin"},{"last_name":"Heemskerk","first_name":"Idse","full_name":"Heemskerk, Idse"},{"first_name":"Aryeh","last_name":"Warmflash","full_name":"Warmflash, Aryeh"},{"full_name":"Bocanegra, Laura","last_name":"Bocanegra","id":"4896F754-F248-11E8-B48F-1D18A9856A87","first_name":"Laura"},{"first_name":"Kasumi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi","full_name":"Kishi, Kasumi"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva"},{"full_name":"Long, Yuchen","last_name":"Long","first_name":"Yuchen"},{"full_name":"Fruleux, Antoine","last_name":"Fruleux","first_name":"Antoine"},{"full_name":"Boudaoud, Arezki","last_name":"Boudaoud","first_name":"Arezki"},{"full_name":"Saunders, Timothy E.","first_name":"Timothy E.","last_name":"Saunders"},{"last_name":"Caldarelli","first_name":"Paolo","full_name":"Caldarelli, Paolo"},{"full_name":"Michaut, Arthur","last_name":"Michaut","first_name":"Arthur"},{"first_name":"Jerome","last_name":"Gros","full_name":"Gros, Jerome"},{"full_name":"Maroudas-Sacks, Yonit","first_name":"Yonit","last_name":"Maroudas-Sacks"},{"first_name":"Kinneret","last_name":"Keren","full_name":"Keren, Kinneret"},{"last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"first_name":"Zev J.","last_name":"Gartner","full_name":"Gartner, Zev J."},{"full_name":"Stormo, Benjamin","last_name":"Stormo","first_name":"Benjamin"},{"full_name":"Gladfelter, Amy","last_name":"Gladfelter","first_name":"Amy"},{"last_name":"Rodrigues","first_name":"Alan","full_name":"Rodrigues, Alan"},{"first_name":"Amy","last_name":"Shyer","full_name":"Shyer, Amy"},{"full_name":"Minc, Nicolas","first_name":"Nicolas","last_name":"Minc"},{"full_name":"Maître, Jean Léon","last_name":"Maître","first_name":"Jean Léon"},{"full_name":"Di Talia, Stefano","last_name":"Di Talia","first_name":"Stefano"},{"first_name":"Bassma","last_name":"Khamaisi","full_name":"Khamaisi, Bassma"},{"first_name":"David","last_name":"Sprinzak","full_name":"Sprinzak, David"},{"full_name":"Tlili, Sham","last_name":"Tlili","first_name":"Sham"}],"article_type":"original","month":"04","date_published":"2021-04-14T00:00:00Z","date_updated":"2023-08-08T13:15:46Z","publisher":"IOP Publishing","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1478-3975"]},"year":"2021","intvolume":"        18","pmid":1,"has_accepted_license":"1","quality_controlled":"1","ec_funded":1,"doi":"10.1088/1478-3975/abd0db","citation":{"ama":"Lenne PF, Munro E, Heemskerk I, et al. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical biology</i>. 2021;18(4). doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>","chicago":"Lenne, Pierre François, Edwin Munro, Idse Heemskerk, Aryeh Warmflash, Laura Bocanegra, Kasumi Kishi, Anna Kicheva, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>.","short":"P.F. Lenne, E. Munro, I. Heemskerk, A. Warmflash, L. Bocanegra, K. Kishi, A. Kicheva, Y. Long, A. Fruleux, A. Boudaoud, T.E. Saunders, P. Caldarelli, A. Michaut, J. Gros, Y. Maroudas-Sacks, K. Keren, E.B. Hannezo, Z.J. Gartner, B. Stormo, A. Gladfelter, A. Rodrigues, A. Shyer, N. Minc, J.L. Maître, S. Di Talia, B. Khamaisi, D. Sprinzak, S. Tlili, Physical Biology 18 (2021).","apa":"Lenne, P. F., Munro, E., Heemskerk, I., Warmflash, A., Bocanegra, L., Kishi, K., … Tlili, S. (2021). Roadmap for the multiscale coupling of biochemical and mechanical signals during development. <i>Physical Biology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1478-3975/abd0db\">https://doi.org/10.1088/1478-3975/abd0db</a>","mla":"Lenne, Pierre François, et al. “Roadmap for the Multiscale Coupling of Biochemical and Mechanical Signals during Development.” <i>Physical Biology</i>, vol. 18, no. 4, 041501, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1478-3975/abd0db\">10.1088/1478-3975/abd0db</a>.","ista":"Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo EB, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S. 2021. Roadmap for the multiscale coupling of biochemical and mechanical signals during development. Physical biology. 18(4), 041501.","ieee":"P. F. Lenne <i>et al.</i>, “Roadmap for the multiscale coupling of biochemical and mechanical signals during development,” <i>Physical biology</i>, vol. 18, no. 4. IOP Publishing, 2021."},"acknowledgement":"The AK group is supported by IST Austria and by the ERC under European Union Horizon 2020 research and innovation programme Grant 680037. Apologies to those whose work could not be mentioned due to limited space. We thank all my lab members, both past and present, for stimulating discussion. This work was funded by a Singapore Ministry of Education Tier 3 Grant, MOE2016-T3-1-005. We thank Francis Corson for continuous discussion and collaboration contributing to these views and for figure 4(A). PC is sponsored by the Institut Pasteur and the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. Research in JG's laboratory is funded by the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement No. 337635, Institut Pasteur, CNRS, Cercle FSER, Fondation pour la Recherche Medicale, the Vallee Foundation and the ANR-19-CE-13-0024 Grant. We thank Erez Braun and Alex Mogilner for comments on the manuscript and Niv Ierushalmi for help with figure 5. