[{"doi":"10.1007/978-3-031-37706-8_20","date_published":"2023-07-17T00:00:00Z","_id":"14259","month":"07","conference":{"name":"CAV: Computer Aided Verification","start_date":"2023-07-17","end_date":"2023-07-22","location":"Paris, France"},"quality_controlled":"1","publication_status":"published","intvolume":"     13964","publication":"35th International Conference on Computer Aided Verification ","oa":1,"alternative_title":["LNCS"],"file_date_updated":"2023-09-06T08:25:50Z","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"language":[{"iso":"eng"}],"type":"conference","file":[{"access_level":"open_access","checksum":"ed66278b61bb869e1baba3d9b9081271","content_type":"application/pdf","success":1,"file_name":"2023_LNCS_CAV_Kretinsky.pdf","date_updated":"2023-09-06T08:25:50Z","creator":"dernst","file_size":428354,"file_id":"14276","relation":"main_file","date_created":"2023-09-06T08:25:50Z"}],"department":[{"_id":"KrCh"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"oa_version":"Published Version","author":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias"},{"full_name":"Prokop, Maximilian","last_name":"Prokop","first_name":"Maximilian"},{"first_name":"Sabine","full_name":"Rieder, Sabine","last_name":"Rieder"}],"has_accepted_license":"1","scopus_import":"1","day":"17","citation":{"short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414.","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>","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.","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>.","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>","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>.","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."},"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"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.","lang":"eng"}],"title":"Guessing winning policies in LTL synthesis by semantic learning","article_processing_charge":"Yes (in subscription journal)","ddc":["000"],"date_updated":"2023-09-06T08:27:33Z","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":13964,"acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","date_created":"2023-09-03T22:01:16Z","year":"2023","page":"390-414","status":"public"},{"article_processing_charge":"Yes (in subscription journal)","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-27T07:46:52Z","ddc":["000"],"year":"2023","date_created":"2023-09-03T22:01:16Z","volume":13964,"status":"public","page":"156-169","scopus_import":"1","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"14995","relation":"research_data"}]},"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.","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>.","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>.","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>","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>","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."},"day":"17","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"}],"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"file":[{"date_created":"2023-09-06T08:16:25Z","relation":"main_file","file_id":"14275","creator":"dernst","file_size":421408,"file_name":"2023_LNCS_Koval.pdf","date_updated":"2023-09-06T08:16:25Z","success":1,"checksum":"c346016393123a0a2338ad4d976f61bc","access_level":"open_access","content_type":"application/pdf"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"author":[{"full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"last_name":"Sokolova","full_name":"Sokolova, Maria","first_name":"Maria"},{"first_name":"Dmitry","last_name":"Tsitelov","full_name":"Tsitelov, Dmitry"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"oa_version":"Published Version","conference":{"end_date":"2023-07-22","location":"Paris, France","name":"CAV: Computer Aided Verification","start_date":"2023-07-17"},"month":"07","_id":"14260","date_published":"2023-07-17T00:00:00Z","doi":"10.1007/978-3-031-37706-8_8","oa":1,"publication":"35th International Conference on Computer Aided Verification ","intvolume":"     13964","publication_status":"published","quality_controlled":"1","alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031377051"]},"file_date_updated":"2023-09-06T08:16:25Z"},{"has_accepted_license":"1","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"isi":1,"day":"11","citation":{"short":"J. Gamper, F. Kluibenschedl, A.K.H. Weiss, T.S. Hofer, Journal of Physical Chemistry Letters 14 (2023) 7395–7403.","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>","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>.","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>","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.","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>.","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."},"ddc":["530","540"],"publisher":"American Chemical Society","date_updated":"2023-09-06T11:04:31Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (in subscription journal)","pmid":1,"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","page":"7395-7403","status":"public","article_type":"original","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.","volume":14,"year":"2023","date_created":"2023-09-03T22:01:16Z","publication_status":"published","quality_controlled":"1","publication":"Journal of Physical Chemistry Letters","oa":1,"intvolume":"        14","_id":"14261","date_published":"2023-08-11T00:00:00Z","doi":"10.1021/acs.jpclett.3c01707","external_id":{"isi":["001048165800001"],"pmid":["37566743"]},"month":"08","file_date_updated":"2023-09-06T07:32:39Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1948-7185"]},"issue":"33","type":"journal_article","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"file_name":"2023_JourPhysChemistry_Gamper.pdf","date_updated":"2023-09-06T07:32:39Z","access_level":"open_access","content_type":"application/pdf","checksum":"637454e2b3a357498d8d622d241c4bf6","success":1,"date_created":"2023-09-06T07:32:39Z","relation":"main_file","file_id":"14272","file_size":4986859,"creator":"dernst"}],"department":[{"_id":"GradSch"}],"author":[{"full_name":"Gamper, Jakob","last_name":"Gamper","first_name":"Jakob"},{"full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl","first_name":"Florian","id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9"},{"first_name":"Alexander K.H.","last_name":"Weiss","full_name":"Weiss, Alexander K.H."},{"last_name":"Hofer","full_name":"Hofer, Thomas S.","first_name":"Thomas S."}],"oa_version":"Published Version"},{"related_material":{"record":[{"id":"14279","relation":"research_data","status":"public"},{"status":"public","id":"14697","relation":"dissertation_contains"}]},"scopus_import":"1","abstract":[{"lang":"eng","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."}],"isi":1,"day":"01","citation":{"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.","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>.","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>","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>.","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>","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)."