[{"article_type":"original","related_material":{"link":[{"url":"https://github.com/danzllab/CATS","relation":"software"}],"record":[{"relation":"research_data","status":"public","id":"13126"}]},"date_updated":"2024-02-21T12:18:18Z","publication":"Nature Biotechnology","year":"2023","oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41587-023-01911-8"}],"publisher":"Springer Nature","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"date_created":"2023-09-03T22:01:15Z","date_published":"2023-08-31T00:00:00Z","external_id":{"isi":["001065254200001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"JoDa"},{"_id":"Bio"},{"_id":"RySh"}],"ec_funded":1,"publication_status":"epub_ahead","status":"public","acknowledgement":"We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).","project":[{"name":"Optical control of synaptic function via adhesion molecules","call_identifier":"FWF","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508"},{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"}],"publication_identifier":{"eissn":["1546-1696"],"issn":["1087-0156"]},"doi":"10.1038/s41587-023-01911-8","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"_id":"14257","author":[{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","full_name":"Michalska, Julia M","last_name":"Michalska","orcid":"0000-0003-3862-1235"},{"full_name":"Lyudchik, Julia","last_name":"Lyudchik","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia"},{"orcid":"0000-0002-2340-7431","last_name":"Velicky","full_name":"Velicky, Philipp","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Korinkova, Hana","last_name":"Korinkova","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed","first_name":"Hana"},{"orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","full_name":"Watson, Jake","last_name":"Watson"},{"last_name":"Cenameri","full_name":"Cenameri, Alban","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105"},{"orcid":"0000-0002-3183-8207","last_name":"Amberg","full_name":"Amberg, Nicole","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","full_name":"Venturino, Alessandro","last_name":"Venturino","orcid":"0000-0003-2356-9403"},{"full_name":"Roessler, Karl","last_name":"Roessler","first_name":"Karl"},{"first_name":"Thomas","full_name":"Czech, Thomas","last_name":"Czech"},{"first_name":"Romana","full_name":"Höftberger, Romana","last_name":"Höftberger"},{"orcid":"0000-0001-8635-0877","last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","full_name":"Jonas, Peter M"},{"orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","last_name":"Danzl","full_name":"Danzl, Johann G"}],"title":"Imaging brain tissue architecture across millimeter to nanometer scales","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","month":"08","day":"31","citation":{"ista":"Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology.","ama":"Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8","short":"J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023).","apa":"Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8","ieee":"J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology. Springer Nature, 2023.","chicago":"Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8.","mla":"Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8."}},{"publisher":"Elsevier","intvolume":" 110","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"MaRo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37543033"]},"date_published":"2023-09-07T00:00:00Z","date_created":"2023-09-03T22:01:15Z","scopus_import":"1","publication":"American Journal of Human Genetics","date_updated":"2024-01-30T13:21:05Z","page":"1549-1563","article_type":"original","oa":1,"year":"2023","file":[{"checksum":"4108b031dc726ae6b4a5ae7e021ba188","content_type":"application/pdf","access_level":"open_access","date_updated":"2024-01-30T13:20:35Z","success":1,"file_size":2551276,"relation":"main_file","creator":"dernst","file_name":"2023_AJHG_Ojavee.pdf","date_created":"2024-01-30T13:20:35Z","file_id":"14912"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":110,"citation":{"apa":"Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., … Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. Elsevier. https://doi.org/10.1016/j.ajhg.2023.07.006","ieee":"S. E. Ojavee et al., “Genetic insights into the age-specific biological mechanisms governing human ovarian aging,” American Journal of Human Genetics, vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023.","short":"S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik, M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563.","ama":"Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. 2023;110(9):1549-1563. doi:10.1016/j.ajhg.2023.07.006","ista":"Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson MR. 2023. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563.","mla":"Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” American Journal of Human Genetics, vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:10.1016/j.ajhg.2023.07.006.","chicago":"Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer, Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” American Journal of Human Genetics. Elsevier, 2023. https://doi.org/10.1016/j.ajhg.2023.07.006."},"day":"07","ddc":["570"],"file_date_updated":"2024-01-30T13:20:35Z","month":"09","pmid":1,"oa_version":"Published Version","publication_identifier":{"eissn":["1537-6605"],"issn":["0002-9297"]},"status":"public","publication_status":"published","acknowledgement":"This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria. K.L. and R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank computations were performed in the High-Performance Computing Center, University of Tartu. We thank Triin Laisk for her valuable insights and comments that helped greatly. We would like to acknowledge the participants and investigators of UK Biobank and Estonian Biobank studies. This project uses UK Biobank data under project number 35520.","title":"Genetic insights into the age-specific biological mechanisms governing human ovarian aging","author":[{"last_name":"Ojavee","full_name":"Ojavee, Sven E.","first_name":"Sven E."},{"last_name":"Darrous","full_name":"Darrous, Liza","first_name":"Liza"},{"first_name":"Marion","last_name":"Patxot","full_name":"Patxot, Marion"},{"full_name":"Läll, Kristi","last_name":"Läll","first_name":"Kristi"},{"last_name":"Fischer","full_name":"Fischer, Krista","first_name":"Krista"},{"first_name":"Reedik","full_name":"Mägi, Reedik","last_name":"Mägi"},{"full_name":"Kutalik, Zoltan","last_name":"Kutalik","first_name":"Zoltan"},{"orcid":"0000-0001-8982-8813","last_name":"Robinson","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"_id":"14258","abstract":[{"lang":"eng","text":"There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data."}],"issue":"9","doi":"10.1016/j.ajhg.2023.07.006"},{"year":"2023","alternative_title":["LNCS"],"oa":1,"page":"390-414","date_updated":"2023-09-06T08:27:33Z","publication":"35th International Conference on Computer Aided Verification ","scopus_import":"1","date_created":"2023-09-03T22:01:16Z","date_published":"2023-07-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","intvolume":" 13964","publisher":"Springer Nature","doi":"10.1007/978-3-031-37706-8_20","abstract":[{"lang":"eng","text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning."}],"_id":"14259","author":[{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer"},{"first_name":"Maximilian","last_name":"Prokop","full_name":"Prokop, Maximilian"},{"last_name":"Rieder","full_name":"Rieder, Sabine","first_name":"Sabine"}],"title":"Guessing winning policies in LTL synthesis by semantic learning","publication_status":"published","status":"public","acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783031377051"]},"conference":{"end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France","name":"CAV: Computer Aided Verification"},"oa_version":"Published Version","file_date_updated":"2023-09-06T08:25:50Z","month":"07","ddc":["000"],"day":"17","citation":{"chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In 35th International Conference on Computer Aided Verification , 13964:390–414. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_20.","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 390–414, doi:10.1007/978-3-031-37706-8_20.","ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in 35th International Conference on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 390–414.","apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., & Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_20","ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: 35th International Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:390-414. doi:10.1007/978-3-031-37706-8_20","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 390–414."},"volume":13964,"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-09-06T08:25:50Z","file_id":"14276","file_size":428354,"relation":"main_file","creator":"dernst","file_name":"2023_LNCS_CAV_Kretinsky.pdf","checksum":"ed66278b61bb869e1baba3d9b9081271","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-09-06T08:25:50Z","success":1}]},{"page":"156-169","related_material":{"record":[{"status":"public","relation":"research_data","id":"14995"}]},"date_updated":"2024-02-27T07:46:52Z","publication":"35th International Conference on Computer Aided Verification ","year":"2023","alternative_title":["LNCS"],"oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","publisher":"Springer Nature","intvolume":" 13964","date_created":"2023-09-03T22:01:16Z","scopus_import":"1","date_published":"2023-07-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"publication_status":"published","status":"public","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377051"],"issn":["0302-9743"]},"doi":"10.1007/978-3-031-37706-8_8","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"}],"_id":"14260","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","full_name":"Koval, Nikita","last_name":"Koval"},{"first_name":"Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","full_name":"Fedorov, Alexander"},{"first_name":"Maria","last_name":"Sokolova","full_name":"Sokolova, Maria"},{"first_name":"Dmitry","last_name":"Tsitelov","full_name":"Tsitelov, Dmitry"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"article_processing_charge":"Yes (in subscription journal)","volume":13964,"has_accepted_license":"1","file":[{"access_level":"open_access","checksum":"c346016393123a0a2338ad4d976f61bc","content_type":"application/pdf","success":1,"date_updated":"2023-09-06T08:16:25Z","file_name":"2023_LNCS_Koval.pdf","creator":"dernst","file_size":421408,"relation":"main_file","file_id":"14275","date_created":"2023-09-06T08:16:25Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","conference":{"name":"CAV: Computer Aided Verification","location":"Paris, France","start_date":"2023-07-17","end_date":"2023-07-22"},"file_date_updated":"2023-09-06T08:16:25Z","month":"07","ddc":["000"],"citation":{"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 35th International Conference on Computer Aided Verification , 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8.","mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8","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 35th International Conference on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 156–169.","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: 35th International Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:156-169. doi:10.1007/978-3-031-37706-8_8","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"},{"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"publisher":"American Chemical Society","intvolume":" 14","date_created":"2023-09-03T22:01:16Z","scopus_import":"1","date_published":"2023-08-11T00:00:00Z","external_id":{"pmid":["37566743"],"isi":["001048165800001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GradSch"}],"page":"7395-7403","article_type":"original","date_updated":"2023-09-06T11:04:31Z","publication":"Journal of Physical Chemistry Letters","year":"2023","oa":1,"article_processing_charge":"Yes (in subscription journal)","volume":14,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"14272","date_created":"2023-09-06T07:32:39Z","file_name":"2023_JourPhysChemistry_Gamper.pdf","creator":"dernst","file_size":4986859,"relation":"main_file","success":1,"date_updated":"2023-09-06T07:32:39Z","access_level":"open_access","checksum":"637454e2b3a357498d8d622d241c4bf6","content_type":"application/pdf"}],"oa_version":"Published Version","file_date_updated":"2023-09-06T07:32:39Z","ddc":["530","540"],"month":"08","pmid":1,"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. Journal of Physical Chemistry Letters. 2023;14(33):7395-7403. doi:10.1021/acs.jpclett.3c01707","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.","apa":"Gamper, J., Kluibenschedl, F., Weiss, A. K. H., & 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. Journal of Physical Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.3c01707","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,” Journal of Physical Chemistry Letters, vol. 14, no. 33. American Chemical Society, pp. 7395–7403, 2023.","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.” Journal of Physical Chemistry Letters, vol. 14, no. 33, American Chemical Society, 2023, pp. 7395–403, doi:10.1021/acs.jpclett.3c01707.","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.” Journal of Physical Chemistry Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpclett.3c01707."},"day":"11","status":"public","publication_status":"published","acknowledgement":"Financial supports for this work via a PhD scholarship for J. Gamper issued by the Leopold-Franzens-University of Innsbruck (Vicerector Prof. Dr Ulrike Tanzer) are gratefully acknowledged. The computational results presented have been achieved (in part) using the HPC infrastructure of the University of Innsbruck.","publication_identifier":{"eissn":["1948-7185"]},"doi":"10.1021/acs.jpclett.3c01707","abstract":[{"lang":"eng","text":"In this work, a generalized, adapted Numerov implementation capable of determining band structures of periodic quantum systems is outlined. Based on the input potential, the presented approach numerically solves the Schrödinger equation in position space at each momentum space point. Thus, in addition to the band structure, the method inherently provides information about the state functions and probability densities in position space at each momentum space point considered. The generalized, adapted Numerov framework provided reliable estimates for a variety of increasingly complex test suites in one, two, and three dimensions. The accuracy of the proposed methodology was benchmarked against results obtained for the analytically solvable Kronig-Penney model. Furthermore, the presented numerical solver was applied to a model potential representing a 2D optical lattice being a challenging application relevant, for example, in the field of quantum computing."