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. ERC-2018-COG Grant 819174-HydraMechanics awarded to KK. EH thanks all lab members, as well as Pierre Recho, Tsuyoshi Hirashima, Diana Pinheiro and Carl-Philip Heisenberg, for fruitful discussions on these topics—and apologize for not being able to cite many very relevant publications due to the strict 10-reference limit. EH acknowledges the support of Austrian Science Fund (FWF) (P 31639) and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreements (851288). The authors acknowledge the inspiring scientists whose work could not be cited in this perspective due to space constraints; the members of the Gartner Lab for helpful discussions; the Barbara and Gerson Bakar Foundation, the Chan Zuckerberg Biohub Investigators Programme, the National Institute of Health, and the Centre for Cellular Construction, an NSF Science and Technology Centre. The Minc laboratory is currently funded by the CNRS and the European Research Council (CoG Forcaster No. 647073). Research in the lab of J-LM is supported by the Institut Curie, the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé Et de la Recherche Médicale (INSERM), and is funded by grants from the ATIP-Avenir programme, the Fondation Schlumberger pour l'Éducation et la Recherche via the Fondation pour la Recherche Médicale, the European Research Council Starting Grant ERC-2017-StG 757557, the European Molecular Biology Organization Young Investigator programme (EMBO YIP), the INSERM transversal programme Human Development Cell Atlas (HuDeCA), Paris Sciences Lettres (PSL) 'nouvelle équipe' and QLife (17-CONV-0005) grants and Labex DEEP (ANR-11-LABX-0044) which are part of the IDEX PSL (ANR-10-IDEX-0001-02). We acknowledge useful discussions with Massimo Vergassola, Sebastian Streichan and my lab members. Work in my laboratory on Drosophila embryogenesis is partly supported by NIH-R01GM122936. The authors acknowledge the support by a grant from the European Research Council (Grant No. 682161). Lenne group is funded by a grant from the 'Investissements d'Avenir' French Government programme managed by the French National Research Agency (ANR-16-CONV-0001) and by the Excellence Initiative of Aix-Marseille University—A*MIDEX, and ANR projects MechaResp (ANR-17-CE13-0032) and AdGastrulo (ANR-19-CE13-0022).","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13081"}]},"file":[{"creator":"cziletti","checksum":"4f52082549d3561c4c15d4d8d84ca5d8","file_size":6296324,"date_updated":"2021-04-27T08:38:35Z","date_created":"2021-04-27T08:38:35Z","access_level":"open_access","file_id":"9355","file_name":"2021_PhysBio_Lenne.pdf","relation":"main_file","success":1,"content_type":"application/pdf"}],"abstract":[{"lang":"eng","text":"The way in which interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image analysis have greatly enhanced our ability to observe and quantify spatiotemporal patterns of signalling, force generation, deformation, and flow in living cells and tissues. Powerful new tools for genetic, biophysical and optogenetic manipulation are allowing us to perturb the underlying machinery that generates these patterns in increasingly sophisticated ways. Rapid advances in theory and computing have made it possible to construct predictive models that describe how cell and tissue organization and dynamics emerge from the local coupling of biochemistry and mechanics. Together, these advances have opened up a wealth of new opportunities to explore how mechanochemical patterning shapes organismal development. In this roadmap, we present a series of forward-looking case studies on mechanochemical patterning in development, written by scientists working at the interface between the physical and biological sciences, and covering a wide range of spatial and temporal scales, organisms, and modes of development. Together, these contributions highlight the many ways in which the dynamic coupling of mechanics and biochemistry shapes biological dynamics: from mechanoenzymes that sense force to tune their activity and motor output, to collectives of cells in tissues that flow and redistribute biochemical signals during development."