[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Fabian","last_name":"Brauneis","full_name":"Brauneis, Fabian"},{"full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Ghazaryan","first_name":"Areg"},{"last_name":"Hammer","first_name":"Hans-Werner","full_name":"Hammer, Hans-Werner"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev"}],"oa":1,"volume":6,"intvolume":"         6","arxiv":1,"publication":"Communications Physics","date_updated":"2023-12-13T12:21:09Z","department":[{"_id":"MiLe"}],"article_type":"original","publication_identifier":{"issn":["2399-3650"]},"acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.\r\nWe would like to thank Jonas Jager for sharing his data with us in the early stages of this project. We thank Joachim Brand and Ray Yang for sharing with us data from Yang et al.46. This work has received funding from the DFG Project no. 413495248 [VO 2437/1-1] (F.B., H.-W.H., A.G.V.). We acknowledge support from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) and the Open Access Publishing Fund of the Technical University of Darmstadt.","doi":"10.1038/s42005-023-01281-2","scopus_import":"1","file_date_updated":"2023-09-05T08:45:49Z","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","title":"Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux","publication_status":"published","abstract":[{"text":"The model of a ring threaded by the Aharonov-Bohm flux underlies our understanding of a coupling between gauge potentials and matter. The typical formulation of the model is based upon a single particle picture, and should be extended when interactions with other particles become relevant. Here, we illustrate such an extension for a particle in an Aharonov-Bohm ring subject to interactions with a weakly interacting Bose gas. We show that the ground state of the system can be described using the Bose-polaron concept—a particle dressed by interactions with a bosonic environment. We connect the energy spectrum to the effective mass of the polaron, and demonstrate how to change currents in the system by tuning boson-particle interactions. Our results suggest the Aharonov-Bohm ring as a platform for studying coherence and few- to many-body crossover of quasi-particles that arise from an impurity immersed in a medium.","lang":"eng"}],"year":"2023","article_number":"224","citation":{"mla":"Brauneis, Fabian, et al. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” <i>Communications Physics</i>, vol. 6, 224, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s42005-023-01281-2\">10.1038/s42005-023-01281-2</a>.","short":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics 6 (2023).","apa":"Brauneis, F., Ghazaryan, A., Hammer, H.-W., &#38; Volosniev, A. (2023). Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. <i>Communications Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42005-023-01281-2\">https://doi.org/10.1038/s42005-023-01281-2</a>","chicago":"Brauneis, Fabian, Areg Ghazaryan, Hans-Werner Hammer, and Artem Volosniev. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” <i>Communications Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42005-023-01281-2\">https://doi.org/10.1038/s42005-023-01281-2</a>.","ama":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. <i>Communications Physics</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s42005-023-01281-2\">10.1038/s42005-023-01281-2</a>","ieee":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, and A. Volosniev, “Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux,” <i>Communications Physics</i>, vol. 6. Springer Nature, 2023.","ista":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. 2023. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 6, 224."},"_id":"14246","date_created":"2023-08-28T12:36:49Z","file":[{"file_size":855960,"date_updated":"2023-09-05T08:45:49Z","date_created":"2023-09-05T08:45:49Z","relation":"main_file","access_level":"open_access","success":1,"file_name":"2023_CommPhysics_Brauneis.pdf","checksum":"6edfc59b0ee7dc406d0968b05236e83d","creator":"dernst","file_id":"14268","content_type":"application/pdf"}],"publisher":"Springer Nature","date_published":"2023-08-22T00:00:00Z","external_id":{"arxiv":["2301.10488"],"isi":["001052577500002"]},"type":"journal_article","keyword":["General Physics and Astronomy"],"language":[{"iso":"eng"}],"ddc":["530"],"status":"public","month":"08","isi":1,"day":"22","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"type":"journal_article","date_published":"2023-08-26T00:00:00Z","external_id":{"pmid":["37633939"]},"pmid":1,"publisher":"Springer Nature","month":"08","status":"public","ddc":["570"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"26","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","volume":14,"oa":1,"author":[{"first_name":"Nicholas C.","last_name":"Vierra","full_name":"Vierra, Nicholas C."},{"full_name":"Ribeiro-Silva, Luisa","last_name":"Ribeiro-Silva","first_name":"Luisa"},{"full_name":"Kirmiz, Michael","last_name":"Kirmiz","first_name":"Michael"},{"full_name":"Van Der List, Deborah","last_name":"Van Der List","first_name":"Deborah"},{"orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep","first_name":"Pradeep","last_name":"Bhandari"},{"last_name":"Mack","first_name":"Olivia A.","full_name":"Mack, Olivia A."},{"full_name":"Carroll, James","last_name":"Carroll","first_name":"James"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","full_name":"Le Monnier, Elodie","first_name":"Elodie","last_name":"Le Monnier"},{"full_name":"Aicher, Sue A.","first_name":"Sue A.","last_name":"Aicher"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Trimmer, James S.","first_name":"James S.","last_name":"Trimmer"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RySh"}],"date_updated":"2023-09-06T06:53:32Z","publication":"Nature Communications","intvolume":"        14","publication_status":"published","title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","oa_version":"Published Version","article_processing_charge":"Yes","file_date_updated":"2023-09-06T06:50:07Z","scopus_import":"1","doi":"10.1038/s41467-023-40930-6","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.).","article_type":"original","file":[{"file_id":"14270","creator":"dernst","content_type":"application/pdf","checksum":"6ab8aab4e957f626a09a1c73db3388fb","success":1,"access_level":"open_access","file_name":"2023_NatureComm_Vierra.pdf","relation":"main_file","date_created":"2023-09-06T06:50:07Z","date_updated":"2023-09-06T06:50:07Z","file_size":9412549}],"date_created":"2023-09-03T22:01:14Z","_id":"14253","citation":{"mla":"Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” <i>Nature Communications</i>, vol. 14, 5231, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-40930-6\">10.1038/s41467-023-40930-6</a>.","apa":"Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-40930-6\">https://doi.org/10.1038/s41467-023-40930-6</a>","short":"N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023).","chicago":"Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-40930-6\">https://doi.org/10.1038/s41467-023-40930-6</a>.","ama":"Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-40930-6\">10.1038/s41467-023-40930-6</a>","ieee":"N. C. Vierra <i>et al.</i>, “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231."},"article_number":"5231","year":"2023","abstract":[{"text":"Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell.","lang":"eng"}]},{"issue":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"15","quality_controlled":"1","language":[{"iso":"eng"}],"ddc":["510"],"month":"11","isi":1,"status":"public","publisher":"Elsevier","external_id":{"arxiv":["2303.04504"],"isi":["001071552300001"]},"date_published":"2023-11-15T00:00:00Z","type":"journal_article","article_number":"110129","year":"2023","citation":{"mla":"Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” <i>Journal of Functional Analysis</i>, vol. 285, no. 10, 110129, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">10.1016/j.jfa.2023.110129</a>.","short":"R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (2023).","chicago":"Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">https://doi.org/10.1016/j.jfa.2023.110129</a>.","apa":"Seiringer, R., &#38; Solovej, J. P. (2023). A simple approach to Lieb-Thirring type inequalities. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">https://doi.org/10.1016/j.jfa.2023.110129</a>","ieee":"R. Seiringer and J. P. Solovej, “A simple approach to Lieb-Thirring type inequalities,” <i>Journal of Functional Analysis</i>, vol. 285, no. 10. Elsevier, 2023.","ista":"Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. 