}],"issue":"33","_id":"14261","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","author":[{"first_name":"Jakob","last_name":"Gamper","full_name":"Gamper, Jakob"},{"id":"7499e70e-eb2c-11ec-b98b-f925648bc9d9","first_name":"Florian","full_name":"Kluibenschedl, Florian","last_name":"Kluibenschedl"},{"first_name":"Alexander K.H.","full_name":"Weiss, Alexander K.H.","last_name":"Weiss"},{"last_name":"Hofer","full_name":"Hofer, Thomas S.","first_name":"Thomas S."}]},{"date_created":"2023-09-06T08:07:51Z","scopus_import":"1","external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"date_published":"2023-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"American Association for the Advancement of Science","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciimmunol.adc9584"}],"intvolume":" 8","keyword":["General Medicine","Immunology"],"year":"2023","oa":1,"article_number":"adc9584","article_type":"original","related_material":{"record":[{"id":"14279","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14697"}]},"date_updated":"2023-12-21T14:30:01Z","publication":"Science Immunology","oa_version":"Published Version","pmid":1,"month":"09","citation":{"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).","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. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584","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. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","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.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584."},"day":"01","article_processing_charge":"No","volume":8,"doi":"10.1126/sciimmunol.adc9584","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."}],"issue":"87","_id":"14274","title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","author":[{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","first_name":"Jonna H","full_name":"Alanko, Jonna H","last_name":"Alanko","orcid":"0000-0002-7698-3061"},{"orcid":"0000-0003-0506-4217","last_name":"Ucar","full_name":"Ucar, Mehmet C","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425"},{"orcid":"0000-0002-8518-5926","last_name":"Canigova","full_name":"Canigova, Nikola","first_name":"Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stopp","full_name":"Stopp, Julian A","first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schwarz","full_name":"Schwarz, Jan","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","last_name":"Merrin","full_name":"Merrin, Jack","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"}],"ec_funded":1,"status":"public","publication_status":"published","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.","project":[{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["2470-9468"]}},{"article_type":"original","article_number":"013001","publication":"PRX Life","date_updated":"2023-09-15T06:39:17Z","year":"2023","oa":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":" 1","publisher":"American Physical Society","date_published":"2023-07-20T00:00:00Z","date_created":"2023-09-06T08:30:59Z","department":[{"_id":"EdHa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","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.","ec_funded":1,"publication_identifier":{"issn":["2835-8279"]},"project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"}],"issue":"1","abstract":[{"lang":"eng","text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels."}],"doi":"10.1103/prxlife.1.013001","author":[{"full_name":"Boocock, Daniel R","last_name":"Boocock","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R","orcid":"0000-0002-1585-2631"},{"first_name":"Tsuyoshi","full_name":"Hirashima, Tsuyoshi","last_name":"Hirashima"},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo"}],"title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","_id":"14277","has_accepted_license":"1","article_processing_charge":"Yes","volume":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2023-09-15T06:30:50Z","file_id":"14335","checksum":"f881d98c89eb9f1aa136d7b781511553","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-09-15T06:30:50Z","success":1,"relation":"main_file","creator":"dernst","file_size":2559520,"file_name":"2023_PRXLife_Boocock.pdf"}],"oa_version":"Published Version","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.","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","apa":"Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” PRX Life, vol. 1, no. 1. American Physical Society, 2023.","mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:10.1103/prxlife.1.013001.","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001."},"month":"07","file_date_updated":"2023-09-15T06:30:50Z","ddc":["570"]},{"status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14274"}]},"date_updated":"2023-10-03T11:42:58Z","year":"2023","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."}],"doi":"10.5281/ZENODO.8133960","author":[{"orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C","full_name":"Ucar, Mehmet C","last_name":"Ucar"}],"title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","oa":1,"_id":"14279","has_accepted_license":"1","type":"research_data_reference","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Zenodo","date_published":"2023-07-11T00:00:00Z","oa_version":"Published Version","date_created":"2023-09-06T08:39:25Z","day":"11","department":[{"_id":"EdHa"}],"citation":{"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:10.5281/ZENODO.8133960","short":"M.C. Ucar, (2023).","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960.","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. https://doi.org/10.5281/ZENODO.8133960","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.","mla":"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, doi:10.5281/ZENODO.8133960.","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. https://doi.org/10.5281/ZENODO.8133960."},"month":"07","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file":[{"file_name":"PhD Thesis_Philipp Radler_20231004.docx","relation":"source_file","creator":"pradler","file_size":114932847,"access_level":"closed","checksum":"87eef11fbc5c7df0826f12a3a629b444","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2023-10-04T10:28:35Z","file_id":"14390","date_created":"2023-10-04T10:11:53Z"},{"date_updated":"2023-10-04T10:28:35Z","access_level":"closed","checksum":"3253e099b7126469d941fd9419d68b4f","content_type":"application/pdf","embargo":"2024-10-04","file_name":"PhD Thesis_Philipp Radler_20231004.pdf","relation":"main_file","creator":"pradler","file_size":37838778,"file_id":"14391","date_created":"2023-10-04T10:11:21Z","embargo_to":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","ddc":["572"],"file_date_updated":"2023-10-04T10:28:35Z","month":"09","day":"25","citation":{"mla":"Radler, Philipp. Spatiotemporal Signaling during Assembly of the Bacterial Divisome. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14280.","chicago":"Radler, Philipp. “Spatiotemporal Signaling during Assembly of the Bacterial Divisome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14280.","apa":"Radler, P. (2023). Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14280","ieee":"P. Radler, “Spatiotemporal signaling during assembly of the bacterial divisome,” Institute of Science and Technology Austria, 2023.","short":"P. Radler, Spatiotemporal Signaling during Assembly of the Bacterial Divisome, Institute of Science and Technology Austria, 2023.","ama":"Radler P. Spatiotemporal signaling during assembly of the bacterial divisome. 2023. doi:10.15479/at:ista:14280","ista":"Radler P. 2023. Spatiotemporal signaling during assembly of the bacterial divisome. Institute of Science and Technology Austria."