[{"publisher":"Public Library of Science","department":[{"_id":"CaHe"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","volume":21,"date_updated":"2023-08-02T06:33:14Z","date_created":"2023-07-16T22:01:09Z","author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"full_name":"Hofmann, Laura","last_name":"Hofmann","first_name":"Laura","id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031"},{"full_name":"Steccari, Irene","last_name":"Steccari","first_name":"Irene","id":"2705C766-9FE2-11EA-B224-C6773DDC885E"},{"full_name":"Kardos, Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland","last_name":"Kardos"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"ec_funded":1,"file_date_updated":"2023-07-18T07:59:58Z","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37289834"],"isi":["001003199100005"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.3002146","publication_identifier":{"eissn":["1545-7885"]},"month":"06","intvolume":" 21","title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13229","file":[{"access_level":"open_access","file_name":"2023_PloSBiology_Shamipour.pdf","creator":"dernst","content_type":"application/pdf","file_size":4431723,"file_id":"13246","relation":"main_file","success":1,"checksum":"8e88cb0e5a6433a2f1939a9030bed384","date_created":"2023-07-18T07:59:58Z","date_updated":"2023-07-18T07:59:58Z"}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation."}],"page":"e3002146","article_type":"original","citation":{"chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pbio.3002146.","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” PLoS Biology, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:10.1371/journal.pbio.3002146.","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146.","ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.","ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” PLoS Biology, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., & Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3002146","ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 2023;21(6):e3002146. doi:10.1371/journal.pbio.3002146"},"publication":"PLoS Biology","date_published":"2023-06-08T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"08"},{"ec_funded":1,"file_date_updated":"2023-07-07T12:49:51Z","article_number":"065601","volume":7,"date_updated":"2023-08-02T06:34:47Z","date_created":"2023-07-07T12:48:01Z","author":[{"full_name":"Grosjean, Galien M","orcid":"0000-0001-5154-417X","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","last_name":"Grosjean","first_name":"Galien M"},{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2299-3176","first_name":"Scott R","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R"}],"department":[{"_id":"ScWa"}],"publisher":"American Physical Society","publication_status":"published","year":"2023","acknowledgement":"This project has received funding from the European Research Council Grant Agreement No. 949120 and from\r\nthe European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant\r\nAgreement No. 754411. ","publication_identifier":{"issn":["2475-9953"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1103/physrevmaterials.7.065601","project":[{"call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","grant_number":"949120"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["2304.12861"],"isi":["001019565900002"]},"oa":1,"issue":"6","abstract":[{"lang":"eng","text":"Nominally identical materials exchange net electric charge during contact through a mechanism that is still debated. ‘Mosaic models’, in which surfaces are presumed to consist of a random patchwork of microscopic donor/acceptor sites, offer an appealing explanation for this phenomenon. However, recent experiments have shown that global differences persist even between same-material samples, which the standard mosaic framework does not account for. Here, we expand the mosaic framework by incorporating global differences in the densities of donor/acceptor sites. We develop\r\nan analytical model, backed by numerical simulations, that smoothly connects the global and deterministic charge transfer of different materials to the local and stochastic mosaic picture normally associated with identical materials. Going further, we extend our model to explain the effect of contact asymmetries during sliding, providing a plausible explanation for reversal of charging sign that has been observed experimentally."}],"type":"journal_article","oa_version":"Submitted Version","file":[{"date_updated":"2023-07-07T12:49:51Z","date_created":"2023-07-07T12:49:51Z","checksum":"75584730d9cdd50eeccb4c52c509776d","success":1,"relation":"main_file","file_id":"13198","content_type":"application/pdf","file_size":1127040,"creator":"ggrosjea","file_name":"Mosaic_asymmetries.pdf","access_level":"open_access"}],"intvolume":" 7","ddc":["537"],"title":"Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts","status":"public","_id":"13197","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"13","keyword":["Physics and Astronomy (miscellaneous)","General Materials Science"],"date_published":"2023-06-13T00:00:00Z","article_type":"original","citation":{"ieee":"G. M. Grosjean and S. R. Waitukaitis, “Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts,” Physical Review Materials, vol. 7, no. 6. American Physical Society, 2023.","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. American Physical Society. https://doi.org/10.1103/physrevmaterials.7.065601","ista":"Grosjean GM, Waitukaitis SR. 2023. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 7(6), 065601.","ama":"Grosjean GM, Waitukaitis SR. Asymmetries in triboelectric charging: Generalizing mosaic models to different-material samples and sliding contacts. Physical Review Materials. 2023;7(6). doi:10.1103/physrevmaterials.7.065601","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials. American Physical Society, 2023. https://doi.org/10.1103/physrevmaterials.7.065601.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Materials 7 (2023).","mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Asymmetries in Triboelectric Charging: Generalizing Mosaic Models to Different-Material Samples and Sliding Contacts.” Physical Review Materials, vol. 7, no. 6, 065601, American Physical Society, 2023, doi:10.1103/physrevmaterials.7.065601."},"publication":"Physical Review Materials"},{"issue":"6","abstract":[{"text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-07-18T08:07:59Z","date_created":"2023-07-18T08:07:59Z","checksum":"800761fa2c647fabd6ad034589bc526e","success":1,"relation":"main_file","file_id":"13247","content_type":"application/pdf","file_size":2281868,"creator":"dernst","file_name":"2023_PloSCompBio_Charlton.pdf","access_level":"open_access"}],"intvolume":" 19","title":"Environmental dynamics shape perceptual decision bias","ddc":["570"],"status":"public","_id":"13230","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"08","scopus_import":"1","date_published":"2023-06-08T00:00:00Z","article_type":"original","citation":{"short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023).","mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:10.1371/journal.pcbi.1011104.","chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” PLoS Computational Biology. Public Library of Science, 2023. https://doi.org/10.1371/journal.pcbi.1011104.","ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 2023;19(6). doi:10.1371/journal.pcbi.1011104","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” PLoS Computational Biology, vol. 19, no. 6. Public Library of Science, 2023.","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., & Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011104","ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104."},"publication":"PLoS Computational Biology","file_date_updated":"2023-07-18T08:07:59Z","article_number":"e1011104","volume":19,"date_created":"2023-07-16T22:01:09Z","date_updated":"2023-08-02T06:33:50Z","author":[{"last_name":"Charlton","first_name":"Julie A.","full_name":"Charlton, Julie A."},{"last_name":"Mlynarski","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F"},{"last_name":"Bai","first_name":"Yoon H.","full_name":"Bai, Yoon H."},{"full_name":"Hermundstad, Ann M.","first_name":"Ann M.","last_name":"Hermundstad"},{"full_name":"Goris, Robbe L.T.","first_name":"Robbe L.T.","last_name":"Goris"}],"department":[{"_id":"MaJö"}],"publisher":"Public Library of Science","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","publication_identifier":{"eissn":["1553-7358"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1011104","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["001003410200003"],"pmid":["37289753"]}},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-06-01T00:00:00Z","citation":{"mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines, vol. 11, no. 6, 1014, MDPI, 2023, doi:10.3390/vaccines11061014.","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).","chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” Vaccines. MDPI, 2023. https://doi.org/10.3390/vaccines11061014.","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 2023;11(6). doi:10.3390/vaccines11061014","ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","ieee":"D. Dormeshkin et al., “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” Vaccines, vol. 11, no. 6. MDPI, 2023.","apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. MDPI. https://doi.org/10.3390/vaccines11061014"},"publication":"Vaccines","article_type":"original","issue":"6","abstract":[{"lang":"eng","text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study."}],"type":"journal_article","file":[{"date_updated":"2023-07-18T07:25:43Z","date_created":"2023-07-18T07:25:43Z","checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","success":1,"relation":"main_file","file_id":"13244","file_size":2339746,"content_type":"application/pdf","creator":"dernst","file_name":"2023_Vaccines_Dormeshkin.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13232","intvolume":" 11","status":"public","title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","ddc":["570"],"publication_identifier":{"eissn":["2076-393X"]},"month":"06","doi":"10.3390/vaccines11061014","language":[{"iso":"eng"}],"external_id":{"isi":["001017740000001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2023-07-18T07:25:43Z","article_number":"1014","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"full_name":"Katsin, Mikalai","first_name":"Mikalai","last_name":"Katsin"},{"first_name":"Maria","last_name":"Stegantseva","full_name":"Stegantseva, Maria"},{"full_name":"Golenchenko, Sergey","first_name":"Sergey","last_name":"Golenchenko"},{"last_name":"Shapira","first_name":"Michail","full_name":"Shapira, Michail"},{"full_name":"Dubovik, Simon","first_name":"Simon","last_name":"Dubovik"},{"full_name":"Lutskovich, Dzmitry","last_name":"Lutskovich","first_name":"Dzmitry"},{"full_name":"Kavaleuski, Anton","orcid":"0000-0003-2091-526X","id":"62304f89-eb97-11eb-a6c2-8903dd183976","last_name":"Kavaleuski","first_name":"Anton"},{"full_name":"Meleshko, Alexander","last_name":"Meleshko","first_name":"Alexander"}],"volume":11,"date_created":"2023-07-16T22:01:10Z","date_updated":"2023-08-02T06:31:19Z","year":"2023","acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","publisher":"MDPI","department":[{"_id":"LeSa"}],"publication_status":"published"},{"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.01545"}],"oa":1,"external_id":{"arxiv":["2301.01545"],"isi":["001020265000002"]},"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevE.107.065207","language":[{"iso":"eng"}],"article_number":"065207","acknowledgement":"We want to thank P. Sperling, B. Witte, M. French, G. Röpke, H. J. Lee and A. Cangi for many helpful discussions. M. S. and R. R. acknowledge support by the Deutsche Forschungsgemeinschaft (DFG) within the Research Unit FOR 2440. All simulations and analyses were performed at the North-German Supercomputing Alliance (HLRN) and the ITMZ of the University of Rostock. M. B. gratefully acknowledges support by the European Horizon 2020 programme within the Marie Sklodowska-Curie actions (xICE grant 894725) and the\r\nNOMIS foundation. The work of T. D. was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344.","year":"2023","publisher":"American Physical Society","department":[{"_id":"BiCh"}],"publication_status":"published","author":[{"full_name":"Schörner, Maximilian","last_name":"Schörner","first_name":"Maximilian"},{"id":"201939f4-803f-11ed-ab7e-d8da4bd1517f","orcid":"0000-0002-1838-2129","first_name":"Mandy","last_name":"Bethkenhagen","full_name":"Bethkenhagen, Mandy"},{"first_name":"Tilo","last_name":"Döppner","full_name":"Döppner, Tilo"},{"full_name":"Kraus, Dominik","first_name":"Dominik","last_name":"Kraus"},{"first_name":"Luke B.","last_name":"Fletcher","full_name":"Fletcher, Luke B."},{"last_name":"Glenzer","first_name":"Siegfried H.","full_name":"Glenzer, Siegfried H."},{"full_name":"Redmer, Ronald","first_name":"Ronald","last_name":"Redmer"}],"volume":107,"date_created":"2023-07-16T22:01:10Z","date_updated":"2023-08-02T06:30:46Z","scopus_import":"1","article_processing_charge":"No","day":"14","citation":{"chicago":"Schörner, Maximilian, Mandy Bethkenhagen, Tilo Döppner, Dominik Kraus, Luke B. Fletcher, Siegfried H. Glenzer, and Ronald Redmer. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.065207.","mla":"Schörner, Maximilian, et al. “X-Ray Thomson Scattering Spectra from Density Functional Theory Molecular Dynamics Simulations Based on a Modified Chihara Formula.” Physical Review E, vol. 107, no. 6, 065207, American Physical Society, 2023, doi:10.1103/PhysRevE.107.065207.","short":"M. Schörner, M. Bethkenhagen, T. Döppner, D. Kraus, L.B. Fletcher, S.H. Glenzer, R. Redmer, Physical Review E 107 (2023).","ista":"Schörner M, Bethkenhagen M, Döppner T, Kraus D, Fletcher LB, Glenzer SH, Redmer R. 2023. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 107(6), 065207.","apa":"Schörner, M., Bethkenhagen, M., Döppner, T., Kraus, D., Fletcher, L. B., Glenzer, S. H., & Redmer, R. (2023). X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.065207","ieee":"M. Schörner et al., “X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula,” Physical Review E, vol. 107, no. 6. American Physical Society, 2023.","ama":"Schörner M, Bethkenhagen M, Döppner T, et al. X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula. Physical Review E. 2023;107(6). doi:10.1103/PhysRevE.107.065207"},"publication":"Physical Review E","article_type":"original","date_published":"2023-06-14T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"We study ab initio approaches for calculating x-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula that expresses the inelastic contribution in terms of the dielectric function. We study the electronic dynamic structure factor computed from the Mermin dielectric function using an ab initio electron-ion collision frequency in comparison to computations using a linear-response time-dependent density functional theory (LR-TDDFT) framework for hydrogen and beryllium and investigate the dispersion of free-free and bound-free contributions to the scattering signal. A separate treatment of these contributions, where only the free-free part follows the Mermin dispersion, shows good agreement with LR-TDDFT results for ambient-density beryllium, but breaks down for highly compressed matter where the bound states become pressure ionized. LR-TDDFT is used to reanalyze x-ray Thomson scattering experiments on beryllium demonstrating strong deviations from the plasma conditions inferred with traditional analytic models at small scattering angles.