285(10), 110129.","ama":"Seiringer R, Solovej JP. A simple approach to Lieb-Thirring type inequalities. <i>Journal of Functional Analysis</i>. 2023;285(10). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110129\">10.1016/j.jfa.2023.110129</a>"},"abstract":[{"lang":"eng","text":"In [10] Nam proved a Lieb–Thirring Inequality for the kinetic energy of a fermionic quantum system, with almost optimal (semi-classical) constant and a gradient correction term. We present a stronger version of this inequality, with a much simplified proof. As a corollary we obtain a simple proof of the original Lieb–Thirring inequality."}],"_id":"14254","date_created":"2023-09-03T22:01:14Z","file":[{"file_id":"14915","creator":"dernst","content_type":"application/pdf","checksum":"28e424ad91be6219e9d321054ce3a412","access_level":"open_access","success":1,"file_name":"2023_JourFunctionalAnalysis_Seiringer.pdf","date_updated":"2024-01-30T14:15:16Z","date_created":"2024-01-30T14:15:16Z","file_size":232934,"relation":"main_file"}],"doi":"10.1016/j.jfa.2023.110129","scopus_import":"1","article_type":"original","publication_identifier":{"issn":["0022-1236"],"eissn":["1096-0783"]},"acknowledgement":"J.P.S. thanks the Institute of Science and Technology Austria for the hospitality and support during a visit where this work was done. J.P.S. was also partially supported by the VILLUM Centre of Excellence for the Mathematics of Quantum Theory (QMATH) (grant No. 10059).","publication_status":"published","title":"A simple approach to Lieb-Thirring type inequalities","file_date_updated":"2024-01-30T14:15:16Z","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","arxiv":1,"intvolume":"       285","department":[{"_id":"RoSe"}],"publication":"Journal of Functional Analysis","date_updated":"2024-01-30T14:17:23Z","author":[{"last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"},{"first_name":"Jan Philip","last_name":"Solovej","full_name":"Solovej, Jan Philip"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":285},{"pmid":1,"publisher":"Public Library of Science","type":"journal_article","date_published":"2023-08-14T00:00:00Z","external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"ddc":["570"],"language":[{"iso":"eng"}],"isi":1,"month":"08","status":"public","day":"14","quality_controlled":"1","issue":"8","project":[{"call_identifier":"FWF","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","author":[{"full_name":"Koch, Jana","last_name":"Koch","first_name":"Jana"},{"last_name":"Xin","first_name":"Qilin","full_name":"Xin, Qilin"},{"first_name":"Martin","last_name":"Obr","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1756-6564","full_name":"Obr, Martin"},{"first_name":"Alicia","last_name":"Schäfer","full_name":"Schäfer, Alicia"},{"first_name":"Nina","last_name":"Rolfs","full_name":"Rolfs, Nina"},{"last_name":"Anagho","first_name":"Holda A.","full_name":"Anagho, Holda A."},{"last_name":"Kudulyte","first_name":"Aiste","full_name":"Kudulyte, Aiste"},{"full_name":"Woltereck, Lea","last_name":"Woltereck","first_name":"Lea"},{"full_name":"Kummer, Susann","first_name":"Susann","last_name":"Kummer"},{"first_name":"Joaquin","last_name":"Campos","full_name":"Campos, Joaquin"},{"last_name":"Uckeley","first_name":"Zina M.","full_name":"Uckeley, Zina M."},{"full_name":"Bell-Sakyi, Lesley","first_name":"Lesley","last_name":"Bell-Sakyi"},{"full_name":"Kräusslich, Hans Georg","first_name":"Hans Georg","last_name":"Kräusslich"},{"full_name":"Schur, Florian Km","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian Km"},{"first_name":"Claudio","last_name":"Acuna","full_name":"Acuna, Claudio"},{"full_name":"Lozach, Pierre Yves","last_name":"Lozach","first_name":"Pierre Yves"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"EM-Fac"}],"volume":19,"oa":1,"intvolume":"        19","department":[{"_id":"FlSc"}],"date_updated":"2023-12-13T12:22:22Z","publication":"PLoS Pathogens","scopus_import":"1","doi":"10.1371/journal.ppat.1011562","acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"article_type":"original","publication_status":"published","title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","article_processing_charge":"Yes","oa_version":"Published Version","file_date_updated":"2023-09-06T06:41:52Z","citation":{"mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>.","short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” <i>PLoS Pathogens</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>.","apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1011562\">https://doi.org/10.1371/journal.ppat.1011562</a>","ieee":"J. Koch <i>et al.</i>, “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” <i>PLoS Pathogens</i>, vol. 19, no. 8. Public Library of Science, 2023.","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562.","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. <i>PLoS Pathogens</i>. 2023;19(8). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1011562\">10.1371/journal.ppat.1011562</a>"},"year":"2023","article_number":"e1011562","abstract":[{"text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells.","lang":"eng"}],"file":[{"date_created":"2023-09-06T06:41:52Z","date_updated":"2023-09-06T06:41:52Z","relation":"main_file","file_size":4458336,"file_name":"2023_PloSPathogens_Koch.pdf","success":1,"access_level":"open_access","checksum":"47ca3bb54b27f28b05644be0ad064bc6","content_type":"application/pdf","file_id":"14269","creator":"dernst"}],"date_created":"2023-09-03T22:01:14Z","_id":"14255"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"S.","last_name":"Mathis","full_name":"Mathis, S."},{"orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501","full_name":"Bugnet, Lisa Annabelle","first_name":"Lisa Annabelle","last_name":"Bugnet"}],"oa":1,"volume":676,"intvolume":"       676","arxiv":1,"publication":"Astronomy and Astrophysics","date_updated":"2023-09-06T11:05:58Z","department":[{"_id":"LiBu"}],"article_type":"letter_note","acknowledgement":"The authors are grateful to the referee for her/his detailed and constructive report, which has allowed us to improve our article. S. M. acknowledges support from the CNES GOLF-SOHO and PLATO grants at CEA/DAp and PNPS (CNRS/INSU). We thank R. A. Garcia for fruitful discussions and suggestions.","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"doi":"10.1051/0004-6361/202346832","scopus_import":"1","file_date_updated":"2023-09-06T07:13:19Z","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","title":"Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields","publication_status":"published","abstract":[{"text":"Context. Space asteroseismology is revolutionizing our knowledge of the internal structure and dynamics of stars. A breakthrough is ongoing with the recent discoveries of signatures of strong magnetic fields in the core of red giant stars. The key signature for such a detection is the asymmetry these fields induce in the frequency splittings of observed dipolar mixed gravito-acoustic modes.\r\nAims. We investigate the ability of the observed asymmetries of the frequency splittings of dipolar mixed modes to constrain the geometrical properties of deep magnetic fields.\r\nMethods. We used the powerful analytical Racah-Wigner algebra used in quantum mechanics to characterize the geometrical couplings of dipolar mixed oscillation modes with various realistically plausible topologies of fossil magnetic fields. We also computed the induced perturbation of their frequencies.\r\nResults. First, in the case of an oblique magnetic dipole, we provide the exact analytical expression of the asymmetry as a function of the angle between the rotation and magnetic axes. Its value provides a direct measure of this angle. Second, considering a combination of axisymmetric dipolar and quadrupolar fields, we show how the asymmetry is blind to the unraveling of the relative strength and sign of each component. Finally, in the case of a given multipole, we show that a negative asymmetry is a signature of non-axisymmetric topologies.\r\nConclusions. Asymmetries of dipolar mixed modes provide a key bit of information on the geometrical topology of deep fossil magnetic fields, but this is insufficient on its own. Asteroseismic constraints should therefore be combined with spectropolarimetric observations and numerical simulations, which aim to predict the more probable stable large-scale geometries.","lang":"eng"}],"article_number":"L9","year":"2023","citation":{"chicago":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” <i>Astronomy and Astrophysics</i>. EDP Sciences, 2023. <a href=\"https://doi.org/10.1051/0004-6361/202346832\">https://doi.org/10.1051/0004-6361/202346832</a>.","apa":"Mathis, S., &#38; Bugnet, L. A. (2023). Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. <i>Astronomy and Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202346832\">https://doi.org/10.1051/0004-6361/202346832</a>","short":"S. Mathis, L.A. Bugnet, Astronomy and Astrophysics 676 (2023).","mla":"Mathis, S., and Lisa Annabelle Bugnet. “Asymmetries of Frequency Splittings of Dipolar Mixed Modes: A Window on the Topology of Deep Magnetic Fields.” <i>Astronomy and Astrophysics</i>, vol. 676, L9, EDP Sciences, 2023, doi:<a href=\"https://doi.org/10.1051/0004-6361/202346832\">10.1051/0004-6361/202346832</a>.","ama":"Mathis S, Bugnet LA. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. <i>Astronomy and Astrophysics</i>. 2023;676. doi:<a href=\"https://doi.org/10.1051/0004-6361/202346832\">10.1051/0004-6361/202346832</a>","ieee":"S. Mathis and L. A. Bugnet, “Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields,” <i>Astronomy and Astrophysics</i>, vol. 676. EDP Sciences, 2023.","ista":"Mathis S, Bugnet LA. 2023. Asymmetries of frequency splittings of dipolar mixed modes: A window on the topology of deep magnetic fields. Astronomy and Astrophysics. 676, L9."},"_id":"14256","file":[{"file_id":"14271","creator":"dernst","content_type":"application/pdf","checksum":"7b30d26fb2b7bcb5b5be1414950615f9","file_name":"2023_AstronomyAstrophysics_Mathis.pdf","access_level":"open_access","success":1,"relation":"main_file","date_created":"2023-09-06T07:13:19Z","file_size":458120,"date_updated":"2023-09-06T07:13:19Z"}],"date_created":"2023-09-03T22:01:15Z","publisher":"EDP Sciences","date_published":"2023-08-01T00:00:00Z","external_id":{"isi":["001046037700007"],"arxiv":["2306.11587"]},"type":"journal_article","language":[{"iso":"eng"}],"ddc":["520"],"status":"public","month":"08","isi":1,"day":"01","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"}},{"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"}],"year":"2023","citation":{"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. <i>Nature Biotechnology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>","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).","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.” <i>Nature Biotechnology</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41587-023-01911-8\">https://doi.org/10.1038/s41587-023-01911-8</a>.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” <i>Nature Biotechnology</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>.","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.","ieee":"J. M. Michalska <i>et al.</i>, “Imaging brain tissue architecture across millimeter to nanometer scales,” <i>Nature Biotechnology</i>. Springer Nature, 2023.","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. <i>Nature Biotechnology</i>. 2023. doi:<a href=\"https://doi.org/10.1038/s41587-023-01911-8\">10.1038/s41587-023-01911-8</a>"},"_id":"14257","date_created":"2023-09-03T22:01:15Z","article_type":"original","publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"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.).","doi":"10.1038/s41587-023-01911-8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41587-023-01911-8"}],"scopus_import":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","publication_status":"epub_ahead","title":"Imaging brain tissue architecture across millimeter to nanometer scales","publication":"Nature Biotechnology","date_updated":"2024-02-21T12:18:18Z","ec_funded":1,"department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Michalska, Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","last_name":"Michalska","first_name":"Julia M"},{"first_name":"Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia"},{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky"},{"id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","full_name":"Korinkova, Hana","first_name":"Hana","last_name":"Korinkova"},{"first_name":"Jake","last_name":"Watson","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","first_name":"Alban","last_name":"Cenameri"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","first_name":"Christoph M","last_name":"Sommer"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"first_name":"Alessandro","last_name":"Venturino","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro"},{"full_name":"Roessler, Karl","last_name":"Roessler","first_name":"Karl"},{"last_name":"Czech","first_name":"Thomas","full_name":"Czech, Thomas"},{"full_name":"Höftberger, Romana","first_name":"Romana","last_name":"Höftberger"},{"orcid":"0000-0001-8635-0877","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra","first_name":"Sandra","last_name":"Siegert"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"},{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/CATS"}],"record":[{"relation":"research_data","status":"public","id":"13126"}]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"project":[{"name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I03600"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24","call_identifier":"FWF"},{"grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"grant_number":"101026635","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry"}],"day":"31","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","month":"08","isi":1,"publisher":"Springer Nature","external_id":{"isi":["001065254200001"]},"date_published":"2023-08-31T00:00:00Z","type":"journal_article"},{"page":"1549-1563","day":"07","quality_controlled":"1","issue":"9","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"pmid":1,"publisher":"Elsevier","type":"journal_article","date_published":"2023-09-07T00:00:00Z","external_id":{"pmid":["37543033"]},"ddc":["570"],"language":[{"iso":"eng"}],"month":"09","status":"public","scopus_import":"1","doi":"10.1016/j.ajhg.2023.07.006","publication_identifier":{"issn":["0002-9297"],"eissn":["1537-6605"]},"acknowledgement":"This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria. K.L. and R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank computations were performed in the High-Performance Computing Center, University of Tartu. We thank Triin Laisk for her valuable insights and comments that helped greatly. We would like to acknowledge the participants and investigators of UK Biobank and Estonian Biobank studies. This project uses UK Biobank data under project number 35520.","article_type":"original","title":"Genetic insights into the age-specific biological mechanisms governing human ovarian aging","publication_status":"published","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2024-01-30T13:20:35Z","citation":{"short":"S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik, M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563.","apa":"Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., … Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms governing human ovarian aging. <i>American Journal of Human Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">https://doi.org/10.1016/j.ajhg.2023.07.006</a>","chicago":"Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer, Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” <i>American Journal of Human Genetics</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">https://doi.org/10.1016/j.ajhg.2023.07.006</a>.","mla":"Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” <i>American Journal of Human Genetics</i>, vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">10.1016/j.ajhg.2023.07.006</a>.","ista":"Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson MR. 2023. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563.","ieee":"S. E. Ojavee <i>et al.</i>, “Genetic insights into the age-specific biological mechanisms governing human ovarian aging,” <i>American Journal of Human Genetics</i>, vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023.","ama":"Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. <i>American Journal of Human Genetics</i>. 2023;110(9):1549-1563. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2023.07.006\">10.1016/j.ajhg.2023.07.006</a>"},"year":"2023","abstract":[{"text":"There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data.","lang":"eng"}],"date_created":"2023-09-03T22:01:15Z","file":[{"file_size":2551276,"date_updated":"2024-01-30T13:20:35Z","date_created":"2024-01-30T13:20:35Z","relation":"main_file","file_name":"2023_AJHG_Ojavee.pdf","success":1,"access_level":"open_access","checksum":"4108b031dc726ae6b4a5ae7e021ba188","creator":"dernst","file_id":"14912","content_type":"application/pdf"}],"_id":"14258","author":[{"full_name":"Ojavee, Sven E.","first_name":"Sven E.","last_name":"Ojavee"},{"first_name":"Liza","last_name":"Darrous","full_name":"Darrous, Liza"},{"full_name":"Patxot, Marion","last_name":"Patxot","first_name":"Marion"},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"full_name":"Fischer, Krista","last_name":"Fischer","first_name":"Krista"},{"full_name":"Mägi, Reedik","first_name":"Reedik","last_name":"Mägi"},{"full_name":"Kutalik, Zoltan","last_name":"Kutalik","first_name":"Zoltan"},{"first_name":"Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":110,"oa":1,"intvolume":"       110","department":[{"_id":"MaRo"}],"date_updated":"2024-01-30T13:21:05Z","publication":"American Journal of Human Genetics"},{"month":"07","status":"public","language":[{"iso":"eng"}],"ddc":["000"],"alternative_title":["LNCS"],"date_published":"2023-07-17T00:00:00Z","type":"conference","publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","quality_controlled":"1","page":"390-414","day":"17","department":[{"_id":"KrCh"}],"publication":"35th International Conference on Computer Aided Verification ","date_updated":"2023-09-06T08:27:33Z","intvolume":"     13964","oa":1,"volume":13964,"author":[{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","first_name":"Tobias","last_name":"Meggendorfer"},{"last_name":"Prokop","first_name":"Maximilian","full_name":"Prokop, Maximilian"},{"full_name":"Rieder, Sabine","last_name":"Rieder","first_name":"Sabine"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2023-07-22","name":"CAV: Computer Aided Verification","location":"Paris, France","start_date":"2023-07-17"},"_id":"14259","date_created":"2023-09-03T22:01:16Z","file":[{"date_created":"2023-09-06T08:25:50Z","file_size":428354,"date_updated":"2023-09-06T08:25:50Z","relation":"main_file","file_name":"2023_LNCS_CAV_Kretinsky.pdf","access_level":"open_access","success":1,"checksum":"ed66278b61bb869e1baba3d9b9081271","content_type":"application/pdf","creator":"dernst","file_id":"14276"}],"year":"2023","citation":{"ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 390–414.","ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:390-414. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>","apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., &#38; Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:390–414. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>.","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 390–414, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>."},"abstract":[{"lang":"eng","text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning."}],"publication_status":"published","title":"Guessing winning policies in LTL synthesis by semantic learning","file_date_updated":"2023-09-06T08:25:50Z","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","doi":"10.1007/978-3-031-37706-8_20","scopus_import":"1","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377051"],"issn":["0302-9743"]},"acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro)."},{"type":"conference","date_published":"2023-07-17T00:00:00Z","publisher":"Springer Nature","status":"public","month":"07","alternative_title":["LNCS"],"ddc":["000"],"language":[{"iso":"eng"}],"quality_controlled":"1","day":"17","page":"156-169","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"volume":13964,"oa":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"14995"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","first_name":"Nikita"},{"last_name":"Fedorov","first_name":"Alexander","full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"full_name":"Sokolova, Maria","first_name":"Maria","last_name":"Sokolova"},{"full_name":"Tsitelov, Dmitry","first_name":"Dmitry","last_name":"Tsitelov"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian"}],"date_updated":"2024-02-27T07:46:52Z","publication":"35th International Conference on Computer Aided Verification ","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"intvolume":"     13964","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","file_date_updated":"2023-09-06T08:16:25Z","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"scopus_import":"1","doi":"10.1007/978-3-031-37706-8_8","date_created":"2023-09-03T22:01:16Z","file":[{"date_created":"2023-09-06T08:16:25Z","relation":"main_file","date_updated":"2023-09-06T08:16:25Z","file_size":421408,"file_name":"2023_LNCS_Koval.pdf","success":1,"access_level":"open_access","checksum":"c346016393123a0a2338ad4d976f61bc","content_type":"application/pdf","file_id":"14275","creator":"dernst"}],"_id":"14260","conference":{"start_date":"2023-07-17","location":"Paris, France","name":"CAV: Computer Aided Verification","end_date":"2023-07-22"},"abstract":[{"text":"This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness.","lang":"eng"}],"citation":{"ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in <i>35th International Conference on Computer Aided Verification </i>, Paris, France, 2023, vol. 13964, pp. 156–169.","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: <i>35th International Conference on Computer Aided Verification </i>. Vol 13964. Springer Nature; 2023:156-169. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In <i>35th International Conference on Computer Aided Verification </i> (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In <i>35th International Conference on Computer Aided Verification </i>, 13964:156–69. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>.","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 156–169.","mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” <i>35th International Conference on Computer Aided Verification </i>, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>."},"year":"2023"},{"acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","publication_identifier":{"eissn":["1948-7185"]},"article_type":"original","scopus_import":"1","doi":"10.1021/acs.jpclett.3c01707","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2023-09-06T07:32:39Z","title":"Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems","publication_status":"published","abstract":[{"lang":"eng","text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing."}],"citation":{"ista":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. 2023. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. Journal of Physical Chemistry Letters. 14(33), 7395–7403.","ieee":"J. Gamper, F. Kluibenschedl, A. K. H. Weiss, and T. S. Hofer, “Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems,” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","ama":"Gamper J, Kluibenschedl F, Weiss AKH, Hofer TS. Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. 2023;14(33):7395-7403. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., &#38; Hofer, T. S. (2023). Accessing position space wave functions in band structure calculations of periodic systems - a generalized, adapted numerov implementation for one-, two-, and three-dimensional quantum problems. <i>Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>","chicago":"Gamper, Jakob, Florian Kluibenschedl, Alexander K.H. Weiss, and Thomas S. Hofer. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">https://doi.org/10.1021/acs.jpclett.3c01707</a>.","short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","mla":"Gamper, Jakob, et al. “Accessing Position Space Wave Functions in Band Structure Calculations of Periodic Systems - a Generalized, Adapted Numerov Implementation for One-, Two-, and Three-Dimensional Quantum Problems.” <i>Journal of Physical Chemistry Letters</i>, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01707\">10.1021/acs.jpclett.3c01707</a>."},"year":"2023","date_created":"2023-09-03T22:01:16Z","file":[{"relation":"main_file","date_created":"2023-09-06T07:32:39Z","date_updated":"2023-09-06T07:32:39Z","file_size":4986859,"file_name":"2023_JourPhysChemistry_Gamper.pdf","success":1,"access_level":"open_access","checksum":"637454e2b3a357498d8d622d241c4bf6","creator":"dernst","file_id":"14272","content_type":"application/pdf"}],"_id":"14261","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Gamper","first_name":"Jakob","full_name":"Gamper, Jakob"},{"full_name":"Kluibenschedl, Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","last_name":"Kluibenschedl","first_name":"Florian"},{"full_name":"Weiss, Alexander K.H.","last_name":"Weiss","first_name":"Alexander K.H."