},"oa_version":"Published Version","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","grant_number":"679239","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020"},{"_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607","name":"Understanding bacterial cell division by in vitro\r\nreconstitution"},{"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"}],"publication_identifier":{"isbn":["978-3-99078-033-6"],"issn":["2663-337X"]},"ec_funded":1,"publication_status":"published","status":"public","_id":"14280","author":[{"last_name":"Radler","full_name":"Radler, Philipp","first_name":"Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 "}],"supervisor":[{"full_name":"Loose, Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724"}],"title":"Spatiotemporal signaling during assembly of the bacterial divisome","doi":"10.15479/at:ista:14280","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"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"MaLo"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"date_created":"2023-09-06T10:58:25Z","date_published":"2023-09-25T00:00:00Z","date_updated":"2024-02-21T12:35:18Z","page":"156","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11373"},{"id":"7387","relation":"part_of_dissertation","status":"public"},{"relation":"research_data","status":"public","id":"10934"}]},"keyword":["Cell Division","Reconstitution","FtsZ","FtsA","Divisome","E.coli"],"alternative_title":["ISTA Thesis"],"year":"2023"},{"publisher":"Oxford Academic","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.08503"}],"intvolume":" 2023","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"TiBr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000773116000001"],"arxiv":["1901.08503"]},"date_published":"2023-04-01T00:00:00Z","date_created":"2021-01-22T09:31:09Z","publication":"International Mathematics Research Notices","date_updated":"2023-08-01T12:23:55Z","page":"6780-6808","article_type":"original","oa":1,"year":"2023","arxiv":1,"volume":2023,"article_processing_charge":"No","citation":{"mla":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices, vol. 2023, no. 8, Oxford Academic, 2023, pp. 6780–808, doi:10.1093/imrn/rnac048.","chicago":"Wilsch, Florian Alexander. “Integral Points of Bounded Height on a Log Fano Threefold.” International Mathematics Research Notices. Oxford Academic, 2023. https://doi.org/10.1093/imrn/rnac048.","short":"F.A. Wilsch, International Mathematics Research Notices 2023 (2023) 6780–6808.","ista":"Wilsch FA. 2023. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023(8), 6780–6808.","ama":"Wilsch FA. Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. 2023;2023(8):6780-6808. doi:10.1093/imrn/rnac048","apa":"Wilsch, F. A. (2023). Integral points of bounded height on a log Fano threefold. International Mathematics Research Notices. Oxford Academic. https://doi.org/10.1093/imrn/rnac048","ieee":"F. A. Wilsch, “Integral points of bounded height on a log Fano threefold,” International Mathematics Research Notices, vol. 2023, no. 8. Oxford Academic, pp. 6780–6808, 2023."},"day":"01","month":"04","oa_version":"Preprint","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"acknowledgement":"This work was supported by the German Academic Exchange Service. Parts of this article were prepared at the Institut de Mathémathiques de Jussieu—Paris Rive Gauche. I wish to thank Antoine Chambert-Loir for his remarks and the institute for its hospitality, as well as the anonymous referee for several useful remarks and suggestions for improvements.","publication_status":"published","status":"public","title":"Integral points of bounded height on a log Fano threefold","author":[{"orcid":"0000-0001-7302-8256","last_name":"Wilsch","full_name":"Wilsch, Florian Alexander","first_name":"Florian Alexander","id":"560601DA-8D36-11E9-A136-7AC1E5697425"}],"_id":"9034","abstract":[{"lang":"eng","text":"We determine an asymptotic formula for the number of integral points of bounded height on a blow-up of P3 outside certain planes using universal torsors."}],"issue":"8","doi":"10.1093/imrn/rnac048"},{"article_processing_charge":"Yes (via OA deal)","arxiv":1,"oa_version":"Published Version","day":"17","citation":{"short":"M. Dymond, V. Kaluza, Geometriae Dedicata (2023).","ista":"Dymond M, Kaluza V. 2023. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata., 15.","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 2023. doi:10.1007/s10711-023-00862-3","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata. Springer Nature, 2023.","apa":"Dymond, M., & Kaluza, V. (2023). Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3","mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata, 15, Springer Nature, 2023, doi:10.1007/s10711-023-00862-3.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature, 2023. https://doi.org/10.1007/s10711-023-00862-3."},"month":"11","status":"public","publication_status":"epub_ahead","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","publication_identifier":{"eissn":["1572-9168"],"issn":["0046-5755"]},"abstract":[{"lang":"eng","text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence."}],"doi":"10.1007/s10711-023-00862-3","author":[{"first_name":"Michael","full_name":"Dymond, Michael","last_name":"Dymond"},{"full_name":"Kaluza, Vojtech","last_name":"Kaluza","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","first_name":"Vojtech","orcid":"0000-0002-2512-8698"}],"title":"Divergence of separated nets with respect to displacement equivalence","_id":"9651","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1007/s10711-023-00862-3","open_access":"1"}],"publisher":"Springer Nature","external_id":{"arxiv":["2102.13046"],"isi":["001105681500001"]},"date_published":"2023-11-17T00:00:00Z","scopus_import":"1","date_created":"2021-07-14T07:01:27Z","department":[{"_id":"UlWa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_type":"original","article_number":"15","publication":"Geometriae Dedicata","date_updated":"2024-01-11T13:06:32Z","year":"2023","oa":1},{"abstract":[{"text":"In 1998 Burago and Kleiner and (independently) McMullen gave examples of separated nets in Euclidean space which are non-bilipschitz equivalent to the integer lattice. We study weaker notions of equivalence of separated nets and demonstrate that such notions also give rise to distinct equivalence classes. Put differently, we find occurrences of particularly strong divergence of separated nets from the integer lattice. Our approach generalises that of Burago and Kleiner and McMullen which takes place largely in a continuous setting. Existence of irregular separated nets is verified via the existence of non-realisable density functions ρ:[0,1]d→(0,∞). In the present work we obtain stronger types of non-realisable densities.","lang":"eng"}],"doi":"10.1007/s11856-022-2448-6","title":"Highly irregular separated nets","author":[{"first_name":"Michael","last_name":"Dymond","full_name":"Dymond, Michael"},{"first_name":"Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","last_name":"Kaluza","full_name":"Kaluza, Vojtech","orcid":"0000-0002-2512-8698"}],"_id":"9652","acknowledgement":"This work was done while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35.","status":"public","publication_status":"published","publication_identifier":{"eissn":["1565-8511"]},"oa_version":"Submitted Version","citation":{"ieee":"M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.","apa":"Dymond, M., & Kaluza, V. (2023). Highly irregular separated nets. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-022-2448-6","short":"M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554.","ista":"Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554.","ama":"Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics. 2023;253:501-554. doi:10.1007/s11856-022-2448-6","mla":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics, vol. 253, Springer Nature, 2023, pp. 501–54, doi:10.1007/s11856-022-2448-6.","chicago":"Dymond, Michael, and Vojtech Kaluza. “Highly Irregular Separated Nets.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-022-2448-6."},"day":"01","month":"03","file_date_updated":"2021-07-14T07:41:50Z","ddc":["515","516"],"has_accepted_license":"1","volume":253,"article_processing_charge":"No","file":[{"file_id":"9653","date_created":"2021-07-14T07:41:50Z","access_level":"open_access","checksum":"6fa0a3207dd1d6467c309fd1bcc867d1","content_type":"application/pdf","date_updated":"2021-07-14T07:41:50Z","file_name":"separated_nets.pdf","file_size":900422,"relation":"main_file","creator":"vkaluza"}],"arxiv":1,"year":"2023","keyword":["Lipschitz","bilipschitz","bounded displacement","modulus of continuity","separated net","non-realisable density","Burago--Kleiner construction"],"oa":1,"page":"501-554","article_type":"original","publication":"Israel Journal of Mathematics","date_updated":"2023-08-14T11:26:34Z","date_published":"2023-03-01T00:00:00Z","external_id":{"isi":["000904950300003"],"arxiv":["1903.05923"]},"date_created":"2021-07-14T07:01:28Z","scopus_import":"1","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Springer Nature","intvolume":" 253"},{"oa":1,"year":"2023","date_updated":"2023-10-04T09:19:12Z","publication":"Potential Analysis","article_type":"original","page":"573-615","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}],"scopus_import":"1","date_created":"2021-10-17T22:01:17Z","date_published":"2023-03-01T00:00:00Z","external_id":{"arxiv":["2003.01366"],"isi":["000704213400001"]},"intvolume":" 58","publisher":"Springer Nature","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"_id":"10145","author":[{"orcid":"0000-0002-9881-6870","first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","full_name":"Dello Schiavo, Lorenzo"}],"title":"Ergodic decomposition of Dirichlet forms via direct integrals and applications","doi":"10.1007/s11118-021-09951-y","abstract":[{"lang":"eng","text":"We study direct integrals of quadratic and Dirichlet forms. We show that each quasi-regular Dirichlet space over a probability space admits a unique representation as a direct integral of irreducible Dirichlet spaces, quasi-regular for the same underlying topology. The same holds for each quasi-regular strongly local Dirichlet space over a metrizable Luzin σ-finite Radon measure space, and admitting carré du champ operator. In this case, the representation is only projectively unique."}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"publication_identifier":{"eissn":["1572-929X"],"issn":["0926-2601"]},"ec_funded":1,"status":"public","acknowledgement":"The author is grateful to Professors Sergio Albeverio and Andreas Eberle, and to Dr. Kohei Suzuki, for fruitful conversations on the subject of the present work, and for respectively pointing out the references [1, 13], and [3, 20]. Finally, he is especially grateful to an anonymous Reviewer for their very careful reading and their suggestions which improved the readability of the paper.","publication_status":"published","month":"03","ddc":["510"],"file_date_updated":"2023-10-04T09:18:59Z","day":"01","citation":{"ista":"Dello Schiavo L. 2023. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 58, 573–615.","ama":"Dello Schiavo L. Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. 2023;58:573-615. doi:10.1007/s11118-021-09951-y","short":"L. Dello Schiavo, Potential Analysis 58 (2023) 573–615.","apa":"Dello Schiavo, L. (2023). Ergodic decomposition of Dirichlet forms via direct integrals and applications. Potential Analysis. Springer Nature. https://doi.org/10.1007/s11118-021-09951-y","ieee":"L. Dello Schiavo, “Ergodic decomposition of Dirichlet forms via direct integrals and applications,” Potential Analysis, vol. 58. Springer Nature, pp. 573–615, 2023.","mla":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis, vol. 58, Springer Nature, 2023, pp. 573–615, doi:10.1007/s11118-021-09951-y.","chicago":"Dello Schiavo, Lorenzo. “Ergodic Decomposition of Dirichlet Forms via Direct Integrals and Applications.” Potential Analysis. Springer Nature, 2023. https://doi.org/10.1007/s11118-021-09951-y."},"oa_version":"Published Version","arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/pdf","checksum":"625526482be300ca7281c91c30d41725","access_level":"open_access","date_updated":"2023-10-04T09:18:59Z","success":1,"file_size":806391,"relation":"main_file","creator":"dernst","file_name":"2023_PotentialAnalysis_DelloSchiavo.pdf","date_created":"2023-10-04T09:18:59Z","file_id":"14387"}],"volume":58,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1"},{"isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":" 11","publisher":"Springer Nature","date_published":"2023-09-01T00:00:00Z","external_id":{"arxiv":["2102.07452"],"isi":["000799715600001"]},"scopus_import":"1","date_created":"2021-10-23T10:50:22Z","department":[{"_id":"JuFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","page":"1254–1378","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","date_updated":"2023-08-14T11:51:47Z","year":"2023","oa":1,"has_accepted_license":"1","volume":11,"article_processing_charge":"Yes (via OA deal)","file":[{"date_created":"2023-08-14T11:51:04Z","file_id":"14052","date_updated":"2023-08-14T11:51:04Z","success":1,"content_type":"application/pdf","checksum":"f83dcaecdbd3ace862c4ed97a20e8501","access_level":"open_access","creator":"dernst","file_size":1635193,"relation":"main_file","file_name":"2023_StochPartialDiffEquations_Clozeau.pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"oa_version":"Published Version","day":"01","citation":{"ieee":"N. Clozeau, “Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields,” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11. Springer Nature, pp. 1254–1378, 2023.","apa":"Clozeau, N. (2023). Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00254-w","short":"N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378.","ama":"Clozeau N. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 2023;11:1254–1378. doi:10.1007/s40072-022-00254-w","ista":"Clozeau N. 2023. Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields. Stochastics and Partial Differential Equations: Analysis and Computations. 11, 1254–1378.","chicago":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-022-00254-w.","mla":"Clozeau, Nicolas. “Optimal Decay of the Parabolic Semigroup in Stochastic Homogenization for Correlated Coefficient Fields.” Stochastics and Partial Differential Equations: Analysis and Computations, vol. 11, Springer Nature, 2023, pp. 1254–1378, doi:10.1007/s40072-022-00254-w."},"file_date_updated":"2023-08-14T11:51:04Z","ddc":["510"],"month":"09","acknowledgement":"I would like to thank my advisor Antoine Gloria for suggesting this problem to me, as well for many interesting discussions and suggestions.