}],"oa":1,"ddc":["570"],"external_id":{"pmid":["33276350"],"isi":["000640396400001"]},"isi":1},{"month":"10","date_published":"2021-10-05T00:00:00Z","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Biophysical Society","date_updated":"2023-08-08T13:14:10Z","main_file_link":[{"open_access":"1","url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view"}],"scopus_import":"1","day":"05","title":"Holding it together: when cadherin meets cadherin","volume":120,"status":"public","date_created":"2021-04-25T22:01:30Z","oa_version":"Published Version","_id":"9350","article_processing_charge":"No","type":"journal_article","publication":"Biophysical Journal","author":[{"full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","last_name":"Arslan"},{"full_name":"Eckert, Julia","first_name":"Julia","last_name":"Eckert"},{"full_name":"Schmidt, Thomas","first_name":"Thomas","last_name":"Schmidt"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"department":[{"_id":"CaHe"}],"oa":1,"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"}],"page":"4182-4192","isi":1,"external_id":{"pmid":["33794149"],"isi":["000704646900006"]},"year":"2021","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"pmid":1,"intvolume":"       120","doi":"10.1016/j.bpj.2021.03.025","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.","ista":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together: when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192.","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>.","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>","short":"F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal 120 (2021) 4182–4192.","chicago":"Arslan, Feyza N, Julia Eckert, Thomas Schmidt, and Carl-Philipp J Heisenberg. “Holding It Together: When Cadherin Meets Cadherin.” <i>Biophysical Journal</i>. Biophysical Society, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2021.03.025\">https://doi.org/10.1016/j.bpj.2021.03.025</a>.","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>"},"quality_controlled":"1","related_material":{"record":[{"status":"public","id":"12368","relation":"dissertation_contains"}]},"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_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"year":"2021","arxiv":1,"intvolume":"        22","has_accepted_license":"1","ec_funded":1,"quality_controlled":"1","doi":"10.1007/s00023-021-01044-1","citation":{"mla":"Kirkpatrick, Kay, et al. “A Large Deviation Principle in Many-Body Quantum Dynamics.” <i>Annales Henri Poincare</i>, vol. 22, Springer Nature, 2021, pp. 2595–618, doi:<a href=\"https://doi.org/10.1007/s00023-021-01044-1\">10.1007/s00023-021-01044-1</a>.","ista":"Kirkpatrick K, Rademacher SAE, Schlein B. 2021. A large deviation principle in many-body quantum dynamics. Annales Henri Poincare. 22, 2595–2618.","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.","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>.","short":"K. Kirkpatrick, S.A.E. Rademacher, B. Schlein, Annales Henri Poincare 22 (2021) 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>","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>"},"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).","file":[{"date_updated":"2021-10-15T11:15:40Z","creator":"cchlebak","checksum":"1a0fb963f2f415ba470881a794f20eb6","file_size":522669,"file_name":"2021_Annales_Kirkpatrick.pdf","relation":"main_file","success":1,"content_type":"application/pdf","access_level":"open_access","date_created":"2021-10-15T11:15:40Z","file_id":"10143"}],"abstract":[{"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. ","lang":"eng"}],"ddc":["530"],"oa":1,"external_id":{"isi":["000638022600001"],"arxiv":["2010.13754"]},"page":"2595-2618","isi":1,"day":"08","status":"public","volume":22,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"A large deviation principle in many-body quantum dynamics","publication":"Annales Henri Poincare","file_date_updated":"2021-10-15T11:15:40Z","type":"journal_article","_id":"9351","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","date_created":"2021-04-25T22:01:30Z","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"department":[{"_id":"RoSe"}],"author":[{"full_name":"Kirkpatrick, Kay","first_name":"Kay","last_name":"Kirkpatrick"},{"full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466","last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"}],"article_type":"original","month":"04","date_published":"2021-04-08T00:00:00Z","date_updated":"2023-08-08T13:14:40Z","publisher":"Springer Nature","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1"},{"intvolume":"        59","arxiv":1,"year":"2021","publication_identifier":{"issn":["0036-1429"]},"language":[{"iso":"eng"}],"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.","citation":{"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.","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.","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>.","apa":"Fischer, J. L., Gallistl, D., &#38; Peterseim, D. (2021). A priori error analysis of a numerical stochastic homogenization method. <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/19M1308992\">https://doi.org/10.1137/19M1308992</a>","chicago":"Fischer, Julian L, Dietmar Gallistl, and Dietmar Peterseim. “A Priori Error Analysis of a Numerical Stochastic Homogenization Method.