[{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2023-12-01T00:00:00Z","publication":"Journal of Applied Crystallography","citation":{"ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 2023;56(6):1618-1629. doi:10.1107/S1600576723008324","ista":"Pauw BR, Smales GJ, Anker AS, Annadurai V, Balazs D, Bienert R, Bouwman WG, Breßler I, Breternitz J, Brok ES, Bryant G, Clulow AJ, Crater ER, De Geuser F, Giudice AD, Deumer J, Disch S, Dutt S, Frank K, Fratini E, Garcia PRAF, Gilbert EP, Hahn MB, Hallett J, Hohenschutz M, Hollamby M, Huband S, Ilavsky J, Jochum JK, Juelsholt M, Mansel BW, Penttilä P, Pittkowski RK, Portale G, Pozzo LD, Rochels L, Rosalie JM, Saloga PEJ, Seibt S, Smith AJ, Smith GN, Spiering GA, Stawski TM, Taché O, Thünemann AF, Toth K, Whitten AE, Wuttke J. 2023. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 56(6), 1618–1629.","ieee":"B. R. Pauw et al., “The human factor: Results of a small-angle scattering data analysis round robin,” Journal of Applied Crystallography, vol. 56, no. 6. pp. 1618–1629, 2023.","apa":"Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert, R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. https://doi.org/10.1107/S1600576723008324","mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, vol. 56, no. 6, 2023, pp. 1618–29, doi:10.1107/S1600576723008324.","short":"B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert, W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R. Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E. Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz, M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P. Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J. Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché, A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography 56 (2023) 1618–1629.","chicago":"Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai, Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, 2023. https://doi.org/10.1107/S1600576723008324."},"article_type":"original","page":"1618-1629","abstract":[{"lang":"eng","text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed."}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2024-01-17T07:47:35Z","date_created":"2024-01-17T07:47:35Z","checksum":"dab30d4556360f2cecf99f4b7efb0ee9","success":1,"relation":"main_file","file_id":"14822","file_size":2165864,"content_type":"application/pdf","creator":"dernst","file_name":"2023_JourApplCrystallography_Pauw.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14799","status":"public","ddc":["540"],"title":"The human factor: Results of a small-angle scattering data analysis round robin","intvolume":" 56","month":"12","publication_identifier":{"issn":["0021-8898"],"eissn":["1600-5767"]},"doi":"10.1107/S1600576723008324","language":[{"iso":"eng"}],"external_id":{"arxiv":["2303.03772"]},"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","file_date_updated":"2024-01-17T07:47:35Z","author":[{"first_name":"Brian R.","last_name":"Pauw","full_name":"Pauw, Brian R."},{"full_name":"Smales, Glen J.","last_name":"Smales","first_name":"Glen J."},{"full_name":"Anker, Andy S.","first_name":"Andy S.","last_name":"Anker"},{"last_name":"Annadurai","first_name":"Venkatasamy","full_name":"Annadurai, Venkatasamy"},{"full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","first_name":"Daniel","last_name":"Balazs"},{"full_name":"Bienert, Ralf","last_name":"Bienert","first_name":"Ralf"},{"full_name":"Bouwman, Wim G.","first_name":"Wim G.","last_name":"Bouwman"},{"full_name":"Breßler, Ingo","first_name":"Ingo","last_name":"Breßler"},{"first_name":"Joachim","last_name":"Breternitz","full_name":"Breternitz, Joachim"},{"first_name":"Erik S.","last_name":"Brok","full_name":"Brok, Erik S."},{"full_name":"Bryant, Gary","last_name":"Bryant","first_name":"Gary"},{"full_name":"Clulow, Andrew J.","first_name":"Andrew J.","last_name":"Clulow"},{"full_name":"Crater, Erin R.","first_name":"Erin R.","last_name":"Crater"},{"full_name":"De Geuser, Frédéric","last_name":"De Geuser","first_name":"Frédéric"},{"last_name":"Giudice","first_name":"Alessandra Del","full_name":"Giudice, Alessandra Del"},{"full_name":"Deumer, Jérôme","last_name":"Deumer","first_name":"Jérôme"},{"full_name":"Disch, Sabrina","last_name":"Disch","first_name":"Sabrina"},{"first_name":"Shankar","last_name":"Dutt","full_name":"Dutt, Shankar"},{"full_name":"Frank, Kilian","first_name":"Kilian","last_name":"Frank"},{"first_name":"Emiliano","last_name":"Fratini","full_name":"Fratini, Emiliano"},{"full_name":"Garcia, Paulo R.A.F.","last_name":"Garcia","first_name":"Paulo R.A.F."},{"full_name":"Gilbert, Elliot P.","last_name":"Gilbert","first_name":"Elliot P."},{"full_name":"Hahn, Marc B.","last_name":"Hahn","first_name":"Marc B."},{"full_name":"Hallett, James","first_name":"James","last_name":"Hallett"},{"full_name":"Hohenschutz, Max","first_name":"Max","last_name":"Hohenschutz"},{"full_name":"Hollamby, Martin","last_name":"Hollamby","first_name":"Martin"},{"full_name":"Huband, Steven","last_name":"Huband","first_name":"Steven"},{"full_name":"Ilavsky, Jan","first_name":"Jan","last_name":"Ilavsky"},{"full_name":"Jochum, Johanna K.","last_name":"Jochum","first_name":"Johanna K."},{"full_name":"Juelsholt, Mikkel","last_name":"Juelsholt","first_name":"Mikkel"},{"full_name":"Mansel, Bradley W.","first_name":"Bradley W.","last_name":"Mansel"},{"first_name":"Paavo","last_name":"Penttilä","full_name":"Penttilä, Paavo"},{"full_name":"Pittkowski, Rebecca K.","first_name":"Rebecca K.","last_name":"Pittkowski"},{"full_name":"Portale, Giuseppe","last_name":"Portale","first_name":"Giuseppe"},{"first_name":"Lilo D.","last_name":"Pozzo","full_name":"Pozzo, Lilo D."},{"last_name":"Rochels","first_name":"Leonhard","full_name":"Rochels, Leonhard"},{"first_name":"Julian M.","last_name":"Rosalie","full_name":"Rosalie, Julian M."},{"first_name":"Patrick E.J.","last_name":"Saloga","full_name":"Saloga, Patrick E.J."},{"full_name":"Seibt, Susanne","first_name":"Susanne","last_name":"Seibt"},{"full_name":"Smith, Andrew J.","last_name":"Smith","first_name":"Andrew J."},{"full_name":"Smith, Gregory N.","first_name":"Gregory N.","last_name":"Smith"},{"full_name":"Spiering, Glenn A.","last_name":"Spiering","first_name":"Glenn A."},{"full_name":"Stawski, Tomasz M.","last_name":"Stawski","first_name":"Tomasz M."},{"last_name":"Taché","first_name":"Olivier","full_name":"Taché, Olivier"},{"full_name":"Thünemann, Andreas F.","last_name":"Thünemann","first_name":"Andreas F."},{"last_name":"Toth","first_name":"Kristof","full_name":"Toth, Kristof"},{"last_name":"Whitten","first_name":"Andrew E.","full_name":"Whitten, Andrew E."},{"full_name":"Wuttke, Joachim","last_name":"Wuttke","first_name":"Joachim"}],"date_updated":"2024-01-17T07:49:52Z","date_created":"2024-01-14T23:00:57Z","volume":56,"acknowledgement":"KT acknowledges the NIST–NRC postdoctoral fellowship program for support. This work was partially funded through the European Metrology Programme for Innovation and Research (EMPIR) project No. 17NRM04.\r\nCertain commercial equipment, instruments, materials or software are identified in this article in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Open access funding enabled and organized by Projekt DEAL.","year":"2023","publication_status":"published","department":[{"_id":"LifeSc"}]},{"_id":"13312","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas","status":"public","ddc":["530"],"oa_version":"Preprint","type":"preprint","abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest in the past years. Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform.","lang":"eng"}],"citation":{"ieee":"M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. .","apa":"Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109","ista":"Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109.","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","mla":"Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109."},"publication":"arXiv","date_published":"2023-06-13T00:00:00Z","keyword":["Mesoscale and Nanoscale Physics"],"article_processing_charge":"No","day":"13","year":"2023","acknowledgement":"The authors acknowledge Alexander Brinkmann, Alessandro Crippa, Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM analysis. This research and related results were made\r\npossible with the support of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication facility, the European Union’s Horizon 2020\r\nresearch and innovation programme under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento Program” Project No.\r\n2022-T1/IND-24070.","department":[{"_id":"GeKa"},{"_id":"M-Shop"}],"publication_status":"submitted","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"13286"}]},"author":[{"full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","first_name":"Marco","last_name":"Valentini"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver","last_name":"Sagi","full_name":"Sagi, Oliver"},{"first_name":"Levon","last_name":"Baghumyan","full_name":"Baghumyan, Levon"},{"first_name":"Thijs de","last_name":"Gijsel","full_name":"Gijsel, Thijs de"},{"first_name":"Jason","last_name":"Jung","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87","full_name":"Jung, Jason"},{"full_name":"Calcaterra, Stefano","first_name":"Stefano","last_name":"Calcaterra"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"full_name":"Servin, Juan Aguilera","first_name":"Juan Aguilera","last_name":"Servin"},{"last_name":"Aggarwal","first_name":"Kushagra","orcid":"0000-0001-9985-9293","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","full_name":"Aggarwal, Kushagra"},{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","last_name":"Janik","first_name":"Marian","full_name":"Janik, Marian"},{"full_name":"Adletzberger, Thomas","id":"38756BB2-F248-11E8-B48F-1D18A9856A87","last_name":"Adletzberger","first_name":"Thomas"},{"full_name":"Souto, Rubén Seoane","first_name":"Rubén Seoane","last_name":"Souto"},{"full_name":"Leijnse, Martin","first_name":"Martin","last_name":"Leijnse"},{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"full_name":"Schrade, Constantin","last_name":"Schrade","first_name":"Constantin"},{"full_name":"Bakkers, Erik","first_name":"Erik","last_name":"Bakkers"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"full_name":"Isella, Giovanni","first_name":"Giovanni","last_name":"Isella"},{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"date_created":"2023-07-26T11:17:20Z","date_updated":"2024-02-07T07:52:32Z","article_number":"2306.07109","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.07109"}],"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":{"arxiv":["2306.07109"]},"oa":1,"project":[{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"},{"call_identifier":"FWF","name":"Towards scalable hut wire quantum devices","grant_number":"P32235","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"name":"Conventional and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"_id":"bd5b4ec5-d553-11ed-ba76-a6eedb083344","name":"Protected states of quantum matter"}],"doi":"10.48550/arXiv.2306.07109","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"month":"06"},{"date_published":"2023-08-04T00:00:00Z","citation":{"short":"J.G. Danzl, (2023).","mla":"Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126.","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126","ista":"Danzl JG. 2023. 