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13231","intvolume":" 107","title":"X-ray Thomson scattering spectra from density functional theory molecular dynamics simulations based on a modified Chihara formula","status":"public","oa_version":"Preprint"},{"type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We study the impact of finite-range physics on the zero-range-model analysis of three-body recombination in ultracold atoms. We find that temperature dependence of the zero-range parameters can vary from one set of measurements to another as it may be driven by the distribution of error bars in the experiment, and not by the underlying three-body physics. To study finite-temperature effects in three-body recombination beyond the zero-range physics, we introduce and examine a finite-range model based upon a hyperspherical formalism. The systematic error discussed in this Letter may provide a significant contribution to the error bars of measured three-body parameters."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"13233","intvolume":" 107","status":"public","title":"Finite-range bias in fitting three-body loss to the zero-range model","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"20","citation":{"mla":"Agafonova, Sofya, et al. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A, vol. 107, no. 6, L061304, American Physical Society, 2023, doi:10.1103/PhysRevA.107.L061304.","short":"S. Agafonova, M. Lemeshko, A. Volosniev, Physical Review A 107 (2023).","chicago":"Agafonova, Sofya, Mikhail Lemeshko, and Artem Volosniev. “Finite-Range Bias in Fitting Three-Body Loss to the Zero-Range Model.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/PhysRevA.107.L061304.","ama":"Agafonova S, Lemeshko M, Volosniev A. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 2023;107(6). doi:10.1103/PhysRevA.107.L061304","ista":"Agafonova S, Lemeshko M, Volosniev A. 2023. Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. 107(6), L061304.","ieee":"S. Agafonova, M. Lemeshko, and A. Volosniev, “Finite-range bias in fitting three-body loss to the zero-range model,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","apa":"Agafonova, S., Lemeshko, M., & Volosniev, A. (2023). Finite-range bias in fitting three-body loss to the zero-range model. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.107.L061304"},"publication":"Physical Review A","article_type":"letter_note","date_published":"2023-06-20T00:00:00Z","article_number":"L061304","ec_funded":1,"year":"2023","acknowledgement":"We thank Jan Arlt, Hans-Werner Hammer, and Karsten Riisager for useful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","department":[{"_id":"MiLe"},{"_id":"OnHo"}],"publisher":"American Physical Society","publication_status":"published","author":[{"full_name":"Agafonova, Sofya","last_name":"Agafonova","first_name":"Sofya","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80"},{"first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem"}],"volume":107,"date_updated":"2023-08-02T06:31:52Z","date_created":"2023-07-16T22:01:10Z","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"month":"06","external_id":{"isi":["001019748000005"],"arxiv":["2302.01022"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2302.01022","open_access":"1"}],"project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevA.107.L061304","language":[{"iso":"eng"}]},{"day":"08","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2023-07-08T00:00:00Z","publication":"npj Climate and Atmospheric Science","citation":{"chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science. Springer Nature, 2023. https://doi.org/10.1038/s41612-023-00411-5.","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” Npj Climate and Atmospheric Science, vol. 6, 82, Springer Nature, 2023, doi:10.1038/s41612-023-00411-5.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023).","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","apa":"GOSWAMI, B. B., & An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. Npj Climate and Atmospheric Science. Springer Nature. https://doi.org/10.1038/s41612-023-00411-5","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” npj Climate and Atmospheric Science, vol. 6. Springer Nature, 2023.","ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 2023;6. doi:10.1038/s41612-023-00411-5"},"article_type":"original","abstract":[{"text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.","lang":"eng"}],"type":"journal_article","file":[{"date_updated":"2023-07-31T08:00:01Z","date_created":"2023-07-31T08:00:01Z","checksum":"e9967d436a83b8ffcc6f58782e1f7500","success":1,"relation":"main_file","file_id":"13326","content_type":"application/pdf","file_size":1750712,"creator":"dernst","file_name":"2023_npjclimate_Goswami.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"13256","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["550"],"title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","status":"public","intvolume":" 6","month":"07","publication_identifier":{"eissn":["2397-3722"]},"doi":"10.1038/s41612-023-00411-5","language":[{"iso":"eng"}],"external_id":{"isi":["001024920300002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2023-07-31T08:00:01Z","article_number":"82","author":[{"full_name":"Goswami, Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","last_name":"Goswami","first_name":"Bidyut B"},{"last_name":"An","first_name":"Soon Il","full_name":"An, Soon Il"}],"date_created":"2023-07-23T22:01:10Z","date_updated":"2023-08-02T06:38:07Z","volume":6,"acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","year":"2023","publication_status":"published","department":[{"_id":"CaMu"}],"publisher":"Springer Nature"},{"publication_identifier":{"eissn":["1759-6653"]},"month":"07","isi":1,"quality_controlled":"1","external_id":{"isi":["001023444700003"],"pmid":["37341535"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evad113","article_number":"evad113","file_date_updated":"2023-08-01T06:58:34Z","publisher":"Oxford Academic","department":[{"_id":"BeVi"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","volume":15,"date_updated":"2023-08-02T06:42:35Z","date_created":"2023-07-23T22:01:11Z","related_material":{"link":[{"relation":"software","url":"https://github.com/carolbarata/dpseudo-n-beyond"}]},"author":[{"full_name":"De Castro Barbosa Rodrigues Barata, Carolina","first_name":"Carolina","last_name":"De Castro Barbosa Rodrigues Barata","id":"20565186-803f-11ed-ab7e-96a4ff7694ef"},{"last_name":"Snook","first_name":"Rhonda R.","full_name":"Snook, Rhonda R."},{"full_name":"Ritchie, Michael G.","last_name":"Ritchie","first_name":"Michael G."},{"last_name":"Kosiol","first_name":"Carolin","full_name":"Kosiol, Carolin"}],"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"01","article_type":"original","citation":{"ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., & Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome Biology and Evolution. Oxford Academic. https://doi.org/10.1093/gbe/evad113","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” Genome biology and evolution, vol. 15, no. 7. Oxford Academic, 2023.","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 2023;15(7). doi:10.1093/gbe/evad113","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution. Oxford Academic, 2023. https://doi.org/10.1093/gbe/evad113.","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” Genome Biology and Evolution, vol. 15, no. 7, evad113, Oxford Academic, 2023, doi:10.1093/gbe/evad113.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023)."},"publication":"Genome biology and evolution","date_published":"2023-07-01T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines.","lang":"eng"}],"intvolume":" 15","status":"public","title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","ddc":["570"],"_id":"13260","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_size":2382587,"content_type":"application/pdf","file_name":"2023_GBE_Barata.pdf","access_level":"open_access","date_updated":"2023-08-01T06:58:34Z","date_created":"2023-08-01T06:58:34Z","success":1,"checksum":"70de3c4878de6efe00dc56de2df8812f","file_id":"13339","relation":"main_file"}],"oa_version":"Published Version"},{"article_processing_charge":"No","month":"07","day":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.03237"}],"citation":{"ista":"Huber D, Pinsonneault M, Beck P, Bedding TR, Joss Bland-Hawthorn JB-H, Breton SN, Bugnet LA, Chaplin WJ, Garcia RA, Grunblatt SK, Guzik JA, Hekker S, Kawaler SD, Mathis S, Mathur S, Metcalfe T, Mosser B, Ness MK, Piro AL, Serenelli A, Sharma S, Soderblom DR, Stassun KG, Stello D, Tayar J, Belle GT van, Zinn JC. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv, 2307.03237.","apa":"Huber, D., Pinsonneault, M., Beck, P., Bedding, T. R., Joss Bland-Hawthorn, J. B.-H., Breton, S. N., … Zinn, J. C. (n.d.). Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. https://doi.org/10.48550/arXiv.2307.03237","ieee":"D. Huber et al., “Asteroseismology with the Roman galactic bulge time-domain survey,” arXiv. .","ama":"Huber D, Pinsonneault M, Beck P, et al. Asteroseismology with the Roman galactic bulge time-domain survey. arXiv. doi:10.48550/arXiv.2307.03237","chicago":"Huber, Daniel, Marc Pinsonneault, Paul Beck, Timothy R. Bedding, Joss Bland-Hawthorn Joss Bland-Hawthorn, Sylvain N. Breton, Lisa Annabelle Bugnet, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.03237.","mla":"Huber, Daniel, et al. “Asteroseismology with the Roman Galactic Bulge Time-Domain Survey.” ArXiv, 2307.03237, doi:10.48550/arXiv.2307.03237.","short":"D. Huber, M. Pinsonneault, P. Beck, T.R. Bedding, J.B.-H. Joss Bland-Hawthorn, S.N. Breton, L.A. Bugnet, W.J. Chaplin, R.A. Garcia, S.K. Grunblatt, J.A. Guzik, S. Hekker, S.D. Kawaler, S. Mathis, S. Mathur, T. Metcalfe, B. Mosser, M.K. Ness, A.L. Piro, A. Serenelli, S. Sharma, D.R. Soderblom, K.G. Stassun, D. Stello, J. Tayar, G.T. van Belle, J.C. Zinn, ArXiv (n.d.)."},"external_id":{"arxiv":["2307.03237"]},"oa":1,"publication":"arXiv","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.2307.03237","date_published":"2023-07-06T00:00:00Z","type":"preprint","article_number":"2307.03237","abstract":[{"lang":"eng","text":"Asteroseismology has transformed stellar astrophysics. Red giant asteroseismology is a prime example, with oscillation periods and amplitudes that are readily detectable with time-domain space-based telescopes. These oscillations can be used to infer masses, ages and radii for large numbers of stars, providing unique constraints on stellar populations in our galaxy. The cadence, duration, and spatial resolution of the Roman galactic bulge time-domain survey (GBTDS) are well-suited for asteroseismology and will probe an important population not studied by prior missions. We identify photometric precision as a key requirement for realizing the potential of asteroseismology with Roman. A precision of 1 mmag per 15-min cadence or better for saturated stars will enable detections of the populous red clump star population in the Galactic bulge. If the survey efficiency is better than expected, we argue for repeat observations of the same fields to improve photometric precision, or covering additional fields to expand the stellar population reach if the photometric precision for saturated stars is better than 1 mmag. Asteroseismology is relatively insensitive to the timing of the observations during the mission, and the prime red clump targets can be observed in a single 70 day campaign in any given field. Complementary stellar characterization, particularly astrometry tied to the Gaia system, will also dramatically expand the diagnostic power of asteroseismology. We also highlight synergies to Roman GBTDS exoplanet science using transits and microlensing."}],"department":[{"_id":"LiBu"}],"title":"Asteroseismology with the Roman galactic bulge time-domain survey","status":"public","publication_status":"submitted","year":"2023","_id":"13447","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","date_created":"2023-08-02T07:30:43Z","date_updated":"2023-08-02T07:36:00Z","author":[{"full_name":"Huber, Daniel","last_name":"Huber","first_name":"Daniel"},{"last_name":"Pinsonneault","first_name":"Marc","full_name":"Pinsonneault, Marc"},{"full_name":"Beck, Paul","first_name":"Paul","last_name":"Beck"},{"full_name":"Bedding, Timothy R.","last_name":"Bedding","first_name":"Timothy R."},{"last_name":"Joss Bland-Hawthorn","first_name":"Joss Bland-Hawthorn","full_name":"Joss Bland-Hawthorn, Joss Bland-Hawthorn"},{"first_name":"Sylvain N.","last_name":"Breton","full_name":"Breton, Sylvain N."},{"full_name":"Bugnet, Lisa Annabelle","last_name":"Bugnet","first_name":"Lisa Annabelle","orcid":"0000-0003-0142-4000","id":"d9edb345-f866-11ec-9b37-d119b5234501"},{"first_name":"William J.","last_name":"Chaplin","full_name":"Chaplin, William J."},{"last_name":"Garcia","first_name":"Rafael A.","full_name":"Garcia, Rafael A."},{"full_name":"Grunblatt, Samuel K.","first_name":"Samuel K.","last_name":"Grunblatt"},{"last_name":"Guzik","first_name":"Joyce A.","full_name":"Guzik, Joyce A."},{"full_name":"Hekker, Saskia","last_name":"Hekker","first_name":"Saskia"},{"first_name":"Steven D.","last_name":"Kawaler","full_name":"Kawaler, Steven D."},{"first_name":"Stephane","last_name":"Mathis","full_name":"Mathis, Stephane"},{"first_name":"Savita","last_name":"Mathur","full_name":"Mathur, Savita"},{"full_name":"Metcalfe, Travis","first_name":"Travis","last_name":"Metcalfe"},{"full_name":"Mosser, Benoit","first_name":"Benoit","last_name":"Mosser"},{"full_name":"Ness, Melissa K.","first_name":"Melissa K.","last_name":"Ness"},{"last_name":"Piro","first_name":"Anthony L.","full_name":"Piro, Anthony L."},{"first_name":"Aldo","last_name":"Serenelli","full_name":"Serenelli, Aldo"},{"full_name":"Sharma, Sanjib","first_name":"Sanjib","last_name":"Sharma"},{"full_name":"Soderblom, David R.","last_name":"Soderblom","first_name":"David R."},{"last_name":"Stassun","first_name":"Keivan G.","full_name":"Stassun, Keivan G."},{"last_name":"Stello","first_name":"Dennis","full_name":"Stello, Dennis"},{"first_name":"Jamie","last_name":"Tayar","full_name":"Tayar, Jamie"},{"full_name":"Belle, Gerard T. van","first_name":"Gerard T. van","last_name":"Belle"},{"first_name":"Joel C.","last_name":"Zinn","full_name":"Zinn, Joel C."}]},{"file":[{"file_id":"13087","relation":"main_file","success":1,"checksum":"6b3354968403cb9d48cc5a83611fb571","date_created":"2023-05-24T16:11:16Z","date_updated":"2023-05-24T16:11:16Z","access_level":"open_access","file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","creator":"epeste","content_type":"application/pdf","file_size":2152072},{"date_created":"2023-05-24T16:12:59Z","date_updated":"2023-05-24T16:12:59Z","checksum":"8d0df94bbcf4db72c991f22503b3fd60","relation":"source_file","file_id":"13088","content_type":"application/zip","file_size":1658293,"creator":"epeste","file_name":"PhD_Thesis_APeste.zip","access_level":"closed"}],"oa_version":"Published Version","title":"Efficiency and generalization of sparse neural networks","ddc":["000"],"status":"public","_id":"13074","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2023-05-23T00:00:00Z","page":"147","citation":{"chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13074.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","mla":"Peste, Elena-Alexandra. Efficiency and Generalization of Sparse Neural Networks. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13074.","apa":"Peste, E.-A. (2023). Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13074","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria.","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:10.15479/at:ista:13074"},"article_processing_charge":"No","has_accepted_license":"1","day":"23","date_created":"2023-05-23T17:07:53Z","date_updated":"2023-08-04T10:33:27Z","related_material":{"record":[{"id":"11458","relation":"part_of_dissertation","status":"public"},{"id":"13053","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"12299"}]},"author":[{"last_name":"Peste","first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publication_status":"published","year":"2023","ec_funded":1,"file_date_updated":"2023-05-24T16:12:59Z","language":[{"iso":"eng"}],"supervisor":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.15479/at:ista:13074","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"05"},{"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"08","doi":"10.1103/physrevb.108.054201","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2303.16876"]},"project":[{"grant_number":"850899","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020"}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-08-07T09:48:08Z","article_number":"054201","author":[{"full_name":"Brighi, Pietro","last_name":"Brighi","first_name":"Pietro","orcid":"0000-0002-7969-2729","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87"},{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina","first_name":"Marko","full_name":"Ljubotina, Marko"},{"full_name":"Abanin, Dmitry A.","last_name":"Abanin","first_name":"Dmitry A."},{"full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym"}],"volume":108,"date_created":"2023-08-05T18:25:22Z","date_updated":"2023-08-07T09:51:39Z","year":"2023","acknowledgement":"We thank A. A. Michailidis and A. Mirlin for insightful discussions. P.B., M.L., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). D.A. was\r\nsupported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 864597) and by the Swiss National Science Foundation. P.B., M.L., and M.S. acknowledge PRACE for awarding us access to Joliot-Curie at GENCI@CEA, France, where the TEBD simulations were performed. The TEBD simulations were performed using the ITensor library [60].","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-08-01T00:00:00Z","citation":{"ieee":"P. Brighi, M. Ljubotina, D. A. Abanin, and M. Serbyn, “Many-body localization proximity effect in a two-species bosonic Hubbard model,” Physical Review B, vol. 108, no. 5. American Physical Society, 2023.","apa":"Brighi, P., Ljubotina, M., Abanin, D. A., & Serbyn, M. (2023). Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.108.054201","ista":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. 2023. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 108(5), 054201.","ama":"Brighi P, Ljubotina M, Abanin DA, Serbyn M. Many-body localization proximity effect in a two-species bosonic Hubbard model. Physical Review B. 2023;108(5). doi:10.1103/physrevb.108.054201","chicago":"Brighi, Pietro, Marko Ljubotina, Dmitry A. Abanin, and Maksym Serbyn. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/physrevb.108.054201.","short":"P. Brighi, M. Ljubotina, D.A. Abanin, M. Serbyn, Physical Review B 108 (2023).","mla":"Brighi, Pietro, et al. “Many-Body Localization Proximity Effect in a Two-Species Bosonic Hubbard Model.” Physical Review B, vol. 108, no. 5, 054201, American Physical Society, 2023, doi:10.1103/physrevb.108.054201."},"publication":"Physical Review B","article_type":"original","issue":"5","abstract":[{"text":"The many-body localization (MBL) proximity effect is an intriguing phenomenon where a thermal bath localizes due to the interaction with a disordered system. The interplay of thermal and nonergodic behavior in these systems gives rise to a rich phase diagram, whose exploration is an active field of research. In this paper, we study a bosonic Hubbard model featuring two particle species representing the bath and the disordered system. Using state-of-the-art numerical techniques, we investigate the dynamics of the model in different regimes, based on which we obtain a tentative phase diagram as a function of coupling strength and bath size. When the bath is composed of a single particle, we observe clear signatures of a transition from an MBL proximity effect to a delocalized phase. Increasing the bath size, however, its thermalizing effect becomes stronger and eventually the whole system delocalizes in the range of moderate interaction strengths studied. In this regime, we characterize particle transport, revealing diffusive behavior of the originally localized bosons.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2023-08-07T09:48:08Z","date_updated":"2023-08-07T09:48:08Z","success":1,"checksum":"f763000339b5fd543c14377109920690","file_id":"13981","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":3051398,"file_name":"2023_PhysRevB_Brighi.pdf","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13963","intvolume":" 108","status":"public","ddc":["530"],"title":"Many-body localization proximity effect in a two-species bosonic Hubbard model"},{"doi":"10.1103/PhysRevB.108.045115","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2203.12666"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.12666","open_access":"1"}],"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"A path-integral approach to composite impurities","_id":"26986C82-B435-11E9-9278-68D0E5697425","grant_number":"M02641"},{"name":"Algebro-Geometric Applications of Factorization Homology","call_identifier":"FWF","_id":"26B96266-B435-11E9-9278-68D0E5697425","grant_number":"M02751"},{"grant_number":"P29902","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment","call_identifier":"FWF"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"month":"07","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"author":[{"orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","last_name":"Bighin","first_name":"Giacomo","full_name":"Bighin, Giacomo"},{"id":"3DD82E3C-F248-11E8-B48F-1D18A9856A87","first_name":"Quoc P","last_name":"Ho","full_name":"Ho, Quoc P"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"full_name":"Tscherbul, T. V.","last_name":"Tscherbul","first_name":"T. V."}],"date_created":"2023-08-06T22:01:10Z","date_updated":"2023-08-07T08:41:29Z","volume":108,"year":"2023","acknowledgement":"We acknowledge stimulating discussions with Sergey Varganov, Artur Izmaylov, Jacek Kłos, Piotr Żuchowski, Dominika Zgid, Nikolay Prokof'ev, Boris Svistunov, Robert Parrish, and Andreas Heßelmann. G.B. and Q.P.H. acknowledge support from the Austrian Science Fund (FWF) under Projects No. M2641-N27 and No. M2751. M.L. acknowledges support by the FWF under Project No. P29902-N27, and by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). T.V.T. was supported by the NSF CAREER award No. PHY-2045681. This work is supported by the German Research Foundation (DFG) under Germany's Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster). The authors acknowledge support by the state of Baden-Württemberg through bwHPC.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"},{"_id":"TaHa"}],"ec_funded":1,"article_number":"045115","date_published":"2023-07-15T00:00:00Z","publication":"Physical Review B","citation":{"chicago":"Bighin, Giacomo, Quoc P Ho, Mikhail Lemeshko, and T. V. Tscherbul. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.045115.","short":"G. Bighin, Q.P. Ho, M. Lemeshko, T.V. Tscherbul, Physical Review B 108 (2023).","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo for Electronic Correlation in Molecules: High-Order Many-Body Perturbation Theory with Low Scaling.” Physical Review B, vol. 108, no. 4, 045115, American Physical Society, 2023, doi:10.1103/PhysRevB.108.045115.","apa":"Bighin, G., Ho, Q. P., Lemeshko, M., & Tscherbul, T. V. (2023). Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.045115","ieee":"G. Bighin, Q. P. Ho, M. Lemeshko, and T. V. Tscherbul, “Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling,” Physical Review B, vol. 108, no. 4. American Physical Society, 2023.","ista":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. 2023. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 108(4), 045115.","ama":"Bighin G, Ho QP, Lemeshko M, Tscherbul TV. Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling. Physical Review B. 2023;108(4). doi:10.1103/PhysRevB.108.045115"},"article_type":"original","day":"15","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13966","title":"Diagrammatic Monte Carlo for electronic correlation in molecules: High-order many-body perturbation theory with low scaling","status":"public","intvolume":" 108","abstract":[{"text":"We present a low-scaling diagrammatic Monte Carlo approach to molecular correlation energies. Using combinatorial graph theory to encode many-body Hugenholtz diagrams, we sample the Møller-Plesset (MPn) perturbation series, obtaining accurate correlation energies up to n=5, with quadratic scaling in the number of basis functions. Our technique reduces the computational complexity of the molecular many-fermion correlation problem, opening up the possibility of low-scaling, accurate stochastic computations for a wide class of many-body systems described by Hugenholtz diagrams.","lang":"eng"}],"issue":"4","type":"journal_article"},{"language":[{"iso":"eng"}],"doi":"10.15227/orgsyn.100.0271","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.15227/orgsyn.100.0271"}],"oa":1,"publication_identifier":{"issn":["0078-6209"],"eissn":["2333-3553"]},"month":"07","volume":100,"date_updated":"2023-08-07T08:21:45Z","date_created":"2023-08-06T22:01:11Z","author":[{"first_name":"Amiera","last_name":"Madani","full_name":"Madani, Amiera"},{"full_name":"Sletten, Eric T.","last_name":"Sletten","first_name":"Eric T."},{"last_name":"Cavedon","first_name":"Cristian","full_name":"Cavedon, Cristian"},{"full_name":"Seeberger, Peter H.","last_name":"Seeberger","first_name":"Peter H."},{"last_name":"Pieber","first_name":"Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus"}],"publisher":"Organic Syntheses","department":[{"_id":"BaPi"}],"publication_status":"published","year":"2023","date_published":"2023-07-01T00:00:00Z","page":"271-286","article_type":"original","citation":{"short":"A. Madani, E.T. Sletten, C. Cavedon, P.H. Seeberger, B. Pieber, Organic Syntheses 100 (2023) 271–286.","mla":"Madani, Amiera, et al. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses, vol. 100, Organic Syntheses, 2023, pp. 271–86, doi:10.15227/orgsyn.100.0271.","chicago":"Madani, Amiera, Eric T. Sletten, Cristian Cavedon, Peter H. Seeberger, and Bartholomäus Pieber. “Visible-Light-Mediated Oxidative Debenzylation of 3-O-Benzyl-1,2:5,6-Di-O-Isopropylidene-α-D-Glucofuranose.” Organic Syntheses. Organic Syntheses, 2023. https://doi.org/10.15227/orgsyn.100.0271.","ama":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 2023;100:271-286. doi:10.15227/orgsyn.100.0271","ieee":"A. Madani, E. T. Sletten, C. Cavedon, P. H. Seeberger, and B. Pieber, “Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose,” Organic Syntheses, vol. 100. Organic Syntheses, pp. 271–286, 2023.","apa":"Madani, A., Sletten, E. T., Cavedon, C., Seeberger, P. H., & Pieber, B. (2023). Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. Organic Syntheses. https://doi.org/10.15227/orgsyn.100.0271","ista":"Madani A, Sletten ET, Cavedon C, Seeberger PH, Pieber B. 2023. Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose. Organic Syntheses. 100, 271–286."},"publication":"Organic Syntheses","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","intvolume":" 100","status":"public","title":"Visible-light-mediated oxidative debenzylation of 3-O-Benzyl-1,2:5,6-di-O-isopropylidene-α-D-glucofuranose","_id":"13970","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article"},{"date_published":"2023-06-03T00:00:00Z","publication":"Nature Communications","citation":{"ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y.","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023)."},"article_type":"original","day":"03","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"13132","relation":"main_file","date_created":"2023-06-13T08:05:46Z","date_updated":"2023-06-13T08:05:46Z","success":1,"checksum":"4af0393e3ed47b3fc46e68b81c3c1007","file_name":"2023_NatureComm_CasillasPerez.pdf","access_level":"open_access","creator":"dernst","file_size":2358167,"content_type":"application/pdf"}],"_id":"13127","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","status":"public","ddc":["570"],"intvolume":" 14","abstract":[{"text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense.","lang":"eng"}],"type":"journal_article","doi":"10.1038/s41467-023-38947-y","acknowledged_ssus":[{"_id":"LifeSc"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["37270641"],"isi":["001002562700005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"},{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"month":"06","publication_identifier":{"eissn":["2041-1723"]},"author":[{"full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E"},{"full_name":"Bod'Ová, Katarína","last_name":"Bod'Ová","first_name":"Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"12945"}]},"date_updated":"2023-08-07T13:09:09Z","date_created":"2023-06-11T22:00:40Z","volume":14,"acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","year":"2023","pmid":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"file_date_updated":"2023-06-13T08:05:46Z","ec_funded":1,"article_number":"3232"},{"citation":{"chicago":"Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12945.","short":"S. Cremer, (2023).","mla":"Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12945.","ieee":"S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.","apa":"Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12945","ista":"Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12945.","ama":"Cremer S. 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This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. "}],"title":"Nanoparticle-based semiconductor solids: From synthesis to consolidation","ddc":["546","541"],"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12885","oa_version":"Published Version","file":[{"access_level":"closed","file_name":"Thesis_Calcabrini.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":99627036,"creator":"mcalcabr","relation":"source_file","file_id":"12887","checksum":"9347b0e09425f56fdcede5d3528404dc","date_created":"2023-05-02T07:43:18Z","date_updated":"2023-05-02T07:43:18Z"},{"success":1,"checksum":"2d188b76621086cd384f0b9264b0a576","date_created":"2023-05-02T07:42:45Z","date_updated":"2023-05-02T07:42:45Z","file_id":"12888","relation":"main_file","creator":"mcalcabr","content_type":"application/pdf","file_size":8742220,"access_level":"open_access","file_name":"Thesis_Calcabrini_pdfa.pdf"}],"has_accepted_license":"1","article_processing_charge":"No","day":"28","page":"82","citation":{"mla":"Calcabrini, Mariano. Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12885.","short":"M. Calcabrini, Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation, Institute of Science and Technology Austria, 2023.","chicago":"Calcabrini, Mariano. “Nanoparticle-Based Semiconductor Solids: From Synthesis to Consolidation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12885.","ama":"Calcabrini M. Nanoparticle-based semiconductor solids: From synthesis to consolidation. 2023. doi:10.15479/at:ista:12885","ista":"Calcabrini M. 2023. Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria.","apa":"Calcabrini, M. (2023). Nanoparticle-based semiconductor solids: From synthesis to consolidation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12885","ieee":"M. Calcabrini, “Nanoparticle-based semiconductor solids: From synthesis to consolidation,” Institute of Science and Technology Austria, 2023."},"date_published":"2023-04-28T00:00:00Z"},{"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","article_type":"original","page":"717-750","publication":"Annales Henri Poincare","citation":{"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.","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","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.","short":"M. Wirth, H. Zhang, Annales Henri Poincare 24 (2023) 717–750.","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."