},"date_updated":"2023-12-21T14:30:01Z","publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"adc9584","article_processing_charge":"No","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","pmid":1,"project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"status":"public","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}],"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.","volume":8,"year":"2023","date_created":"2023-09-06T08:07:51Z","publication_status":"published","quality_controlled":"1","publication":"Science Immunology","oa":1,"intvolume":"         8","_id":"14274","date_published":"2023-09-01T00:00:00Z","doi":"10.1126/sciimmunol.adc9584","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"month":"09","publication_identifier":{"issn":["2470-9468"]},"language":[{"iso":"eng"}],"keyword":["General Medicine","Immunology"],"issue":"87","type":"journal_article","ec_funded":1,"department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","last_name":"Alanko","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061"},{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"last_name":"Canigova","orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola"},{"first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","last_name":"Stopp"},{"last_name":"Schwarz","full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"oa_version":"Published Version"},{"file_date_updated":"2023-09-15T06:30:50Z","publication_identifier":{"issn":["2835-8279"]},"language":[{"iso":"eng"}],"issue":"1","type":"journal_article","_id":"14277","date_published":"2023-07-20T00:00:00Z","doi":"10.1103/prxlife.1.013001","month":"07","publication_status":"published","quality_controlled":"1","intvolume":"         1","publication":"PRX Life","oa":1,"author":[{"last_name":"Boocock","orcid":"0000-0002-1585-2631","full_name":"Boocock, Daniel R","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R"},{"first_name":"Tsuyoshi","last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"}],"oa_version":"Published Version","file":[{"file_size":2559520,"creator":"dernst","date_created":"2023-09-15T06:30:50Z","relation":"main_file","file_id":"14335","date_updated":"2023-09-15T06:30:50Z","file_name":"2023_PRXLife_Boocock.pdf","access_level":"open_access","content_type":"application/pdf","checksum":"f881d98c89eb9f1aa136d7b781511553","success":1}],"ec_funded":1,"department":[{"_id":"EdHa"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"day":"20","citation":{"ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","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>","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>","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>.","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","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.","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":[{"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.","lang":"eng"}],"has_accepted_license":"1","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.","volume":1,"year":"2023","date_created":"2023-09-06T08:30:59Z","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"status":"public","article_type":"original","article_number":"013001","article_processing_charge":"Yes","title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","ddc":["570"],"date_updated":"2023-09-15T06:39:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society"},{"date_updated":"2023-10-03T11:42:58Z","publisher":"Zenodo","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ddc":["570"],"department":[{"_id":"EdHa"}],"title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","article_processing_charge":"No","author":[{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"}],"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"status":"public","date_created":"2023-09-06T08:39:25Z","year":"2023","oa":1,"month":"07","doi":"10.5281/ZENODO.8133960","related_material":{"record":[{"status":"public","id":"14274","relation":"used_in_publication"}]},"date_published":"2023-07-11T00:00:00Z","_id":"14279","has_accepted_license":"1","type":"research_data_reference","abstract":[{"lang":"eng","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."}],"citation":{"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>.","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.","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>.","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>","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>","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>."},"day":"11"},{"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"file_date_updated":"2023-10-04T10:28:35Z","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"type":"dissertation","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","date_published":"2023-09-25T00:00:00Z","doi":"10.15479/at:ista:14280","_id":"14280","month":"09","oa_version":"Published Version","author":[{"first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","last_name":"Radler"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"creator":"pradler","file_size":114932847,"date_created":"2023-10-04T10:11:53Z","relation":"source_file","file_id":"14390","date_updated":"2023-10-04T10:28:35Z","file_name":"PhD Thesis_Philipp Radler_20231004.docx","checksum":"87eef11fbc5c7df0826f12a3a629b444","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"},{"embargo_to":"open_access","file_size":37838778,"creator":"pradler","date_created":"2023-10-04T10:11:21Z","relation":"main_file","file_id":"14391","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","date_updated":"2023-10-04T10:28:35Z","embargo":"2024-10-04","access_level":"closed","checksum":"3253e099b7126469d941fd9419d68b4f","content_type":"application/pdf"}],"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"day":"25","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>","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>.","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>","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","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>."},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11373"},{"status":"public","relation":"part_of_dissertation","id":"7387"},{"status":"public","relation":"research_data","id":"10934"}]},"has_accepted_license":"1","page":"156","status":"public","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"},{"name":"Reconstitution of bacterial cell wall sythesis","_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016"}],"date_created":"2023-09-06T10:58:25Z","year":"2023","ddc":["572"],"supervisor":[{"last_name":"Loose","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"date_updated":"2024-02-21T12:35:18Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","title":"Spatiotemporal signaling during assembly of the bacterial divisome","article_processing_charge":"No"},{"citation":{"ama":"Praetorius FM, Leung PJY, Tessmer MH, et al. Design of stimulus-responsive two-state hinge proteins. <i>Science</i>. 