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We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"file_date_updated":"2023-08-04T13:19:47Z"},{"abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","_id":"14257","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Imaging brain tissue architecture across millimeter to nanometer scales","status":"public","day":"31","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2023-08-31T00:00:00Z","publication":"Nature Biotechnology","citation":{"ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8","ieee":"J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology. Springer Nature, 2023.","ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology.","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8."},"article_type":"original","ec_funded":1,"author":[{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","first_name":"Julia M","last_name":"Michalska"},{"first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia"},{"id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2340-7431","first_name":"Philipp","last_name":"Velicky","full_name":"Velicky, Philipp"},{"id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","last_name":"Korinkova","first_name":"Hana","full_name":"Korinkova, Hana"},{"first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake"},{"full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg"},{"full_name":"Venturino, Alessandro","first_name":"Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403"},{"first_name":"Karl","last_name":"Roessler","full_name":"Roessler, Karl"},{"full_name":"Czech, Thomas","last_name":"Czech","first_name":"Thomas"},{"first_name":"Romana","last_name":"Höftberger","full_name":"Höftberger, Romana"},{"first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"},{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13126"}],"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}]},"date_created":"2023-09-03T22:01:15Z","date_updated":"2024-02-21T12:18:18Z","year":"2023","acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","publication_status":"epub_ahead","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"publisher":"Springer Nature","month":"08","publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"doi":"10.1038/s41587-023-01911-8","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001065254200001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41587-023-01911-8"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","call_identifier":"FWF","name":"Optical control of synaptic function via adhesion molecules"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","name":"Molecular Drug Targets","call_identifier":"FWF"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","call_identifier":"H2020"},{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"},{"call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","grant_number":"101026635"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"13044","status":"public","title":"Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Singlet oxygen (1O2) formation is now recognised as a key aspect of non-aqueous oxygen redox chemistry. For identifying 1O2, chemical trapping via 9,10-dimethylanthracene (DMA) to form the endoperoxide (DMA-O2) has become the mainstay method due to its sensitivity, selectivity, and ease of use. While DMA has been shown to be selective for 1O2, rather than forming DMA-O2 with a wide variety of potentially reactive O-containing species, false positives might hypothetically be obtained in the presence of previously overlooked species. Here, we first give unequivocal direct spectroscopic proof by the 1O2-specific near infrared (NIR) emission at 1270 nm for the previously proposed 1O2 formation pathways, which centre around superoxide disproportionation. We then show that peroxocarbonates, common intermediates in metal-O2 and metal carbonate electrochemistry, do not produce false-positive DMA-O2. Moreover, we identify a previously unreported 1O2-forming pathway through the reaction of CO2 with superoxide. Overall, we give unequivocal proof for 1O2 formation in non-aqueous oxygen redox and show that chemical trapping with DMA is a reliable method to assess 1O2 formation."}],"publication":"Faraday Discussions","citation":{"ista":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. 2023. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions.","apa":"Mondal, S., Jethwa, R. B., Pant, B., Hauschild, R., & Freunberger, S. A. (2023). Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd00088e","ieee":"S. Mondal, R. B. Jethwa, B. Pant, R. Hauschild, and S. A. Freunberger, “Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes,” Faraday Discussions. Royal Society of Chemistry, 2023.","ama":"Mondal S, Jethwa RB, Pant B, Hauschild R, Freunberger SA. Singlet oxygen in non-aqueous oxygen redox: Direct spectroscopic evidence for formation pathways and reliability of chemical probes. Faraday Discussions. 2023. doi:10.1039/d3fd00088e","chicago":"Mondal, Soumyadip, Rajesh B Jethwa, Bhargavi Pant, Robert Hauschild, and Stefan Alexander Freunberger. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd00088e.","mla":"Mondal, Soumyadip, et al. “Singlet Oxygen in Non-Aqueous Oxygen Redox: Direct Spectroscopic Evidence for Formation Pathways and Reliability of Chemical Probes.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd00088e.","short":"S. Mondal, R.B. Jethwa, B. Pant, R. Hauschild, S.A. Freunberger, Faraday Discussions (2023)."},"article_type":"original","date_published":"2023-05-17T00:00:00Z","keyword":["Physical and Theoretical Chemistry"],"day":"17","article_processing_charge":"Yes (via OA deal)","year":"2023","publication_status":"epub_ahead","publisher":"Royal Society of Chemistry","department":[{"_id":"StFr"},{"_id":"Bio"}],"author":[{"full_name":"Mondal, Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","first_name":"Soumyadip"},{"first_name":"Rajesh B","last_name":"Jethwa","id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B"},{"first_name":"Bhargavi","last_name":"Pant","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112","full_name":"Pant, Bhargavi"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"date_created":"2023-05-22T06:53:34Z","date_updated":"2024-03-20T13:10:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","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,"main_file_link":[{"url":"https://doi.org/10.1039/d3fd00088e","open_access":"1"}],"external_id":{"isi":["001070423500001"]},"quality_controlled":"1","isi":1,"doi":"10.1039/d3fd00088e","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["1359-6640"],"eissn":["1364-5498"]}},{"date_created":"2022-02-16T11:18:21Z","date_updated":"2023-01-31T07:33:07Z","volume":2,"author":[{"last_name":"Dubini","first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A."},{"first_name":"Eva","last_name":"Korytiaková","full_name":"Korytiaková, Eva"},{"first_name":"Thea","last_name":"Schinkel","full_name":"Schinkel, Thea"},{"full_name":"Heinrichs, Pia","last_name":"Heinrichs","first_name":"Pia"},{"full_name":"Carell, Thomas","first_name":"Thomas","last_name":"Carell"},{"first_name":"Petra","last_name":"Rovo","id":"c316e53f-b965-11eb-b128-bb26acc59c00","orcid":"0000-0001-8729-7326","full_name":"Rovo, Petra"}],"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.12.14.472563","relation":"earlier_version"}]},"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"NMR"}],"acknowledgement":"We thank Markus Müller for valued discussions and Felix Xu for assistance in the measurement of UV/vis melting profiles. This work was supported in part by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1309-325871075, EU-ITN LightDyNAmics (ID: 765266), the ERC-AG EpiR (ID: 741912), the Center for NanoScience, the Excellence Clusters CIPSM, and the Fonds der Chemischen Industrie. Open access funding provided by Institute of Science and Technology Austria (ISTA).\r\n\r\n","year":"2022","pmid":1,"file_date_updated":"2022-07-29T07:53:20Z","language":[{"iso":"eng"}],"doi":"10.1021/acsphyschemau.1c00050","quality_controlled":"1","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"oa":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":{"pmid":["35637781"]},"month":"02","publication_identifier":{"eissn":["2694-2445"]},"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11692","date_updated":"2022-07-29T07:53:20Z","date_created":"2022-07-29T07:53:20Z","checksum":"5ce3f907848f5c7caf77f1adfe5826c6","success":1,"file_name":"2022_ACSPhysChemAU_Dubini.