},{"full_name":"Hofer, Thomas S.","first_name":"Thomas S.","last_name":"Hofer"}],"volume":14,"oa":1,"intvolume":"        14","date_updated":"2023-09-06T11:04:31Z","publication":"Journal of Physical Chemistry Letters","department":[{"_id":"GradSch"}],"day":"11","page":"7395-7403","quality_controlled":"1","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"issue":"33","pmid":1,"publisher":"American Chemical Society","type":"journal_article","external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"date_published":"2023-08-11T00:00:00Z","ddc":["530","540"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"08"},{"project":[{"name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373"},{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020"},{"grant_number":"W01250-B20","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems"},{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"issue":"87","day":"01","quality_controlled":"1","keyword":["General Medicine","Immunology"],"language":[{"iso":"eng"}],"status":"public","isi":1,"month":"09","pmid":1,"publisher":"American Association for the Advancement of Science","type":"journal_article","date_published":"2023-09-01T00:00:00Z","external_id":{"pmid":["37656776"],"isi":["001062110600003"]},"abstract":[{"text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization.","lang":"eng"}],"citation":{"apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>","chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">https://doi.org/10.1126/sciimmunol.adc9584</a>.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” <i>Science Immunology</i>, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>.","ieee":"J. H. Alanko <i>et al.</i>, “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” <i>Science Immunology</i>, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. <i>Science Immunology</i>. 2023;8(87). doi:<a href=\"https://doi.org/10.1126/sciimmunol.adc9584\">10.1126/sciimmunol.adc9584</a>"},"article_number":"adc9584","year":"2023","date_created":"2023-09-06T08:07:51Z","_id":"14274","publication_identifier":{"issn":["2470-9468"]},"acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","article_type":"original","scopus_import":"1","doi":"10.1126/sciimmunol.adc9584","main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"article_processing_charge":"No","oa_version":"Published Version","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","publication_status":"published","intvolume":"         8","ec_funded":1,"date_updated":"2023-12-21T14:30:01Z","publication":"Science Immunology","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","last_name":"Alanko","first_name":"Jonna H"},{"id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","last_name":"Ucar"},{"first_name":"Nikola","last_name":"Canigova","orcid":"0000-0002-8518-5926","id":"3795523E-F248-11E8-B48F-1D18A9856A87","full_name":"Canigova, Nikola"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","first_name":"Julian A","last_name":"Stopp"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan","first_name":"Jan","last_name":"Schwarz"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin"},{"last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt"}],"volume":8,"related_material":{"record":[{"status":"public","relation":"research_data","id":"14279"},{"id":"14697","relation":"dissertation_contains","status":"public"}]},"oa":1},{"_id":"14277","file":[{"relation":"main_file","date_updated":"2023-09-15T06:30:50Z","date_created":"2023-09-15T06:30:50Z","file_size":2559520,"file_name":"2023_PRXLife_Boocock.pdf","access_level":"open_access","success":1,"checksum":"f881d98c89eb9f1aa136d7b781511553","content_type":"application/pdf","creator":"dernst","file_id":"14335"}],"date_created":"2023-09-06T08:30:59Z","year":"2023","article_number":"013001","citation":{"ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” <i>PRX Life</i>, vol. 1, no. 1. American Physical Society, 2023.","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. 2023;1(1). doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","apa":"Boocock, D. R., Hirashima, T., &#38; Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/prxlife.1.013001\">https://doi.org/10.1103/prxlife.1.013001</a>.","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” <i>PRX Life</i>, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/prxlife.1.013001\">10.1103/prxlife.1.013001</a>."},"abstract":[{"lang":"eng","text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels."}],"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","publication_status":"published","file_date_updated":"2023-09-15T06:30:50Z","oa_version":"Published Version","article_processing_charge":"Yes","doi":"10.1103/prxlife.1.013001","article_type":"original","acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","publication_identifier":{"issn":["2835-8279"]},"department":[{"_id":"EdHa"}],"publication":"PRX Life","date_updated":"2023-09-15T06:39:17Z","ec_funded":1,"intvolume":"         1","oa":1,"volume":1,"author":[{"full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1585-2631","last_name":"Boocock","first_name":"Daniel R"},{"full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Hirashima"},{"first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020"}],"has_accepted_license":"1","quality_controlled":"1","day":"20","month":"07","status":"public","language":[{"iso":"eng"}],"ddc":["570"],"date_published":"2023-07-20T00:00:00Z","type":"journal_article","publisher":"American Physical Society"},{"day":"11","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"doi":"10.5281/ZENODO.8133960","oa_version":"Published Version","article_processing_charge":"No","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","abstract":[{"text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt.","lang":"eng"}],"year":"2023","citation":{"ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>.","ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>","short":"M.C. Ucar, (2023).","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>.","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8133960\">https://doi.org/10.5281/ZENODO.8133960</a>","mla":"Ucar, Mehmet C. <i>Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.”</i> Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8133960\">10.5281/ZENODO.8133960</a>."},"_id":"14279","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_created":"2023-09-06T08:39:25Z","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","author":[{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","last_name":"Ucar"}],"related_material":{"record":[{"id":"14274","relation":"used_in_publication","status":"public"}]},"oa":1,"date_published":"2023-07-11T00:00:00Z","type":"research_data_reference","ddc":["570"],"status":"public","date_updated":"2023-10-03T11:42:58Z","month":"07","department":[{"_id":"EdHa"}]},{"project":[{"grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607"},{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163"},{"grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall sythesis","_id":"259B655A-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","day":"25","page":"156","alternative_title":["ISTA Thesis"],"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"ddc":["572"],"language":[{"iso":"eng"}],"status":"public","month":"09","publisher":"Institute of Science and Technology Austria","type":"dissertation","date_published":"2023-09-25T00:00:00Z","supervisor":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin"}],"abstract":[{"lang":"eng","text":"Cell division in Escherichia coli is performed by the divisome, a multi-protein complex composed of more than 30 proteins. The divisome spans from the cytoplasm through the inner membrane to the cell wall and the outer membrane. Divisome assembly is initiated by a cytoskeletal structure, the so-called Z-ring, which localizes at the center of the E. coli cell and determines the position of the future cell septum. The Z-ring is composed of the highly conserved bacterial tubulin homologue FtsZ, which forms treadmilling filaments. These filaments are recruited to the inner membrane by FtsA, a highly conserved bacterial actin homologue. FtsA interacts with other proteins in the periplasm and thus connects the cytoplasmic and periplasmic components of the divisome. \r\nA previous model postulated that FtsA regulates maturation of the divisome by switching from an oligomeric, inactive state to a monomeric and active state. This model was based mostly on in vivo studies, as a biochemical characterization of FtsA has been hampered by difficulties in purifying the protein. Here, we studied FtsA using an in vitro reconstitution approach and aimed to answer two questions: (i) How are dynamics from cytoplasmic, treadmilling FtsZ filaments coupled to proteins acting in the periplasmic space and (ii) How does FtsA regulate the maturation of the divisome?