2023;381(6659):754-760. doi:<a href=\"https://doi.org/10.1126/science.adg7731\">10.1126/science.adg7731</a>","ista":"Praetorius FM, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. 2023. Design of stimulus-responsive two-state hinge proteins. Science. 381(6659), 754–760.","chicago":"Praetorius, Florian M, Philip J. Y. Leung, Maxx H. Tessmer, Adam Broerman, Cullen Demakis, Acacia F. Dishman, Arvind Pillai, et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adg7731\">https://doi.org/10.1126/science.adg7731</a>.","apa":"Praetorius, F. M., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., … Baker, D. (2023). Design of stimulus-responsive two-state hinge proteins. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg7731\">https://doi.org/10.1126/science.adg7731</a>","short":"F.M. Praetorius, P.J.Y. Leung, M.H. Tessmer, A. Broerman, C. Demakis, A.F. Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P.M. Levine, M. Lamb, R.K. Ballard, S.R. Gerben, H. Nguyen, A. Kang, B. Sankaran, A.K. Bera, B.F. Volkman, J. Nivala, S. Stoll, D. Baker, Science 381 (2023) 754–760.","ieee":"F. M. Praetorius <i>et al.</i>, “Design of stimulus-responsive two-state hinge proteins,” <i>Science</i>, vol. 381, no. 6659. American Association for the Advancement of Science, pp. 754–760, 2023.","mla":"Praetorius, Florian M., et al. “Design of Stimulus-Responsive Two-State Hinge Proteins.” <i>Science</i>, vol. 381, no. 6659, American Association for the Advancement of Science, 2023, pp. 754–60, doi:<a href=\"https://doi.org/10.1126/science.adg7731\">10.1126/science.adg7731</a>."},"day":"17","abstract":[{"text":"In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of “hinge” proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.","lang":"eng"}],"scopus_import":"1","date_created":"2023-09-06T12:04:23Z","year":"2023","volume":381,"article_type":"original","status":"public","page":"754-760","pmid":1,"title":"Design of stimulus-responsive two-state hinge proteins","article_processing_charge":"No","date_updated":"2023-11-07T12:42:09Z","publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","issue":"6659","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"language":[{"iso":"eng"}],"month":"08","external_id":{"pmid":["37590357"]},"extern":"1","doi":"10.1126/science.adg7731","date_published":"2023-08-17T00:00:00Z","_id":"14281","publication":"Science","intvolume":"       381","quality_controlled":"1","publication_status":"published","oa_version":"None","author":[{"id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M","last_name":"Praetorius","full_name":"Praetorius, Florian M"},{"first_name":"Philip J. Y.","last_name":"Leung","full_name":"Leung, Philip J. Y."},{"full_name":"Tessmer, Maxx H.","last_name":"Tessmer","first_name":"Maxx H."},{"first_name":"Adam","last_name":"Broerman","full_name":"Broerman, Adam"},{"full_name":"Demakis, Cullen","last_name":"Demakis","first_name":"Cullen"},{"full_name":"Dishman, Acacia F.","last_name":"Dishman","first_name":"Acacia F."},{"first_name":"Arvind","full_name":"Pillai, Arvind","last_name":"Pillai"},{"first_name":"Abbas","full_name":"Idris, Abbas","last_name":"Idris"},{"first_name":"David","last_name":"Juergens","full_name":"Juergens, David"},{"first_name":"Justas","last_name":"Dauparas","full_name":"Dauparas, Justas"},{"first_name":"Xinting","last_name":"Li","full_name":"Li, Xinting"},{"last_name":"Levine","full_name":"Levine, Paul M.","first_name":"Paul M."},{"full_name":"Lamb, Mila","last_name":"Lamb","first_name":"Mila"},{"last_name":"Ballard","full_name":"Ballard, Ryanne K.","first_name":"Ryanne K."},{"first_name":"Stacey R.","full_name":"Gerben, Stacey R.","last_name":"Gerben"},{"full_name":"Nguyen, Hannah","last_name":"Nguyen","first_name":"Hannah"},{"full_name":"Kang, Alex","last_name":"Kang","first_name":"Alex"},{"first_name":"Banumathi","full_name":"Sankaran, Banumathi","last_name":"Sankaran"},{"first_name":"Asim K.","full_name":"Bera, Asim K.","last_name":"Bera"},{"full_name":"Volkman, Brian F.","last_name":"Volkman","first_name":"Brian F."},{"full_name":"Nivala, Jeff","last_name":"Nivala","first_name":"Jeff"},{"full_name":"Stoll, Stefan","last_name":"Stoll","first_name":"Stefan"},{"first_name":"David","last_name":"Baker","full_name":"Baker, David"}]},{"month":"03","date_published":"2023-03-15T00:00:00Z","extern":"1","doi":"10.1101/2023.03.14.532666","_id":"14294","oa":1,"publication":"bioRxiv","publication_status":"submitted","citation":{"ieee":"N. I. Edman <i>et al.</i>, “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies,” <i>bioRxiv</i>. .","mla":"Edman, Natasha I., et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>.","ista":"Edman NI, Redler RL, Phal A, Schlichthaerle T, Srivatsan SR, Etemadi A, An S, Favor A, Ehnes D, Li Z, Praetorius FM, Gordon M, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray AN, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. bioRxiv, <a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>.","chicago":"Edman, Natasha I, Rachel L Redler, Ashish Phal, Thomas Schlichthaerle, Sanjay R Srivatsan, Ali Etemadi, Seong An, et al. “Modulation of FGF Pathway Signaling and Vascular Differentiation Using Designed Oligomeric Assemblies.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.03.14.532666\">https://doi.org/10.1101/2023.03.14.532666</a>.","apa":"Edman, N. I., Redler, R. L., Phal, A., Schlichthaerle, T., Srivatsan, S. R., Etemadi, A., … Baker, D. (n.d.). Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.03.14.532666\">https://doi.org/10.1101/2023.03.14.532666</a>","ama":"Edman NI, Redler RL, Phal A, et al. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.03.14.532666\">10.1101/2023.03.14.532666</a>","short":"N.I. Edman, R.L. Redler, A. Phal, T. Schlichthaerle, S.R. Srivatsan, A. Etemadi, S. An, A. Favor, D. Ehnes, Z. Li, F.M. Praetorius, M. Gordon, W. Yang, B. Coventry, D.R. Hicks, L. Cao, N. Bethel, P. Heine, A.N. Murray, S. Gerben, L. Carter, M. Miranda, B. Negahdari, S. Lee, C. Trapnell, L. Stewart, D.C. Ekiert, J. Schlessinger, J. Shendure, G. Bhabha, H. Ruohola-Baker, D. Baker, BioRxiv (n.d.)."},"day":"15","type":"preprint","abstract":[{"lang":"eng","text":"Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways."}],"language":[{"iso":"eng"}],"title":"Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-11-07T12:21:58Z","date_created":"2023-09-06T12:31:49Z","year":"2023","oa_version":"Preprint","author":[{"first_name":"Natasha I","full_name":"Edman, Natasha I","last_name":"Edman"},{"full_name":"Redler, Rachel L","last_name":"Redler","first_name":"Rachel L"},{"last_name":"Phal","full_name":"Phal, Ashish","first_name":"Ashish"},{"first_name":"Thomas","full_name":"Schlichthaerle, Thomas","last_name":"Schlichthaerle"},{"full_name":"Srivatsan, Sanjay R","last_name":"Srivatsan","first_name":"Sanjay R"},{"first_name":"Ali","full_name":"Etemadi, Ali","last_name":"Etemadi"},{"full_name":"An, Seong","last_name":"An","first_name":"Seong"},{"last_name":"Favor","full_name":"Favor, Andrew","first_name":"Andrew"},{"full_name":"Ehnes, Devon","last_name":"Ehnes","first_name":"Devon"},{"first_name":"Zhe","full_name":"Li, Zhe","last_name":"Li"},{"last_name":"Praetorius","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M"},{"first_name":"Max","full_name":"Gordon, Max","last_name":"Gordon"},{"first_name":"Wei","last_name":"Yang","full_name":"Yang, Wei"},{"first_name":"Brian","last_name":"Coventry","full_name":"Coventry, Brian"},{"first_name":"Derrick R","full_name":"Hicks, Derrick R","last_name":"Hicks"},{"first_name":"Longxing","full_name":"Cao, Longxing","last_name":"Cao"},{"full_name":"Bethel, Neville","last_name":"Bethel","first_name":"Neville"},{"first_name":"Piper","full_name":"Heine, Piper","last_name":"Heine"},{"first_name":"Analisa N","last_name":"Murray","full_name":"Murray, Analisa N"},{"first_name":"Stacey","last_name":"Gerben","full_name":"Gerben, Stacey"},{"first_name":"Lauren","last_name":"Carter","full_name":"Carter, Lauren"},{"full_name":"Miranda, Marcos","last_name":"Miranda","first_name":"Marcos"},{"full_name":"Negahdari, Babak","last_name":"Negahdari","first_name":"Babak"},{"first_name":"Sangwon","full_name":"Lee, Sangwon","last_name":"Lee"},{"first_name":"Cole","full_name":"Trapnell, Cole","last_name":"Trapnell"},{"first_name":"Lance","last_name":"Stewart","full_name":"Stewart, Lance"},{"full_name":"Ekiert, Damian C","last_name":"Ekiert","first_name":"Damian C"},{"first_name":"Joseph","last_name":"Schlessinger","full_name":"Schlessinger, Joseph"},{"first_name":"Jay","full_name":"Shendure, Jay","last_name":"Shendure"},{"first_name":"Gira","last_name":"Bhabha","full_name":"Bhabha, Gira"},{"first_name":"Hannele","full_name":"Ruohola-Baker, Hannele","last_name":"Ruohola-Baker"},{"full_name":"Baker, David","last_name":"Baker","first_name":"David"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.14.532666"}],"status":"public"},{"oa_version":"Submitted Version","author":[{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas","last_name":"Fiedler","full_name":"Fiedler, Lukas"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"department":[{"_id":"JiFr"}],"file":[{"file_size":737872,"creator":"amally","file_id":"14482","date_created":"2023-11-02T17:03:20Z","relation":"main_file","checksum":"1c476c3414d2dfb0c85db0cb6cfd8a28","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"Fiedler CurrOpinOlantBiol 2023_revised.pdf","date_updated":"2023-11-02T17:03:20Z"}],"issue":"10","type":"journal_article","file_date_updated":"2023-11-02T17:03:20Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1369-5266"]},"intvolume":"        75","oa":1,"publication":"Current Opinion in Plant Biology","publication_status":"published","quality_controlled":"1","external_id":{"pmid":["37666097"]},"month":"10","_id":"14313","doi":"10.1016/j.pbi.2023.102443","date_published":"2023-10-01T00:00:00Z","status":"public","article_type":"review","year":"2023","date_created":"2023-09-10T22:01:11Z","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.","volume":75,"date_updated":"2023-11-07T08:17:13Z","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["580"],"article_processing_charge":"No","pmid":1,"title":"Rapid auxin signaling: Unknowns old and new","article_number":"102443","abstract":[{"lang":"eng","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."}],"citation":{"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>.","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.","short":"L. Fiedler, J. Friml, Current Opinion in Plant Biology 75 (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>","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>.","ista":"Fiedler L, Friml J. 2023. Rapid auxin signaling: Unknowns old and new. Current Opinion in Plant Biology. 75(10), 102443.","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>"},"day":"01","scopus_import":"1","has_accepted_license":"1"},{"title":"Theta oscillations as a substrate for medial prefrontal-hippocampal assembly interactions","pmid":1,"article_processing_charge":"Yes","article_number":"113015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-15T07:14:12Z","publisher":"Elsevier","ddc":["570"],"date_created":"2023-09-10T22:01:11Z","year":"2023","volume":42,"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","status":"public","project":[{"grant_number":"607616","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Inter-and intracellular signalling in schizophrenia"}],"scopus_import":"1","has_accepted_license":"1","citation":{"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.","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>.","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>","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>","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>.","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.","short":"M. Nardin, K. Käfer, F. Stella, J.L. Csicsvari, Cell Reports 42 (2023)."},"day":"26","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."}],"department":[{"_id":"JoCs"}],"ec_funded":1,"file":[{"date_updated":"2023-09-15T07:12:46Z","file_name":"2023_CellPress_Nardin.pdf","checksum":"ca77a304fb813c292550b8604b0fb41d","content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"14337","date_created":"2023-09-15T07:12:46Z","relation":"main_file","file_size":4879455,"creator":"dernst"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele"},{"full_name":"Käfer, Karola","last_name":"Käfer","first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","last_name":"Stella","first_name":"Federico","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","month":"09","external_id":{"pmid":["37632747"]},"doi":"10.1016/j.celrep.2023.113015","date_published":"2023-09-26T00:00:00Z","_id":"14314","publication":"Cell Reports","oa":1,"intvolume":"        42","quality_controlled":"1","publication_status":"published","type":"journal_article","issue":"9","file_date_updated":"2023-09-15T07:12:46Z","publication_identifier":{"eissn":["2211-1247"]},"language":[{"iso":"eng"}]},{"date_created":"2023-09-10T22:01:11Z","year":"2023","volume":12,"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.","article_type":"original","status":"public","title":"Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress","pmid":1,"article_processing_charge":"Yes","article_number":"RP89066","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-15T07:07:10Z","publisher":"eLife Sciences Publications","ddc":["570"],"citation":{"short":"U.H. Cho, M. Hetzer, ELife 12 (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>","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>.","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>","ista":"Cho UH, Hetzer M. 2023. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife. 12, RP89066.","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>.","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."