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics, 2021. <a href=\"https://doi.org/10.1137/19M1308992\">https://doi.org/10.1137/19M1308992</a>.","short":"J.L. Fischer, D. Gallistl, D. Peterseim, SIAM Journal on Numerical Analysis 59 (2021) 660–674.","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>"},"doi":"10.1137/19M1308992","quality_controlled":"1","oa":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."}],"isi":1,"page":"660-674","external_id":{"isi":["000646030400003"],"arxiv":["1912.11646"]},"volume":59,"title":"A priori error analysis of a numerical stochastic homogenization method","status":"public","day":"09","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X"},{"full_name":"Gallistl, Dietmar","last_name":"Gallistl","first_name":"Dietmar"},{"full_name":"Peterseim, Dietmar","first_name":"Dietmar","last_name":"Peterseim"}],"department":[{"_id":"JuFi"}],"oa_version":"Preprint","date_created":"2021-04-25T22:01:31Z","issue":"2","_id":"9352","type":"journal_article","article_processing_charge":"No","publication":"SIAM Journal on Numerical Analysis","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","date_updated":"2023-08-08T13:13:37Z","date_published":"2021-03-09T00:00:00Z","month":"03","article_type":"original","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.11646"}]},{"external_id":{"isi":["000947350400021"],"arxiv":["2105.08353"]},"isi":1,"file":[{"creator":"esarac","file_size":641990,"checksum":"6e4cba3f72775f479c5b1b75d1a4a0c4","date_updated":"2021-06-16T08:23:54Z","access_level":"open_access","date_created":"2021-06-16T08:23:54Z","file_id":"9557","file_name":"qam.pdf","relation":"main_file","success":1,"content_type":"application/pdf"}],"ddc":["000"],"oa":1,"abstract":[{"text":"In runtime verification, a monitor watches a trace of a system and, if possible, decides after observing each finite prefix whether or not the unknown infinite trace satisfies a given specification. We generalize the theory of runtime verification to monitors that attempt to estimate numerical values of quantitative trace properties (instead of attempting to conclude boolean values of trace specifications), such as maximal or average response time along a trace. Quantitative monitors are approximate: with every finite prefix, they can improve their estimate of the infinite trace's unknown property value. Consequently, quantitative monitors can be compared with regard to a precision-cost trade-off: better approximations of the property value require more monitor resources, such as states (in the case of finite-state monitors) or registers, and additional resources yield better approximations. We introduce a formal framework for quantitative and approximate monitoring, show how it conservatively generalizes the classical boolean setting for monitoring, and give several precision-cost trade-offs for monitors. For example, we prove that there are quantitative properties for which every additional register improves monitoring precision.","lang":"eng"}],"conference":{"name":"LICS: Symposium on Logic in Computer Science","location":"Online","start_date":"2021-06-29","end_date":"2021-07-02"},"acknowledgement":"We thank the anonymous reviewers for their helpful comments. This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","citation":{"ama":"Henzinger TA, Sarac NE. Quantitative and approximate monitoring. In: <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Institute of Electrical and Electronics Engineers; 2021. doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470547\">10.1109/LICS52264.2021.9470547</a>","ieee":"T. A. Henzinger and N. E. Sarac, “Quantitative and approximate monitoring,” in <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, Online, 2021.","ista":"Henzinger TA, Sarac NE. 2021. Quantitative and approximate monitoring. Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science, 9470547.","mla":"Henzinger, Thomas A., and Naci E. Sarac. “Quantitative and Approximate Monitoring.” <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>, 9470547, Institute of Electrical and Electronics Engineers, 2021, doi:<a href=\"https://doi.org/10.1109/LICS52264.2021.9470547\">10.1109/LICS52264.2021.9470547</a>.","apa":"Henzinger, T. A., &#38; Sarac, N. E. (2021). Quantitative and approximate monitoring. In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Online: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470547\">https://doi.org/10.1109/LICS52264.2021.9470547</a>","short":"T.A. Henzinger, N.E. Sarac, in:, Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2021.","chicago":"Henzinger, Thomas A, and Naci E Sarac. “Quantitative and Approximate Monitoring.” In <i>Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science</i>. Institute of Electrical and Electronics Engineers, 2021. <a href=\"https://doi.org/10.1109/LICS52264.2021.9470547\">https://doi.org/10.1109/LICS52264.2021.9470547</a>."