[{"article_number":"109125","file_date_updated":"2021-04-19T08:30:22Z","ec_funded":1,"year":"2021","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari, Christoph Lampert, and Federico Stella for critically reading previous manuscript versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help with applying the Bayesian detection method to our data. We also thank Florian Marr for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the Scientific Service Units of IST Austria for efficient support.","publication_status":"published","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publisher":"Elsevier","author":[{"id":"423EC9C2-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaomin","last_name":"Zhang","full_name":"Zhang, Xiaomin"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois","last_name":"Schlögl","full_name":"Schlögl, Alois"},{"last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-07T14:36:14Z","date_created":"2021-04-18T22:01:39Z","volume":357,"month":"03","publication_identifier":{"eissn":["1872-678X"],"issn":["0165-0270"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000661088500005"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.jneumeth.2021.109125","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"type":"journal_article","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"}],"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9329","status":"public","title":"MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo","ddc":["570"],"intvolume":" 357","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2021_JourNeuroscienceMeth_Zhang.pdf","content_type":"application/pdf","file_size":6924738,"creator":"dernst","relation":"main_file","file_id":"9339","checksum":"2a5800d91b96d08b525e17319dcd5e44","success":1,"date_updated":"2021-04-19T08:30:22Z","date_created":"2021-04-19T08:30:22Z"}],"scopus_import":"1","day":"09","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Journal of Neuroscience Methods","citation":{"ieee":"X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo,” Journal of Neuroscience Methods, vol. 357, no. 6. Elsevier, 2021.","apa":"Zhang, X., Schlögl, A., Vandael, D. H., & Jonas, P. M. (2021). MOD: A novel machine-learning optimal-filtering method for accurate and efficient detection of subthreshold synaptic events in vivo. Journal of Neuroscience Methods. Elsevier. https://doi.org/10.1016/j.jneumeth.2021.109125","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.","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. Journal of Neuroscience Methods. 2021;357(6). doi:10.1016/j.jneumeth.2021.109125","chicago":"Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods. Elsevier, 2021. https://doi.org/10.1016/j.jneumeth.2021.109125.","short":"X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods 357 (2021).","mla":"Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods, vol. 357, no. 6, 109125, Elsevier, 2021, doi:10.1016/j.jneumeth.2021.109125."},"article_type":"original","date_published":"2021-03-09T00:00:00Z"},{"year":"2021","acknowledgement":"We thank Arnold Schwartz for providing α2δ-1 knockout mice; Ariane Benedetti, Sabine Baumgartner, Sandra Demetz, and Irene Mahlknecht for technical support; Nadine Ortner and Andreas Lieb for electrophysiological experiments; the team of the Electron Microscopy Facility at the Institute of Science and Technology Austria for technical support related to ultrastructural analysis; Hermann Dietrich and Anja Beierfuß and her team for animal care; Jutta Engel and Jörg Striessnig for critical discussions; and Bruno Benedetti and Bernhard Flucher for critical discussions and reading the manuscript. This study was supported by Austrian Science Fund Grants P24079, F44060, F44150, and DOC30-B30 (to G.J.O.) and T855 (to M.C.), European Research Council Grant AdG 694539 (to R.S.), Deutsche Forschungsgemeinschaft\r\nGrant SFB1348-TP A03 (to M.M.), and Interdisziplinäre Zentrum für Klinische Forschung Münster Grant Mi3/004/19 (to M.M.). This work is part of the PhD theses of C.L.S., S.M.G., and C.A.","publication_status":"published","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publisher":"National Academy of Sciences","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.","first_name":"Stefanie M.","last_name":"Geisler"},{"full_name":"Stanika, Ruslan I.","last_name":"Stanika","first_name":"Ruslan I."},{"full_name":"Campiglio, Marta","last_name":"Campiglio","first_name":"Marta"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benedikt","last_name":"Nimmervoll","full_name":"Nimmervoll, Benedikt"},{"last_name":"Schlick","first_name":"Bettina","full_name":"Schlick, Bettina"},{"first_name":"Johannes","last_name":"Brockhaus","full_name":"Brockhaus, Johannes"},{"last_name":"Missler","first_name":"Markus","full_name":"Missler, Markus"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"first_name":"Gerald J.","last_name":"Obermair","full_name":"Obermair, Gerald J."