},"day":"04","abstract":[{"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.","lang":"eng"}],"scopus_import":"1","has_accepted_license":"1","author":[{"first_name":"Ukrae H.","full_name":"Cho, Ukrae H.","last_name":"Cho"},{"id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","last_name":"Hetzer","full_name":"Hetzer, Martin W","orcid":"0000-0002-2111-992X"}],"oa_version":"Published Version","department":[{"_id":"MaHe"}],"file":[{"creator":"dernst","file_size":3703097,"date_created":"2023-09-15T06:59:10Z","file_id":"14336","relation":"main_file","date_updated":"2023-09-15T06:59:10Z","file_name":"2023_eLife_Cho.pdf","success":1,"checksum":"db24bf3d595507387b48d3799c33e289","access_level":"open_access","content_type":"application/pdf"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"type":"journal_article","file_date_updated":"2023-09-15T06:59:10Z","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"month":"09","external_id":{"pmid":["37665327"]},"doi":"10.7554/eLife.89066","date_published":"2023-09-04T00:00:00Z","_id":"14315","oa":1,"intvolume":"        12","publication":"eLife","quality_controlled":"1","publication_status":"published"},{"scopus_import":"1","citation":{"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>","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>.","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>","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.","short":"M. Nagano, K. Aoshima, H. Shimamura, D.E. Siekhaus, J.Y. Toshima, J. Toshima, Journal of Cell Science 136 (2023).","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.","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>."},"day":"01","abstract":[{"lang":"eng","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."}],"pmid":1,"title":"Distinct role of TGN-resident clathrin adaptors for Vps21p activation in the TGN-endosome trafficking pathway","article_processing_charge":"No","article_number":"jcs261448","date_updated":"2023-09-20T09:14:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"The Company of Biologists","date_created":"2023-09-10T22:01:12Z","year":"2023","volume":136,"article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2023.03.27.534325"}],"status":"public","month":"09","external_id":{"pmid":["37539494"]},"date_published":"2023-09-01T00:00:00Z","doi":"10.1242/jcs.261448","_id":"14316","oa":1,"intvolume":"       136","publication":"Journal of Cell Science","quality_controlled":"1","publication_status":"published","type":"journal_article","issue":"17","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"language":[{"iso":"eng"}],"department":[{"_id":"DaSi"}],"author":[{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"last_name":"Aoshima","full_name":"Aoshima, Kaito","first_name":"Kaito"},{"first_name":"Hiroki","last_name":"Shimamura","full_name":"Shimamura, Hiroki"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus"},{"first_name":"Junko Y.","full_name":"Toshima, Junko Y.","last_name":"Toshima"},{"first_name":"Jiro","last_name":"Toshima","full_name":"Toshima, Jiro"}],"oa_version":"Preprint"},{"publisher":"Springer Nature","date_updated":"2025-07-14T09:09:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"article_processing_charge":"Yes (in subscription journal)","title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"}],"status":"public","page":"86-112","year":"2023","date_created":"2023-09-10T22:01:12Z","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.","volume":13966,"scopus_import":"1","has_accepted_license":"1","abstract":[{"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.","lang":"eng"}],"citation":{"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>.","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.","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>.","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>","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>","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."},"day":"17","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"ec_funded":1,"department":[{"_id":"KrCh"}],"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"f143c8eedf609f20f2aad2eeb496d53f","success":1,"file_name":"2023_LNCS_Akshay.pdf","date_updated":"2023-09-20T08:46:43Z","creator":"dernst","file_size":531745,"file_id":"14349","relation":"main_file","date_created":"2023-09-20T08:46:43Z"}],"author":[{"last_name":"Akshay","full_name":"Akshay, S.","first_name":"S."},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","publication":"International Conference on Computer Aided Verification","intvolume":"     13966","oa":1,"publication_status":"published","quality_controlled":"1","conference":{"end_date":"2023-07-22","location":"Paris, France","name":"CAV: Computer Aided Verification","start_date":"2023-07-17"},"month":"07","_id":"14317","date_published":"2023-07-17T00:00:00Z","doi":"10.1007/978-3-031-37709-9_5","type":"conference","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031377082"]},"language":[{"iso":"eng"}],"file_date_updated":"2023-09-20T08:46:43Z","alternative_title":["LNCS"]},{"quality_controlled":"1","publication_status":"published","intvolume":"     13966","publication":"Computer Aided Verification","oa":1,"doi":"10.1007/978-3-031-37709-9_2","date_published":"2023-07-17T00:00:00Z","_id":"14318","month":"07","conference":{"start_date":"2023-07-17","name":"CAV: Computer Aided Verification","end_date":"2023-07-22","location":"Paris, France"},"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377082"]},"file_date_updated":"2023-09-20T08:24:47Z","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"checksum":"42917e086f8c7699f3bccf84f74fe000","content_type":"application/pdf","access_level":"open_access","success":1,"date_updated":"2023-09-20T08:24:47Z","file_name":"2023_LNCS_Sun.pdf","file_size":624647,"creator":"dernst","relation":"main_file","file_id":"14348","date_created":"2023-09-20T08:24:47Z"}],"department":[{"_id":"KrCh"}],"ec_funded":1,"oa_version":"Published Version","author":[{"first_name":"Yican","last_name":"Sun","full_name":"Sun, Yican"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/boyvolcano/PRR"}]},"has_accepted_license":"1","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"day":"17","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>.","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.","short":"Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Computer Aided Verification, Springer Nature, 2023, 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>","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>.","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>"},"ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-14T09:09:57Z","publisher":"Springer Nature","title":"Automated tail bound analysis for probabilistic recurrence relations","article_processing_charge":"Yes (in subscription journal)","page":"16-39","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"status":"public","volume":13966,"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.","date_created":"2023-09-10T22:01:12Z","year":"2023"},{"doi":"10.37236/11714","date_published":"2023-07-28T00:00:00Z","_id":"14319","month":"07","external_id":{"arxiv":["2212.03100"]},"arxiv":1,"quality_controlled":"1","publication_status":"published","publication":"Electronic Journal of Combinatorics","intvolume":"        30","oa":1,"file_date_updated":"2023-09-15T08:02:09Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1077-8926"]},"type":"journal_article","issue":"3","file":[{"date_updated":"2023-09-15T08:02:09Z","file_name":"2023_elecJournCombinatorics_Anastos.