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2351220,"creator":"dernst"}],"title":"1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives","ddc":["540"],"status":"public","intvolume":" 2","_id":"10758","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"5-Carboxycytosine (5caC) is a rare epigenetic modification found in nucleic acids of all domains of life. Despite its sparse genomic abundance, 5caC is presumed to play essential regulatory roles in transcription, maintenance and base-excision processes in DNA. In this work, we utilize nuclear magnetic resonance (NMR) spectroscopy to address the effects of 5caC incorporation into canonical DNA strands at multiple pH and temperature conditions. Our results demonstrate that 5caC has a pH-dependent global destabilizing and a base-pair mobility enhancing local impact on dsDNA, albeit without any detectable influence on the ground-state B-DNA structure. Measurement of hybridization thermodynamics and kinetics of 5caC-bearing DNA duplexes highlighted how acidic environment (pH 5.8 and 4.7) destabilizes the double-stranded structure by ∼10–20 kJ mol–1 at 37 °C when compared to the same sample at neutral pH. Protonation of 5caC results in a lower activation energy for the dissociation process and a higher barrier for annealing. Studies on conformational exchange on the microsecond time scale regime revealed a sharply localized base-pair motion involving exclusively the modified site and its immediate surroundings. By direct comparison with canonical and 5-formylcytosine (5fC)-edited strands, we were able to address the impact of the two most oxidized naturally occurring cytosine derivatives in the genome. These insights on 5caC’s subtle sensitivity to acidic pH contribute to the long-standing questions of its capacity as a substrate in base excision repair processes and its purpose as an independent, stable epigenetic mark.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2022-02-11T00:00:00Z","article_type":"original","page":"237-246","publication":"ACS Physical Chemistry Au","citation":{"chicago":"Dubini, Romeo C. A., Eva Korytiaková, Thea Schinkel, Pia Heinrichs, Thomas Carell, and Petra Rovo. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au. American Chemical Society, 2022. https://doi.org/10.1021/acsphyschemau.1c00050.","short":"R.C.A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, P. Rovo, ACS Physical Chemistry Au 2 (2022) 237–246.","mla":"Dubini, Romeo C. A., et al. “1H NMR Chemical Exchange Techniques Reveal Local and Global Effects of Oxidized Cytosine Derivatives.” ACS Physical Chemistry Au, vol. 2, no. 3, American Chemical Society, 2022, pp. 237–46, doi:10.1021/acsphyschemau.1c00050.","ieee":"R. C. A. Dubini, E. Korytiaková, T. Schinkel, P. Heinrichs, T. Carell, and P. Rovo, “1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives,” ACS Physical Chemistry Au, vol. 2, no. 3. American Chemical Society, pp. 237–246, 2022.","apa":"Dubini, R. C. A., Korytiaková, E., Schinkel, T., Heinrichs, P., Carell, T., & Rovo, P. (2022). 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. American Chemical Society. https://doi.org/10.1021/acsphyschemau.1c00050","ista":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 2022. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2(3), 237–246.","ama":"Dubini RCA, Korytiaková E, Schinkel T, Heinrichs P, Carell T, Rovo P. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Physical Chemistry Au. 2022;2(3):237-246. doi:10.1021/acsphyschemau.1c00050"},"day":"11","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1"},{"quality_controlled":"1","oa":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":{"pmid":["35384410"]},"language":[{"iso":"eng"}],"doi":"10.1002/cpz1.407","publication_identifier":{"eissn":["2691-1299"]},"month":"04","department":[{"_id":"NanoFab"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2022","acknowledgement":"We thank Kasia Stefanowski for excellent technical assistance, and the Core Facility Bioimaging of the Biomedical Center (BMC) of the Ludwig-Maximilian University for excellent support. We gratefully acknowledge financial support from the Peter Hans Hofschneider Professorship of the Stiftung Experimentelle Biomedizin (to J.R), from the DFG (Collaborative Research Center SFB914, project A12; and Priority Programme SPP2332, project 492014049; both to J.R) and from the LMU Institutional Strategy LMU-Excellent within the framework of the German Excellence Initiative (to J.R).\r\nOpen access funding enabled and organized by Projekt DEAL.","volume":2,"date_created":"2022-04-17T22:01:46Z","date_updated":"2022-05-02T08:18:00Z","author":[{"last_name":"Kroll","first_name":"Janina","full_name":"Kroll, Janina"},{"first_name":"Mauricio J.A.","last_name":"Ruiz-Fernandez","full_name":"Ruiz-Fernandez, Mauricio J.A."},{"first_name":"Malte B.","last_name":"Braun","full_name":"Braun, Malte B."},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack"},{"first_name":"Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"}],"article_number":"e407","file_date_updated":"2022-05-02T08:16:10Z","article_type":"original","citation":{"chicago":"Kroll, Janina, Mauricio J.A. Ruiz-Fernandez, Malte B. Braun, Jack Merrin, and Jörg Renkawitz. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols. Wiley, 2022. https://doi.org/10.1002/cpz1.407.","mla":"Kroll, Janina, et al. “Quantifying the Probing and Selection of Microenvironmental Pores by Motile Immune Cells.” Current Protocols, vol. 2, no. 4, e407, Wiley, 2022, doi:10.1002/cpz1.407.","short":"J. Kroll, M.J.A. Ruiz-Fernandez, M.B. Braun, J. Merrin, J. Renkawitz, Current Protocols 2 (2022).","ista":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. 2022. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2(4), e407.","ieee":"J. Kroll, M. J. A. Ruiz-Fernandez, M. B. Braun, J. Merrin, and J. Renkawitz, “Quantifying the probing and selection of microenvironmental pores by motile immune cells,” Current Protocols, vol. 2, no. 4. Wiley, 2022.","apa":"Kroll, J., Ruiz-Fernandez, M. J. A., Braun, M. B., Merrin, J., & Renkawitz, J. (2022). Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. Wiley. https://doi.org/10.1002/cpz1.407","ama":"Kroll J, Ruiz-Fernandez MJA, Braun MB, Merrin J, Renkawitz J. Quantifying the probing and selection of microenvironmental pores by motile immune cells. Current Protocols. 2022;2(4). doi:10.1002/cpz1.407"},"publication":"Current Protocols","date_published":"2022-04-05T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"05","intvolume":" 2","ddc":["570"],"title":"Quantifying the probing and selection of microenvironmental pores by motile immune cells","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11182","file":[{"access_level":"open_access","file_name":"2022_CurrentProtocols_Kroll.pdf","content_type":"application/pdf","file_size":2142703,"creator":"dernst","relation":"main_file","file_id":"11347","checksum":"72152d005c367777f6cf2f6a477f0d52","success":1,"date_created":"2022-05-02T08:16:10Z","date_updated":"2022-05-02T08:16:10Z"}],"oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"text":"Immune cells are constantly on the move through multicellular organisms to explore and respond to pathogens and other harmful insults. While moving, immune cells efficiently traverse microenvironments composed of tissue cells and extracellular fibers, which together form complex environments of various porosity, stiffness, topography, and chemical composition. In this protocol we describe experimental procedures to investigate immune cell migration through microenvironments of heterogeneous porosity. In particular, we describe micro-channels, micro-pillars, and collagen networks as cell migration paths with alternative pore size choices. Employing micro-channels or micro-pillars that divide at junctions into alternative paths with initially differentially sized pores allows us to precisely (1) measure the cellular translocation time through these porous path junctions, (2) quantify the cellular preference for individual pore sizes, and (3) image cellular components like the nucleus and the cytoskeleton. This reductionistic experimental setup thus can elucidate how immune cells perform decisions in complex microenvironments of various porosity like the interstitium. The setup further allows investigation of the underlying forces of cellular squeezing and the consequences of cellular deformation on the integrity of the cell and its organelles. As a complementary approach that does not require any micro-engineering expertise, we describe the usage of three-dimensional collagen networks with different pore sizes. Whereas we here focus on dendritic cells as a model for motile immune cells, the described protocols are versatile as they are also applicable for other immune cell types like neutrophils and non-immune cell types such as mesenchymal and cancer cells. In summary, we here describe protocols to identify the mechanisms and principles of cellular probing, decision making, and squeezing during cellular movement through microenvironments of heterogeneous porosity.","lang":"eng"}]},{"year":"2022","publication_status":"published","publisher":"Edinburgh University Press","department":[{"_id":"E-Lib"}],"author":[{"full_name":"Chlebak, Clara A","id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","orcid":"0000-0002-3385-3865","first_name":"Clara A","last_name":"Chlebak"},{"first_name":"Peter H.","last_name":"Reid","full_name":"Reid, Peter H."}],"date_created":"2022-06-12T22:01:45Z","date_updated":"2023-02-21T09:51:29Z","volume":38,"month":"04","publication_identifier":{"eissn":["1758-3497"],"issn":["1758-3489"]},"main_file_link":[{"url":"https://rgu-repository.worktribe.com/output/1635939","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.3366/lih.2022.0097","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"This article investigates library-related documents written by Gerard van Swieten (1700–72) during his tenure as Library Prefect in the Imperial Library of Vienna (1745–72). Van Swieten’s time as Library Prefect is considered through a textual analysis. Handwritten letters were deconstructed in terms of their appearance, layout, and tone in order to mine them for meaning. Furthermore, the contents were examined for library matters such as censorship, catalogues, and collection development. The Imperial Court Library held a prominent role as a repository for rare and valuable works, later becoming the National Library of Austria.