\r\nWe found that the cytoplasmic peptides of the transmembrane proteins FtsN and FtsQ interact directly with FtsA and can follow the spatiotemporal signal of FtsA/Z filaments. When we investigated the underlying mechanism by imaging single molecules of FtsNcyto, we found the peptide to interact transiently with FtsA. An in depth analysis of the single molecule trajectories helped to postulate a model where PG synthases follow the dynamics of FtsZ by a diffusion and capture mechanism. \r\nFollowing up on these findings we were interested in how the self-interaction of FtsA changes when it encounters FtsNcyto and if we can confirm the proposed oligomer-monomer switch. For this, we compared the behavior of the previously identified, hyperactive mutant FtsA R286W with wildtype FtsA. The mutant outperforms WT in mirroring and transmitting the spatiotemporal signal of treadmilling FtsZ filaments. Surprisingly however, we found that this was not due to a difference in the self-interaction strength of the two variants, but a difference in their membrane residence time. Furthermore, in contrast to our expectations, upon binding of FtsNcyto the measured self-interaction of FtsA actually increased. \r\nWe propose that FtsNcyto induces a rearrangement of the oligomeric architecture of FtsA. In further consequence this change leads to more persistent FtsZ filaments which results in a defined signalling zone, allowing formation of the mature divisome. The observed difference between FtsA WT and R286W is due to the vastly different membrane turnover of the proteins. R286W cycles 5-10x faster compared to WT which allows to sample FtsZ filaments at faster frequencies. These findings can explain the observed differences in toxicity for overexpression of FtsA WT and R286W and help to understand how FtsA regulates divisome maturation."}],"citation":{"ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","mla":"Radler, Philipp. <i>Spatiotemporal Signaling during Assembly of the Bacterial Divisome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14280\">10.15479/at:ista:14280</a>.","apa":"Radler, P. (2023). <i>Spatiotemporal signaling during assembly of the bacterial divisome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14280\">https://doi.org/10.15479/at:ista:14280</a>."},"year":"2023","date_created":"2023-09-06T10:58:25Z","file":[{"file_name":"PhD Thesis_Philipp Radler_20231004.docx","access_level":"closed","relation":"source_file","date_created":"2023-10-04T10:11:53Z","date_updated":"2023-10-04T10:28:35Z","file_size":114932847,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"pradler","file_id":"14390","checksum":"87eef11fbc5c7df0826f12a3a629b444"},{"checksum":"3253e099b7126469d941fd9419d68b4f","content_type":"application/pdf","file_id":"14391","creator":"pradler","embargo":"2024-10-04","embargo_to":"open_access","relation":"main_file","date_updated":"2023-10-04T10:28:35Z","file_size":37838778,"date_created":"2023-10-04T10:11:21Z","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","access_level":"closed"}],"_id":"14280","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-033-6"]},"doi":"10.15479/at:ista:14280","article_processing_charge":"No","oa_version":"Published Version","file_date_updated":"2023-10-04T10:28:35Z","title":"Spatiotemporal signaling during assembly of the bacterial divisome","publication_status":"published","degree_awarded":"PhD","ec_funded":1,"date_updated":"2024-02-21T12:35:18Z","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Philipp","last_name":"Radler","orcid":"0000-0001-9198-2182 ","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp"}],"related_material":{"record":[{"id":"11373","relation":"part_of_dissertation","status":"public"},{"id":"7387","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"research_data","id":"10934"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}]},{"publication_identifier":{"issn":["1369-5266"]},"acknowledgement":"The opening quote is not intended to reflect any political views of the authors. The authors by no means endorse the rhetoric of Donald Rumsfeld or the 2003 invasion of Iraq by the United States. Nevertheless, Rumsfeld's quote led to both public and academic debates on the concept of known and unknown unknowns, which can be applied to the recent unexpected developments in the auxin signaling field. We thank Linlin Qi and Huihuang Chen for their suggestions on figure presentation and inspiring discussions of TIR1/AFB signaling. Finally, we thank Aroosa Hussain for discussion of Greek mythology.","article_type":"review","scopus_import":"1","doi":"10.1016/j.pbi.2023.102443","article_processing_charge":"No","oa_version":"Submitted Version","file_date_updated":"2023-11-02T17:03:20Z","title":"Rapid auxin signaling: Unknowns old and new","publication_status":"published","abstract":[{"text":"To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling.","lang":"eng"}],"citation":{"chicago":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>.","apa":"Fiedler, L., &#38; Friml, J. (2023). Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">https://doi.org/10.1016/j.pbi.2023.102443</a>","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (2023).","mla":"Fiedler, Lukas, and Jiří Friml. “Rapid Auxin Signaling: Unknowns Old and New.” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10, 102443, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>.","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.","ieee":"L. Fiedler and J. Friml, “Rapid auxin signaling: Unknowns old and new,” <i>Current Opinion in Plant Biology</i>, vol. 75, no. 10. Elsevier, 2023.","ama":"Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. <i>Current Opinion in Plant Biology</i>. 2023;75(10). doi:<a href=\"https://doi.org/10.1016/j.pbi.2023.102443\">10.1016/j.pbi.2023.102443</a>"},"year":"2023","article_number":"102443","file":[{"checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","content_type":"application/pdf","creator":"amally","file_id":"14482","date_created":"2023-11-02T17:03:20Z","file_size":737872,"date_updated":"2023-11-02T17:03:20Z","relation":"main_file","success":1,"access_level":"open_access","file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf"}],"date_created":"2023-09-10T22:01:11Z","_id":"14313","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Fiedler","first_name":"Lukas","full_name":"Fiedler, Lukas","id":"7c417475-8972-11ed-ae7b-8b674ca26986"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"volume":75,"oa":1,"intvolume":"        75","date_updated":"2023-11-07T08:17:13Z","publication":"Current Opinion in Plant Biology","department":[{"_id":"JiFr"}],"day":"01","quality_controlled":"1","has_accepted_license":"1","issue":"10","pmid":1,"publisher":"Elsevier","type":"journal_article","external_id":{"pmid":["37666097"]},"date_published":"2023-10-01T00:00:00Z","ddc":["580"],"language":[{"iso":"eng"}],"status":"public","month":"10"},{"quality_controlled":"1","day":"26","project":[{"grant_number":"607616","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","name":"Inter-and intracellular signalling in schizophrenia"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","issue":"9","type":"journal_article","external_id":{"pmid":["37632747"]},"date_published":"2023-09-26T00:00:00Z","pmid":1,"publisher":"Elsevier","status":"public","month":"09","ddc":["570"],"language":[{"iso":"eng"}],"article_processing_charge":"Yes","oa_version":"Published Version","file_date_updated":"2023-09-15T07:12:46Z","publication_status":"published","title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","publication_identifier":{"eissn":["2211-1247"]},"acknowledgement":"We thank A. Cumpelik, H. Chiossi, and L. Bollman for comments on an earlier version of this manuscript. This work was funded by EU-FP7 MC-ITN IN-SENS (grant 607616).","article_type":"original","scopus_import":"1","doi":"10.1016/j.celrep.2023.113015","file":[{"file_name":"2023_CellPress_Nardin.pdf","access_level":"open_access","success":1,"file_size":4879455,"date_created":"2023-09-15T07:12:46Z","date_updated":"2023-09-15T07:12:46Z","relation":"main_file","creator":"dernst","file_id":"14337","content_type":"application/pdf","checksum":"ca77a304fb813c292550b8604b0fb41d"}],"date_created":"2023-09-10T22:01:11Z","_id":"14314","abstract":[{"lang":"eng","text":"The execution of cognitive functions requires coordinated circuit activity across different brain areas that involves the associated firing of neuronal assemblies. Here, we tested the circuit mechanism behind assembly interactions between the hippocampus and the medial prefrontal cortex (mPFC) of adult rats by recording neuronal populations during a rule-switching task. We identified functionally coupled CA1-mPFC cells that synchronized their activity beyond that expected from common spatial coding or oscillatory firing. When such cell pairs fired together, the mPFC cell strongly phase locked to CA1 theta oscillations and maintained consistent theta firing phases, independent of the theta timing of their CA1 counterpart. These functionally connected CA1-mPFC cells formed interconnected assemblies. While firing together with their CA1 assembly partners, mPFC cells fired along specific theta sequences. Our results suggest that upregulated theta oscillatory firing of mPFC cells can signal transient interactions with specific CA1 assemblies, thus enabling distributed computations."