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","publication_status":"published","status":"public","publication_identifier":{"issn":["2194-0401"]},"abstract":[{"text":"We study the large scale behavior of elliptic systems with stationary random coefficient that have only slowly decaying correlations. To this aim we analyze the so-called corrector equation, a degenerate elliptic equation posed in the probability space. In this contribution, we use a parabolic approach and optimally quantify the time decay of the semigroup. For the theoretical point of view, we prove an optimal decay estimate of the gradient and flux of the corrector when spatially averaged over a scale R larger than 1. For the numerical point of view, our results provide convenient tools for the analysis of various numerical methods.","lang":"eng"}],"doi":"10.1007/s40072-022-00254-w","author":[{"id":"fea1b376-906f-11eb-847d-b2c0cf46455b","first_name":"Nicolas","full_name":"Clozeau, Nicolas","last_name":"Clozeau"}],"title":"Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields","_id":"10173"},{"year":"2023","oa":1,"page":"946-1034","article_type":"original","date_updated":"2023-10-04T09:22:55Z","publication":"Communications on Pure and Applied Mathematics","date_created":"2021-12-05T23:01:41Z","scopus_import":"1","external_id":{"arxiv":["1912.04100"],"isi":["000724652500001"]},"date_published":"2023-05-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"publisher":"Wiley","intvolume":" 76","doi":"10.1002/cpa.22028","abstract":[{"lang":"eng","text":"We consider large non-Hermitian random matrices X with complex, independent, identically distributed centred entries and show that the linear statistics of their eigenvalues are asymptotically Gaussian for test functions having 2+ϵ derivatives. Previously this result was known only for a few special cases; either the test functions were required to be analytic [72], or the distribution of the matrix elements needed to be Gaussian [73], or at least match the Gaussian up to the first four moments [82, 56]. We find the exact dependence of the limiting variance on the fourth cumulant that was not known before. The proof relies on two novel ingredients: (i) a local law for a product of two resolvents of the Hermitisation of X with different spectral parameters and (ii) a coupling of several weakly dependent Dyson Brownian motions. These methods are also the key inputs for our analogous results on the linear eigenvalue statistics of real matrices X that are presented in the companion paper [32]. "}],"issue":"5","_id":"10405","title":"Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices","author":[{"orcid":"0000-0002-4901-7992","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","full_name":"Schröder, Dominik J","last_name":"Schröder","orcid":"0000-0002-2904-1856"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"L.E. would like to thank Nathanaël Berestycki and D.S.would like to thank Nina Holden for valuable discussions on the Gaussian freefield.G.C. and L.E. are partially supported by ERC Advanced Grant No. 338804.G.C. received funding from the European Union’s Horizon 2020 research and in-novation programme under the Marie Skłodowska-Curie Grant Agreement No.665385. D.S. is supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"publication_identifier":{"issn":["0010-3640"],"eissn":["1097-0312"]},"oa_version":"Published Version","ddc":["510"],"month":"05","file_date_updated":"2023-10-04T09:21:48Z","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics. Wiley, 2023. https://doi.org/10.1002/cpa.22028.","mla":"Cipolloni, Giorgio, et al. “Central Limit Theorem for Linear Eigenvalue Statistics of Non-Hermitian Random Matrices.” Communications on Pure and Applied Mathematics, vol. 76, no. 5, Wiley, 2023, pp. 946–1034, doi:10.1002/cpa.22028.","ama":"Cipolloni G, Erdös L, Schröder DJ. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 2023;76(5):946-1034. doi:10.1002/cpa.22028","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. 76(5), 946–1034.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Communications on Pure and Applied Mathematics 76 (2023) 946–1034.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.22028","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Central limit theorem for linear eigenvalue statistics of non-Hermitian random matrices,” Communications on Pure and Applied Mathematics, vol. 76, no. 5. Wiley, pp. 946–1034, 2023."},"day":"01","article_processing_charge":"Yes (via OA deal)","volume":76,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"arxiv":1,"file":[{"file_id":"14388","date_created":"2023-10-04T09:21:48Z","file_name":"2023_CommPureMathematics_Cipolloni.pdf","creator":"dernst","file_size":803440,"relation":"main_file","success":1,"date_updated":"2023-10-04T09:21:48Z","access_level":"open_access","checksum":"8346bc2642afb4ccb7f38979f41df5d9","content_type":"application/pdf"}]},{"year":"2023","oa":1,"article_number":"66","article_type":"original","date_updated":"2023-08-01T14:40:33Z","publication":"Journal of Nonlinear Science","date_created":"2021-12-16T12:15:35Z","scopus_import":"1","external_id":{"isi":["001002343400002"],"arxiv":["2109.12019"]},"date_published":"2023-06-07T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JuFi"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"publisher":"Springer Nature","intvolume":" 33","doi":"10.1007/s00332-023-09926-w","abstract":[{"text":"The global existence of renormalised solutions and convergence to equilibrium for reaction-diffusion systems with non-linear diffusion are investigated. The system is assumed to have quasi-positive non-linearities and to satisfy an entropy inequality. The difficulties in establishing global renormalised solutions caused by possibly degenerate diffusion are overcome by introducing a new class of weighted truncation functions. By means of the obtained global renormalised solutions, we study the large-time behaviour of complex balanced systems arising from chemical reaction network theory with non-linear diffusion. When the reaction network does not admit boundary equilibria, the complex balanced equilibrium is shown, by using the entropy method, to exponentially attract all renormalised solutions in the same compatibility class. This convergence extends even to a range of non-linear diffusion, where global existence is an open problem, yet we are able to show that solutions to approximate systems converge exponentially to equilibrium uniformly in the regularisation parameter.","lang":"eng"}],"_id":"10550","title":"Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion","author":[{"first_name":"Klemens","last_name":"Fellner","full_name":"Fellner, Klemens"},{"last_name":"Fischer","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"},{"first_name":"Michael","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","last_name":"Kniely","full_name":"Kniely, Michael","orcid":"0000-0001-5645-4333"},{"full_name":"Tang, Bao Quoc","last_name":"Tang","first_name":"Bao Quoc"}],"status":"public","acknowledgement":"We thank the referees for their valuable comments and suggestions. A major part of this work was carried out when B. Q. Tang visited the Institute of Science and Technology Austria (ISTA). The hospitality of ISTA is greatly acknowledged. This work was partially supported by NAWI Graz.\r\nOpen access funding provided by University of Graz.","publication_status":"published","publication_identifier":{"issn":["0938-8974"],"eissn":["1432-1467"]},"oa_version":"Published Version","ddc":["510"],"month":"06","file_date_updated":"2023-06-19T07:33:53Z","citation":{"mla":"Fellner, Klemens, et al. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science, vol. 33, 66, Springer Nature, 2023, doi:10.1007/s00332-023-09926-w.","chicago":"Fellner, Klemens, Julian L Fischer, Michael Kniely, and Bao Quoc Tang. “Global Renormalised Solutions and Equilibration of Reaction-Diffusion Systems with Non-Linear Diffusion.” Journal of Nonlinear Science. Springer Nature, 2023. https://doi.org/10.1007/s00332-023-09926-w.","ieee":"K. Fellner, J. L. Fischer, M. Kniely, and B. Q. Tang, “Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion,” Journal of Nonlinear Science, vol. 33. Springer Nature, 2023.","apa":"Fellner, K., Fischer, J. L., Kniely, M., & Tang, B. Q. (2023). Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. Springer Nature. https://doi.org/10.1007/s00332-023-09926-w","ama":"Fellner K, Fischer JL, Kniely M, Tang BQ. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 2023;33. doi:10.1007/s00332-023-09926-w","ista":"Fellner K, Fischer JL, Kniely M, Tang BQ. 2023. Global renormalised solutions and equilibration of reaction-diffusion systems with non-linear diffusion. Journal of Nonlinear Science. 33, 66.","short":"K. Fellner, J.L. Fischer, M. Kniely, B.Q. Tang, Journal of Nonlinear Science 33 (2023)."},"day":"07","volume":33,"article_processing_charge":"No","has_accepted_license":"1","file":[{"content_type":"application/pdf","checksum":"f3f0f0886098e31c81116cff8183750b","access_level":"open_access","date_updated":"2023-06-19T07:33:53Z","success":1,"relation":"main_file","creator":"dernst","file_size":742315,"file_name":"2023_JourNonlinearScience_Fellner.pdf","date_created":"2023-06-19T07:33:53Z","file_id":"13149"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"file_name":"2023_ArchiveRationalMech_Cornalba.pdf","file_size":1851185,"relation":"main_file","creator":"dernst","success":1,"date_updated":"2024-01-30T12:09:34Z","access_level":"open_access","content_type":"application/pdf","checksum":"4529eeff170b6745a461d397ee611b5a","file_id":"14904","date_created":"2024-01-30T12:09:34Z"}],"article_processing_charge":"Yes (via OA deal)","volume":247,"has_accepted_license":"1","ddc":["510"],"file_date_updated":"2024-01-30T12:09:34Z","month":"08","day":"04","citation":{"chicago":"Cornalba, Federico, and Julian L Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01903-7.","mla":"Cornalba, Federico, and Julian L. Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive for Rational Mechanics and Analysis, vol. 247, no. 5, 76, Springer Nature, 2023, doi:10.1007/s00205-023-01903-7.","ieee":"F. Cornalba and J. L. Fischer, “The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles,” Archive for Rational Mechanics and Analysis, vol. 247, no. 5. Springer Nature, 2023.","apa":"Cornalba, F., & Fischer, J. L. (2023). The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01903-7","short":"F. Cornalba, J.L. Fischer, Archive for Rational Mechanics and Analysis 247 (2023).","ista":"Cornalba F, Fischer JL. 2023. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 247(5), 76.","ama":"Cornalba F, Fischer JL. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 2023;247(5). doi:10.1007/s00205-023-01903-7"},"oa_version":"Published Version","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"}],"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"We thank the anonymous referee for his/her careful reading of the manuscript and valuable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Austrian Science Fund (FWF).","_id":"10551","author":[{"first_name":"Federico","id":"2CEB641C-A400-11E9-A717-D712E6697425","last_name":"Cornalba","full_name":"Cornalba, Federico","orcid":"0000-0002-6269-5149"},{"orcid":"0000-0002-0479-558X","last_name":"Fischer","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"title":"The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles","doi":"10.1007/s00205-023-01903-7","issue":"5","abstract":[{"text":"The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of fluctuating hydrodynamics; it has been proposed in the physics literature to describe the fluctuations of the density of N independent diffusing particles in the regime of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation presents a substantial challenge for both its analysis and its rigorous mathematical justification. Besides being non-renormalisable by the theory of regularity structures by Hairer et al., it has recently been shown to not even admit nontrivial martingale solutions. In the present work, we give a rigorous and fully quantitative justification of the Dean–Kawasaki equation by considering the natural regularisation provided by standard numerical discretisations: We show that structure-preserving discretisations of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting diffusing particles to arbitrary order in N−1 (in suitable weak metrics). In other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate and efficient numerical simulations of the density fluctuations of independent diffusing particles.","lang":"eng"}],"intvolume":" 247","publisher":"Springer Nature","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JuFi"}],"scopus_import":"1","date_created":"2021-12-16T12:16:03Z","date_published":"2023-08-04T00:00:00Z","external_id":{"arxiv":["2109.06500"],"isi":["001043086800001"]},"date_updated":"2024-01-30T12:10:10Z","publication":"Archive for Rational Mechanics and Analysis","article_type":"original","article_number":"76","oa":1,"year":"2023"},{"has_accepted_license":"1","volume":69,"article_processing_charge":"Yes (in subscription journal)","arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"12006","date_created":"2022-08-29T11:23:15Z","file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","relation":"main_file","file_size":1002218,"creator":"alisjak","access_level":"open_access","content_type":"application/pdf","checksum":"def7ae3b28d9fd6aec16450e40090302","success":1,"date_updated":"2022-08-29T11:23:15Z"}],"oa_version":"Published Version","day":"01","citation":{"chicago":"Arroyo Guevara, Alan M, Fabian Klute, Irene Parada, Birgit Vogtenhuber, Raimund Seidel, and Tilo Wiedera. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-022-00394-9.","mla":"Arroyo Guevara, Alan M., et al. “Inserting One Edge into a Simple Drawing Is Hard.” Discrete and Computational Geometry, vol. 69, Springer Nature, 2023, pp. 745–770, doi:10.1007/s00454-022-00394-9.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","ama":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 2023;69:745–770. doi:10.1007/s00454-022-00394-9","ista":"Arroyo Guevara AM, Klute F, Parada I, Vogtenhuber B, Seidel R, Wiedera T. 2023. Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. 69, 745–770.","apa":"Arroyo Guevara, A. M., Klute, F., Parada, I., Vogtenhuber, B., Seidel, R., & Wiedera, T. (2023). Inserting one edge into a simple drawing is hard. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-022-00394-9","ieee":"A. M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, and T. Wiedera, “Inserting one edge into a simple drawing is hard,” Discrete and Computational Geometry, vol. 69. Springer Nature, pp. 745–770, 2023."