}],"date_created":"2021-04-18T22:01:40Z","date_updated":"2023-08-08T13:08:47Z","volume":118,"file_date_updated":"2021-04-19T10:10:56Z","ec_funded":1,"external_id":{"isi":["000637398300002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"}],"doi":"10.1073/pnas.1920827118","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["1091-6490"]},"_id":"9330","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Presynaptic α2δ subunits are key organizers of glutamatergic synapses","intvolume":" 118","file":[{"file_id":"9340","relation":"main_file","success":1,"checksum":"dd014f68ae9d7d8d8fc4139a24e04506","date_updated":"2021-04-19T10:10:56Z","date_created":"2021-04-19T10:10:56Z","access_level":"open_access","file_name":"2021_PNAS_Schoepf.pdf","creator":"dernst","content_type":"application/pdf","file_size":2603911}],"oa_version":"Published Version","type":"journal_article","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"}],"issue":"14","publication":"PNAS","citation":{"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).","mla":"Schöpf, Clemens L., et al. “Presynaptic Α2δ Subunits Are Key Organizers of Glutamatergic Synapses.” PNAS, vol. 118, no. 14, National Academy of Sciences, 2021, doi:10.1073/pnas.1920827118.","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.” PNAS. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.1920827118.","ama":"Schöpf CL, Ablinger C, Geisler SM, et al. Presynaptic α2δ subunits are key organizers of glutamatergic synapses. PNAS. 2021;118(14). doi:10.1073/pnas.1920827118","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. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1920827118","ieee":"C. L. Schöpf et al., “Presynaptic α2δ subunits are key organizers of glutamatergic synapses,” PNAS, vol. 118, no. 14. National Academy of Sciences, 2021.","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)."},"article_type":"original","date_published":"2021-04-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"No","has_accepted_license":"1"},{"day":"02","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2021-04-02T00:00:00Z","article_type":"original","publication":"Science Advances","citation":{"ista":"Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 7(14), eabf2690.","apa":"Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez, J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abf2690","ieee":"J. Duan et al., “Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition,” Science Advances, vol. 7, no. 14. AAAS, 2021.","ama":"Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 2021;7(14). doi:10.1126/sciadv.abf2690","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.” Science Advances. AAAS, 2021. https://doi.org/10.1126/sciadv.abf2690.","mla":"Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” Science Advances, vol. 7, no. 14, eabf2690, AAAS, 2021, doi:10.1126/sciadv.abf2690.","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)."},"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"}],"issue":"14","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2021_ScienceAdv_Duan.pdf","access_level":"open_access","creator":"dernst","file_size":717489,"content_type":"application/pdf","file_id":"9343","relation":"main_file","date_created":"2021-04-19T11:17:29Z","date_updated":"2021-04-19T11:17:29Z","success":1,"checksum":"4b383d4a1d484a71bbc64ecf401bbdbb"}],"ddc":["530"],"title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","status":"public","intvolume":" 7","_id":"9334","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"04","publication_identifier":{"eissn":["23752548"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.abf2690","quality_controlled":"1","isi":1,"external_id":{"isi":["000636455600027"],"pmid":["33811076"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"file_date_updated":"2021-04-19T11:17:29Z","article_number":"eabf2690","date_updated":"2023-08-08T13:11:31Z","date_created":"2021-04-18T22:01:42Z","volume":7,"author":[{"full_name":"Duan, J.","first_name":"J.","last_name":"Duan"},{"full_name":"Álvarez-Pérez, G.","first_name":"G.","last_name":"Álvarez-Pérez"},{"full_name":"Voronin, K. V.","last_name":"Voronin","first_name":"K. V."},{"full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Prieto Gonzalez","first_name":"Ivan"},{"full_name":"Taboada-Gutiérrez, J.","first_name":"J.","last_name":"Taboada-Gutiérrez"},{"full_name":"Volkov, V. S.","last_name":"Volkov","first_name":"V. S."},{"full_name":"Martín-Sánchez, J.","first_name":"J.","last_name":"Martín-Sánchez"},{"first_name":"A. Y.","last_name":"Nikitin","full_name":"Nikitin, A. Y."},{"last_name":"Alonso-González","first_name":"P.","full_name":"Alonso-González, P."