},"doi":"10.1109/LICS52264.2021.9470547","quality_controlled":"1","arxiv":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"year":"2021","scopus_import":"1","publisher":"Institute of Electrical and Electronics Engineers","date_updated":"2023-08-08T13:52:56Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","date_published":"2021-06-29T00:00:00Z","month":"06","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"author":[{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"full_name":"Sarac, Naci E","first_name":"Naci E","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","last_name":"Sarac"}],"article_processing_charge":"No","_id":"9356","type":"conference","file_date_updated":"2021-06-16T08:23:54Z","publication":"Proceedings of the 36th Annual ACM/IEEE Symposium on Logic in Computer Science","project":[{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"}],"date_created":"2021-04-30T17:30:47Z","oa_version":"Published Version","article_number":"9470547","status":"public","title":"Quantitative and approximate monitoring","day":"29"},{"isi":1,"page":"813-912","external_id":{"arxiv":["1802.07948"],"isi":["000682738600005"]},"oa":1,"ddc":["514","516","512"],"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"}],"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","creator":"qho","checksum":"643a8d2d6f06f0888dcd7503f55d0920","file_size":479268,"relation":"main_file","file_name":"densities.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2021-05-03T06:54:06Z","file_id":"9366"}],"citation":{"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>","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>.","ista":"Ho QP. 2021. Homological stability and densities of generalized configuration spaces. Geometry &#38; Topology. 25(2), 813–912.","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.","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>.","short":"Q.P. Ho, Geometry &#38; Topology 25 (2021) 813–912.","apa":"Ho, Q. P. (2021). Homological stability and densities of generalized configuration spaces. <i>Geometry &#38; Topology</i>. Mathematical Sciences Publishers. <a href=\"https://doi.org/10.2140/gt.2021.25.813\">https://doi.org/10.2140/gt.2021.25.813</a>"},"doi":"10.2140/gt.2021.25.813","ec_funded":1,"quality_controlled":"1","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.","year":"2021","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1364-0380"]},"has_accepted_license":"1","intvolume":"        25","arxiv":1,"month":"04","date_published":"2021-04-27T00:00:00Z","article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"Mathematical Sciences Publishers","date_updated":"2023-08-08T13:28:59Z","project":[{"_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7","grant_number":"320593"},{"_id":"26B96266-B435-11E9-9278-68D0E5697425","name":"Algebro-Geometric Applications of Factorization Homology","call_identifier":"FWF","grant_number":"M02751"}],"date_created":"2021-05-02T06:59:33Z","oa_version":"Submitted Version","type":"journal_article","_id":"9359","article_processing_charge":"No","issue":"2","publication":"Geometry & Topology","file_date_updated":"2021-05-03T06:54:06Z","author":[{"last_name":"Ho","first_name":"Quoc P","id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Ho, Quoc P"}],"department":[{"_id":"TaHa"}],"day":"27","volume":25,"title":"Homological stability and densities of generalized configuration spaces","status":"public"},{"publication_identifier":{"eissn":["23795042"]},"language":[{"iso":"eng"}],"year":"2021","intvolume":"         6","pmid":1,"has_accepted_license":"1","quality_controlled":"1","citation":{"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>","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>.","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.