}],"citation":{"ista":"Nardin M, Käfer K, Stella F, Csicsvari JL. 2023. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. Cell Reports. 42(9), 113015.","ieee":"M. Nardin, K. Käfer, F. Stella, and J. L. Csicsvari, “Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions,” <i>Cell Reports</i>, vol. 42, no. 9. Elsevier, 2023.","ama":"Nardin M, Käfer K, Stella F, Csicsvari JL. Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. 2023;42(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>","mla":"Nardin, Michele, et al. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>, vol. 42, no. 9, 113015, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">10.1016/j.celrep.2023.113015</a>.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023).","chicago":"Nardin, Michele, Karola Käfer, Federico Stella, and Jozsef L Csicsvari. “Theta Oscillations as a Substrate for Medial Prefrontal-Hippocampal Assembly Interactions.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>.","apa":"Nardin, M., Käfer, K., Stella, F., &#38; Csicsvari, J. L. (2023). Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113015\">https://doi.org/10.1016/j.celrep.2023.113015</a>"},"article_number":"113015","year":"2023","volume":42,"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Nardin","first_name":"Michele","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570"},{"last_name":"Käfer","first_name":"Karola","full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9439-3148","full_name":"Stella, Federico","first_name":"Federico","last_name":"Stella"},{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari"}],"date_updated":"2023-09-15T07:14:12Z","ec_funded":1,"publication":"Cell Reports","department":[{"_id":"JoCs"}],"intvolume":"        42"},{"pmid":1,"publisher":"eLife Sciences Publications","type":"journal_article","external_id":{"pmid":["37665327"]},"date_published":"2023-09-04T00:00:00Z","ddc":["570"],"language":[{"iso":"eng"}],"month":"09","status":"public","day":"04","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","author":[{"first_name":"Ukrae H.","last_name":"Cho","full_name":"Cho, Ukrae H."},{"last_name":"Hetzer","first_name":"Martin W","full_name":"Hetzer, Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":12,"oa":1,"intvolume":"        12","department":[{"_id":"MaHe"}],"date_updated":"2023-09-15T07:07:10Z","publication":"eLife","scopus_import":"1","doi":"10.7554/eLife.89066","acknowledgement":"We thank the members of the Hetzer laboratory, Tony Hunter (Salk), Lorenzo Puri (Sanford Burnham Prebys), and Jongmin Kim (Massachusetts General Hospital) for the critical reading of the manuscript; Kenneth Diffenderfer and Aimee Pankonin (Stem Cell Core at the Salk Institute) for help with neurogenesis; Carol Marchetto and Fred Gage (Salk) for providing H9 embryonic stem cells; Lorenzo Puri, Alexandra Sacco, and Luca Caputo (Sanford Burnham Prebys) for helpful discussions and sharing mouse primary myoblasts. This work was supported by a Glenn Foundation for Medical Research Postdoctoral Fellowship in Aging Research (UHC), the NOMIS foundation (MWH), and the National Institutes of Health (R01 NS096786 to MWH and K01 AR080828 to UHC). This work was also supported by the Mass Spectrometry Core of the Salk Institute with funding from NIH-NCI CCSG: P30 014195 and the Helmsley Center for Genomic Medicine. We thank Jolene Diedrich and Antonio Pinto for technical support.","publication_identifier":{"eissn":["2050-084X"]},"article_type":"original","publication_status":"published","title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","oa_version":"Published Version","article_processing_charge":"Yes","file_date_updated":"2023-09-15T06:59:10Z","citation":{"ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","ieee":"U. H. Cho and M. Hetzer, “Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress,” <i>eLife</i>, vol. 12. eLife Sciences Publications, 2023.","ama":"Cho UH, Hetzer M. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>eLife</i>. 2023;12. doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>","mla":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>, vol. 12, RP89066, eLife Sciences Publications, 2023, doi:<a href=\"https://doi.org/10.7554/eLife.89066\">10.7554/eLife.89066</a>.","apa":"Cho, U. H., &#38; Hetzer, M. (2023). Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>","chicago":"Cho, Ukrae H., and Martin Hetzer. “Caspase-Mediated Nuclear Pore Complex Trimming in Cell Differentiation and Endoplasmic Reticulum Stress.” <i>ELife</i>. eLife Sciences Publications, 2023. <a href=\"https://doi.org/10.7554/eLife.89066\">https://doi.org/10.7554/eLife.89066</a>.","short":"U.H. Cho, M. Hetzer, ELife 12 (2023)."},"article_number":"RP89066","year":"2023","abstract":[{"lang":"eng","text":"During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. ‘Trimmed’ NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels."}],"file":[{"content_type":"application/pdf","creator":"dernst","file_id":"14336","checksum":"db24bf3d595507387b48d3799c33e289","file_name":"2023_eLife_Cho.pdf","success":1,"access_level":"open_access","relation":"main_file","date_created":"2023-09-15T06:59:10Z","file_size":3703097,"date_updated":"2023-09-15T06:59:10Z"}],"date_created":"2023-09-10T22:01:11Z","_id":"14315"},{"publisher":"The Company of Biologists","pmid":1,"date_published":"2023-09-01T00:00:00Z","external_id":{"pmid":["37539494"]},"type":"journal_article","language":[{"iso":"eng"}],"month":"09","status":"public","day":"01","quality_controlled":"1","issue":"17","author":[{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"last_name":"Aoshima","first_name":"Kaito","full_name":"Aoshima, Kaito"},{"full_name":"Shimamura, Hiroki","first_name":"Hiroki","last_name":"Shimamura"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E"},{"full_name":"Toshima, Junko Y.","first_name":"Junko Y.","last_name":"Toshima"},{"last_name":"Toshima","first_name":"Jiro","full_name":"Toshima, Jiro"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":136,"intvolume":"       136","department":[{"_id":"DaSi"}],"publication":"Journal of Cell Science","date_updated":"2023-09-20T09:14:15Z","main_file_link":[{"url":"https://doi.org/10.1101/2023.03.27.534325","open_access":"1"}],"doi":"10.1242/jcs.261448","scopus_import":"1","article_type":"original","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"publication_status":"published","title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","article_processing_charge":"No","oa_version":"Preprint","year":"2023","article_number":"jcs261448","citation":{"ista":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. 2023. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. Journal of Cell Science. 136(17), jcs261448.","ieee":"M. Nagano, K. Aoshima, H. Shimamura, D. E. Siekhaus, J. Y. Toshima, and J. Toshima, “Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway,” <i>Journal of Cell Science</i>, vol. 136, no. 17. The Company of Biologists, 2023.","ama":"Nagano M, Aoshima K, Shimamura H, Siekhaus DE, Toshima JY, Toshima J. Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. 2023;136(17). doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>","mla":"Nagano, Makoto, et al. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>, vol. 136, no. 17, jcs261448, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261448\">10.1242/jcs.261448</a>.","apa":"Nagano, M., Aoshima, K., Shimamura, H., Siekhaus, D. E., Toshima, J. Y., &#38; Toshima, J. (2023). Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","chicago":"Nagano, Makoto, Kaito Aoshima, Hiroki Shimamura, Daria E Siekhaus, Junko Y. Toshima, and Jiro Toshima. “Distinct Role of TGN-Resident Clathrin Adaptors for Vps21p Activation in the TGN-Endosome Trafficking Pathway.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261448\">https://doi.org/10.1242/jcs.261448</a>."