}],"publication_status":"published","department":[{"_id":"NanoFab"}],"publisher":"AAAS","year":"2021","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. ","pmid":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000640606700001"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pgen.1009479","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["15537404"]},"month":"04","year":"2021","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.","publisher":"Public Library of Science","department":[{"_id":"EM-Fac"},{"_id":"LoSw"},{"_id":"DaSi"}],"publication_status":"published","author":[{"first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"last_name":"Furthmann","first_name":"Nikolas","full_name":"Furthmann, Nikolas"},{"last_name":"Crossman","first_name":"Samuel H.","full_name":"Crossman, Samuel H."},{"first_name":"Alexandra Madelaine","last_name":"Tichy","full_name":"Tichy, Alexandra Madelaine"},{"first_name":"Nina","last_name":"Hoyer","full_name":"Hoyer, Nina"},{"last_name":"Petersen","first_name":"Meike","full_name":"Petersen, Meike"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","last_name":"Zheden","first_name":"Vanessa","full_name":"Zheden, Vanessa"},{"id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Bicher","full_name":"Bicher, Julia"},{"full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"György, Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1819-198X","first_name":"Attila","last_name":"György"},{"full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus"},{"first_name":"Peter","last_name":"Soba","full_name":"Soba, Peter"},{"last_name":"Winklhofer","first_name":"Konstanze F.","full_name":"Winklhofer, Konstanze F."},{"full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"volume":17,"date_updated":"2023-08-08T13:17:47Z","date_created":"2021-05-02T22:01:29Z","file_date_updated":"2021-05-04T09:05:27Z","citation":{"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 et al., “Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease,” PLoS genetics, vol. 17, no. 4. Public Library of Science, p. e1009479, 2021.","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. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1009479","ama":"Inglés Prieto Á, Furthmann N, Crossman SH, et al. Optogenetic delivery of trophic signals in a genetic model of Parkinson’s disease. PLoS genetics. 2021;17(4):e1009479. doi:10.1371/journal.pgen.1009479","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.” PLoS Genetics. Public Library of Science, 2021. https://doi.org/10.1371/journal.pgen.1009479.","mla":"Inglés Prieto, Álvaro, et al. “Optogenetic Delivery of Trophic Signals in a Genetic Model of Parkinson’s Disease.” PLoS Genetics, vol. 17, no. 4, Public Library of Science, 2021, p. e1009479, doi:10.1371/journal.pgen.1009479.","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."},"publication":"PLoS genetics","page":"e1009479","date_published":"2021-04-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","_id":"9363","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 17","title":"Optogenetic delivery of trophic signals in a genetic model of Parkinson's disease","status":"public","ddc":["570"],"oa_version":"Published Version","file":[{"file_name":"2021_PLOS_Ingles-Prieto.pdf","access_level":"open_access","creator":"kschuh","file_size":3072764,"content_type":"application/pdf","file_id":"9369","relation":"main_file","date_updated":"2021-05-04T09:05:27Z","date_created":"2021-05-04T09:05:27Z","success":1,"checksum":"82a74668f863e8dfb22fdd4f845c92ce"}],"type":"journal_article","issue":"4","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."}]},{"date_created":"2021-05-02T22:01:28Z","date_updated":"2023-08-08T13:26:12Z","volume":6,"author":[{"first_name":"Matthieu","last_name":"Gast","full_name":"Gast, Matthieu"},{"last_name":"Kadzioch","first_name":"Nicole P.","full_name":"Kadzioch, Nicole P."},{"first_name":"Doreen","last_name":"Milius","id":"384050BC-F248-11E8-B48F-1D18A9856A87","full_name":"Milius, Doreen"},{"full_name":"Origgi, Francesco","last_name":"Origgi","first_name":"Francesco"},{"full_name":"Plattet, Philippe","first_name":"Philippe","last_name":"Plattet"}],"publication_status":"published","publisher":"American Society for Microbiology","department":[{"_id":"Bio"}],"acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","year":"2021","pmid":1,"file_date_updated":"2021-05-04T12:41:38Z","article_number":"e01024-20","language":[{"iso":"eng"}],"doi":"10.1128/mSphere.01024-20","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000663823400025"],"pmid":["33853875"]},"month":"04","publication_identifier":{"eissn":["23795042"]},"oa_version":"Published Version","file":[{"file_size":3379349,"content_type":"application/pdf","creator":"kschuh","file_name":"2021_mSphere_Gast.pdf","access_level":"open_access","date_updated":"2021-05-04T12:41:38Z","date_created":"2021-05-04T12:41:38Z","checksum":"310748d140c8838335c1314431095898","success":1,"relation":"main_file","file_id":"9370"}],"status":"public","title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","ddc":["570"],"intvolume":" 6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9361","abstract":[{"lang":"eng","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."