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","checksum":"52c46c8cb329f9aaee9ade01525f317b","file_size":247917,"creator":"dernst","date_created":"2023-09-15T08:02:09Z","file_id":"14338","relation":"main_file"}],"department":[{"_id":"MaKw"}],"ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png"},"oa_version":"Published Version","author":[{"last_name":"Anastos","full_name":"Anastos, Michael","id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael"},{"first_name":"David","last_name":"Fabian","full_name":"Fabian, David"},{"first_name":"Alp","last_name":"Müyesser","full_name":"Müyesser, Alp"},{"full_name":"Szabó, Tibor","last_name":"Szabó","first_name":"Tibor"}],"has_accepted_license":"1","scopus_import":"1","day":"28","citation":{"short":"M. Anastos, D. Fabian, A. Müyesser, T. Szabó, Electronic Journal of Combinatorics 30 (2023).","apa":"Anastos, M., Fabian, D., Müyesser, A., &#38; Szabó, T. (2023). Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>","chicago":"Anastos, Michael, David Fabian, Alp Müyesser, and Tibor Szabó. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2023. <a href=\"https://doi.org/10.37236/11714\">https://doi.org/10.37236/11714</a>.","ista":"Anastos M, Fabian D, Müyesser A, Szabó T. 2023. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. Electronic Journal of Combinatorics. 30(3), P3.10.","ama":"Anastos M, Fabian D, Müyesser A, Szabó T. Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets. <i>Electronic Journal of Combinatorics</i>. 2023;30(3). doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>","mla":"Anastos, Michael, et al. “Splitting Matchings and the Ryser-Brualdi-Stein Conjecture for Multisets.” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3, P3.10, Electronic Journal of Combinatorics, 2023, doi:<a href=\"https://doi.org/10.37236/11714\">10.37236/11714</a>.","ieee":"M. Anastos, D. Fabian, A. Müyesser, and T. Szabó, “Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets,” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 3. Electronic Journal of Combinatorics, 2023."},"license":"https://creativecommons.org/licenses/by-nd/4.0/","abstract":[{"text":"We study multigraphs whose edge-sets are the union of three perfect matchings, M1, M2, and M3. Given such a graph G and any a1; a2; a3 2 N with a1 +a2 +a3 6 n - 2, we show there exists a matching M of G with jM \\ Mij = ai for each i 2 f1; 2; 3g. The bound n - 2 in the theorem is best possible in general. We conjecture however that if G is bipartite, the same result holds with n - 2 replaced by n - 1. We give a construction that shows such a result would be tight. We\r\nalso make a conjecture generalising the Ryser-Brualdi-Stein conjecture with colour\r\nmultiplicities.","lang":"eng"}],"article_number":"P3.10","title":"Splitting matchings and the Ryser-Brualdi-Stein conjecture for multisets","article_processing_charge":"Yes","ddc":["510"],"date_updated":"2023-09-15T08:12:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Electronic Journal of Combinatorics","volume":30,"acknowledgement":"Anastos has received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Sk lodowska-Curie grant agreement No 101034413.Fabian’s research is supported by the Deutsche Forschungsgemeinschaft (DFG, GermanResearch Foundation) Graduiertenkolleg “Facets of Complexity” (GRK 2434).","date_created":"2023-09-10T22:01:12Z","year":"2023","article_type":"original","status":"public","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}]},{"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.06310","open_access":"1"}],"article_type":"original","status":"public","volume":108,"acknowledgement":"A.F.Y. acknowledges primary support from the Department of Energy under award DE-SC0020043, and additional support from the Gordon and Betty Moore Foundation under award GBMF9471 for group operations.","date_created":"2023-09-12T07:12:12Z","year":"2023","date_updated":"2023-09-20T09:38:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","article_number":"125411","title":"Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The development of two-dimensional materials has resulted in a diverse range of novel, high-quality compounds with increasing complexity. A key requirement for a comprehensive quantitative theory is the accurate determination of these materials' band structure parameters. However, this task is challenging due to the intricate band structures and the indirect nature of experimental probes. In this work, we introduce a general framework to derive band structure parameters from experimental data using deep neural networks. We applied our method to the penetration field capacitance measurement of trilayer graphene, an effective probe of its density of states. First, we demonstrate that a trained deep network gives accurate predictions for the penetration field capacitance as a function of tight-binding parameters. Next, we use the fast and accurate predictions from the trained network to automatically determine tight-binding parameters directly from experimental data, with extracted parameters being in a good agreement with values in the literature. We conclude by discussing potential applications of our method to other materials and experimental techniques beyond penetration field capacitance."}],"day":"15","citation":{"ista":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. 2023. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. Physical Review B. 108(12), 125411.","apa":"Henderson, P. M., Ghazaryan, A., Zibrov, A. A., Young, A. F., &#38; Serbyn, M. (2023). Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>","ama":"Henderson PM, Ghazaryan A, Zibrov AA, Young AF, Serbyn M. Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene. <i>Physical Review B</i>. 2023;108(12). doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>","chicago":"Henderson, Paul M, Areg Ghazaryan, Alexander A. Zibrov, Andrea F. Young, and Maksym Serbyn. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/physrevb.108.125411\">https://doi.org/10.1103/physrevb.108.125411</a>.","short":"P.M. Henderson, A. Ghazaryan, A.A. Zibrov, A.F. Young, M. Serbyn, Physical Review B 108 (2023).","ieee":"P. M. Henderson, A. Ghazaryan, A. A. Zibrov, A. F. Young, and M. Serbyn, “Deep learning extraction of band structure parameters from density of states: A case study on trilayer graphene,” <i>Physical Review B</i>, vol. 108, no. 12. American Physical Society, 2023.","mla":"Henderson, Paul M., et al. “Deep Learning Extraction of Band Structure Parameters from Density of States: A Case Study on Trilayer Graphene.” <i>Physical Review B</i>, vol. 108, no. 12, 125411, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/physrevb.108.125411\">10.1103/physrevb.108.125411</a>."