},"abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"14051","relation":"main_file","date_updated":"2023-08-14T11:38:28Z","date_created":"2023-08-14T11:38:28Z","success":1,"checksum":"8c7b185eba5ccd92ef55c120f654222c","file_name":"2023_AnnalesHenriPoincare_Wirth.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":554871}],"ddc":["510"],"status":"public","title":"Curvature-dimension conditions for symmetric quantum Markov semigroups","intvolume":" 24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12087","month":"03","publication_identifier":{"issn":["1424-0637"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00023-022-01220-x","quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Curvature-dimension in noncommutative analysis","_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","grant_number":"M03337"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2105.08303"],"isi":["000837499800002"]},"oa":1,"file_date_updated":"2023-08-14T11:38:28Z","ec_funded":1,"date_created":"2022-09-11T22:01:57Z","date_updated":"2023-08-14T11:39:28Z","volume":24,"author":[{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior","orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"},{"full_name":"Zhang, Haonan","first_name":"Haonan","last_name":"Zhang","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"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).","year":"2023"},{"doi":"10.1007/s11856-022-2448-6","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000904950300003"],"arxiv":["1903.05923"]},"quality_controlled":"1","isi":1,"month":"03","publication_identifier":{"eissn":["1565-8511"]},"author":[{"first_name":"Michael","last_name":"Dymond","full_name":"Dymond, Michael"},{"last_name":"Kaluza","first_name":"Vojtech","orcid":"0000-0002-2512-8698","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E","full_name":"Kaluza, Vojtech"}],"date_created":"2021-07-14T07:01:28Z","date_updated":"2023-08-14T11:26:34Z","volume":253,"year":"2023","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.","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","file_date_updated":"2021-07-14T07:41:50Z","date_published":"2023-03-01T00:00:00Z","publication":"Israel Journal of Mathematics","citation":{"ista":"Dymond M, Kaluza V. 2023. Highly irregular separated nets. Israel Journal of Mathematics. 253, 501–554.","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","ieee":"M. Dymond and V. Kaluza, “Highly irregular separated nets,” Israel Journal of Mathematics, vol. 253. Springer Nature, pp. 501–554, 2023.","ama":"Dymond M, Kaluza V. Highly irregular separated nets. Israel Journal of Mathematics. 2023;253:501-554. 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.","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.","short":"M. Dymond, V. Kaluza, Israel Journal of Mathematics 253 (2023) 501–554."},"article_type":"original","page":"501-554","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["Lipschitz","bilipschitz","bounded displacement","modulus of continuity","separated net","non-realisable density","Burago--Kleiner construction"],"oa_version":"Submitted Version","file":[{"file_name":"separated_nets.pdf","access_level":"open_access","creator":"vkaluza","content_type":"application/pdf","file_size":900422,"file_id":"9653","relation":"main_file","date_created":"2021-07-14T07:41:50Z","date_updated":"2021-07-14T07:41:50Z","checksum":"6fa0a3207dd1d6467c309fd1bcc867d1"}],"_id":"9652","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["515","516"],"title":"Highly irregular separated nets","status":"public","intvolume":" 253","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"}],"type":"journal_article"},{"year":"2023","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","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","author":[{"full_name":"Clozeau, Nicolas","last_name":"Clozeau","first_name":"Nicolas","id":"fea1b376-906f-11eb-847d-b2c0cf46455b"}],"date_created":"2021-10-23T10:50:22Z","date_updated":"2023-08-14T11:51:47Z","volume":11,"file_date_updated":"2023-08-14T11:51:04Z","external_id":{"arxiv":["2102.07452"],"isi":["000799715600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1007/s40072-022-00254-w","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2194-0401"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10173","title":"Optimal decay of the parabolic semigroup in stochastic homogenization for correlated coefficient fields","ddc":["510"],"status":"public","intvolume":" 11","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1635193,"creator":"dernst","file_name":"2023_StochPartialDiffEquations_Clozeau.pdf","access_level":"open_access","date_updated":"2023-08-14T11:51:04Z","date_created":"2023-08-14T11:51:04Z","checksum":"f83dcaecdbd3ace862c4ed97a20e8501","success":1,"relation":"main_file","file_id":"14052"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"publication":"Stochastics and Partial Differential Equations: Analysis and Computations","citation":{"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.","short":"N. Clozeau, Stochastics and Partial Differential Equations: Analysis and Computations 11 (2023) 1254–1378.","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.","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","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"},"article_type":"original","page":"1254–1378","date_published":"2023-09-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"publication_identifier":{"issn":["0178-8051"],"eissn":["1432-2064"]},"month":"04","doi":"10.1007/s00440-022-01156-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000830344500001"],"arxiv":["2106.10200"]},"quality_controlled":"1","isi":1,"file_date_updated":"2023-08-14T12:47:32Z","author":[{"full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni","first_name":"Giorgio"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"},{"first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J"}],"volume":185,"date_created":"2022-08-07T22:02:00Z","date_updated":"2023-08-14T12:48:09Z","acknowledgement":"The authors are indebted to Sourav Chatterjee for forwarding the very inspiring question that Stephen Shenker originally addressed to him which initiated the current paper. They are also grateful that the authors of [23] kindly shared their preliminary numerical results in June 2021.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","year":"2023","department":[{"_id":"LaEr"}],"publisher":"Springer Nature","publication_status":"published","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 2023;185:1183–1218. doi:10.1007/s00440-022-01156-7","ista":"Cipolloni G, Erdös L, Schröder DJ. 2023. Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. 185, 1183–1218.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Quenched universality for deformed Wigner matrices,” Probability Theory and Related Fields, vol. 185. Springer Nature, pp. 1183–1218, 2023.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2023). Quenched universality for deformed Wigner matrices. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-022-01156-7","mla":"Cipolloni, Giorgio, et al. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields, vol. 185, Springer Nature, 2023, pp. 1183–1218, doi:10.1007/s00440-022-01156-7.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Probability Theory and Related Fields 185 (2023) 1183–1218.","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Quenched Universality for Deformed Wigner Matrices.” Probability Theory and Related Fields. Springer Nature, 2023. https://doi.org/10.1007/s00440-022-01156-7."},"publication":"Probability Theory and Related Fields","page":"1183–1218","article_type":"original","abstract":[{"lang":"eng","text":"Following E. Wigner’s original vision, we prove that sampling the eigenvalue gaps within the bulk spectrum of a fixed (deformed) Wigner matrix H yields the celebrated Wigner-Dyson-Mehta universal statistics with high probability. Similarly, we prove universality for a monoparametric family of deformed Wigner matrices H+xA with a deterministic Hermitian matrix A and a fixed Wigner matrix H, just using the randomness of a single scalar real random variable x. Both results constitute quenched versions of bulk universality that has so far only been proven in annealed sense with respect to the probability space of the matrix ensemble."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-08-14T12:47:32Z","date_created":"2023-08-14T12:47:32Z","checksum":"b9247827dae5544d1d19c37abe547abc","success":1,"relation":"main_file","file_id":"14054","content_type":"application/pdf","file_size":782278,"creator":"dernst","file_name":"2023_ProbabilityTheory_Cipolloni.pdf","access_level":"open_access"}],"_id":"11741","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 185","title":"Quenched universality for deformed Wigner matrices","ddc":["510"],"status":"public"},{"file_date_updated":"2023-08-14T12:57:25Z","author":[{"full_name":"Wang, Siqi","first_name":"Siqi","last_name":"Wang"},{"id":"9E331C2E-9F27-11E9-AE48-5033E6697425","orcid":"0000-0002-9515-4277","first_name":"Cheng","last_name":"Chang","full_name":"Chang, Cheng"},{"full_name":"Bai, Shulin","first_name":"Shulin","last_name":"Bai"},{"last_name":"Qin","first_name":"Bingchao","full_name":"Qin, Bingchao"},{"first_name":"Yingcai","last_name":"Zhu","full_name":"Zhu, Yingcai"},{"first_name":"Shaoping","last_name":"Zhan","full_name":"Zhan, Shaoping"},{"full_name":"Zheng, Junqing","first_name":"Junqing","last_name":"Zheng"},{"full_name":"Tang, Shuwei","first_name":"Shuwei","last_name":"Tang"},{"last_name":"Zhao","first_name":"Li Dong","full_name":"Zhao, Li Dong"}],"volume":35,"date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-14T12:57:44Z","year":"2023","acknowledgement":"The National Key Research and Development Program of China (2018YFA0702100), the Basic Science Center Project of the National Natural Science Foundation of China (51788104), the National Natural Science Foundation of China (51571007 and 51772012), the Beijing Natural Science Foundation (JQ18004), the 111 Project (B17002), the National Science Fund for Distinguished Young Scholars (51925101), and the FWF “Lise Meitner Fellowship” (grant agreement M2889-N). Open Access is funded by the Austrian Science Fund (FWF).","department":[{"_id":"MaIb"}],"publisher":"American Chemical Society","publication_status":"published","publication_identifier":{"issn":["0897-4756"],"eissn":["1520-5002"]},"month":"01","doi":"10.1021/acs.chemmater.2c03542","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000914749700001"]},"project":[{"_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A","grant_number":"M02889","name":"Bottom-up Engineering for Thermoelectric Applications"}],"isi":1,"quality_controlled":"1","issue":"2","abstract":[{"lang":"eng","text":"High carrier mobility is critical to improving thermoelectric performance over a broad temperature range. However, traditional doping inevitably deteriorates carrier mobility. Herein, we develop a strategy for fine tuning of defects to improve carrier mobility. To begin, n-type PbTe is created by compensating for the intrinsic Pb vacancy in bare PbTe. Excess Pb2+ reduces vacancy scattering, resulting in a high carrier mobility of ∼3400 cm2 V–1 s–1. Then, excess Ag is introduced to compensate for the remaining intrinsic Pb vacancies. We find that excess Ag exhibits a dynamic doping process with increasing temperatures, increasing both the carrier concentration and carrier mobility throughout a wide temperature range; specifically, an ultrahigh carrier mobility ∼7300 cm2 V–1 s–1 is obtained for Pb1.01Te + 0.002Ag at 300 K. Moreover, the dynamic doping-induced high carrier concentration suppresses the bipolar thermal conductivity at high temperatures. The final step is using iodine to optimize the carrier concentration to ∼1019 cm–3. Ultimately, a maximum ZT value of ∼1.5 and a large average ZTave value of ∼1.0 at 300–773 K are obtained for Pb1.01Te0.998I0.002 + 0.002Ag. These findings demonstrate that fine tuning of defects with <0.5% impurities can remarkably enhance carrier mobility and improve thermoelectric performance."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2961043,"creator":"dernst","access_level":"open_access","file_name":"2023_ChemistryMaterials_Wang.pdf","checksum":"b21dca2aa7a80c068bc256bdd1fea9df","success":1,"date_updated":"2023-08-14T12:57:25Z","date_created":"2023-08-14T12:57:25Z","relation":"main_file","file_id":"14055"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12331","intvolume":" 35","ddc":["540"],"title":"Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"24","scopus_import":"1","date_published":"2023-01-24T00:00:00Z","citation":{"mla":"Wang, Siqi, et al. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials, vol. 35, no. 2, American Chemical Society, 2023, pp. 755–63, doi:10.1021/acs.chemmater.2c03542.","short":"S. Wang, C. Chang, S. Bai, B. Qin, Y. Zhu, S. Zhan, J. Zheng, S. Tang, L.D. Zhao, Chemistry of Materials 35 (2023) 755–763.","chicago":"Wang, Siqi, Cheng Chang, Shulin Bai, Bingchao Qin, Yingcai Zhu, Shaoping Zhan, Junqing Zheng, Shuwei Tang, and Li Dong Zhao. “Fine Tuning of Defects Enables High Carrier Mobility and Enhanced Thermoelectric Performance of N-Type PbTe.” Chemistry of Materials. American Chemical Society, 2023. https://doi.org/10.1021/acs.chemmater.2c03542.","ama":"Wang S, Chang C, Bai S, et al. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 2023;35(2):755-763. doi:10.1021/acs.chemmater.2c03542","ista":"Wang S, Chang C, Bai S, Qin B, Zhu Y, Zhan S, Zheng J, Tang S, Zhao LD. 2023. Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. 