}],"issue":"2","type":"journal_article","date_published":"2021-04-14T00:00:00Z","publication":"mSphere","citation":{"chicago":"Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere. American Society for Microbiology, 2021. https://doi.org/10.1128/mSphere.01024-20.","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” MSphere, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:10.1128/mSphere.01024-20.","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,” mSphere, vol. 6, no. 2. American Society for Microbiology, 2021.","apa":"Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., & Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. MSphere. American Society for Microbiology. https://doi.org/10.1128/mSphere.01024-20","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.","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. mSphere. 2021;6(2). doi:10.1128/mSphere.01024-20"},"day":"14","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"publication_identifier":{"eissn":["2041-1723"]},"month":"06","isi":1,"quality_controlled":"1","external_id":{"pmid":["34108481"],"isi":["000664874700014"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1038/s41467-021-23854-x","article_number":"3483","file_date_updated":"2021-06-15T18:55:59Z","publisher":"Springer Nature","department":[{"_id":"EM-Fac"}],"publication_status":"published","pmid":1,"acknowledgement":"We are deeply grateful to the late Gregor Högenauer who built the foundation for this study with his visionary work on the inhibitor diazaborine and its bacterial target. We thank Rolf Breinbauer for insightful discussions on boron chemistry. We thank Anton Meinhart and Tim Clausen for the valuable discussion of the manuscript. We are indebted to Thomas Köcher for the MS measurement of the diazaborine-ATPγS adduct. We thank the team of the VBCF for support during early phases of this work and the IST Austria Electron Microscopy Facility for providing equipment. The lab of D.H. is supported by Boehringer Ingelheim. The work was funded by FWF projects P32536 and P32977 (to H.B.).","year":"2021","volume":12,"date_updated":"2023-08-08T14:05:26Z","date_created":"2021-06-10T14:57:45Z","author":[{"full_name":"Prattes, Michael","last_name":"Prattes","first_name":"Michael"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"first_name":"Victor-Valentin","last_name":"Hodirnau","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"first_name":"Ingrid","last_name":"Rössler","full_name":"Rössler, Ingrid"},{"full_name":"Klein, Isabella","last_name":"Klein","first_name":"Isabella"},{"first_name":"Christina","last_name":"Hetzmannseder","full_name":"Hetzmannseder, Christina"},{"full_name":"Zisser, Gertrude","last_name":"Zisser","first_name":"Gertrude"},{"full_name":"Gruber, Christian C.","first_name":"Christian C.","last_name":"Gruber"},{"full_name":"Gruber, Karl","first_name":"Karl","last_name":"Gruber"},{"full_name":"Haselbach, David","first_name":"David","last_name":"Haselbach"},{"last_name":"Bergler","first_name":"Helmut","full_name":"Bergler, Helmut"}],"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"has_accepted_license":"1","article_processing_charge":"No","day":"09","article_type":"original","citation":{"mla":"Prattes, Michael, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications, vol. 12, no. 1, 3483, Springer Nature, 2021, doi:10.1038/s41467-021-23854-x.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, I. Rössler, I. Klein, C. Hetzmannseder, G. Zisser, C.C. Gruber, K. Gruber, D. Haselbach, H. Bergler, Nature Communications 12 (2021).","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Ingrid Rössler, Isabella Klein, Christina Hetzmannseder, Gertrude Zisser, et al. “Structural Basis for Inhibition of the AAA-ATPase Drg1 by Diazaborine.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-23854-x.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-23854-x","ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. 2021. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. 12(1), 3483.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Rössler, I., Klein, I., Hetzmannseder, C., … Bergler, H. (2021). Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-23854-x","ieee":"M. Prattes et al., “Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021."},"publication":"Nature Communications","date_published":"2021-06-09T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2′-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases.","lang":"eng"}],"intvolume":" 12","title":"Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9540","file":[{"file_name":"2021_NatureComm_Prattes.