},"abstract":[{"text":"Clathrin-mediated vesicle trafficking plays central roles in post-Golgi transport. In yeast (Saccharomyces cerevisiae), the AP-1 complex and GGA adaptors are predicted to generate distinct transport vesicles at the trans-Golgi network (TGN), and the epsin-related proteins Ent3p and Ent5p (collectively Ent3p/5p) act as accessories for these adaptors. Recently, we showed that vesicle transport from the TGN is crucial for yeast Rab5 (Vps21p)-mediated endosome formation, and that Ent3p/5p are crucial for this process, whereas AP-1 and GGA adaptors are dispensable. However, these observations were incompatible with previous studies showing that these adaptors are required for Ent3p/5p recruitment to the TGN, and thus the overall mechanism responsible for regulation of Vps21p activity remains ambiguous. Here, we investigated the functional relationships between clathrin adaptors in post-Golgi-mediated Vps21p activation. We show that AP-1 disruption in the ent3Δ5Δ mutant impaired transport of the Vps21p guanine nucleotide exchange factor Vps9p transport to the Vps21p compartment and severely reduced Vps21p activity. Additionally, GGA adaptors, the phosphatidylinositol-4-kinase Pik1p and Rab11 GTPases Ypt31p and Ypt32p were found to have partially overlapping functions for recruitment of AP-1 and Ent3p/5p to the TGN. These findings suggest a distinct role of clathrin adaptors for Vps21p activation in the TGN–endosome trafficking pathway.","lang":"eng"}],"_id":"14316","date_created":"2023-09-10T22:01:12Z"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"has_accepted_license":"1","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","call_identifier":"H2020"},{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818"}],"quality_controlled":"1","day":"17","page":"86-112","status":"public","month":"07","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"ddc":["000"],"date_published":"2023-07-17T00:00:00Z","type":"conference","publisher":"Springer Nature","_id":"14317","date_created":"2023-09-10T22:01:12Z","file":[{"relation":"main_file","file_size":531745,"date_created":"2023-09-20T08:46:43Z","date_updated":"2023-09-20T08:46:43Z","success":1,"access_level":"open_access","file_name":"2023_LNCS_Akshay.pdf","checksum":"f143c8eedf609f20f2aad2eeb496d53f","file_id":"14349","creator":"dernst","content_type":"application/pdf"}],"conference":{"end_date":"2023-07-22","name":"CAV: Computer Aided Verification","location":"Paris, France","start_date":"2023-07-17"},"abstract":[{"lang":"eng","text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples."}],"year":"2023","citation":{"ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in <i>International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 86–112.","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:86-112. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 13966:86–112. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>."},"file_date_updated":"2023-09-20T08:46:43Z","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","publication_status":"published","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377082"],"issn":["0302-9743"]},"acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","doi":"10.1007/978-3-031-37709-9_5","scopus_import":"1","publication":"International Conference on Computer Aided Verification","date_updated":"2025-07-14T09:09:56Z","ec_funded":1,"department":[{"_id":"KrCh"}],"intvolume":"     13966","oa":1,"volume":13966,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Akshay, S.","last_name":"Akshay","first_name":"S."},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","first_name":"Tobias"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","last_name":"Zikelic","first_name":"Dorde"}]},{"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377082"]},"acknowledgement":"We thank Prof. Bican Xia for valuable information on the exponential theory of reals. The work is partially supported by the National Natural Science Foundation of China (NSFC) with Grant No. 62172271, ERC CoG 863818 (ForM-SMArt), the Hong Kong Research Grants Council ECS Project Number 26208122, the HKUST-Kaisa Joint Research Institute Project Grant HKJRI3A-055 and the HKUST Startup Grant R9272.","scopus_import":"1","doi":"10.1007/978-3-031-37709-9_2","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2023-09-20T08:24:47Z","title":"Automated tail bound analysis for probabilistic recurrence relations","publication_status":"published","abstract":[{"lang":"eng","text":"Probabilistic recurrence relations (PRRs) are a standard formalism for describing the runtime of a randomized algorithm. Given a PRR and a time limit κ, we consider the tail probability Pr[T≥κ], i.e., the probability that the randomized runtime T of the PRR exceeds κ. Our focus is the formal analysis of tail bounds that aims at finding a tight asymptotic upper bound u≥Pr[T≥κ]. To address this problem, the classical and most well-known approach is the cookbook method by Karp (JACM 1994), while other approaches are mostly limited to deriving tail bounds of specific PRRs via involved custom analysis.\r\nIn this work, we propose a novel approach for deriving the common exponentially-decreasing tail bounds for PRRs whose preprocessing time and random passed sizes observe discrete or (piecewise) uniform distribution and whose recursive call is either a single procedure call or a divide-and-conquer. We first establish a theoretical approach via Markov’s inequality, and then instantiate the theoretical approach with a template-based algorithmic approach via a refined treatment of exponentiation. Experimental evaluation shows that our algorithmic approach is capable of deriving tail bounds that are (i) asymptotically tighter than Karp’s method, (ii) match the best-known manually-derived asymptotic tail bound for QuickSelect, and (iii) is only slightly worse (with a loglogn factor) than the manually-proven optimal asymptotic tail bound for QuickSort. Moreover, our algorithmic approach handles all examples (including realistic PRRs such as QuickSort, QuickSelect, DiameterComputation, etc.) in less than 0.1 s, showing that our approach is efficient in practice."}],"citation":{"mla":"Sun, Yican, et al. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” <i>Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 16–39, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>.","apa":"Sun, Y., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2023). Automated tail bound analysis for probabilistic recurrence relations. In <i>Computer Aided Verification</i> (Vol. 13966, pp. 16–39). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>","chicago":"Sun, Yican, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Automated Tail Bound Analysis for Probabilistic Recurrence Relations.” In <i>Computer Aided Verification</i>, 13966:16–39. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">https://doi.org/10.1007/978-3-031-37709-9_2</a>.","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, pp. 16–39.","ieee":"Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Automated tail bound analysis for probabilistic recurrence relations,” in <i>Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 16–39.","ista":"Sun Y, Fu H, Chatterjee K, Goharshady AK. 2023. Automated tail bound analysis for probabilistic recurrence relations. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 16–39.","ama":"Sun Y, Fu H, Chatterjee K, Goharshady AK. Automated tail bound analysis for probabilistic recurrence relations. In: <i>Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:16-39. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_2\">10.1007/978-3-031-37709-9_2</a>"},"year":"2023","date_created":"2023-09-10T22:01:12Z","file":[{"checksum":"42917e086f8c7699f3bccf84f74fe000","file_id":"14348","creator":"dernst","content_type":"application/pdf","relation":"main_file","date_created":"2023-09-20T08:24:47Z","file_size":624647,"date_updated":"2023-09-20T08:24:47Z","file_name":"2023_LNCS_Sun.pdf","success":1,"access_level":"open_access"}],"_id":"14318","conference":{"start_date":"2023-07-17","location":"Paris, France","name":"CAV: Computer Aided Verification","end_date":"2023-07-22"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Sun","first_name":"Yican","full_name":"Sun, Yican"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Goharshady","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584"}],"volume":13966,"related_material":{"link":[{"relation":"software","url":"https://github.com/boyvolcano/PRR"}]},"oa":1,"intvolume":"     13966","date_updated":"2025-07-14T09:09:57Z","ec_funded":1,"publication":"Computer Aided Verification","department":[{"_id":"KrCh"}],"day":"17","page":"16-39","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818"}],"has_accepted_license":"1","publisher":"Springer Nature","type":"conference","date_published":"2023-07-17T00:00:00Z","alternative_title":["LNCS"],"ddc":["000"],"language":[{"iso":"eng"}],"status":"public","month":"07"}]