},"scopus_import":"1","author":[{"orcid":"0000-0002-5198-7445","full_name":"Henderson, Paul M","last_name":"Henderson","first_name":"Paul M","id":"13C09E74-18D9-11E9-8878-32CFE5697425"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"first_name":"Alexander A.","full_name":"Zibrov, Alexander A.","last_name":"Zibrov"},{"full_name":"Young, Andrea F.","last_name":"Young","first_name":"Andrea F."},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"oa_version":"Preprint","department":[{"_id":"MaSe"},{"_id":"ChLa"},{"_id":"MiLe"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"type":"journal_article","issue":"12","quality_controlled":"1","publication_status":"published","intvolume":"       108","publication":"Physical Review B","oa":1,"date_published":"2023-09-15T00:00:00Z","doi":"10.1103/physrevb.108.125411","_id":"14320","month":"09","external_id":{"arxiv":["2210.06310"]},"arxiv":1},{"abstract":[{"text":"We demonstrate the possibility of a coupling between the magnetization direction of a ferromagnet and the tilting angle of adsorbed achiral molecules. To illustrate the mechanism of the coupling, we analyze a minimal Stoner model that includes Rashba spin–orbit coupling due to the electric field on the surface of the ferromagnet. The proposed mechanism allows us to study magnetic anisotropy of the system with an extended Stoner–Wohlfarth model and argue that adsorbed achiral molecules can change magnetocrystalline anisotropy of the substrate. Our research aims to motivate further experimental studies of the current-free chirality induced spin selectivity effect involving both enantiomers.","lang":"eng"}],"citation":{"ieee":"R. Al Hyder, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Achiral dipoles on a ferromagnet can affect its magnetization direction,” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10. AIP Publishing, 2023.","mla":"Al Hyder, Ragheed, et al. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>, vol. 159, no. 10, 104103, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>.","ista":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. 2023. Achiral dipoles on a ferromagnet can affect its magnetization direction. The Journal of Chemical Physics. 159(10), 104103.","ama":"Al Hyder R, Cappellaro A, Lemeshko M, Volosniev A. Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. 2023;159(10). doi:<a href=\"https://doi.org/10.1063/5.0165806\">10.1063/5.0165806</a>","chicago":"Al Hyder, Ragheed, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Achiral Dipoles on a Ferromagnet Can Affect Its Magnetization Direction.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>.","apa":"Al Hyder, R., Cappellaro, A., Lemeshko, M., &#38; Volosniev, A. (2023). Achiral dipoles on a ferromagnet can affect its magnetization direction. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0165806\">https://doi.org/10.1063/5.0165806</a>","short":"R. Al Hyder, A. Cappellaro, M. Lemeshko, A. Volosniev, The Journal of Chemical Physics 159 (2023)."},"day":"11","scopus_import":"1","has_accepted_license":"1","article_type":"original","status":"public","project":[{"name":"Non-equilibrium Field Theory of Molecular Rotations","grant_number":"101062862","_id":"bd7b5202-d553-11ed-ba76-9b1c1b258338"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"date_created":"2023-09-13T09:25:09Z","year":"2023","volume":159,"acknowledgement":"We thank Zhanybek Alpichshev, Mohammad Reza Safari, Binghai Yan, and Yossi Paltiel for enlightening discussions.\r\nM.L. acknowledges support from the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). A. C. received funding from the European Union’s Horizon Europe research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101062862 - NeqMolRot.","date_updated":"2023-09-20T09:48:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"AIP Publishing","ddc":["530"],"pmid":1,"title":"Achiral dipoles on a ferromagnet can affect its magnetization direction","article_processing_charge":"Yes (in subscription journal)","article_number":"104103","type":"journal_article","issue":"10","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"file_date_updated":"2023-09-13T09:34:20Z","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"language":[{"iso":"eng"}],"intvolume":"       159","oa":1,"publication":"The Journal of Chemical Physics","quality_controlled":"1","publication_status":"published","month":"09","external_id":{"pmid":["37694742"],"arxiv":["2306.17592"]},"arxiv":1,"date_published":"2023-09-11T00:00:00Z","doi":"10.1063/5.0165806","_id":"14321","author":[{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed"},{"orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","last_name":"Cappellaro","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"},{"last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"department":[{"_id":"MiLe"}],"ec_funded":1,"file":[{"relation":"main_file","date_created":"2023-09-13T09:34:20Z","file_id":"14322","creator":"acappell","file_size":5749653,"success":1,"access_level":"open_access","content_type":"application/pdf","checksum":"507ab65ab29e2c987c94cabad7c5370b","date_updated":"2023-09-13T09:34:20Z","file_name":"104103_1_5.0165806.pdf"}]},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"department":[{"_id":"GradSch"},{"_id":"AnKi"}],"file":[{"embargo_to":"open_access","file_size":10147911,"creator":"kkuzmicz","file_id":"14324","relation":"main_file","date_created":"2023-09-13T09:52:52Z","file_name":"PhDThesis_KK_final_pdfA.pdf","date_updated":"2023-09-13T10:08:25Z","content_type":"application/pdf","access_level":"closed","checksum":"bd83596869c814b24aeff7077d031c0e","embargo":"2025-03-13"},{"file_size":103980668,"creator":"kkuzmicz","date_created":"2023-09-13T09:53:29Z","relation":"source_file","file_id":"14325","file_name":"thesis_KK_final_corrections_092023.docx","date_updated":"2023-09-13T09:53:29Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"aa2757ae4c3478041fd7e62c587d3e4d"}],"oa_version":"Published Version","author":[{"full_name":"Kuzmicz-Kowalska, Katarzyna","last_name":"Kuzmicz-Kowalska","first_name":"Katarzyna","id":"4CED352A-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","month":"09","doi":"10.15479/at:ista:14323","date_published":"2023-09-13T00:00:00Z","_id":"14323","type":"dissertation","language":[{"iso":"eng"}],"file_date_updated":"2023-09-13T10:08:25Z","publication_identifier":{"issn":["2663 - 337X"]},"alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"supervisor":[{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"}],"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-03-07T15:02:59Z","ddc":["570"],"title":"Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord","article_processing_charge":"No","project":[{"name":"The role of morphogens in the regulation of neural tube