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3397292,"creator":"cziletti","relation":"main_file","file_id":"9556","date_updated":"2021-06-15T18:55:59Z","date_created":"2021-06-15T18:55:59Z","checksum":"40fc24c1310930990b52a8ad1142ee97","success":1}],"oa_version":"Published Version"},{"publication_identifier":{"eissn":["2050084X"]},"month":"05","doi":"10.7554/eLife.63294","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000661272000001"],"pmid":["34028353"]},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2021-06-28T11:35:30Z","author":[{"full_name":"Bespalov, Anton","last_name":"Bespalov","first_name":"Anton"},{"full_name":"Bernard, René","last_name":"Bernard","first_name":"René"},{"full_name":"Gilis, Anja","first_name":"Anja","last_name":"Gilis"},{"last_name":"Gerlach","first_name":"Björn","full_name":"Gerlach, Björn"},{"last_name":"Guillén","first_name":"Javier","full_name":"Guillén, Javier"},{"full_name":"Castagné, Vincent","first_name":"Vincent","last_name":"Castagné"},{"first_name":"Isabel A.","last_name":"Lefevre","full_name":"Lefevre, Isabel A."},{"last_name":"Ducrey","first_name":"Fiona","full_name":"Ducrey, Fiona"},{"first_name":"Lee","last_name":"Monk","full_name":"Monk, Lee"},{"full_name":"Bongiovanni, Sandrine","first_name":"Sandrine","last_name":"Bongiovanni"},{"first_name":"Bruce","last_name":"Altevogt","full_name":"Altevogt, Bruce"},{"full_name":"Arroyo-Araujo, María","last_name":"Arroyo-Araujo","first_name":"María"},{"full_name":"Bikovski, Lior","first_name":"Lior","last_name":"Bikovski"},{"last_name":"De Bruin","first_name":"Natasja","full_name":"De Bruin, Natasja"},{"first_name":"Esmeralda","last_name":"Castaños-Vélez","full_name":"Castaños-Vélez, Esmeralda"},{"last_name":"Dityatev","first_name":"Alexander","full_name":"Dityatev, Alexander"},{"first_name":"Christoph H.","last_name":"Emmerich","full_name":"Emmerich, Christoph H."},{"full_name":"Fares, Raafat","last_name":"Fares","first_name":"Raafat"},{"full_name":"Ferland-Beckham, Chantelle","last_name":"Ferland-Beckham","first_name":"Chantelle"},{"first_name":"Christelle","last_name":"Froger-Colléaux","full_name":"Froger-Colléaux, Christelle"},{"first_name":"Valerie","last_name":"Gailus-Durner","full_name":"Gailus-Durner, Valerie"},{"last_name":"Hölter","first_name":"Sabine M.","full_name":"Hölter, Sabine M."},{"full_name":"Hofmann, Martine Cj","first_name":"Martine Cj","last_name":"Hofmann"},{"full_name":"Kabitzke, Patricia","first_name":"Patricia","last_name":"Kabitzke"},{"last_name":"Kas","first_name":"Martien Jh","full_name":"Kas, Martien Jh"},{"first_name":"Claudia","last_name":"Kurreck","full_name":"Kurreck, Claudia"},{"full_name":"Moser, Paul","last_name":"Moser","first_name":"Paul"},{"first_name":"Malgorzata","last_name":"Pietraszek","full_name":"Pietraszek, Malgorzata"},{"full_name":"Popik, Piotr","last_name":"Popik","first_name":"Piotr"},{"full_name":"Potschka, Heidrun","first_name":"Heidrun","last_name":"Potschka"},{"full_name":"Prado Montes De Oca, Ernesto","first_name":"Ernesto","last_name":"Prado Montes De Oca"},{"full_name":"Restivo, Leonardo","first_name":"Leonardo","last_name":"Restivo"},{"last_name":"Riedel","first_name":"Gernot","full_name":"Riedel, Gernot"},{"last_name":"Ritskes-Hoitinga","first_name":"Merel","full_name":"Ritskes-Hoitinga, Merel"},{"last_name":"Samardzic","first_name":"Janko","full_name":"Samardzic, Janko"},{"orcid":"0000-0003-4326-5300","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","last_name":"Schunn","first_name":"Michael","full_name":"Schunn, Michael"},{"full_name":"Stöger, Claudia","first_name":"Claudia","last_name":"Stöger"},{"first_name":"Vootele","last_name":"Voikar","full_name":"Voikar, Vootele"},{"full_name":"Vollert, Jan","first_name":"Jan","last_name":"Vollert"},{"first_name":"Kimberley E.","last_name":"Wever","full_name":"Wever, Kimberley E."},{"full_name":"Wuyts, Kathleen","first_name":"Kathleen","last_name":"Wuyts"},{"last_name":"Macleod","first_name":"Malcolm R.","full_name":"Macleod, Malcolm R."},{"full_name":"Dirnagl, Ulrich","last_name":"Dirnagl","first_name":"Ulrich"},{"first_name":"Thomas","last_name":"Steckler","full_name":"Steckler, Thomas"}],"volume":10,"date_created":"2021-06-27T22:01:49Z","date_updated":"2023-08-10T13:36:50Z","pmid":1,"acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","year":"2021","publisher":"eLife Sciences Publications","department":[{"_id":"PreCl"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"24","scopus_import":"1","date_published":"2021-05-24T00:00:00Z","citation":{"chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.63294.","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” ELife, vol. 10, eLife Sciences Publications, 2021, doi:10.7554/eLife.63294.","short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.63294","ieee":"A. Bespalov et al., “Introduction to the EQIPD quality system,” eLife, vol. 10. eLife Sciences Publications, 2021.","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. eLife. 2021;10. doi:10.7554/eLife.63294"},"publication":"eLife","article_type":"original","abstract":[{"lang":"eng","text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use."