35(2), 755–763.","ieee":"S. Wang et al., “Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe,” Chemistry of Materials, vol. 35, no. 2. American Chemical Society, pp. 755–763, 2023.","apa":"Wang, S., Chang, C., Bai, S., Qin, B., Zhu, Y., Zhan, S., … Zhao, L. D. (2023). Fine tuning of defects enables high carrier mobility and enhanced thermoelectric performance of n-type PbTe. Chemistry of Materials. American Chemical Society. https://doi.org/10.1021/acs.chemmater.2c03542"},"publication":"Chemistry of Materials","page":"755-763","article_type":"original"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","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.","short":"A.M. Arroyo Guevara, F. Klute, I. Parada, B. Vogtenhuber, R. Seidel, T. Wiedera, Discrete and Computational Geometry 69 (2023) 745–770.","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.","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.","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","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.","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"},"publication":"Discrete and Computational Geometry","page":"745–770","article_type":"original","date_published":"2023-04-01T00:00:00Z","type":"journal_article","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"}],"_id":"11999","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 69","status":"public","title":"Inserting one edge into a simple drawing is hard","ddc":["510"],"file":[{"creator":"alisjak","content_type":"application/pdf","file_size":1002218,"file_name":"2022_DiscreteandComputionalGeometry_Arroyo.pdf","access_level":"open_access","date_updated":"2022-08-29T11:23:15Z","date_created":"2022-08-29T11:23:15Z","success":1,"checksum":"def7ae3b28d9fd6aec16450e40090302","file_id":"12006","relation":"main_file"}],"oa_version":"Published Version","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"month":"04","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000840292800001"],"arxiv":["1909.07347"]},"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s00454-022-00394-9","language":[{"iso":"eng"}],"ec_funded":1,"file_date_updated":"2022-08-29T11:23:15Z","year":"2023","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.","publisher":"Springer Nature","department":[{"_id":"UlWa"}],"publication_status":"published","author":[{"full_name":"Arroyo Guevara, Alan M","first_name":"Alan M","last_name":"Arroyo Guevara","id":"3207FDC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2401-8670"},{"first_name":"Fabian","last_name":"Klute","full_name":"Klute, Fabian"},{"first_name":"Irene","last_name":"Parada","full_name":"Parada, Irene"},{"full_name":"Vogtenhuber, Birgit","last_name":"Vogtenhuber","first_name":"Birgit"},{"full_name":"Seidel, Raimund","first_name":"Raimund","last_name":"Seidel"},{"full_name":"Wiedera, Tilo","last_name":"Wiedera","first_name":"Tilo"}],"volume":69,"date_updated":"2023-08-14T12:51:25Z","date_created":"2022-08-28T22:02:01Z"},{"oa_version":"Preprint","title":"The splay-list: A distribution-adaptive concurrent skip-list","status":"public","intvolume":" 36","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12330","abstract":[{"text":"The design and implementation of efficient concurrent data structures has seen significant attention. However, most of this work has focused on concurrent data structures providing good worst-case guarantees, although, in real workloads, objects are often accessed at different rates. Efficient distribution-adaptive data structures, such as splay-trees, are known in the sequential case; however, they often are hard to translate efficiently to the concurrent case. We investigate distribution-adaptive concurrent data structures, and propose a new design called the splay-list. At a high level, the splay-list is similar to a standard skip-list, with the key distinction that the height of each element adapts dynamically to its access rate: popular elements “move up,” whereas rarely-accessed elements decrease in height. We show that the splay-list provides order-optimal amortized complexity bounds for a subset of operations, while being amenable to efficient concurrent implementation. Experiments show that the splay-list can leverage distribution-adaptivity for performance, and can outperform the only previously-known distribution-adaptive concurrent design in certain workloads.","lang":"eng"}],"type":"journal_article","date_published":"2023-09-01T00:00:00Z","article_type":"original","page":"395-418","publication":"Distributed Computing","citation":{"short":"V. Aksenov, D.-A. Alistarh, A. Drozdova, A. Mohtashami, Distributed Computing 36 (2023) 395–418.","mla":"Aksenov, Vitalii, et al. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 395–418, doi:10.1007/s00446-022-00441-x.","chicago":"Aksenov, Vitalii, Dan-Adrian Alistarh, Alexandra Drozdova, and Amirkeivan Mohtashami. “The Splay-List: A Distribution-Adaptive Concurrent Skip-List.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00441-x.","ama":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 2023;36:395-418. doi:10.1007/s00446-022-00441-x","ieee":"V. Aksenov, D.-A. Alistarh, A. Drozdova, and A. Mohtashami, “The splay-list: A distribution-adaptive concurrent skip-list,” Distributed Computing, vol. 36. Springer Nature, pp. 395–418, 2023.","apa":"Aksenov, V., Alistarh, D.-A., Drozdova, A., & Mohtashami, A. (2023). The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00441-x","ista":"Aksenov V, Alistarh D-A, Drozdova A, Mohtashami A. 2023. The splay-list: A distribution-adaptive concurrent skip-list. Distributed Computing. 36, 395–418."},"day":"01","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-08-14T12:54:32Z","date_created":"2023-01-22T23:00:55Z","volume":36,"author":[{"full_name":"Aksenov, Vitalii","id":"2980135A-F248-11E8-B48F-1D18A9856A87","first_name":"Vitalii","last_name":"Aksenov"},{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"full_name":"Drozdova, Alexandra","last_name":"Drozdova","first_name":"Alexandra"},{"full_name":"Mohtashami, Amirkeivan","last_name":"Mohtashami","first_name":"Amirkeivan"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"DaAl"}],"year":"2023","language":[{"iso":"eng"}],"doi":"10.1007/s00446-022-00441-x","quality_controlled":"1","isi":1,"external_id":{"isi":["000913424000001"],"arxiv":["2008.01009"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2008.01009","open_access":"1"}],"month":"09","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]}},{"article_type":"original","page":"1441-1457","publication":"Molecular Ecology","citation":{"chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16793.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” Molecular Ecology, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:10.1111/mec.16793.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” Molecular Ecology, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., & Barton, N. H. (2023). On the origin and structure of haplotype blocks. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16793","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. Molecular Ecology. 2023;32(6):1441-1457. doi:10.1111/mec.16793"},"date_published":"2023-03-01T00:00:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","title":"On the origin and structure of haplotype blocks","ddc":["570"],"status":"public","intvolume":" 32","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12159","file":[{"access_level":"open_access","file_name":"2023_MolecularEcology_Shipilina.pdf","creator":"dernst","content_type":"application/pdf","file_size":7144607,"file_id":"14062","relation":"main_file","success":1,"checksum":"b10e0f8fa3dc4d72aaf77a557200978a","date_created":"2023-08-16T08:15:41Z","date_updated":"2023-08-16T08:15:41Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies."}],"issue":"6","isi":1,"quality_controlled":"1","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["36433653"],"isi":["000900762000001"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.16793","month":"03","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2023","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","pmid":1,"date_updated":"2023-08-16T08:18:47Z","date_created":"2023-01-12T12:09:17Z","volume":32,"author":[{"first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"first_name":"Arka","last_name":"Pal","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank","last_name":"Chan"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"file_date_updated":"2023-08-16T08:15:41Z"},{"publication_identifier":{"issn":["2590-1524"]},"month":"01","doi":"10.1016/j.yjsbx.2022.100079","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["36578472"]},"quality_controlled":"1","file_date_updated":"2023-08-16T09:36:28Z","article_number":"100079","author":[{"last_name":"Gauto","first_name":"Diego F.","full_name":"Gauto, Diego F."},{"full_name":"Lebedenko, Olga O.","last_name":"Lebedenko","first_name":"Olga O."},{"first_name":"Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151","full_name":"Becker, Lea Marie"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"last_name":"Skrynnikov","first_name":"Nikolai R.","full_name":"Skrynnikov, Nikolai R."},{"full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"}],"volume":7,"date_updated":"2023-08-16T09:37:25Z","date_created":"2023-01-12T11:55:38Z","pmid":1,"year":"2023","acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","department":[{"_id":"PaSc"}],"publisher":"Elsevier","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","keyword":["Structural Biology"],"date_published":"2023-01-01T00:00:00Z","citation":{"ieee":"D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079."},"publication":"Journal of Structural Biology: X","article_type":"original","abstract":[{"lang":"eng","text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects."}],"type":"journal_article","file":[{"file_name":"2023_JourStrucBiologyX_Gauto.pdf","access_level":"open_access","creator":"dernst","file_size":5132322,"content_type":"application/pdf","file_id":"14064","relation":"main_file","date_created":"2023-08-16T09:36:28Z","date_updated":"2023-08-16T09:36:28Z","success":1,"checksum":"b4b1c10a31018aafe053b7d55a470e54"}],"oa_version":"Published Version","_id":"12114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","ddc":["570"],"title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","status":"public"},{"month":"03","publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"doi":"10.1002/1873-3468.14540","language":[{"iso":"eng"}],"external_id":{"pmid":["36448231"],"isi":["000891573000001"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2023-08-16T08:31:04Z","author":[{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"first_name":"Albert","last_name":"Auer","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3580-2906","full_name":"Auer, Albert"},{"full_name":"Brognara, Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","first_name":"Gabriel","last_name":"Brognara"},{"id":"55380f95-15b2-11ec-abd3-aff8e230696b","first_name":"Hanifatul R","last_name":"Budiman","full_name":"Budiman, Hanifatul R"},{"first_name":"Lukasz M","last_name":"Kowalski","id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","full_name":"Kowalski, Lukasz M"},{"full_name":"Matijevic, Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","last_name":"Matijevic"}],"date_created":"2023-01-12T12:09:58Z","date_updated":"2023-08-16T08:32:29Z","volume":597,"acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","year":"2023","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"MaLo"}],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"],"date_published":"2023-03-01T00:00:00Z","publication":"FEBS Letters","citation":{"chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540"},"article_type":"review","page":"762-777","abstract":[{"lang":"eng","text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time."}],"issue":"6","type":"journal_article","file":[{"relation":"main_file","file_id":"14063","date_created":"2023-08-16T08:31:04Z","date_updated":"2023-08-16T08:31:04Z","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","success":1,"file_name":"2023_FEBSLetters_Loose.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3148143,"creator":"dernst"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12163","status":"public","ddc":["570"],"title":"In vitro reconstitution of small GTPase regulation","intvolume":" 597"},{"acknowledgement":"A preliminary version of this work appeared in DISC’19. Mirza Ahad Baig, Alessia Milani and Corentin Travers are supported by ANR projects Descartes and FREDDA. Mirza Ahad Baig is supported by UMI Relax. Danny Hendler is supported by the Israel Science Foundation (Grants 380/18 and 1425/22).","year":"2023","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","author":[{"full_name":"Baig, Mirza Ahad","first_name":"Mirza Ahad","last_name":"Baig","id":"3EDE6DE4-AA5A-11E9-986D-341CE6697425"},{"first_name":"Danny","last_name":"Hendler","full_name":"Hendler, Danny"},{"full_name":"Milani, Alessia","last_name":"Milani","first_name":"Alessia"},{"full_name":"Travers, Corentin","last_name":"Travers","first_name":"Corentin"}],"date_updated":"2023-08-16T08:39:36Z","date_created":"2023-01-12T12:10:08Z","volume":36,"oa":1,"external_id":{"isi":["000890138700001"]},"main_file_link":[{"url":"https://drops.dagstuhl.de/opus/volltexte/2019/11310/","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1007/s00446-022-00439-5","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0178-2770"],"eissn":["1432-0452"]},"_id":"12164","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Long-lived counters with polylogarithmic amortized step complexity","intvolume":" 36","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"A shared-memory counter is a widely-used and well-studied concurrent object. It supports two operations: An Inc operation that increases its value by 1 and a Read operation that returns its current value. In Jayanti et al (SIAM J Comput, 30(2), 2000), Jayanti, Tan and Toueg proved a linear lower bound on the worst-case step complexity of obstruction-free implementations, from read-write registers, of a large class of shared objects that includes counters. The lower bound leaves open the question of finding counter implementations with sub-linear amortized step complexity. In this work, we address this gap. We show that n-process, wait-free and linearizable counters can be implemented from read-write registers with O(log2n) amortized step complexity. This is the first counter algorithm from read-write registers that provides sub-linear amortized step complexity in executions of arbitrary length. Since a logarithmic lower bound on the amortized step complexity of obstruction-free counter implementations exists, our upper bound is within a logarithmic factor of the optimal. The worst-case step complexity of the construction remains linear, which is optimal. This is obtained thanks to a new max register construction with O(logn) amortized step complexity in executions of arbitrary length in which the value stored in the register does not grow too quickly. We then leverage an existing counter algorithm by Aspnes, Attiya and Censor-Hillel [1] in which we “plug” our max register implementation to show that it remains linearizable while achieving O(log2n) amortized step complexity.","lang":"eng"}],"publication":"Distributed Computing","citation":{"short":"M.A. Baig, D. Hendler, A. Milani, C. Travers, Distributed Computing 36 (2023) 29–43.","mla":"Baig, Mirza Ahad, et al. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing, vol. 36, Springer Nature, 2023, pp. 29–43, doi:10.1007/s00446-022-00439-5.","chicago":"Baig, Mirza Ahad, Danny Hendler, Alessia Milani, and Corentin Travers. “Long-Lived Counters with Polylogarithmic Amortized Step Complexity.” Distributed Computing. Springer Nature, 2023. https://doi.org/10.1007/s00446-022-00439-5.","ama":"Baig MA, Hendler D, Milani A, Travers C. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 2023;36:29-43. doi:10.1007/s00446-022-00439-5","ieee":"M. A. Baig, D. Hendler, A. Milani, and C. Travers, “Long-lived counters with polylogarithmic amortized step complexity,” Distributed Computing, vol. 36. Springer Nature, pp. 29–43, 2023.","apa":"Baig, M. A., Hendler, D., Milani, A., & Travers, C. (2023). Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. Springer Nature. https://doi.org/10.1007/s00446-022-00439-5","ista":"Baig MA, Hendler D, Milani A, Travers C. 2023. Long-lived counters with polylogarithmic amortized step complexity. Distributed Computing. 36, 29–43."},"article_type":"original","page":"29-43","date_published":"2023-03-01T00:00:00Z","scopus_import":"1","keyword":["Computational Theory and Mathematics","Computer Networks and Communications","Hardware and Architecture","Theoretical Computer Science"],"day":"01","article_processing_charge":"No"},{"author":[{"full_name":"Ortiz-Leal, Irene","first_name":"Irene","last_name":"Ortiz-Leal"},{"last_name":"Torres","first_name":"Mateo V.","full_name":"Torres, Mateo V."},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","last_name":"Vargas Barroso","first_name":"Victor M","full_name":"Vargas Barroso, Victor M"},{"first_name":"Luis Eusebio","last_name":"Fidalgo","full_name":"Fidalgo, Luis Eusebio"},{"last_name":"López-Beceiro","first_name":"Ana María","full_name":"López-Beceiro, Ana María"},{"full_name":"Larriva-Sahd, Jorge A.","last_name":"Larriva-Sahd","first_name":"Jorge A."