\r\nGerard van Swieten’s work as a librarian tends to be overlooked, perhaps because he is better known as the private physician of Maria Theresia, as well as a medical reformer. Nevertheless, he was a hard-working chief librarian deeply involved in all aspects of librarianship. Van Swieten endorsed modern scientific works, which were otherwise banned officially by the censorship commission, for the use of scholars in the library, expanded the collection by acquiring books through his network of scholars and publishers, and reissued library catalogues. He also provided for the comfort of users in the library reading room, at a time when such considerations were unusual. In conclusion, a proposal is made that van Swieten viewed his role as librarian with some importance and pride."}],"issue":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11444","title":"From the prefect’s desk: Gerard van Swieten’s library correspondence","status":"public","intvolume":" 38","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Library and Information History","citation":{"short":"C.A. Chlebak, P.H. Reid, Library and Information History 38 (2022) 23–41.","mla":"Chlebak, Clara A., and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” Library and Information History, vol. 38, no. 1, Edinburgh University Press, 2022, pp. 23–41, doi:10.3366/lih.2022.0097.","chicago":"Chlebak, Clara A, and Peter H. Reid. “From the Prefect’s Desk: Gerard van Swieten’s Library Correspondence.” Library and Information History. Edinburgh University Press, 2022. https://doi.org/10.3366/lih.2022.0097.","ama":"Chlebak CA, Reid PH. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 2022;38(1):23-41. doi:10.3366/lih.2022.0097","ieee":"C. A. Chlebak and P. H. Reid, “From the prefect’s desk: Gerard van Swieten’s library correspondence,” Library and Information History, vol. 38, no. 1. Edinburgh University Press, pp. 23–41, 2022.","apa":"Chlebak, C. A., & Reid, P. H. (2022). From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. Edinburgh University Press. https://doi.org/10.3366/lih.2022.0097","ista":"Chlebak CA, Reid PH. 2022. From the prefect’s desk: Gerard van Swieten’s library correspondence. Library and Information History. 38(1), 23–41."},"article_type":"original","page":"23-41","date_published":"2022-04-01T00:00:00Z"},{"doi":"10.25365/phaidra.337","conference":{"name":"ASHPC: Austrian-Slovenian HPC Meeting","start_date":"2022-05-31","location":"Grundlsee, Austria","end_date":"2022-06-02"},"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"},"oa":1,"publication_identifier":{"isbn":["978-3-200-08499-5"]},"month":"06","author":[{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Hornoiu, Andrei","first_name":"Andrei","last_name":"Hornoiu","id":"77129392-B450-11EA-8745-D4653DDC885E"},{"full_name":"Elefante, Stefano","first_name":"Stefano","last_name":"Elefante","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stadlbauer, Stephan","last_name":"Stadlbauer","first_name":"Stephan","id":"4D0BC184-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-05-05T09:13:42Z","date_updated":"2023-05-16T07:42:56Z","acknowledgement":"The abstracts in this booklet are licenced under a CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/legalcode), except Markus Wallerberger’s contribution at page 21, licenced under a CC BY-SA 4.0 licence (https://creativecommons.org/licenses/by-sa/4.0/legalcode).\r\n","year":"2022","department":[{"_id":"ScienComp"}],"publisher":"EuroCC Austria c/o Universität Wien","publication_status":"published","file_date_updated":"2023-05-05T09:06:00Z","date_published":"2022-06-02T00:00:00Z","citation":{"short":"A. Schlögl, A. Hornoiu, S. Elefante, S. Stadlbauer, in:, ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7.","mla":"Schlögl, Alois, et al. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” ASHPC22 - Austrian-Slovenian HPC Meeting 2022, EuroCC Austria c/o Universität Wien, 2022, p. 7, doi:10.25365/phaidra.337.","chicago":"Schlögl, Alois, Andrei Hornoiu, Stefano Elefante, and Stephan Stadlbauer. “Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.” In ASHPC22 - Austrian-Slovenian HPC Meeting 2022, 7. EuroCC Austria c/o Universität Wien, 2022. https://doi.org/10.25365/phaidra.337.","ama":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. Where is the sweet spot? A procurement story of general purpose compute nodes. In: ASHPC22 - Austrian-Slovenian HPC Meeting 2022. EuroCC Austria c/o Universität Wien; 2022:7. doi:10.25365/phaidra.337","ieee":"A. Schlögl, A. Hornoiu, S. Elefante, and S. Stadlbauer, “Where is the sweet spot? A procurement story of general purpose compute nodes,” in ASHPC22 - Austrian-Slovenian HPC Meeting 2022, Grundlsee, Austria, 2022, p. 7.","apa":"Schlögl, A., Hornoiu, A., Elefante, S., & Stadlbauer, S. (2022). Where is the sweet spot? A procurement story of general purpose compute nodes. In ASHPC22 - Austrian-Slovenian HPC Meeting 2022 (p. 7). Grundlsee, Austria: EuroCC Austria c/o Universität Wien. https://doi.org/10.25365/phaidra.337","ista":"Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. 2022. Where is the sweet spot? A procurement story of general purpose compute nodes. ASHPC22 - Austrian-Slovenian HPC Meeting 2022. ASHPC: Austrian-Slovenian HPC Meeting, 7."},"publication":"ASHPC22 - Austrian-Slovenian HPC Meeting 2022","page":"7","article_processing_charge":"No","has_accepted_license":"1","day":"02","oa_version":"Published Version","file":[{"file_size":7180531,"content_type":"application/pdf","creator":"schloegl","access_level":"open_access","file_name":"BOOKLET_ASHPC22.pdf","checksum":"e3f8c240b85422ce2190e7b203cc2563","success":1,"date_updated":"2023-05-05T09:06:00Z","date_created":"2023-05-05T09:06:00Z","relation":"main_file","file_id":"12895"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12894","status":"public","title":"Where is the sweet spot? A procurement story of general purpose compute nodes","ddc":["000"],"type":"conference_abstract"},{"abstract":[{"lang":"eng","text":"Lymph nodes (LNs) comprise two main structural elements: fibroblastic reticular cells that form dedicated niches for immune cell interaction and capsular fibroblasts that build a shell around the organ. Immunological challenge causes LNs to increase more than tenfold in size within a few days. Here, we characterized the biomechanics of LN swelling on the cellular and organ scale. We identified lymphocyte trapping by influx and proliferation as drivers of an outward pressure force, causing fibroblastic reticular cells of the T-zone (TRCs) and their associated conduits to stretch. After an initial phase of relaxation, TRCs sensed the resulting strain through cell matrix adhesions, which coordinated local growth and remodeling of the stromal network. While the expanded TRC network readopted its typical configuration, a massive fibrotic reaction of the organ capsule set in and countered further organ expansion. Thus, different fibroblast populations mechanically control LN swelling in a multitier fashion."}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"628e7b49809f22c75b428842efe70c68","date_updated":"2022-07-25T07:11:32Z","date_created":"2022-07-25T07:11:32Z","file_id":"11642","relation":"main_file","creator":"dernst","file_size":11475325,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_NatureImmunology_Assen.pdf"}],"intvolume":" 23","ddc":["570"],"status":"public","title":"Multitier mechanics control stromal adaptations in swelling lymph nodes","_id":"9794","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"11","scopus_import":"1","date_published":"2022-07-11T00:00:00Z","page":"1246-1255","article_type":"original","citation":{"chicago":"Assen, Frank P, Jun Abe, Miroslav Hons, Robert Hauschild, Shayan Shamipour, Walter Kaufmann, Tommaso Costanzo, et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology. Springer Nature, 2022. https://doi.org/10.1038/s41590-022-01257-4.","mla":"Assen, Frank P., et al. “Multitier Mechanics Control Stromal Adaptations in Swelling Lymph Nodes.” Nature Immunology, vol. 23, Springer Nature, 2022, pp. 1246–55, doi:10.1038/s41590-022-01257-4.","short":"F.P. Assen, J. Abe, M. Hons, R. Hauschild, S. Shamipour, W. Kaufmann, T. Costanzo, G. Krens, M. Brown, B. Ludewig, S. Hippenmeyer, C.-P.J. Heisenberg, W. Weninger, E.B. Hannezo, S.A. Luther, J.V. Stein, M.K. Sixt, Nature Immunology 23 (2022) 1246–1255.","ista":"Assen FP, Abe J, Hons M, Hauschild R, Shamipour S, Kaufmann W, Costanzo T, Krens G, Brown M, Ludewig B, Hippenmeyer S, Heisenberg C-PJ, Weninger W, Hannezo EB, Luther SA, Stein JV, Sixt MK. 2022. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 23, 1246–1255.","ieee":"F. P. Assen et al., “Multitier mechanics control stromal adaptations in swelling lymph nodes,” Nature Immunology, vol. 23. Springer Nature, pp. 1246–1255, 2022.","apa":"Assen, F. P., Abe, J., Hons, M., Hauschild, R., Shamipour, S., Kaufmann, W., … Sixt, M. K. (2022). Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. Springer Nature. https://doi.org/10.1038/s41590-022-01257-4","ama":"Assen FP, Abe J, Hons M, et al. Multitier mechanics control stromal adaptations in swelling lymph nodes. Nature Immunology. 2022;23:1246-1255. doi:10.1038/s41590-022-01257-4"},"publication":"Nature Immunology","ec_funded":1,"file_date_updated":"2022-07-25T07:11:32Z","volume":23,"date_updated":"2023-08-02T06:53:07Z","date_created":"2021-08-06T09:09:11Z","author":[{"full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","last_name":"Assen","first_name":"Frank P"},{"full_name":"Abe, Jun","last_name":"Abe","first_name":"Jun"},{"full_name":"Hons, Miroslav","last_name":"Hons","first_name":"Miroslav","orcid":"0000-0002-6625-3348","id":"4167FE56-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan","full_name":"Shamipour, Shayan"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","first_name":"Tommaso","full_name":"Costanzo, Tommaso"},{"orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","last_name":"Krens","first_name":"Gabriel","full_name":"Krens, Gabriel"},{"full_name":"Brown, Markus","first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ludewig, Burkhard","last_name":"Ludewig","first_name":"Burkhard"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Weninger, Wolfgang","last_name":"Weninger","first_name":"Wolfgang"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Luther, Sanjiv A.","first_name":"Sanjiv A.","last_name":"Luther"},{"first_name":"Jens V.","last_name":"Stein","full_name":"Stein, Jens V."