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","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>.","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>"},"doi":"10.1128/mSphere.01024-20","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","file":[{"date_updated":"2021-05-04T12:41:38Z","creator":"kschuh","file_size":3379349,"checksum":"310748d140c8838335c1314431095898","file_name":"2021_mSphere_Gast.pdf","relation":"main_file","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2021-05-04T12:41:38Z","file_id":"9370"}],"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"}],"ddc":["570"],"oa":1,"external_id":{"isi":["000663823400025"],"pmid":["33853875"]},"isi":1,"day":"14","status":"public","article_number":"e01024-20","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":6,"title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","file_date_updated":"2021-05-04T12:41:38Z","publication":"mSphere","issue":"2","_id":"9361","article_processing_charge":"No","type":"journal_article","oa_version":"Published Version","date_created":"2021-05-02T22:01:28Z","department":[{"_id":"Bio"}],"author":[{"last_name":"Gast","first_name":"Matthieu","full_name":"Gast, Matthieu"},{"last_name":"Kadzioch","first_name":"Nicole P.","full_name":"Kadzioch, Nicole P."},{"full_name":"Milius, Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87","first_name":"Doreen","last_name":"Milius"},{"full_name":"Origgi, Francesco","last_name":"Origgi","first_name":"Francesco"},{"full_name":"Plattet, Philippe","first_name":"Philippe","last_name":"Plattet"}],"month":"04","date_published":"2021-04-14T00:00:00Z","date_updated":"2023-08-08T13:26:12Z","publisher":"American Society for Microbiology","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1"},{"scopus_import":"1","article_type":"original","date_published":"2021-04-15T00:00:00Z","month":"04","date_updated":"2023-10-18T08:17:42Z","publisher":"Public Library of Science","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"PLoS ONE","file_date_updated":"2021-05-04T13:22:19Z","_id":"9362","article_processing_charge":"No","issue":"4","type":"journal_article","date_created":"2021-05-02T22:01:28Z","oa_version":"Published Version","department":[{"_id":"GaTk"}],"author":[{"orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","last_name":"Chalk"},{"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"}],"day":"15","status":"public","article_number":"e0248940","volume":16,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Inferring the function performed by a recurrent neural network","external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"isi":1,"file":[{"file_name":"2021_pone_Chalk.pdf","relation":"main_file","content_type":"application/pdf","success":1,"date_created":"2021-05-04T13:22:19Z","access_level":"open_access","file_id":"9371","date_updated":"2021-05-04T13:22:19Z","creator":"kschuh","file_size":2768282,"checksum":"c52da133850307d2031f552d998f00e8"}],"abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"oa":1,"ddc":["570"],"quality_controlled":"1","doi":"10.1371/journal.pone.0248940","citation":{"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>.","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.","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","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>","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>"},"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["19326203"]},"year":"2021","intvolume":"        16","pmid":1,"has_accepted_license":"1"},{"date_published":"2021-04-01T00:00:00Z","month":"04","publisher":"Public Library of Science","date_updated":"2023-08-08T13:17:47Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","scopus_import":"1","day":"01","status":"public","volume":17,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","_id":"9363","article_processing_charge":"No","type":"journal_article","issue":"4","file_date_updated":"2021-05-04T09:05:27Z","publication":"PLoS genetics","date_created":"2021-05-02T22:01:29Z","oa_version":"Published Version","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"author":[{"full_name":"Inglés Prieto, Álvaro","orcid":"0000-0002-5409-8571","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","last_name":"Inglés Prieto"},{"last_name":"Furthmann","first_name":"Nikolas","full_name":"Furthmann, Nikolas"},{"full_name":"Crossman, Samuel H.","last_name":"Crossman","first_name":"Samuel H."},{"last_name":"Tichy","first_name":"Alexandra Madelaine","full_name":"Tichy, Alexandra Madelaine"},{"full_name":"Hoyer, Nina","first_name":"Nina","last_name":"Hoyer"},{"full_name":"Petersen, Meike","last_name":"Petersen","first_name":"Meike"},{"first_name":"Vanessa","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","full_name":"Zheden, Vanessa"},{"full_name":"Bicher, Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Bicher"},{"orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"György, Attila","orcid":"0000-0002-1819-198X","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","last_name":"György"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"full_name":"Soba, Peter","first_name":"Peter","last_name":"Soba"},{"full_name":"Winklhofer, Konstanze F.","first_name":"Konstanze F.","last_name":"Winklhofer"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak"}],"file":[{"access_level":"open_access","date_created":"2021-05-04T09:05:27Z","file_id":"9369","relation":"main_file","file_name":"2021_PLOS_Ingles-Prieto.pdf","success":1,"content_type":"application/pdf","creator":"kschuh","checksum":"82a74668f863e8dfb22fdd4f845c92ce","file_size":3072764,"date_updated":"2021-05-04T09:05:27Z"}],"oa":1,"ddc":["570"],"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"]},"isi":1,"page":"e1009479","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15537404"]},"year":"2021","intvolume":"        17","has_accepted_license":"1","doi":"10.1371/journal.pgen.1009479","citation":{"ama":"Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS genetics</i>. 