}],"type":"journal_article","file":[{"creator":"asandaue","file_size":2500720,"content_type":"application/pdf","file_name":"2021_ELife_Bespalov.pdf","access_level":"open_access","date_created":"2021-06-28T11:35:30Z","date_updated":"2021-06-28T11:35:30Z","success":1,"checksum":"885b746051a7a6b6e24e3d2781a48fde","file_id":"9609","relation":"main_file"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9607","intvolume":" 10","status":"public","ddc":["570"],"title":"Introduction to the EQIPD quality system"},{"article_number":"109274","file_date_updated":"2021-06-28T14:06:24Z","ec_funded":1,"publication_status":"published","department":[{"_id":"SiHi"},{"_id":"LoSw"},{"_id":"PreCl"}],"publisher":"Cell Press","year":"2021","acknowledgement":"We thank the Bioimaging, Life Science, and Pre-Clinical Facilities at IST Austria; M.P. Postiglione, C. Simbriger, K. Valoskova, C. Schwayer, T. Hussain, M. Pieber, and V. Wimmer for initial experiments, technical support, and/or assistance; R. Shigemoto for sharing iv (Dnah11 mutant) mice; and M. Sixt and all members of the Hippenmeyer lab for discussion. This work was supported by National Institutes of Health grants ( R01-NS050580 to L.L. and F32MH096361 to L.A.S.). L.L. is an investigator of HHMI. N.A. received support from FWF Firnberg-Programm ( T 1031 ). A.H.H. is a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences . This work also received support from IST Austria institutional funds , FWF SFB F78 to S.H., the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme ( FP7/2007-2013 ) under REA grant agreement no 618444 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 725780 LinPro ) to S.H.","date_updated":"2023-08-10T13:55:00Z","date_created":"2021-06-27T22:01:48Z","volume":35,"author":[{"full_name":"Contreras, Ximena","last_name":"Contreras","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Amberg","first_name":"Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole"},{"first_name":"Amarbayasgalan","last_name":"Davaatseren","id":"70ADC922-B424-11E9-99E3-BA18E6697425","full_name":"Davaatseren, Amarbayasgalan"},{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H"},{"id":"32FE7D7C-F248-11E8-B48F-1D18A9856A87","last_name":"Sonntag","first_name":"Johanna","full_name":"Sonntag, Johanna"},{"full_name":"Andersen, Lill","first_name":"Lill","last_name":"Andersen"},{"first_name":"Tina","last_name":"Bernthaler","full_name":"Bernthaler, Tina"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena","last_name":"Heger","full_name":"Heger, Anna-Magdalena"},{"full_name":"Johnson, Randy L.","first_name":"Randy L.","last_name":"Johnson"},{"full_name":"Schwarz, Lindsay A.","first_name":"Lindsay A.","last_name":"Schwarz"},{"full_name":"Luo, Liqun","last_name":"Luo","first_name":"Liqun"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/boost-for-mouse-genetic-analysis/"}]},"month":"06","publication_identifier":{"eissn":["22111247"]},"quality_controlled":"1","isi":1,"project":[{"_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812","name":"Molecular Mechanisms of Radial Neuronal Migration"},{"grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development","call_identifier":"FP7"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000664463600016"]},"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2021.109274","type":"journal_article","abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division."}],"issue":"12","ddc":["570"],"status":"public","title":"A genome-wide library of MADM mice for single-cell genetic mosaic analysis","intvolume":" 35","_id":"9603","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"9613","relation":"main_file","date_updated":"2021-06-28T14:06:24Z","date_created":"2021-06-28T14:06:24Z","success":1,"checksum":"d49520fdcbbb5c2f883bddb67cee5d77","file_name":"2021_CellReports_Contreras.pdf","access_level":"open_access","creator":"asandaue","content_type":"application/pdf","file_size":7653149}],"scopus_import":"1","day":"22","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Cell Reports","citation":{"mla":"Contreras, Ximena, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports, vol. 35, no. 12, 109274, Cell Press, 2021, doi:10.1016/j.celrep.2021.109274.","short":"X. Contreras, N. Amberg, A. Davaatseren, A.H. Hansen, J. Sonntag, L. Andersen, T. Bernthaler, C. Streicher, A.-M. Heger, R.L. Johnson, L.A. Schwarz, L. Luo, T. Rülicke, S. Hippenmeyer, Cell Reports 35 (2021).","chicago":"Contreras, Ximena, Nicole Amberg, Amarbayasgalan Davaatseren, Andi H Hansen, Johanna Sonntag, Lill Andersen, Tina Bernthaler, et al. “A Genome-Wide Library of MADM Mice for Single-Cell Genetic Mosaic Analysis.” Cell Reports. Cell Press, 2021. https://doi.org/10.1016/j.celrep.2021.109274.","ama":"Contreras X, Amberg N, Davaatseren A, et al. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 2021;35(12). doi:10.1016/j.celrep.2021.109274","ista":"Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A-M, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. 2021. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. 35(12), 109274.","ieee":"X. Contreras et al., “A genome-wide library of MADM mice for single-cell genetic mosaic analysis,” Cell Reports, vol. 35, no. 12. Cell Press, 2021.","apa":"Contreras, X., Amberg, N., Davaatseren, A., Hansen, A. H., Sonntag, J., Andersen, L., … Hippenmeyer, S. (2021). A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2021.109274"},"date_published":"2021-06-22T00:00:00Z"},{"issue":"30","abstract":[{"lang":"eng","text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science."