},"file_date_updated":"2022-08-29T11:23:15Z","month":"04","ddc":["510"],"acknowledgement":"This work was started during the 6th Austrian–Japanese–Mexican–Spanish Workshop on Discrete Geometry in June 2019 in Austria. We thank all the participants for the good atmosphere as well as discussions on the topic. Also, we thank Jan Kynčl for sending us remarks on a preliminary version of this work and an anonymous referee for further helpful comments.Alan Arroyo was funded by the Marie Skłodowska-Curie grant agreement No 754411. Fabian Klute was partially supported by the Netherlands Organisation for Scientific Research (NWO) under project no. 612.001.651 and by the Austrian Science Fund (FWF): J-4510. Irene Parada and Birgit Vogtenhuber were partially supported by the Austrian Science Fund (FWF): W1230 and within the collaborative DACH project Arrangements and Drawings as FWF project I 3340-N35. Irene Parada was also partially supported by the Independent Research Fund Denmark grant 2020-2023 (9131-00044B) Dynamic Network Analysis and by the Margarita Salas Fellowship funded by the Ministry of Universities of Spain and the European Union (NextGenerationEU). Tilo Wiedera was supported by the German Research Foundation (DFG) grant CH 897/2-2.","publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"A simple drawing D(G) of a graph G is one where each pair of edges share at most one point: either a common endpoint or a proper crossing. An edge e in the complement of G can be inserted into D(G) if there exists a simple drawing of G+e extending D(G). As a result of Levi’s Enlargement Lemma, if a drawing is rectilinear (pseudolinear), that is, the edges can be extended into an arrangement of lines (pseudolines), then any edge in the complement of G can be inserted. In contrast, we show that it is NP-complete to decide whether one edge can be inserted into a simple drawing. This remains true even if we assume that the drawing is pseudocircular, that is, the edges can be extended to an arrangement of pseudocircles. On the positive side, we show that, given an arrangement of pseudocircles A and a pseudosegment σ, it can be decided in polynomial time whether there exists a pseudocircle Φσ extending σ for which A∪{Φσ} is again an arrangement of pseudocircles.","lang":"eng"}],"doi":"10.1007/s00454-022-00394-9","author":[{"orcid":"0000-0003-2401-8670","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","first_name":"Alan M","full_name":"Arroyo Guevara, Alan M","last_name":"Arroyo Guevara"},{"first_name":"Fabian","last_name":"Klute","full_name":"Klute, Fabian"},{"first_name":"Irene","full_name":"Parada, Irene","last_name":"Parada"},{"first_name":"Birgit","full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber"},{"first_name":"Raimund","last_name":"Seidel","full_name":"Seidel, Raimund"},{"full_name":"Wiedera, Tilo","last_name":"Wiedera","first_name":"Tilo"}],"title":"Inserting one edge into a simple drawing is hard","_id":"11999","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","intvolume":" 69","publisher":"Springer Nature","date_published":"2023-04-01T00:00:00Z","external_id":{"isi":["000840292800001"],"arxiv":["1909.07347"]},"scopus_import":"1","date_created":"2022-08-28T22:02:01Z","department":[{"_id":"UlWa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","page":"745–770","publication":"Discrete and Computational Geometry","date_updated":"2023-08-14T12:51:25Z","year":"2023","oa":1},{"publication":"Algorithmica","date_updated":"2023-06-27T12:53:43Z","page":"277-295","article_type":"original","oa":1,"year":"2023","publisher":"Springer Nature","intvolume":" 85","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"HeEd"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","date_published":"2023-01-01T00:00:00Z","external_id":{"isi":["000846967100001"]},"date_created":"2022-09-11T22:01:57Z","scopus_import":"1","publication_identifier":{"eissn":["1432-0541"],"issn":["0178-4617"]},"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"publication_status":"published","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","status":"public","ec_funded":1,"title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","last_name":"Osang","full_name":"Osang, Georg F"}],"_id":"12086","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}],"doi":"10.1007/s00453-022-01027-6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"checksum":"71685ca5121f4c837f40c3f8eb50c915","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-20T10:02:48Z","success":1,"creator":"dernst","file_size":911017,"relation":"main_file","file_name":"2023_Algorithmica_Edelsbrunner.pdf","date_created":"2023-01-20T10:02:48Z","file_id":"12322"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":85,"citation":{"chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295.","ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295."},"day":"01","file_date_updated":"2023-01-20T10:02:48Z","month":"01","ddc":["510"],"oa_version":"Published Version"},{"ec_funded":1,"status":"public","acknowledgement":"H.Z. is supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. M.W. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 716117) and from the Austrian Science Fund (FWF) through grant number F65. Both authors would like to thank Jan Maas for fruitful discussions and helpful comments. Open access funding provided by Austrian Science Fund (FWF).","publication_status":"published","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Curvature-dimension in noncommutative analysis","grant_number":"M03337","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"publication_identifier":{"issn":["1424-0637"]},"doi":"10.1007/s00023-022-01220-x","abstract":[{"text":"Following up on the recent work on lower Ricci curvature bounds for quantum systems, we introduce two noncommutative versions of curvature-dimension bounds for symmetric quantum Markov semigroups over matrix algebras. Under suitable such curvature-dimension conditions, we prove a family of dimension-dependent functional inequalities, a version of the Bonnet–Myers theorem and concavity of entropy power in the noncommutative setting. We also provide examples satisfying certain curvature-dimension conditions, including Schur multipliers over matrix algebras, Herz–Schur multipliers over group algebras and generalized depolarizing semigroups.","lang":"eng"}],"_id":"12087","author":[{"orcid":"0000-0002-0519-4241","last_name":"Wirth","full_name":"Wirth, Melchior","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"},{"last_name":"Zhang","full_name":"Zhang, Haonan","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","article_processing_charge":"Yes (via OA deal)","volume":24,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"file":[{"file_size":554871,"creator":"dernst","relation":"main_file","file_name":"2023_AnnalesHenriPoincare_Wirth.pdf","date_updated":"2023-08-14T11:38:28Z","success":1,"content_type":"application/pdf","checksum":"8c7b185eba5ccd92ef55c120f654222c","access_level":"open_access","date_created":"2023-08-14T11:38:28Z","file_id":"14051"}],"oa_version":"Published Version","month":"03","ddc":["510"],"file_date_updated":"2023-08-14T11:38:28Z","day":"01","citation":{"ista":"Wirth M, Zhang H. 2023. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 24, 717–750.","ama":"Wirth M, Zhang H. Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. 2023;24:717-750. doi:10.1007/s00023-022-01220-x","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.","apa":"Wirth, M., & Zhang, H. (2023). Curvature-dimension conditions for symmetric quantum Markov semigroups. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01220-x","ieee":"M. Wirth and H. Zhang, “Curvature-dimension conditions for symmetric quantum Markov semigroups,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 717–750, 2023.","mla":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 717–50, doi:10.1007/s00023-022-01220-x.","chicago":"Wirth, Melchior, and Haonan Zhang. “Curvature-Dimension Conditions for Symmetric Quantum Markov Semigroups.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01220-x."},"article_type":"original","page":"717-750","date_updated":"2023-08-14T11:39:28Z","publication":"Annales Henri Poincare","year":"2023","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"intvolume":" 24","publisher":"Springer Nature","scopus_import":"1","date_created":"2022-09-11T22:01:57Z","external_id":{"arxiv":["2105.08303"],"isi":["000837499800002"]},"date_published":"2023-03-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JaMa"}]}]