2021;17(4):e1009479. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1009479\">10.1371/journal.pgen.1009479</a>","apa":"Inglés Prieto, Á., Furthmann, N., Crossman, S. H., Tichy, A. M., Hoyer, N., Petersen, M., … Janovjak, H. L. (2021). Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1009479\">https://doi.org/10.1371/journal.pgen.1009479</a>","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>.","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.","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.","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>."},"quality_controlled":"1","acknowledgement":"We thank R. Cagan, A. Whitworth and J. Nagpal for fly lines and advice, S. Herlitze for provision of a tissue culture illuminator, and Verian Bader for help with statistical analysis."},{"acknowledgement":"The second author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7-2007-2013) (Grant agreement No. 616160).","doi":"10.1080/02331934.2021.1914035","citation":{"short":"F.U. Ogbuisi, Y. Shehu, J.C. Yao, Optimization (2021).","chicago":"Ogbuisi, Ferdinard U., Yekini Shehu, and Jen Chih Yao. “Convergence Analysis of New Inertial Method for the Split Common Null Point Problem.” <i>Optimization</i>. Taylor and Francis, 2021. <a href=\"https://doi.org/10.1080/02331934.2021.1914035\">https://doi.org/10.1080/02331934.2021.1914035</a>.","apa":"Ogbuisi, F. U., Shehu, Y., &#38; Yao, J. C. (2021). Convergence analysis of new inertial method for the split common null point problem. <i>Optimization</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/02331934.2021.1914035\">https://doi.org/10.1080/02331934.2021.1914035</a>","mla":"Ogbuisi, Ferdinard U., et al. “Convergence Analysis of New Inertial Method for the Split Common Null Point Problem.” <i>Optimization</i>, Taylor and Francis, 2021, doi:<a href=\"https://doi.org/10.1080/02331934.2021.1914035\">10.1080/02331934.2021.1914035</a>.","ieee":"F. U. Ogbuisi, Y. Shehu, and J. C. Yao, “Convergence analysis of new inertial method for the split common null point problem,” <i>Optimization</i>. Taylor and Francis, 2021.","ista":"Ogbuisi FU, Shehu Y, Yao JC. 2021. Convergence analysis of new inertial method for the split common null point problem. Optimization.","ama":"Ogbuisi FU, Shehu Y, Yao JC. Convergence analysis of new inertial method for the split common null point problem. <i>Optimization</i>. 2021. doi:<a href=\"https://doi.org/10.1080/02331934.2021.1914035\">10.1080/02331934.2021.1914035</a>"},"ec_funded":1,"quality_controlled":"1","year":"2021","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1029-4945"],"issn":["0233-1934"]},"isi":1,"external_id":{"isi":["000640109300001"]},"abstract":[{"text":"In this paper, we propose a new iterative method with alternated inertial step for solving split common null point problem in real Hilbert spaces. We obtain weak convergence of the proposed iterative algorithm. Furthermore, we introduce the notion of bounded linear regularity property for the split common null point problem and obtain the linear convergence property for the new algorithm under some mild assumptions. Finally, we provide some numerical examples to demonstrate the performance and efficiency of the proposed method.","lang":"eng"}],"author":[{"full_name":"Ogbuisi, Ferdinard U.","first_name":"Ferdinard U.","last_name":"Ogbuisi"},{"orcid":"0000-0001-9224-7139","full_name":"Shehu, Yekini","last_name":"Shehu","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yao, Jen Chih","last_name":"Yao","first_name":"Jen Chih"}],"department":[{"_id":"VlKo"}],"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"oa_version":"None","date_created":"2021-05-02T22:01:29Z","article_processing_charge":"No","type":"journal_article","_id":"9365","publication":"Optimization","title":"Convergence analysis of new inertial method for the split common null point problem","status":"public","day":"14","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Taylor and Francis","date_updated":"2023-10-10T09:48:41Z","date_published":"2021-04-14T00:00:00Z","month":"04","article_type":"original"}]