}],"type":"journal_article","file":[{"file_id":"9833","relation":"main_file","success":1,"checksum":"b043a91d9f9200e467b970b692687ed3","date_updated":"2021-08-09T09:44:03Z","date_created":"2021-08-09T09:44:03Z","access_level":"open_access","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","creator":"asandaue","file_size":7123293,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"9822","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 13","ddc":["620","570"],"status":"public","title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"04","scopus_import":"1","date_published":"2021-08-04T00:00:00Z","citation":{"ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","ieee":"T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850."},"publication":"ACS Applied Materials and Interfaces","page":"35545–35560","article_type":"original","ec_funded":1,"file_date_updated":"2021-08-09T09:44:03Z","author":[{"first_name":"Themistoklis","last_name":"Zisis","full_name":"Zisis, Themistoklis"},{"last_name":"Schwarz","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan"},{"last_name":"Balles","first_name":"Miriam","full_name":"Balles, Miriam"},{"first_name":"Maibritt","last_name":"Kretschmer","full_name":"Kretschmer, Maibritt"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Nemethova","full_name":"Nemethova, Maria"},{"first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"first_name":"Janina","last_name":"Lange","full_name":"Lange, Janina"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Zahler, Stefan","first_name":"Stefan","last_name":"Zahler"}],"volume":13,"date_created":"2021-08-08T22:01:28Z","date_updated":"2023-08-10T14:22:48Z","pmid":1,"acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","year":"2021","publisher":"American Chemical Society","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"publication_status":"published","publication_identifier":{"issn":["19448244"],"eissn":["19448252"]},"month":"08","doi":"10.1021/acsami.1c09850","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"}],"isi":1,"quality_controlled":"1"},{"issue":"1","abstract":[{"text":"A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 284","status":"public","title":"QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9911","article_processing_charge":"Yes","day":"11","scopus_import":"1","date_published":"2021-08-11T00:00:00Z","page":"56-73","article_type":"original","citation":{"chicago":"Nelson, Glyn, Ulrike Boehm, Steve Bagley, Peter Bajcsy, Johanna Bischof, Claire M. Brown, Aurélien Dauphin, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy. Wiley, 2021. https://doi.org/10.1111/jmi.13041.","mla":"Nelson, Glyn, et al. “QUAREP-LiMi: A Community-Driven Initiative to Establish Guidelines for Quality Assessment and Reproducibility for Instruments and Images in Light Microscopy.” Journal of Microscopy, vol. 284, no. 1, Wiley, 2021, pp. 56–73, doi:10.1111/jmi.13041.","short":"G. Nelson, U. Boehm, S. Bagley, P. Bajcsy, J. Bischof, C.M. Brown, A. Dauphin, I.M. Dobbie, J.E. Eriksson, O. Faklaris, J. Fernandez-Rodriguez, A. Ferrand, L. Gelman, A. Gheisari, H. Hartmann, C. Kukat, A. Laude, M. Mitkovski, S. Munck, A.J. North, T.M. Rasse, U. Resch-Genger, L.C. Schuetz, A. Seitz, C. Strambio-De-Castillia, J.R. Swedlow, I. Alexopoulos, K. Aumayr, S. Avilov, G.J. Bakker, R.R. Bammann, A. Bassi, H. Beckert, S. Beer, Y. Belyaev, J. Bierwagen, K.A. Birngruber, M. Bosch, J. Breitlow, L.A. Cameron, J. Chalfoun, J.J. Chambers, C.L. Chen, E. Conde-Sousa, A.D. Corbett, F.P. Cordelieres, E.D. Nery, R. Dietzel, F. Eismann, E. Fazeli, A. Felscher, H. Fried, N. Gaudreault, W.I. Goh, T. Guilbert, R. Hadleigh, P. Hemmerich, G.A. Holst, M.S. Itano, C.B. Jaffe, H.K. Jambor, S.C. Jarvis, A. Keppler, D. Kirchenbuechler, M. Kirchner, N. Kobayashi, G. Krens, S. Kunis, J. Lacoste, M. Marcello, G.G. Martins, D.J. Metcalf, C.A. Mitchell, J. Moore, T. Mueller, M.S. Nelson, S. Ogg, S. Onami, A.L. Palmer, P. Paul-Gilloteaux, J.A. Pimentel, L. Plantard, S. Podder, E. Rexhepaj, A. Royon, M.A. Saari, D. Schapman, V. Schoonderwoert, B. Schroth-Diez, S. Schwartz, M. Shaw, M. Spitaler, M.T. Stoeckl, D. Sudar, J. Teillon, S. Terjung, R. Thuenauer, C.D. Wilms, G.D. Wright, R. Nitschke, Journal of Microscopy 284 (2021) 56–73.","ista":"Nelson G et al. 2021. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 284(1), 56–73.","apa":"Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., … Nitschke, R. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. Wiley. https://doi.org/10.1111/jmi.13041","ieee":"G. Nelson et al., “QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy,” Journal of Microscopy, vol. 284, no. 1. Wiley, pp. 56–73, 2021.","ama":"Nelson G, Boehm U, Bagley S, et al. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. Journal of Microscopy. 