},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Springer Nature","department":[{"_id":"SiHi"},{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"MiSi"}],"publication_status":"published","year":"2022","acknowledgement":"This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics, Electron Microscopy, Preclinical and Life Science Facilities. We thank C. Moussion for providing anti-PNAd antibody and D. Critchley for Talin1-floxed mice, and E. Papusheva for providing a custom 3D channel alignment script. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. M.H. was supported by Czech Sciencundation GACR 20-24603Y and Charles University PRIMUS/20/MED/013.","publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"month":"07","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"LifeSc"}],"doi":"10.1038/s41590-022-01257-4","project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"isi":1,"quality_controlled":"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":["000822975900002"]},"oa":1},{"article_processing_charge":"No","has_accepted_license":"1","day":"14","scopus_import":"1","date_published":"2022-02-14T00:00:00Z","article_type":"original","citation":{"short":"J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W. Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8, e2122030119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122030119.","chicago":"Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo, Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122030119.","ama":"Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(8). doi:10.1073/pnas.2122030119","apa":"Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens, G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2122030119","ieee":"J. Slovakova et al., “Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 8. Proceedings of the National Academy of Sciences, 2022.","ista":"Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 119(8), e2122030119."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"8","abstract":[{"lang":"eng","text":"Tension of the actomyosin cell cortex plays a key role in determining cell–cell contact growth and size. The level of cortical tension outside of the cell–cell contact, when pulling at the contact edge, scales with the total size to which a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)]. Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell–cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. After tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell–cell contact size is limited by tension-stabilizing E-cadherin–actin complexes at the contact."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"10780","relation":"main_file","success":1,"checksum":"d49f83c3580613966f71768ddb9a55a5","date_created":"2022-02-21T08:45:11Z","date_updated":"2022-02-21T08:45:11Z","access_level":"open_access","file_name":"2022_PNAS_Slovakova.pdf","creator":"dernst","content_type":"application/pdf","file_size":1609678}],"intvolume":" 119","status":"public","ddc":["570"],"title":"Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor cells","_id":"10766","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["10916490"]},"month":"02","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"PreCl"}],"doi":"10.1073/pnas.2122030119","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"name":"Modulation of adhesion function in cell-cell contact formation by cortical tension","grant_number":"187-2013","_id":"2521E28E-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"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"},"oa":1,"external_id":{"isi":["000766926900009"]},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"file_date_updated":"2022-02-21T08:45:11Z","article_number":"e2122030119","volume":119,"date_updated":"2023-08-02T14:26:51Z","date_created":"2022-02-20T23:01:31Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9750"}]},"author":[{"last_name":"Slovakova","first_name":"Jana","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arslan, Feyza N","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","last_name":"Arslan","first_name":"Feyza N"},{"full_name":"Caballero Mancebo, Silvia","last_name":"Caballero Mancebo","first_name":"Silvia","orcid":"0000-0002-5223-3346","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krens","first_name":"Gabriel","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"CaHe"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publication_status":"published","acknowledgement":"We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo, and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour and Daniel Capek for help with data analysis. We also thank the Imaging & Optics, Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute of Science and Technology Austria (ISTA)Nasser Darwish-Miranda for continuous support. We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.), Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced Grant (MECSPEC; to C.-P.H.).","year":"2022"},{"year":"2022","acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","pmid":1,"publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"author":[{"full_name":"Dahhan, DA","last_name":"Dahhan","first_name":"DA"},{"full_name":"Reynolds, GD","first_name":"GD","last_name":"Reynolds"},{"full_name":"Cárdenas, JJ","first_name":"JJ","last_name":"Cárdenas"},{"last_name":"Eeckhout","first_name":"D","full_name":"Eeckhout, D"},{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"first_name":"K","last_name":"Yperman","full_name":"Yperman, K"},{"full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann"},{"last_name":"Vang","first_name":"N","full_name":"Vang, N"},{"last_name":"Yan","first_name":"X","full_name":"Yan, X"},{"last_name":"Hwang","first_name":"I","full_name":"Hwang, I"},{"full_name":"Heese, A","first_name":"A","last_name":"Heese"},{"full_name":"De Jaeger, G","first_name":"G","last_name":"De Jaeger"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"last_name":"Pan","first_name":"J","full_name":"Pan, J"},{"last_name":"Bednarek","first_name":"SY","full_name":"Bednarek, SY"}],"date_updated":"2023-08-02T14:46:48Z","date_created":"2022-03-08T13:47:51Z","volume":34,"month":"06","publication_identifier":{"issn":["1040-4651"],"eissn":["1532-298x"]},"external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"doi":"10.1093/plcell/koac071","acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data.","lang":"eng"}],"issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10841","status":"public","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","intvolume":" 34","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Plant Cell","citation":{"ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. Oxford Academic. https://doi.org/10.1093/plcell/koac071","ieee":"D. Dahhan et al., “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” Plant Cell, vol. 34, no. 6. Oxford Academic, pp. 2150–2173, 2022.","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 2022;34(6):2150-2173. doi:10.1093/plcell/koac071","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell. Oxford Academic, 2022. https://doi.org/10.1093/plcell/koac071.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” Plant Cell, vol. 34, no. 6, Oxford Academic, 2022, pp. 2150–73, doi:10.1093/plcell/koac071.","short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173."},"article_type":"original","page":"2150-2173","date_published":"2022-06-01T00:00:00Z"},{"ddc":["540"],"status":"public","title":"Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance","intvolume":" 61","_id":"11705","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4072650,"file_name":"2022_AngewandteChemieInternat_Chang.pdf","access_level":"open_access","date_created":"2023-02-02T08:01:00Z","date_updated":"2023-02-02T08:01:00Z","success":1,"checksum":"ad601f2b9e26e46ab4785162be58b5ed","file_id":"12476","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The broad implementation of thermoelectricity requires high-performance and low-cost materials. One possibility is employing surfactant-free solution synthesis to produce nanopowders. We propose the strategy of functionalizing “naked” particles’ surface by inorganic molecules to control the nanostructure and, consequently, thermoelectric performance. In particular, we use bismuth thiolates to functionalize surfactant-free SnTe particles’ surfaces. Upon thermal processing, bismuth thiolates decomposition renders SnTe-Bi2S3 nanocomposites with synergistic functions: 1) carrier concentration optimization by Bi doping; 2) Seebeck coefficient enhancement and bipolar effect suppression by energy filtering; and 3) lattice thermal conductivity reduction by small grain domains, grain boundaries and nanostructuration. Overall, the SnTe-Bi2S3 nanocomposites exhibit peak z T up to 1.3 at 873 K and an average z T of ≈0.6 at 300–873 K, which is among the highest reported for solution-processed SnTe."}],"issue":"35","article_type":"original","publication":"Angewandte Chemie - International Edition","citation":{"short":"C. Chang, Y. Liu, S. Lee, M. Spadaro, K.M. Koskela, T. Kleinhanns, T. Costanzo, J. Arbiol, R.L. Brutchey, M. Ibáñez, Angewandte Chemie - International Edition 61 (2022).","mla":"Chang, Cheng, et al. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” Angewandte Chemie - International Edition, vol. 61, no. 35, e202207002, Wiley, 2022, doi:10.1002/anie.202207002.","chicago":"Chang, Cheng, Yu Liu, Seungho Lee, Maria Spadaro, Kristopher M. Koskela, Tobias Kleinhanns, Tommaso Costanzo, Jordi Arbiol, Richard L. Brutchey, and Maria Ibáñez. “Surface Functionalization of Surfactant-Free Particles: A Strategy to Tailor the Properties of Nanocomposites for Enhanced Thermoelectric Performance.” Angewandte Chemie - International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202207002.","ama":"Chang C, Liu Y, Lee S, et al. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 2022;61(35). doi:10.1002/anie.202207002","ieee":"C. Chang et al., “Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance,” Angewandte Chemie - International Edition, vol. 61, no. 35. Wiley, 2022.","apa":"Chang, C., Liu, Y., Lee, S., Spadaro, M., Koskela, K. M., Kleinhanns, T., … Ibáñez, M. (2022). Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. Wiley. https://doi.org/10.1002/anie.202207002","ista":"Chang C, Liu Y, Lee S, Spadaro M, Koskela KM, Kleinhanns T, Costanzo T, Arbiol J, Brutchey RL, Ibáñez M. 2022. Surface functionalization of surfactant-free particles: A strategy to tailor the properties of nanocomposites for enhanced thermoelectric performance. Angewandte Chemie - International Edition. 61(35), e202207002."},"date_published":"2022-08-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication_status":"published","department":[{"_id":"MaIb"},{"_id":"EM-Fac"}],"publisher":"Wiley","year":"2022","acknowledgement":"This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF). This work was financially supported by IST Austria and the Werner Siemens Foundation. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. Lise Meitner Project (M2889-N). Y.L. acknowledges funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754411. R.L.B. thanks the National Science Foundation for support under DMR-1904719. MCS acknowledge MINECO Juan de la Cierva Incorporation fellowship (JdlCI 2019) and Severo Ochoa. M.C.S. and J.A. acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant no. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. This study was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and Generalitat de Catalunya.","date_updated":"2023-08-03T12:23:52Z","date_created":"2022-07-31T22:01:48Z","volume":61,"author":[{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng"},{"full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740"},{"full_name":"Lee, Seungho","first_name":"Seungho","last_name":"Lee","id":"BB243B88-D767-11E9-B658-BC13E6697425","orcid":"0000-0002-6962-8598"},{"last_name":"Spadaro","first_name":"Maria","full_name":"Spadaro, Maria"},{"full_name":"Koskela, Kristopher M.","first_name":"Kristopher M.","last_name":"Koskela"},{"full_name":"Kleinhanns, Tobias","id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","last_name":"Kleinhanns","first_name":"Tobias"},{"last_name":"Costanzo","first_name":"Tommaso","orcid":"0000-0001-9732-3815","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","full_name":"Costanzo, Tommaso"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"full_name":"Brutchey, Richard L.","last_name":"Brutchey","first_name":"Richard L."},{"first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"}],"article_number":"e202207002","file_date_updated":"2023-02-02T08:01:00Z","ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"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":["000828274200001"]},"oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"language":[{"iso":"eng"}],"doi":"10.1002/anie.202207002","month":"08","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]}},{"file_date_updated":"2023-01-20T08:43:51Z","department":[{"_id":"StFr"},{"_id":"EM-Fac"}],"publisher":"American Chemical Society","publication_status":"published","year":"2022","acknowledgement":"S.A.F. and C.P. are indebted to the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 636069). This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant NanoEvolution, Grant Agreement No. 894042. S.A.F. and S.M. are indebted to Institute of Science and Technology Austria (ISTA) for support. This research was supported by the Scientific Service Units of ISTA through resources provided by the Electron Microscopy Facility and the Miba Machine Shop. C.P. thanks Vanessa Wood (ETH Zürich) for her continuing support.","volume":7,"date_created":"2022-09-08T09:51:09Z","date_updated":"2023-08-03T13:47:56Z","author":[{"full_name":"Prehal, Christian","first_name":"Christian","last_name":"Prehal"},{"id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","last_name":"Mondal","first_name":"Soumyadip","full_name":"Mondal, Soumyadip"},{"full_name":"Lovicar, Ludek","first_name":"Ludek","last_name":"Lovicar","id":"36DB3A20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","first_name":"Stefan Alexander","last_name":"Freunberger"}],"publication_identifier":{"eissn":["2380-8195"]},"month":"08","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":["000860787000001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"M-Shop"}],"doi":"10.1021/acsenergylett.2c01711","type":"journal_article","issue":"9","abstract":[{"text":"Capacity, rate performance, and cycle life of aprotic Li–O2 batteries critically depend on reversible electrodeposition of Li2O2. Current understanding states surface-adsorbed versus solvated LiO2 controls Li2O2 growth as surface film or as large particles. Herein, we show that Li2O2 forms across a wide range of electrolytes, carbons, and current densities as particles via solution-mediated LiO2 disproportionation, bringing into question the prevalence of any surface growth under practical conditions. We describe a unified O2 reduction mechanism, which can explain all found capacity relations and Li2O2 morphologies with exclusive solution discharge. Determining particle morphology and achievable capacities are species mobilities, true areal rate, and the degree of LiO2 association in solution. Capacity is conclusively limited by mass transport through the tortuous Li2O2 rather than electron transport through a passivating Li2O2 film. Provided that species mobilities and surface growth are high, high capacities are also achieved with weakly solvating electrolytes, which were previously considered prototypical for low capacity via surface growth.","lang":"eng"}],"intvolume":" 7","ddc":["540"],"title":"Exclusive solution discharge in Li-O₂ batteries?","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12065","file":[{"date_updated":"2023-01-20T08:43:51Z","date_created":"2023-01-20T08:43:51Z","checksum":"cf0bed3a2535c11d27244cd029dbc1d0","success":1,"relation":"main_file","file_id":"12319","content_type":"application/pdf","file_size":3827583,"creator":"dernst","file_name":"2022_ACSEnergyLetters_Prehal.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"29","page":"3112-3119","article_type":"original","citation":{"chicago":"Prehal, Christian, Soumyadip Mondal, Ludek Lovicar, and Stefan Alexander Freunberger. “Exclusive Solution Discharge in Li-O₂ Batteries?” ACS Energy Letters. American Chemical Society, 2022. https://doi.org/10.1021/acsenergylett.2c01711.","short":"C. Prehal, S. Mondal, L. Lovicar, S.A. Freunberger, ACS Energy Letters 7 (2022) 3112–3119.","mla":"Prehal, Christian, et al. “Exclusive Solution Discharge in Li-O₂ Batteries?” ACS Energy Letters, vol. 7, no. 9, American Chemical Society, 2022, pp. 3112–19, doi:10.1021/acsenergylett.2c01711.","ieee":"C. Prehal, S. Mondal, L. Lovicar, and S. A. Freunberger, “Exclusive solution discharge in Li-O₂ batteries?,” ACS Energy Letters, vol. 7, no. 9. American Chemical Society, pp. 3112–3119, 2022.","apa":"Prehal, C., Mondal, S., Lovicar, L., & Freunberger, S. A. (2022). Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. American Chemical Society. https://doi.org/10.1021/acsenergylett.2c01711","ista":"Prehal C, Mondal S, Lovicar L, Freunberger SA. 2022. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 7(9), 3112–3119.","ama":"Prehal C, Mondal S, Lovicar L, Freunberger SA. Exclusive solution discharge in Li-O₂ batteries? ACS Energy Letters. 2022;7(9):3112-3119. doi:10.1021/acsenergylett.2c01711"},"publication":"ACS Energy Letters","date_published":"2022-08-29T00:00:00Z"},{"scopus_import":"1","day":"29","article_processing_charge":"No","article_type":"original","publication":"Physical Review Materials","citation":{"mla":"Pertl, Felix, et al. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” Physical Review Materials, vol. 6, no. 12, 125605, American Physical Society, 2022, doi:10.1103/PhysRevMaterials.6.125605.","short":"F. Pertl, J.C.A. Sobarzo Ponce, L.B. Shafeek, T. Cramer, S.R. Waitukaitis, Physical Review Materials 6 (2022).","chicago":"Pertl, Felix, Juan Carlos A Sobarzo Ponce, Lubuna B Shafeek, Tobias Cramer, and Scott R Waitukaitis. “Quantifying Nanoscale Charge Density Features of Contact-Charged Surfaces with an FEM/KPFM-Hybrid Approach.” Physical Review Materials. American Physical Society, 2022. https://doi.org/10.1103/PhysRevMaterials.6.125605.","ama":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 2022;6(12). doi:10.1103/PhysRevMaterials.6.125605","ista":"Pertl F, Sobarzo Ponce JCA, Shafeek LB, Cramer T, Waitukaitis SR. 2022. Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. 6(12), 125605.","ieee":"F. Pertl, J. C. A. Sobarzo Ponce, L. B. Shafeek, T. Cramer, and S. R. Waitukaitis, “Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach,” Physical Review Materials, vol. 6, no. 12. American Physical Society, 2022.","apa":"Pertl, F., Sobarzo Ponce, J. C. A., Shafeek, L. B., Cramer, T., & Waitukaitis, S. R. (2022). Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.6.125605"},"date_published":"2022-12-29T00:00:00Z","type":"journal_article","abstract":[{"text":"Kelvin probe force microscopy (KPFM) is a powerful tool for studying contact electrification (CE) at the nanoscale, but converting KPFM voltage maps to charge density maps is nontrivial due to long-range forces and complex system geometry. Here we present a strategy using finite-element method (FEM) simulations to determine the Green's function of the KPFM probe/insulator/ground system, which allows us to quantitatively extract surface charge. Testing our approach with synthetic data, we find that accounting for the atomic force microscope (AFM) tip, cone, and cantilever is necessary to recover a known input and that existing methods lead to gross miscalculation or even the incorrect sign of the underlying charge. Applying it to experimental data, we demonstrate its capacity to extract realistic surface charge densities and fine details from contact-charged surfaces. Our method gives a straightforward recipe to convert qualitative KPFM voltage data into quantitative charge data over a range of experimental conditions, enabling quantitative CE at the nanoscale.","lang":"eng"}],"issue":"12","status":"public","title":"Quantifying nanoscale charge density features of contact-charged surfaces with an FEM/KPFM-hybrid approach","intvolume":" 6","_id":"12109","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"12","publication_identifier":{"eissn":["2475-9953"]},"isi":1,"quality_controlled":"1","project":[{"_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","call_identifier":"H2020"}],"external_id":{"isi":["000908384800001"],"arxiv":["2209.01889"]},"oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2209.01889","open_access":"1"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"},{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevMaterials.6.125605","article_number":"125605","ec_funded":1,"publication_status":"published","department":[{"_id":"ScWa"},{"_id":"NanoFab"}],"publisher":"American Physical Society","year":"2022","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\r\nNo. 949120). This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria (ISTA) through resources provided by the Miba Machine\r\nShop, the Nanofabrication Facility, and the Scientific Computing Facility. We thank F. Stumpf from Park Systems for useful discussions and support with scanning probe microscopy.