},{"full_name":"Sánchez-Quinteiro, Pablo","first_name":"Pablo","last_name":"Sánchez-Quinteiro"}],"date_updated":"2023-08-16T11:37:52Z","date_created":"2023-02-05T23:01:00Z","volume":16,"acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","year":"2023","pmid":1,"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Frontiers","file_date_updated":"2023-02-06T07:56:14Z","article_number":"1097467","doi":"10.3389/fnana.2022.1097467","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000919786900001"],"pmid":["36704406"]},"quality_controlled":"1","isi":1,"month":"01","publication_identifier":{"eissn":["1662-5129"]},"file":[{"date_updated":"2023-02-06T07:56:14Z","date_created":"2023-02-06T07:56:14Z","success":1,"checksum":"49cd40f3bda6f267079427042e7d15e3","file_id":"12518","relation":"main_file","creator":"dernst","file_size":21943473,"content_type":"application/pdf","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"12515","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","intvolume":" 16","abstract":[{"text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues.","lang":"eng"}],"type":"journal_article","date_published":"2023-01-10T00:00:00Z","publication":"Frontiers in Neuroanatomy","citation":{"chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers, 2023. https://doi.org/10.3389/fnana.2022.1097467.","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023).","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","ieee":"I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers in Neuroanatomy, vol. 16. Frontiers, 2023.","apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467","ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467"},"article_type":"original","day":"10","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"volume":41,"date_updated":"2023-08-16T11:32:33Z","date_created":"2023-01-08T23:00:53Z","author":[{"full_name":"Yeung, Jake","orcid":"0000-0003-1732-1559","id":"123012b2-db30-11eb-b4d8-a35840c0551b","last_name":"Yeung","first_name":"Jake"},{"full_name":"Florescu, Maria","last_name":"Florescu","first_name":"Maria"},{"first_name":"Peter","last_name":"Zeller","full_name":"Zeller, Peter"},{"first_name":"Buys Anton","last_name":"De Barbanson","full_name":"De Barbanson, Buys Anton"},{"full_name":"Wellenstein, Max D.","last_name":"Wellenstein","first_name":"Max D."},{"full_name":"Van Oudenaarden, Alexander","first_name":"Alexander","last_name":"Van Oudenaarden"}],"department":[{"_id":"ScienComp"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"We thank M. van Loenhout for experimental advice on purifying cell types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat and O. Stegle for discussions on multinomial distributions. This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001) and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is part of the Oncode Institute which is financed partly by the Dutch Cancer Society.","file_date_updated":"2023-08-16T11:30:45Z","language":[{"iso":"eng"}],"doi":"10.1038/s41587-022-01560-3","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000909067600003"]},"oa":1,"publication_identifier":{"issn":["1087-0156"],"eissn":["1546-1696"]},"month":"06","file":[{"file_id":"14066","relation":"main_file","date_updated":"2023-08-16T11:30:45Z","date_created":"2023-08-16T11:30:45Z","success":1,"checksum":"668447a1c8d360b68f8aaf9e08ed644f","file_name":"2023_NatureBioTech_Yeung.pdf","access_level":"open_access","creator":"dernst","file_size":12040976,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 41","ddc":["570"],"title":"scChIX-seq infers dynamic relationships between histone modifications in single cells","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12106","abstract":[{"text":"Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.","lang":"eng"}],"type":"journal_article","date_published":"2023-06-01T00:00:00Z","page":"813–823","article_type":"original","citation":{"mla":"Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.","short":"J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A. Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.","chicago":"Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships between Histone Modifications in Single Cells.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.","ama":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3","ista":"Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden A. 2023. scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. 41, 813–823.","apa":"Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D., & Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between histone modifications in single cells. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-022-01560-3","ieee":"J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823, 2023."},"publication":"Nature Biotechnology","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"author":[{"full_name":"Boccato, Chiara","id":"342E7E22-F248-11E8-B48F-1D18A9856A87","last_name":"Boccato","first_name":"Chiara"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"volume":24,"date_created":"2023-01-15T23:00:52Z","date_updated":"2023-08-16T11:34:03Z","year":"2023","acknowledgement":"Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged.","publisher":"Springer Nature","department":[{"_id":"RoSe"}],"publication_status":"published","ec_funded":1,"doi":"10.1007/s00023-022-01252-3","language":[{"iso":"eng"}],"external_id":{"isi":["000910751800002"],"arxiv":["2205.15284"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2205.15284","open_access":"1"}],"oa":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["1424-0637"]},"month":"05","oa_version":"Preprint","_id":"12183","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","status":"public","title":"The Bose Gas in a box with Neumann boundary conditions","abstract":[{"text":"We consider a gas of n bosonic particles confined in a box [−ℓ/2,ℓ/2]3 with Neumann boundary conditions. We prove Bose–Einstein condensation in the Gross–Pitaevskii regime, with an optimal bound on the condensate depletion. Moreover, our lower bound for the ground state energy in a small box [−ℓ/2,ℓ/2]3 implies (via Neumann bracketing) a lower bound for the ground state energy of N bosons in a large box [−L/2,L/2]3 with density ρ=N/L3 in the thermodynamic limit.","lang":"eng"}],"type":"journal_article","date_published":"2023-05-01T00:00:00Z","citation":{"mla":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare, vol. 24, Springer Nature, 2023, pp. 1505–60, doi:10.1007/s00023-022-01252-3.","short":"C. Boccato, R. Seiringer, Annales Henri Poincare 24 (2023) 1505–1560.","chicago":"Boccato, Chiara, and Robert Seiringer. “The Bose Gas in a Box with Neumann Boundary Conditions.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-022-01252-3.","ama":"Boccato C, Seiringer R. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 2023;24:1505-1560. doi:10.1007/s00023-022-01252-3","ista":"Boccato C, Seiringer R. 2023. The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. 24, 1505–1560.","ieee":"C. Boccato and R. Seiringer, “The Bose Gas in a box with Neumann boundary conditions,” Annales Henri Poincare, vol. 24. Springer Nature, pp. 1505–1560, 2023.","apa":"Boccato, C., & Seiringer, R. (2023). The Bose Gas in a box with Neumann boundary conditions. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-022-01252-3"},"publication":"Annales Henri Poincare","page":"1505-1560","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"volume":63,"date_created":"2023-02-12T23:00:59Z","date_updated":"2023-08-16T12:22:07Z","author":[{"full_name":"Koehl, Patrice","last_name":"Koehl","first_name":"Patrice"},{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"department":[{"_id":"HeEd"}],"publisher":"American Chemical Society","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, 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.\r\nOpen Access is funded by the Austrian Science Fund (FWF).","ec_funded":1,"file_date_updated":"2023-08-16T12:21:13Z","language":[{"iso":"eng"}],"doi":"10.1021/acs.jcim.2c01346","project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000920370700001"],"pmid":["36638318"]},"publication_identifier":{"issn":["1549-9596"],"eissn":["1549-960X"]},"month":"02","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2023_JCIM_Koehl.pdf","creator":"dernst","file_size":8069223,"content_type":"application/pdf","file_id":"14070","relation":"main_file","success":1,"checksum":"7d20562269edff1e31b9d6019d4983b0","date_updated":"2023-08-16T12:21:13Z","date_created":"2023-08-16T12:21:13Z"}],"intvolume":" 63","status":"public","ddc":["510","540"],"title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12544","issue":"3","abstract":[{"lang":"eng","text":"Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software."}],"type":"journal_article","date_published":"2023-02-13T00:00:00Z","page":"973-985","article_type":"original","citation":{"chicago":"Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling. American Chemical Society, 2023. https://doi.org/10.1021/acs.jcim.2c01346.","mla":"Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:10.1021/acs.jcim.2c01346.","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","ista":"Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985.","apa":"Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. American Chemical Society. https://doi.org/10.1021/acs.jcim.2c01346","ieee":"P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023.","ama":"Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346"},"publication":"Journal of Chemical Information and Modeling","article_processing_charge":"No","has_accepted_license":"1","day":"13","scopus_import":"1"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts."}],"intvolume":" 7","status":"public","title":"Pathogen evasion of social immunity","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12543","file":[{"content_type":"application/pdf","file_size":1600499,"creator":"dernst","access_level":"open_access","file_name":"2023_NatureEcoEvo_Stock.pdf","checksum":"8244f4650a0e7aeea488d1bcd4a31702","success":1,"date_updated":"2023-08-16T11:54:59Z","date_created":"2023-08-16T11:54:59Z","relation":"main_file","file_id":"14069"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"450-460","article_type":"original","citation":{"apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6","ieee":"M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460.","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6","chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6."},"publication":"Nature Ecology and Evolution","date_published":"2023-03-01T00:00:00Z","ec_funded":1,"file_date_updated":"2023-08-16T11:54:59Z","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"publisher":"Springer Nature","publication_status":"published","pmid":1,"acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","year":"2023","volume":7,"date_updated":"2023-08-16T11:55:48Z","date_created":"2023-02-12T23:00:59Z","related_material":{"link":[{"url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","relation":"press_release","description":"News on ISTA website"}]},"author":[{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock"},{"full_name":"Milutinovic, Barbara","last_name":"Milutinovic","first_name":"Barbara","orcid":"0000-0002-8214-4758","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"id":"953894f3-25bd-11ec-8556-f70a9d38ef60","last_name":"Hönigsberger","first_name":"Michaela","full_name":"Hönigsberger, Michaela"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"last_name":"Wiesenhofer","first_name":"Florian","id":"39523C54-F248-11E8-B48F-1D18A9856A87","full_name":"Wiesenhofer, Florian"},{"full_name":"Kampleitner, Niklas","id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","last_name":"Kampleitner","first_name":"Niklas"},{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha"},{"full_name":"Schmitt, Thomas","last_name":"Schmitt","first_name":"Thomas"},{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"publication_identifier":{"eissn":["2397-334X"]},"month":"03","project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"},{"name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1038/s41559-023-01981-6"},{"article_number":"qrac004","ec_funded":1,"file_date_updated":"2023-08-16T11:43:33Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2023","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","volume":7,"date_updated":"2023-08-16T11:44:32Z","date_created":"2023-02-06T13:59:12Z","author":[{"last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","full_name":"Mrnjavac, Andrea"},{"full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","first_name":"Kseniia"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"publication_identifier":{"issn":["2056-3744"]},"month":"02","project":[{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"},{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["001021692200001"],"pmid":["37065438"]},"language":[{"iso":"eng"}],"doi":"10.1093/evlett/qrac004","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"intvolume":" 7","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","ddc":["570"],"status":"public","_id":"12521","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_id":"14068","date_created":"2023-08-16T11:43:33Z","date_updated":"2023-08-16T11:43:33Z","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","success":1,"file_name":"2023_EvLetters_Mrnjavac.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2592189,"creator":"dernst"}],"oa_version":"Published Version","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","article_type":"original","citation":{"ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 2023;7(1). doi:10.1093/evlett/qrac004","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” Evolution Letters, vol. 7, no. 1. Oxford University Press, 2023.","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., & Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. Oxford University Press. https://doi.org/10.1093/evlett/qrac004","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:10.1093/evlett/qrac004.","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” Evolution Letters. Oxford University Press, 2023. https://doi.org/10.1093/evlett/qrac004."},"publication":"Evolution Letters","date_published":"2023-02-01T00:00:00Z"},{"year":"2023","acknowledgement":"I wish to thank all current and past members of the Hippenmeyer laboratory at ISTA for exciting discussions on the subject of this review. I apologize to colleagues whose work I could not cite and/or discuss in the frame of the available space. Work in the Hippenmeyer laboratory on the\r\ndiscussed topic is supported by ISTA institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agree-ment no. 725780 LinPro) to SH.","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"}],"author":[{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon"}],"date_updated":"2023-08-16T12:30:25Z","date_created":"2023-02-26T12:24:21Z","volume":79,"article_number":"102695","file_date_updated":"2023-08-16T12:29:06Z","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000953497700001"],"pmid":["36842274"]},"isi":1,"quality_controlled":"1","project":[{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805"},{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.conb.2023.102695","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["0959-4388"]},"_id":"12679","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Principles of neural stem cell lineage progression: Insights from developing cerebral cortex","ddc":["570"],"intvolume":" 79","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14071","checksum":"4d11c4ca87e6cbc4d2ac46d3225ea615","success":1,"date_updated":"2023-08-16T12:29:06Z","date_created":"2023-08-16T12:29:06Z","access_level":"open_access","file_name":"2023_CurrentOpinionNeurobio_Hippenmeyer.pdf","content_type":"application/pdf","file_size":1787894,"creator":"dernst"}],"type":"journal_article","abstract":[{"text":"How to generate a brain of correct size and with appropriate cell-type diversity during development is a major question in Neuroscience. In the developing neocortex, radial glial progenitor (RGP) cells are the main neural stem cells that produce cortical excitatory projection neurons, glial cells, and establish the prospective postnatal stem cell niche in the lateral ventricles. RGPs follow a tightly orchestrated developmental program that when disrupted can result in severe cortical malformations such as microcephaly and megalencephaly. The precise cellular and molecular mechanisms instructing faithful RGP lineage progression are however not well understood. This review will summarize recent conceptual advances that contribute to our understanding of the general principles of RGP lineage progression.","lang":"eng"}],"issue":"4","publication":"Current Opinion in Neurobiology","citation":{"ama":"Hippenmeyer S. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 2023;79(4). doi:10.1016/j.conb.2023.102695","ista":"Hippenmeyer S. 2023. Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. 79(4), 102695.","ieee":"S. Hippenmeyer, “Principles of neural stem cell lineage progression: Insights from developing cerebral cortex,” Current Opinion in Neurobiology, vol. 79, no. 4. Elsevier, 2023.","apa":"Hippenmeyer, S. (2023). Principles of neural stem cell lineage progression: Insights from developing cerebral cortex. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2023.102695","mla":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology, vol. 79, no. 4, 102695, Elsevier, 2023, doi:10.1016/j.conb.2023.102695.","short":"S. Hippenmeyer, Current Opinion in Neurobiology 79 (2023).","chicago":"Hippenmeyer, Simon. “Principles of Neural Stem Cell Lineage Progression: Insights from Developing Cerebral Cortex.” Current Opinion in Neurobiology. Elsevier, 2023. https://doi.org/10.1016/j.conb.2023.102695."},"article_type":"review","date_published":"2023-04-01T00:00:00Z","scopus_import":"1","keyword":["General Neuroscience"],"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"month":"04","publication_identifier":{"issn":["0025-584X"],"eissn":["1522-2616"]},"language":[{"iso":"eng"}],"doi":"10.1002/mana.202100192","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"arxiv":["2104.05063"],"isi":["000914134900001"]},"oa":1,"file_date_updated":"2023-08-16T11:40:02Z","date_created":"2023-01-29T23:00:59Z","date_updated":"2023-08-16T11:41:42Z","volume":296,"author":[{"last_name":"Agresti","first_name":"Antonio","orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio"},{"full_name":"Lindemulder, Nick","first_name":"Nick","last_name":"Lindemulder"},{"first_name":"Mark","last_name":"Veraar","full_name":"Veraar, Mark"}],"publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Wiley","year":"2023","acknowledgement":"The first author has been partially supported by the Nachwuchsring—Network for the promotion of young scientists—at TU Kaiserslautern. The second and third authors were supported by the Vidi subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO).","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2023-04-01T00:00:00Z","article_type":"original","page":"1319-1350","publication":"Mathematische Nachrichten","citation":{"chicago":"Agresti, Antonio, Nick Lindemulder, and Mark Veraar. “On the Trace Embedding and Its Applications to Evolution Equations.” Mathematische Nachrichten. Wiley, 2023. https://doi.org/10.1002/mana.202100192.","short":"A. Agresti, N. Lindemulder, M. Veraar, Mathematische Nachrichten 296 (2023) 1319–1350.","mla":"Agresti, Antonio, et al. “On the Trace Embedding and Its Applications to Evolution Equations.” Mathematische Nachrichten, vol. 296, no. 4, Wiley, 2023, pp. 1319–50, doi:10.1002/mana.202100192.","ieee":"A. Agresti, N. Lindemulder, and M. Veraar, “On the trace embedding and its applications to evolution equations,” Mathematische Nachrichten, vol. 296, no. 4. Wiley, pp. 1319–1350, 2023.","apa":"Agresti, A., Lindemulder, N., & Veraar, M. (2023). On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. Wiley. https://doi.org/10.1002/mana.202100192","ista":"Agresti A, Lindemulder N, Veraar M. 2023. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 296(4), 1319–1350.","ama":"Agresti A, Lindemulder N, Veraar M. On the trace embedding and its applications to evolution equations. Mathematische Nachrichten. 2023;296(4):1319-1350. doi:10.1002/mana.202100192"},"abstract":[{"lang":"eng","text":"In this paper, we consider traces at initial times for functions with mixed time-space smoothness. Such results are often needed in the theory of evolution equations. Our result extends and unifies many previous results. Our main improvement is that we can allow general interpolation couples. The abstract results are applied to regularity problems for fractional evolution equations and stochastic evolution equations, where uniform trace estimates on the half-line are shown."}],"issue":"4","type":"journal_article","file":[{"file_name":"2023_MathNachrichten_Agresti.pdf","access_level":"open_access","file_size":449280,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"14067","date_created":"2023-08-16T11:40:02Z","date_updated":"2023-08-16T11:40:02Z","checksum":"6f099f1d064173784d1a27716a2cc795","success":1}],"oa_version":"Published Version","title":"On the trace embedding and its applications to evolution equations","ddc":["510"],"status":"public","intvolume":" 296","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12429"},{"article_number":"2350006","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"World Scientific Publishing","year":"2023","date_created":"2023-01-29T23:00:59Z","date_updated":"2023-08-16T11:47:27Z","volume":35,"author":[{"last_name":"Falconi","first_name":"Marco","full_name":"Falconi, Marco"},{"first_name":"Nikolai K","last_name":"Leopold","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K"},{"first_name":"David Johannes","last_name":"Mitrouskas","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","full_name":"Mitrouskas, David Johannes"},{"full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrat","first_name":"Sören P"}],"month":"01","publication_identifier":{"issn":["0129-055X"]},"quality_controlled":"1","isi":1,"external_id":{"arxiv":["2110.00458"],"isi":["000909760300001"]},"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2110.00458","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1142/S0129055X2350006X","type":"journal_article","abstract":[{"lang":"eng","text":"We study the time evolution of the Nelson model in a mean-field limit in which N nonrelativistic bosons weakly couple (with respect to the particle number) to a positive or zero mass quantized scalar field. Our main result is the derivation of the Bogoliubov dynamics and higher-order corrections. More precisely, we prove the convergence of the approximate wave function to the many-body wave function in norm, with a convergence rate proportional to the number of corrections taken into account in the approximation. We prove an analogous result for the unitary propagator. As an application, we derive a simple system of partial differential equations describing the time evolution of the first- and second-order approximations to the one-particle reduced density matrices of the particles and the quantum field, respectively."}],"issue":"4","status":"public","title":"Bogoliubov dynamics and higher-order corrections for the regularized Nelson model","intvolume":" 35","_id":"12430","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","day":"09","article_processing_charge":"No","article_type":"original","publication":"Reviews in Mathematical Physics","citation":{"ama":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 2023;35(4). doi:10.1142/S0129055X2350006X","ieee":"M. Falconi, N. K. Leopold, D. J. Mitrouskas, and S. P. Petrat, “Bogoliubov dynamics and higher-order corrections for the regularized Nelson model,” Reviews in Mathematical Physics, vol. 35, no. 4. World Scientific Publishing, 2023.","apa":"Falconi, M., Leopold, N. K., Mitrouskas, D. J., & Petrat, S. P. (2023). Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X2350006X","ista":"Falconi M, Leopold NK, Mitrouskas DJ, Petrat SP. 2023. Bogoliubov dynamics and higher-order corrections for the regularized Nelson model. Reviews in Mathematical Physics. 35(4), 2350006.","short":"M. Falconi, N.K. Leopold, D.J. Mitrouskas, S.P. Petrat, Reviews in Mathematical Physics 35 (2023).","mla":"Falconi, Marco, et al. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” Reviews in Mathematical Physics, vol. 35, no. 4, 2350006, World Scientific Publishing, 2023, doi:10.1142/S0129055X2350006X.","chicago":"Falconi, Marco, Nikolai K Leopold, David Johannes Mitrouskas, and Sören P Petrat. “Bogoliubov Dynamics and Higher-Order Corrections for the Regularized Nelson Model.” Reviews in Mathematical Physics. World Scientific Publishing, 2023. https://doi.org/10.1142/S0129055X2350006X."},"date_published":"2023-01-09T00:00:00Z"},{"publication":"Nature Computational Science","citation":{"chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-023-00410-9","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263.","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9"},"article_type":"original","page":"254-263","date_published":"2023-03-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No","has_accepted_license":"1","_id":"12762","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","ddc":["570"],"intvolume":" 3","file":[{"content_type":"application/pdf","file_size":4474284,"creator":"dernst","file_name":"2023_NatureCompScience_Lombardi.pdf","access_level":"open_access","date_updated":"2023-08-16T12:39:57Z","date_created":"2023-08-16T12:39:57Z","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","success":1,"relation":"main_file","file_id":"14073"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations."}],"external_id":{"arxiv":["2108.06686"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"}],"doi":"10.1038/s43588-023-00410-9","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["2662-8457"]},"acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"author":[{"full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","first_name":"Fabrizio"},{"full_name":"Pepic, Selver","first_name":"Selver","last_name":"Pepic","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","first_name":"Daniele","last_name":"De Martino"}],"date_updated":"2023-08-16T12:41:53Z","date_created":"2023-03-26T22:01:08Z","volume":3,"file_date_updated":"2023-08-16T12:39:57Z","ec_funded":1},{"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"month":"07","external_id":{"unknown":["2211.09606"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.ICALP.2023.69","conference":{"end_date":"2023-07-14","start_date":"2023-07-10","location":"Paderborn, Germany","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"language":[{"iso":"eng"}],"article_number":"69","ec_funded":1,"file_date_updated":"2023-08-21T06:59:05Z","year":"2023","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No.\r\n101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the\r\nAustrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”,\r\nI 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nThis work was done in part while Gramoz Goranci was at Institute for Theoretical Studies, ETH Zurich, Switzerland. There, he was supported by Dr. Max Rössler, the Walter Haefner Foundation and the ETH Zürich Foundation. We also thank Richard Peng, Thatchaphol Saranurak, Sebastian Forster and Sushant Sachdeva for helpful discussions, and the anonymous reviewers for their insightful comments.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"publication_status":"published","author":[{"last_name":"Goranci","first_name":"Gramoz","full_name":"Goranci, Gramoz"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"}],"volume":261,"date_created":"2023-08-20T22:01:14Z","date_updated":"2023-08-21T07:00:49Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","citation":{"mla":"Goranci, Gramoz, and Monika H. Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 69, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.69.","short":"G. Goranci, M.H. Henzinger, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Goranci, Gramoz, and Monika H Henzinger. “Efficient Data Structures for Incremental Exact and Approximate Maximum Flow.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.69.","ama":"Goranci G, Henzinger MH. Efficient data structures for incremental exact and approximate maximum flow. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.69","ista":"Goranci G, Henzinger MH. 2023. Efficient data structures for incremental exact and approximate maximum flow. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 69.","ieee":"G. Goranci and M. H. Henzinger, “Efficient data structures for incremental exact and approximate maximum flow,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","apa":"Goranci, G., & Henzinger, M. H. (2023). Efficient data structures for incremental exact and approximate maximum flow. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.69"},"publication":"50th International Colloquium on Automata, Languages, and Programming","date_published":"2023-07-01T00:00:00Z","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"We show an (1+ϵ)-approximation algorithm for maintaining maximum s-t flow under m edge insertions in m1/2+o(1)ϵ−1/2 amortized update time for directed, unweighted graphs. This constitutes the first sublinear dynamic maximum flow algorithm in general sparse graphs with arbitrarily good approximation guarantee.","lang":"eng"}],"_id":"14085","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 261","ddc":["000"],"title":"Efficient data structures for incremental exact and approximate maximum flow","status":"public","file":[{"file_name":"2023_LIPIcsICALP_Goranci.pdf","access_level":"open_access","content_type":"application/pdf","file_size":875910,"creator":"dernst","relation":"main_file","file_id":"14089","date_created":"2023-08-21T06:59:05Z","date_updated":"2023-08-21T06:59:05Z","checksum":"074177e815a1656de5d4071c7a3dffa6","success":1}],"oa_version":"Published Version"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2007.10824"]},"quality_controlled":"1","conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.4230/LIPIcs.ICALP.2023.72","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"year":"2023","acknowledgement":"We thank Heng Guo for helpful explanations of algorithms for sampling connected subgraphs and matchings, Maksym Serbyn for bringing to our attention the Wang-Landau algorithm and its use in physics.","publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Harris","first_name":"David G.","full_name":"Harris, David G."},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir"}],"date_updated":"2023-08-21T06:49:11Z","date_created":"2023-08-20T22:01:14Z","volume":261,"article_number":"72","file_date_updated":"2023-08-21T06:45:16Z","publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"ista":"Harris DG, Kolmogorov V. 2023. Parameter estimation for Gibbs distributions. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 72.","ieee":"D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","apa":"Harris, D. G., & Kolmogorov, V. (2023). Parameter estimation for Gibbs distributions. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.72","ama":"Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.72","chicago":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.72.","mla":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 72, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.72.","short":"D.G. Harris, V. Kolmogorov, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023."},"date_published":"2023-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","_id":"14084","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","510"],"status":"public","title":"Parameter estimation for Gibbs distributions","intvolume":" 261","file":[{"file_size":917791,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_LIPIcsICALP_Harris.pdf","checksum":"6dee0684245bb1c524b9c955db1e933d","success":1,"date_updated":"2023-08-21T06:45:16Z","date_created":"2023-08-21T06:45:16Z","relation":"main_file","file_id":"14088"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We will consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n].