2021;284(1):56-73. doi:10.1111/jmi.13041"},"publication":"Journal of Microscopy","volume":284,"date_updated":"2023-08-11T10:30:40Z","date_created":"2021-08-15T22:01:29Z","author":[{"first_name":"Glyn","last_name":"Nelson","full_name":"Nelson, Glyn"},{"full_name":"Boehm, Ulrike","first_name":"Ulrike","last_name":"Boehm"},{"first_name":"Steve","last_name":"Bagley","full_name":"Bagley, Steve"},{"full_name":"Bajcsy, Peter","last_name":"Bajcsy","first_name":"Peter"},{"full_name":"Bischof, Johanna","last_name":"Bischof","first_name":"Johanna"},{"full_name":"Brown, Claire M.","last_name":"Brown","first_name":"Claire M."},{"full_name":"Dauphin, Aurélien","first_name":"Aurélien","last_name":"Dauphin"},{"full_name":"Dobbie, Ian M.","last_name":"Dobbie","first_name":"Ian M."},{"full_name":"Eriksson, John E.","first_name":"John E.","last_name":"Eriksson"},{"last_name":"Faklaris","first_name":"Orestis","full_name":"Faklaris, Orestis"},{"first_name":"Julia","last_name":"Fernandez-Rodriguez","full_name":"Fernandez-Rodriguez, Julia"},{"full_name":"Ferrand, Alexia","first_name":"Alexia","last_name":"Ferrand"},{"first_name":"Laurent","last_name":"Gelman","full_name":"Gelman, Laurent"},{"full_name":"Gheisari, Ali","first_name":"Ali","last_name":"Gheisari"},{"full_name":"Hartmann, Hella","last_name":"Hartmann","first_name":"Hella"},{"full_name":"Kukat, Christian","last_name":"Kukat","first_name":"Christian"},{"full_name":"Laude, Alex","first_name":"Alex","last_name":"Laude"},{"full_name":"Mitkovski, Miso","first_name":"Miso","last_name":"Mitkovski"},{"last_name":"Munck","first_name":"Sebastian","full_name":"Munck, Sebastian"},{"full_name":"North, Alison J.","last_name":"North","first_name":"Alison J."},{"first_name":"Tobias M.","last_name":"Rasse","full_name":"Rasse, Tobias M."},{"last_name":"Resch-Genger","first_name":"Ute","full_name":"Resch-Genger, Ute"},{"full_name":"Schuetz, Lucas 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G.","last_name":"Martins"},{"full_name":"Metcalf, Daniel J.","first_name":"Daniel J.","last_name":"Metcalf"},{"full_name":"Mitchell, Claire A.","first_name":"Claire A.","last_name":"Mitchell"},{"full_name":"Moore, Joshua","last_name":"Moore","first_name":"Joshua"},{"last_name":"Mueller","first_name":"Tobias","full_name":"Mueller, Tobias"},{"last_name":"Nelson","first_name":"Michael S.","full_name":"Nelson, Michael S."},{"first_name":"Stephen","last_name":"Ogg","full_name":"Ogg, Stephen"},{"full_name":"Onami, Shuichi","last_name":"Onami","first_name":"Shuichi"},{"last_name":"Palmer","first_name":"Alexandra L.","full_name":"Palmer, Alexandra L."},{"full_name":"Paul-Gilloteaux, Perrine","first_name":"Perrine","last_name":"Paul-Gilloteaux"},{"full_name":"Pimentel, Jaime A.","last_name":"Pimentel","first_name":"Jaime A."},{"full_name":"Plantard, Laure","first_name":"Laure","last_name":"Plantard"},{"first_name":"Santosh","last_name":"Podder","full_name":"Podder, Santosh"},{"last_name":"Rexhepaj","first_name":"Elton","full_name":"Rexhepaj, Elton"},{"full_name":"Royon, Arnaud","first_name":"Arnaud","last_name":"Royon"},{"full_name":"Saari, Markku A.","first_name":"Markku A.","last_name":"Saari"},{"last_name":"Schapman","first_name":"Damien","full_name":"Schapman, Damien"},{"full_name":"Schoonderwoert, Vincent","last_name":"Schoonderwoert","first_name":"Vincent"},{"last_name":"Schroth-Diez","first_name":"Britta","full_name":"Schroth-Diez, Britta"},{"full_name":"Schwartz, Stanley","first_name":"Stanley","last_name":"Schwartz"},{"last_name":"Shaw","first_name":"Michael","full_name":"Shaw, Michael"},{"first_name":"Martin","last_name":"Spitaler","full_name":"Spitaler, Martin"},{"first_name":"Martin T.","last_name":"Stoeckl","full_name":"Stoeckl, Martin T."},{"last_name":"Sudar","first_name":"Damir","full_name":"Sudar, Damir"},{"full_name":"Teillon, Jeremie","first_name":"Jeremie","last_name":"Teillon"},{"first_name":"Stefan","last_name":"Terjung","full_name":"Terjung, Stefan"},{"last_name":"Thuenauer","first_name":"Roland","full_name":"Thuenauer, Roland"},{"full_name":"Wilms, Christian D.","last_name":"Wilms","first_name":"Christian D."},{"last_name":"Wright","first_name":"Graham D.","full_name":"Wright, Graham D."},{"full_name":"Nitschke, Roland","last_name":"Nitschke","first_name":"Roland"}],"department":[{"_id":"Bio"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"We thank https://www.somersault1824.com/somersault18:24 BV (Leuven, Belgium) for help with Figure 1. E. C.-S. was supported by the project PPBI-POCI-01-0145-FEDER-022122, in the scope of Fundação para a Ciência e Tecnologia, Portugal (FCT) National Roadmap of Research Infrastructures. R.N. was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) Grant number Ni 451/9-1 - MIAP-Freiburg.","year":"2021","publication_identifier":{"eissn":["1365-2818"],"issn":["0022-2720"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1111/jmi.13041","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1111/jmi.13041","open_access":"1"}],"external_id":{"isi":["000683702700001"]}}]