\r\nF.P. and J.C.S. contributed equally to this work.","date_updated":"2023-08-03T14:11:29Z","date_created":"2023-01-08T23:00:53Z","volume":6,"author":[{"full_name":"Pertl, Felix","id":"6313aec0-15b2-11ec-abd3-ed67d16139af","last_name":"Pertl","first_name":"Felix"},{"full_name":"Sobarzo Ponce, Juan Carlos A","id":"4B807D68-AE37-11E9-AC72-31CAE5697425","first_name":"Juan Carlos A","last_name":"Sobarzo Ponce"},{"full_name":"Shafeek, Lubuna B","id":"3CD37A82-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7180-6050","first_name":"Lubuna B","last_name":"Shafeek"},{"full_name":"Cramer, Tobias","first_name":"Tobias","last_name":"Cramer"},{"full_name":"Waitukaitis, Scott R","first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176"}]},{"language":[{"iso":"eng"}],"doi":"10.1038/s42003-022-03446-1","quality_controlled":"1","isi":1,"external_id":{"isi":["000811777900003"]},"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,"publication_identifier":{"issn":["2399-3642"]},"month":"06","volume":5,"date_created":"2023-01-16T09:48:19Z","date_updated":"2023-08-04T09:25:59Z","author":[{"full_name":"Muhia, Mary W","id":"ab7ed20f-09f7-11eb-909c-d5d0b443ee9d","last_name":"Muhia","first_name":"Mary W"},{"last_name":"YuanXiang","first_name":"PingAn","full_name":"YuanXiang, PingAn"},{"full_name":"Sedlacik, Jan","first_name":"Jan","last_name":"Sedlacik"},{"last_name":"Schwarz","first_name":"Jürgen R.","full_name":"Schwarz, Jürgen R."},{"first_name":"Frank F.","last_name":"Heisler","full_name":"Heisler, Frank F."},{"last_name":"Gromova","first_name":"Kira V.","full_name":"Gromova, Kira V."},{"full_name":"Thies, Edda","first_name":"Edda","last_name":"Thies"},{"last_name":"Breiden","first_name":"Petra","full_name":"Breiden, Petra"},{"last_name":"Pechmann","first_name":"Yvonne","full_name":"Pechmann, Yvonne"},{"first_name":"Michael R.","last_name":"Kreutz","full_name":"Kreutz, Michael R."},{"last_name":"Kneussel","first_name":"Matthias","full_name":"Kneussel, Matthias"}],"publisher":"Springer Nature","department":[{"_id":"PreCl"}],"publication_status":"published","acknowledgement":"The authors are grateful to the UKE Animal Facilities (Hamburg) for animal husbandry and Dr. Bastian Tiemann for his veterinary expertise and supervision of animal care. We thank Dr. Franco Lombino for critically reading the manuscript and for helpful discussion. This work was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) (FOR2419-KN556/11-1, FOR2419-KN556/11-2, KN556/12-1) and the Landesforschungsförderung Hamburg (LFF-FV76) to M.K.\r\nOpen Access funding enabled and organized by Projekt DEAL.","year":"2022","file_date_updated":"2023-01-27T08:23:46Z","article_number":"589","date_published":"2022-06-15T00:00:00Z","article_type":"original","citation":{"short":"M.W. Muhia, P. YuanXiang, J. Sedlacik, J.R. Schwarz, F.F. Heisler, K.V. Gromova, E. Thies, P. Breiden, Y. Pechmann, M.R. Kreutz, M. Kneussel, Communications Biology 5 (2022).","mla":"Muhia, Mary W., et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” Communications Biology, vol. 5, 589, Springer Nature, 2022, doi:10.1038/s42003-022-03446-1.","chicago":"Muhia, Mary W, PingAn YuanXiang, Jan Sedlacik, Jürgen R. Schwarz, Frank F. Heisler, Kira V. Gromova, Edda Thies, et al. “Muskelin Regulates Actin-Dependent Synaptic Changes and Intrinsic Brain Activity Relevant to Behavioral and Cognitive Processes.” Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03446-1.","ama":"Muhia MW, YuanXiang P, Sedlacik J, et al. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 2022;5. doi:10.1038/s42003-022-03446-1","ieee":"M. W. Muhia et al., “Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes,” Communications Biology, vol. 5. Springer Nature, 2022.","apa":"Muhia, M. W., YuanXiang, P., Sedlacik, J., Schwarz, J. R., Heisler, F. F., Gromova, K. V., … Kneussel, M. (2022). Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03446-1","ista":"Muhia MW, YuanXiang P, Sedlacik J, Schwarz JR, Heisler FF, Gromova KV, Thies E, Breiden P, Pechmann Y, Kreutz MR, Kneussel M. 2022. Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes. Communications Biology. 5, 589."},"publication":"Communications Biology","article_processing_charge":"No","has_accepted_license":"1","day":"15","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology","Medicine (miscellaneous)"],"scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":3968356,"creator":"dernst","file_name":"2022_CommBiology_Muhia.pdf","access_level":"open_access","date_updated":"2023-01-27T08:23:46Z","date_created":"2023-01-27T08:23:46Z","checksum":"bd95be1e77090208b79bc45ea8785d0b","success":1,"relation":"main_file","file_id":"12417"}],"intvolume":" 5","status":"public","ddc":["570"],"title":"Muskelin regulates actin-dependent synaptic changes and intrinsic brain activity relevant to behavioral and cognitive processes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12224","abstract":[{"lang":"eng","text":"Muskelin (Mkln1) is implicated in neuronal function, regulating plasma membrane receptor trafficking. However, its influence on intrinsic brain activity and corresponding behavioral processes remains unclear. Here we show that murine Mkln1 knockout causes non-habituating locomotor activity, increased exploratory drive, and decreased locomotor response to amphetamine. Muskelin deficiency impairs social novelty detection while promoting the retention of spatial reference memory and fear extinction recall. This is strongly mirrored in either weaker or stronger resting-state functional connectivity between critical circuits mediating locomotor exploration and cognition. We show that Mkln1 deletion alters dendrite branching and spine structure, coinciding with enhanced AMPAR-mediated synaptic transmission but selective impairment in synaptic potentiation maintenance. We identify muskelin at excitatory synapses and highlight its role in regulating dendritic spine actin stability. Our findings point to aberrant spine actin modulation and changes in glutamatergic synaptic function as critical mechanisms that contribute to the neurobehavioral phenotype arising from Mkln1 ablation."}],"type":"journal_article"},{"status":"public","ddc":["540"],"title":"Isoxazole nucleosides as building blocks for a plausible proto‐RNA","intvolume":" 61","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12228","file":[{"access_level":"open_access","file_name":"2022_AngewandteChemieInternat_Xu.pdf","creator":"dernst","content_type":"application/pdf","file_size":1076715,"file_id":"12422","relation":"main_file","success":1,"checksum":"4e8152454d12025d13f6e6e9ca06b5d0","date_updated":"2023-01-27T10:28:45Z","date_created":"2023-01-27T10:28:45Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The question of how RNA, as the principal carrier of genetic information evolved is fundamentally important for our understanding of the origin of life. The RNA molecule is far too complex to have formed in one evolutionary step, suggesting that ancestral proto-RNAs (first ancestor of RNA) may have existed, which evolved over time into the RNA of today. Here we show that isoxazole nucleosides, which are quickly formed from hydroxylamine, cyanoacetylene, urea and ribose, are plausible precursors for RNA. The isoxazole nucleoside can rearrange within an RNA-strand to give cytidine, which leads to an increase of pairing stability. If the proto-RNA contains a canonical seed-nucleoside with defined stereochemistry, the seed-nucleoside can control the configuration of the anomeric center that forms during the in-RNA transformation. The results demonstrate that RNA could have emerged from evolutionarily primitive precursor isoxazole ribosides after strand formation."}],"issue":"45","article_type":"original","publication":"Angewandte Chemie International Edition","citation":{"ama":"Xu F, Crisp A, Schinkel T, et al. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. 2022;61(45). doi:10.1002/anie.202211945","ieee":"F. Xu et al., “Isoxazole nucleosides as building blocks for a plausible proto‐RNA,” Angewandte Chemie International Edition, vol. 61, no. 45. Wiley, 2022.","apa":"Xu, F., Crisp, A., Schinkel, T., Dubini, R. C. A., Hübner, S., Becker, S., … Carell, T. (2022). Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202211945","ista":"Xu F, Crisp A, Schinkel T, Dubini RCA, Hübner S, Becker S, Schelter F, Rovo P, Carell T. 2022. Isoxazole nucleosides as building blocks for a plausible proto‐RNA. Angewandte Chemie International Edition. 61(45), e202211945.","short":"F. Xu, A. Crisp, T. Schinkel, R.C.A. Dubini, S. Hübner, S. Becker, F. Schelter, P. Rovo, T. Carell, Angewandte Chemie International Edition 61 (2022).","mla":"Xu, Felix, et al. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” Angewandte Chemie International Edition, vol. 61, no. 45, e202211945, Wiley, 2022, doi:10.1002/anie.202211945.","chicago":"Xu, Felix, Antony Crisp, Thea Schinkel, Romeo C. A. Dubini, Sarah Hübner, Sidney Becker, Florian Schelter, Petra Rovo, and Thomas Carell. “Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA.” Angewandte Chemie International Edition. Wiley, 2022. https://doi.org/10.1002/anie.202211945."