growth","_id":"267AF0E4-B435-11E9-9278-68D0E5697425"}],"status":"public","page":"151","date_created":"2023-09-13T10:07:18Z","year":"2023","related_material":{"record":[{"status":"public","id":"7883","relation":"part_of_dissertation"}]},"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Morphogens are signaling molecules that are known for their prominent role in pattern formation within developing tissues. In addition to patterning, morphogens also control tissue growth. However, the underlying mechanisms are poorly understood. We studied the role of morphogens in regulating tissue growth in the developing vertebrate neural tube. In this system, opposing morphogen gradients of Shh and BMP establish the dorsoventral pattern of neural progenitor domains. Perturbations in these morphogen pathways result in alterations in tissue growth and cell cycle progression, however, it has been unclear what cellular process is affected. To address this, we analysed the rates of cell proliferation and cell death in mouse mutants in which signaling is perturbed, as well as in chick neural plate explants exposed to defined concentrations of signaling activators or inhibitors. Our results indicated that the rate of cell proliferation was not altered in these assays. By contrast, both the Shh and BMP signaling pathways had profound effects on neural progenitor survival. Our results indicate that these pathways synergise to promote cell survival within neural progenitors. Consistent with this, we found that progenitors within the intermediate region of the neural tube, where the combined levels of Shh and BMP are the lowest, are most prone to cell death when signaling activity is inhibited. In addition, we found that downregulation of Shh results in increased apoptosis within the roof plate, which is the dorsal source of BMP ligand production. This revealed a cross-interaction between the Shh and BMP morphogen signaling pathways that may be relevant for understanding how gradients scale in neural tubes with different overall sizes. We further studied the mechanism acting downstream of Shh in cell survival regulation using genetic and genomic approaches. We propose that Shh transcriptionally regulates a non-canonical apoptotic pathway. Altogether, our study points to a novel role of opposing morphogen gradients in tissue size regulation and provides new insights into complex interactions between Shh and BMP signaling gradients in the neural tube."}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","citation":{"short":"K. Kuzmicz-Kowalska, Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord, Institute of Science and Technology Austria, 2023.","apa":"Kuzmicz-Kowalska, K. (2023). <i>Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>","ama":"Kuzmicz-Kowalska K. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>","ista":"Kuzmicz-Kowalska K. 2023. Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord. Institute of Science and Technology Austria.","chicago":"Kuzmicz-Kowalska, Katarzyna. “Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14323\">https://doi.org/10.15479/at:ista:14323</a>.","mla":"Kuzmicz-Kowalska, Katarzyna. <i>Regulation of Neural Progenitor Survival by Shh and BMP in the Developing Spinal Cord</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14323\">10.15479/at:ista:14323</a>.","ieee":"K. Kuzmicz-Kowalska, “Regulation of neural progenitor survival by Shh and BMP in the developing spinal cord,” Institute of Science and Technology Austria, 2023."},"day":"13"},{"publication_status":"submitted","oa":1,"publication":"arXiv","doi":"10.48550/arXiv.2307.09552","extern":"1","date_published":"2023-07-18T00:00:00Z","_id":"14333","month":"07","external_id":{"arxiv":["2307.09552"]},"arxiv":1,"language":[{"iso":"eng"}],"type":"preprint","abstract":[{"lang":"eng","text":"As causal ground truth is incredibly rare, causal discovery algorithms are\r\ncommonly only evaluated on simulated data. This is concerning, given that\r\nsimulations reflect common preconceptions about generating processes regarding\r\nnoise distributions, model classes, and more. In this work, we propose a novel\r\nmethod for falsifying the output of a causal discovery algorithm in the absence\r\nof ground truth. Our key insight is that while statistical learning seeks\r\nstability across subsets of data points, causal learning should seek stability\r\nacross subsets of variables. Motivated by this insight, our method relies on a\r\nnotion of compatibility between causal graphs learned on different subsets of\r\nvariables. We prove that detecting incompatibilities can falsify wrongly\r\ninferred causal relations due to violation of assumptions or errors from finite\r\nsample effects. Although passing such compatibility tests is only a necessary\r\ncriterion for good performance, we argue that it provides strong evidence for\r\nthe causal models whenever compatibility entails strong implications for the\r\njoint distribution. We also demonstrate experimentally that detection of\r\nincompatibilities can aid in causal model selection."}],"day":"18","citation":{"ieee":"P. M. Faller, L. C. Vankadara, A. A. Mastakouri, F. Locatello, and D. Janzing, “Self-compatibility: Evaluating causal discovery without ground truth,” <i>arXiv</i>. .","mla":"Faller, Philipp M., et al. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, 2307.09552, doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>.","ista":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. arXiv, 2307.09552.","apa":"Faller, P. M., Vankadara, L. C., Mastakouri, A. A., Locatello, F., &#38; Janzing, D. (n.d.). Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>","chicago":"Faller, Philipp M., Leena Chennuru Vankadara, Atalanti A. Mastakouri, Francesco Locatello, and Dominik Janzing. “Self-Compatibility: Evaluating Causal Discovery without Ground Truth.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2307.09552\">https://doi.org/10.48550/arXiv.2307.09552</a>.","ama":"Faller PM, Vankadara LC, Mastakouri AA, Locatello F, Janzing D. Self-compatibility: Evaluating causal discovery without ground truth. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2307.09552\">10.48550/arXiv.2307.09552</a>","short":"P.M. Faller, L.C. Vankadara, A.A. Mastakouri, F. Locatello, D. Janzing, ArXiv (n.d.)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-13T12:47:53Z","article_number":"2307.09552","title":"Self-compatibility: Evaluating causal discovery without ground truth","department":[{"_id":"FrLo"}],"article_processing_charge":"No","oa_version":"Preprint","author":[{"last_name":"Faller","full_name":"Faller, Philipp M.","first_name":"Philipp M."},{"last_name":"Vankadara","full_name":"Vankadara, Leena Chennuru","first_name":"Leena Chennuru"},{"full_name":"Mastakouri, Atalanti A.","last_name":"Mastakouri","first_name":"Atalanti A."},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"last_name":"Janzing","full_name":"Janzing, Dominik","first_name":"Dominik"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.09552"}],"status":"public","date_created":"2023-09-13T12:44:59Z","year":"2023"}]