},"date_published":"2022-11-07T00:00:00Z","keyword":["General Chemistry","Catalysis"],"scopus_import":"1","day":"07","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"NMR"}],"publisher":"Wiley","year":"2022","acknowledgement":"We thank Stefan Wiedemann for the synthesis of reference compounds and Pia Heinrichs for assistance in the NMR measurements of the oligonucleotides. We also thank Dr. Luis Escobar and Jonas Feldmann for valued discussions. This work was supported by the German Research Foundation (DFG) for financial support via CRC1309 (Project ID 325871075, A04), CRC1361 (Project ID 893547839, P02) and CRC1032 (Project ID 201269156, A5). This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program under grant agreement No 741912 (EpiR). We are grateful for additional funding from the Volkswagen Foundation (EvoRib). Open Access funding enabled and organized by Projekt DEAL.","date_updated":"2023-08-04T09:32:42Z","date_created":"2023-01-16T09:49:05Z","volume":61,"author":[{"first_name":"Felix","last_name":"Xu","full_name":"Xu, Felix"},{"full_name":"Crisp, Antony","last_name":"Crisp","first_name":"Antony"},{"last_name":"Schinkel","first_name":"Thea","full_name":"Schinkel, Thea"},{"last_name":"Dubini","first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A."},{"full_name":"Hübner, Sarah","last_name":"Hübner","first_name":"Sarah"},{"full_name":"Becker, Sidney","first_name":"Sidney","last_name":"Becker"},{"first_name":"Florian","last_name":"Schelter","full_name":"Schelter, Florian"},{"orcid":"0000-0001-8729-7326","id":"c316e53f-b965-11eb-b128-bb26acc59c00","last_name":"Rovo","first_name":"Petra","full_name":"Rovo, Petra"},{"full_name":"Carell, Thomas","last_name":"Carell","first_name":"Thomas"}],"article_number":"e202211945","file_date_updated":"2023-01-27T10:28:45Z","isi":1,"quality_controlled":"1","oa":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":["000866428500001"]},"language":[{"iso":"eng"}],"doi":"10.1002/anie.202211945","month":"11","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]}},{"publication_identifier":{"issn":["1674-2052"]},"month":"10","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"doi":"10.1016/j.molp.2022.09.003","project":[{"grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","call_identifier":"FWF"}],"isi":1,"quality_controlled":"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":{"pmid":["36081349"],"isi":["000882769800009"]},"file_date_updated":"2023-01-30T07:46:51Z","volume":15,"date_updated":"2023-08-04T09:39:24Z","date_created":"2023-01-16T09:51:49Z","author":[{"first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J"},{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","orcid":"0000-0001-9732-3815","first_name":"Tommaso","last_name":"Costanzo","full_name":"Costanzo, Tommaso"},{"last_name":"Dahhan","first_name":"Dana A.","full_name":"Dahhan, Dana A."},{"last_name":"Bednarek","first_name":"Sebastian Y.","full_name":"Bednarek, Sebastian Y."},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"publication_status":"published","pmid":1,"acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","year":"2022","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"03","keyword":["Plant Science","Molecular Biology"],"scopus_import":"1","date_published":"2022-10-03T00:00:00Z","page":"1533-1542","article_type":"original","citation":{"apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., & Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. Elsevier. https://doi.org/10.1016/j.molp.2022.09.003","ieee":"A. J. Johnson et al., “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” Molecular Plant, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 2022;15(10):1533-1542. doi:10.1016/j.molp.2022.09.003","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant. Elsevier, 2022. https://doi.org/10.1016/j.molp.2022.09.003.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” Molecular Plant, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:10.1016/j.molp.2022.09.003."},"publication":"Molecular Plant","issue":"10","abstract":[{"text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"04d5c12490052d03e4dc4412338a43dd","success":1,"date_updated":"2023-01-30T07:46:51Z","date_created":"2023-01-30T07:46:51Z","relation":"main_file","file_id":"12435","file_size":2307251,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2022_MolecularPlant_Johnson.pdf"}],"intvolume":" 15","status":"public","ddc":["580"],"title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12239"},{"isi":1,"quality_controlled":"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":{"arxiv":["2206.01531"],"isi":["000861009600005"]},"language":[{"iso":"eng"}],"doi":"10.1063/5.0102904","month":"09","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"publication_status":"published","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}],"publisher":"AIP Publishing","year":"2022","acknowledgement":"This work was partially funded by the Institute of Science and Technology Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos and Quantum Analogies.”","date_created":"2023-01-16T09:58:16Z","date_updated":"2023-08-04T09:51:17Z","volume":32,"author":[{"full_name":"Choueiri, George H","last_name":"Choueiri","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"id":"47A5E706-F248-11E8-B48F-1D18A9856A87","last_name":"Suri","first_name":"Balachandra","full_name":"Suri, Balachandra"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"full_name":"Hof, Björn","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"},{"last_name":"Budanur","first_name":"Nazmi B","orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"}],"article_number":"093138","file_date_updated":"2023-01-30T09:41:12Z","article_type":"original","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","citation":{"chicago":"Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2022. https://doi.org/10.1063/5.0102904.","short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","mla":"Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:10.1063/5.0102904.","apa":"Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., & Budanur, N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/5.0102904","ieee":"G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur, “Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 32, no. 9. AIP Publishing, 2022.","ista":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 32(9), 093138.","ama":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2022;32(9). doi:10.1063/5.0102904"},"date_published":"2022-09-26T00:00:00Z","keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"scopus_import":"1","day":"26","article_processing_charge":"No","has_accepted_license":"1","status":"public","title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","ddc":["530"],"intvolume":" 32","_id":"12259","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3209644,"file_name":"2022_Chaos_Choueiri.pdf","access_level":"open_access","date_updated":"2023-01-30T09:41:12Z","date_created":"2023-01-30T09:41:12Z","success":1,"checksum":"17881eff8b21969359a2dd64620120ba","file_id":"12445","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. "}],"issue":"9"},{"date_published":"2022-09-12T00:00:00Z","publication":"Nature Structural & Molecular Biology","citation":{"ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 29(9), 942–953.","ieee":"M. Prattes et al., “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” Nature Structural & Molecular Biology, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00832-5","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 2022;29(9):942-953. doi:10.1038/s41594-022-00832-5","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00832-5.","mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular Biology, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:10.1038/s41594-022-00832-5.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural & Molecular Biology 29 (2022) 942–953."},"article_type":"original","page":"942-953","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["Molecular Biology","Structural Biology"],"file":[{"content_type":"application/pdf","file_size":9935057,"creator":"dernst","access_level":"open_access","file_name":"2022_NatureStrucMolecBio_Prattes.pdf","checksum":"2d5c3ec01718fefd7553052b0b8a0793","success":1,"date_updated":"2023-01-30T10:00:04Z","date_created":"2023-01-30T10:00:04Z","relation":"main_file","file_id":"12447"}],"oa_version":"Published Version","_id":"12262","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","status":"public","ddc":["570"],"intvolume":" 29","abstract":[{"text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.","lang":"eng"}],"issue":"9","type":"journal_article","doi":"10.1038/s41594-022-00832-5","acknowledged_ssus":[{"_id":"EM-Fac"}],"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":["000852942100004"],"pmid":["36097293"]},"oa":1,"quality_controlled":"1","isi":1,"month":"09","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"author":[{"first_name":"Michael","last_name":"Prattes","full_name":"Prattes, Michael"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hetzmannseder, Christina","last_name":"Hetzmannseder","first_name":"Christina"},{"full_name":"Zisser, Gertrude","first_name":"Gertrude","last_name":"Zisser"},{"full_name":"Sailer, Carolin","first_name":"Carolin","last_name":"Sailer"},{"full_name":"Kargas, Vasileios","last_name":"Kargas","first_name":"Vasileios"},{"full_name":"Loibl, Mathias","last_name":"Loibl","first_name":"Mathias"},{"full_name":"Gerhalter, Magdalena","last_name":"Gerhalter","first_name":"Magdalena"},{"full_name":"Kofler, Lisa","last_name":"Kofler","first_name":"Lisa"},{"full_name":"Warren, Alan J.","last_name":"Warren","first_name":"Alan J."},{"first_name":"Florian","last_name":"Stengel","full_name":"Stengel, Florian"},{"full_name":"Haselbach, David","last_name":"Haselbach","first_name":"David"},{"first_name":"Helmut","last_name":"Bergler","full_name":"Bergler, Helmut"}],"date_created":"2023-01-16T09:59:06Z","date_updated":"2023-08-04T09:52:20Z","volume":29,"year":"2022","acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","pmid":1,"publication_status":"published","department":[{"_id":"EM-Fac"}],"publisher":"Springer Nature","file_date_updated":"2023-01-30T10:00:04Z"}]