\r\nThe partition function is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the log partition ratio is defined as q = (log Z(β_max))/Z(β_min)\r\nWe develop a number of algorithms to estimate the counts c_x using roughly Õ(q/ε²) samples for general Gibbs distributions and Õ(n²/ε²) samples for integer-valued distributions (ignoring some second-order terms and parameters), We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs and perfect matchings in a graph."}]},{"year":"2023","acknowledgement":" Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. Jan Vondrák: Supported by NSF Award 2127781.","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"author":[{"full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"full_name":"Liu, Paul","last_name":"Liu","first_name":"Paul"},{"last_name":"Vondrák","first_name":"Jan","full_name":"Vondrák, Jan"},{"first_name":"Da Wei","last_name":"Zheng","full_name":"Zheng, Da Wei"}],"date_created":"2023-08-20T22:01:14Z","date_updated":"2023-08-21T07:05:47Z","volume":261,"article_number":"74","file_date_updated":"2023-08-21T07:04:36Z","ec_funded":1,"external_id":{"arxiv":["2305.00122"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"conference":{"end_date":"2023-07-14","location":"Paderborn, Germany","start_date":"2023-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"doi":"10.4230/LIPIcs.ICALP.2023.74","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"isbn":["9783959772785"],"issn":["18688969"]},"_id":"14086","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000"],"title":"Faster submodular maximization for several classes of matroids","intvolume":" 261","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"14090","checksum":"a5eef225014e003efbfbe4830fdd23cb","success":1,"date_created":"2023-08-21T07:04:36Z","date_updated":"2023-08-21T07:04:36Z","access_level":"open_access","file_name":"2023_LIPIcsICALP_HenzingerM.pdf","content_type":"application/pdf","file_size":930943,"creator":"dernst"}],"type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"The maximization of submodular functions have found widespread application in areas such as machine learning, combinatorial optimization, and economics, where practitioners often wish to enforce various constraints; the matroid constraint has been investigated extensively due to its algorithmic properties and expressive power. Though tight approximation algorithms for general matroid constraints exist in theory, the running times of such algorithms typically scale quadratically, and are not practical for truly large scale settings. Recent progress has focused on fast algorithms for important classes of matroids given in explicit form. Currently, nearly-linear time algorithms only exist for graphic and partition matroids [Alina Ene and Huy L. Nguyen, 2019]. In this work, we develop algorithms for monotone submodular maximization constrained by graphic, transversal matroids, or laminar matroids in time near-linear in the size of their representation. Our algorithms achieve an optimal approximation of 1-1/e-ε and both generalize and accelerate the results of Ene and Nguyen [Alina Ene and Huy L. Nguyen, 2019]. In fact, the running time of our algorithm cannot be improved within the fast continuous greedy framework of Badanidiyuru and Vondrák [Ashwinkumar Badanidiyuru and Jan Vondrák, 2014].\r\nTo achieve near-linear running time, we make use of dynamic data structures that maintain bases with approximate maximum cardinality and weight under certain element updates. These data structures need to support a weight decrease operation and a novel Freeze operation that allows the algorithm to freeze elements (i.e. force to be contained) in its basis regardless of future data structure operations. For the laminar matroid, we present a new dynamic data structure using the top tree interface of Alstrup, Holm, de Lichtenberg, and Thorup [Stephen Alstrup et al., 2005] that maintains the maximum weight basis under insertions and deletions of elements in O(log n) time. This data structure needs to support certain subtree query and path update operations that are performed every insertion and deletion that are non-trivial to handle in conjunction. For the transversal matroid the Freeze operation corresponds to requiring the data structure to keep a certain set S of vertices matched, a property that we call S-stability. While there is a large body of work on dynamic matching algorithms, none are S-stable and maintain an approximate maximum weight matching under vertex updates. We give the first such algorithm for bipartite graphs with total running time linear (up to log factors) in the number of edges."}],"publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"apa":"Henzinger, M. H., Liu, P., Vondrák, J., & Zheng, D. W. (2023). Faster submodular maximization for several classes of matroids. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.74","ieee":"M. H. Henzinger, P. Liu, J. Vondrák, and D. W. Zheng, “Faster submodular maximization for several classes of matroids,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","ista":"Henzinger MH, Liu P, Vondrák J, Zheng DW. 2023. Faster submodular maximization for several classes of matroids. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 74.","ama":"Henzinger MH, Liu P, Vondrák J, Zheng DW. Faster submodular maximization for several classes of matroids. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.74","chicago":"Henzinger, Monika H, Paul Liu, Jan Vondrák, and Da Wei Zheng. “Faster Submodular Maximization for Several Classes of Matroids.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.74.","short":"M.H. Henzinger, P. Liu, J. Vondrák, D.W. Zheng, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Henzinger, Monika H., et al. “Faster Submodular Maximization for Several Classes of Matroids.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 74, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.74."},"date_published":"2023-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1"},{"month":"07","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959772785"]},"quality_controlled":"1","external_id":{"arxiv":["2210.07754"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","location":"Paderborn, Germany","start_date":"2023-07-10","end_date":"2023-07-14"},"doi":"10.4230/LIPIcs.ICALP.2023.99","article_number":"99","file_date_updated":"2023-08-21T07:23:18Z","publication_status":"published","department":[{"_id":"MaMo"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"Nicolas Resch: Research supported in part by ERC H2020 grant No.74079 (ALGSTRONGCRYPTO). Chen Yuan: Research supported in part by the National Key Research and Development Projects under Grant 2022YFA1004900 and Grant 2021YFE0109900, the National Natural Science Foundation of China under Grant 12101403 and Grant 12031011.\r\nAcknowledgements YZ is grateful to Shashank Vatedka, Diyuan Wu and Fengxing Zhu for inspiring discussions.","year":"2023","date_created":"2023-08-20T22:01:13Z","date_updated":"2023-08-21T07:26:01Z","volume":261,"author":[{"first_name":"Nicolas","last_name":"Resch","full_name":"Resch, Nicolas"},{"full_name":"Yuan, Chen","last_name":"Yuan","first_name":"Chen"},{"last_name":"Zhang","first_name":"Yihan","orcid":"0000-0002-6465-6258","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan"}],"scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","publication":"50th International Colloquium on Automata, Languages, and Programming","citation":{"short":"N. Resch, C. Yuan, Y. Zhang, in:, 50th International Colloquium on Automata, Languages, and Programming, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","mla":"Resch, Nicolas, et al. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” 50th International Colloquium on Automata, Languages, and Programming, vol. 261, 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.ICALP.2023.99.","chicago":"Resch, Nicolas, Chen Yuan, and Yihan Zhang. “Zero-Rate Thresholds and New Capacity Bounds for List-Decoding and List-Recovery.” In 50th International Colloquium on Automata, Languages, and Programming, Vol. 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.ICALP.2023.99.","ama":"Resch N, Yuan C, Zhang Y. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In: 50th International Colloquium on Automata, Languages, and Programming. Vol 261. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.ICALP.2023.99","apa":"Resch, N., Yuan, C., & Zhang, Y. (2023). Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. In 50th International Colloquium on Automata, Languages, and Programming (Vol. 261). Paderborn, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2023.99","ieee":"N. Resch, C. Yuan, and Y. Zhang, “Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery,” in 50th International Colloquium on Automata, Languages, and Programming, Paderborn, Germany, 2023, vol. 261.","ista":"Resch N, Yuan C, Zhang Y. 2023. Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery. 50th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 261, 99."},"date_published":"2023-07-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"In this work we consider the list-decodability and list-recoverability of arbitrary q-ary codes, for all integer values of q ≥ 2. A code is called (p,L)_q-list-decodable if every radius pn Hamming ball contains less than L codewords; (p,𝓁,L)_q-list-recoverability is a generalization where we place radius pn Hamming balls on every point of a combinatorial rectangle with side length 𝓁 and again stipulate that there be less than L codewords.\r\nOur main contribution is to precisely calculate the maximum value of p for which there exist infinite families of positive rate (p,𝓁,L)_q-list-recoverable codes, the quantity we call the zero-rate threshold. Denoting this value by p_*, we in fact show that codes correcting a p_*+ε fraction of errors must have size O_ε(1), i.e., independent of n. Such a result is typically referred to as a \"Plotkin bound.\" To complement this, a standard random code with expurgation construction shows that there exist positive rate codes correcting a p_*-ε fraction of errors. We also follow a classical proof template (typically attributed to Elias and Bassalygo) to derive from the zero-rate threshold other tradeoffs between rate and decoding radius for list-decoding and list-recovery.\r\nTechnically, proving the Plotkin bound boils down to demonstrating the Schur convexity of a certain function defined on the q-simplex as well as the convexity of a univariate function derived from it. We remark that an earlier argument claimed similar results for q-ary list-decoding; however, we point out that this earlier proof is flawed.","lang":"eng"}],"ddc":["000"],"status":"public","title":"Zero-rate thresholds and new capacity bounds for list-decoding and list-recovery","intvolume":" 261","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14083","oa_version":"Published Version","file":[{"file_name":"2023_LIPIcsICALP_Resch.pdf","access_level":"open_access","creator":"dernst","file_size":1141497,"content_type":"application/pdf","file_id":"14091","relation":"main_file","date_created":"2023-08-21T07:23:18Z","date_updated":"2023-08-21T07:23:18Z","success":1,"checksum":"a449143fec3fbebb092cb8ef3b53c226"}]},{"month":"03","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"949120","_id":"0aa60e99-070f-11eb-9043-a6de6bdc3afa","call_identifier":"H2020","name":"Tribocharge: a multi-scale approach to an enduring problem in physics"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2211.02488"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2211.02488"],"isi":["000946178200008"]},"language":[{"iso":"eng"}],"doi":"10.1103/physrevlett.130.098202","article_number":"098202","file_date_updated":"2023-02-28T12:37:54Z","ec_funded":1,"publication_status":"published","department":[{"_id":"ScWa"}],"publisher":"American Physical Society","acknowledgement":"We would like to thank Troy Shinbrot, Victor Lee and Daniele Foresti for helpful discussions. This project has received funding from the European Research Council Grant Agreement No. 949120 and from the the Marie Sk lodowska-Curie Grant Agreement No. 754411 under\r\nthe European Union’s Horizon 2020 research and innovation program.","year":"2023","date_updated":"2023-08-22T08:41:32Z","date_created":"2023-02-28T12:14:46Z","volume":130,"author":[{"full_name":"Grosjean, Galien M","first_name":"Galien M","last_name":"Grosjean","id":"0C5FDA4A-9CF6-11E9-8939-FF05E6697425","orcid":"0000-0001-5154-417X"},{"last_name":"Waitukaitis","first_name":"Scott R","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R"}],"related_material":{"record":[{"id":"8101","relation":"research_paper","status":"public"}]},"keyword":["General Physics","Electrostatics","Triboelectricity","Soft Matter","Acoustic Levitation","Granular Materials"],"day":"03","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Physical Review Letters","citation":{"mla":"Grosjean, Galien M., and Scott R. Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters, vol. 130, no. 9, 098202, American Physical Society, 2023, doi:10.1103/physrevlett.130.098202.","short":"G.M. Grosjean, S.R. Waitukaitis, Physical Review Letters 130 (2023).","chicago":"Grosjean, Galien M, and Scott R Waitukaitis. “Single-Collision Statistics Reveal a Global Mechanism Driven by Sample History for Contact Electrification in Granular Media.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.130.098202.","ama":"Grosjean GM, Waitukaitis SR. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 2023;130(9). doi:10.1103/physrevlett.130.098202","ista":"Grosjean GM, Waitukaitis SR. 2023. Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. 130(9), 098202.","apa":"Grosjean, G. M., & Waitukaitis, S. R. (2023). Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.130.098202","ieee":"G. M. Grosjean and S. R. Waitukaitis, “Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media,” Physical Review Letters, vol. 130, no. 9. American Physical Society, 2023."},"date_published":"2023-03-03T00:00:00Z","type":"journal_article","abstract":[{"text":"Models for same-material contact electrification in granular media often rely on a local charge-driving parameter whose spatial variations lead to a stochastic origin for charge exchange. Measuring the charge transfer from individual granular spheres after contacts with substrates of the same material, we find instead a “global” charging behavior, coherent over the sample’s whole surface. Cleaning and baking samples fully resets charging magnitude and direction, which indicates the underlying global parameter is not intrinsic to the material, but acquired from its history. Charging behavior is randomly and irreversibly affected by changes in relative humidity, hinting at a mechanism where adsorbates, in particular, water, are fundamental to the charge-transfer process.","lang":"eng"}],"issue":"9","status":"public","ddc":["530","537"],"title":"Single-collision statistics reveal a global mechanism driven by sample history for contact electrification in granular media","intvolume":" 130","_id":"12697","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"checksum":"c4f2f6eea0408811f8f4898e15890355","date_updated":"2023-02-28T12:20:27Z","date_created":"2023-02-28T12:20:27Z","file_id":"12698","relation":"main_file","creator":"ggrosjea","file_size":2301864,"content_type":"application/pdf","access_level":"open_access","file_name":"Main_Preprint.pdf"},{"access_level":"open_access","file_name":"Suppl_info.pdf","creator":"ggrosjea","content_type":"application/pdf","file_size":1138625,"file_id":"12699","relation":"main_file","success":1,"checksum":"6af6ed6c97a977f923de4162294b43c4","date_created":"2023-02-28T12:20:55Z","date_updated":"2023-02-28T12:20:55Z"},{"file_name":"Suppl_vid1.mp4","access_level":"open_access","file_size":793449,"content_type":"video/mp4","creator":"ggrosjea","relation":"main_file","file_id":"12700","date_created":"2023-02-28T12:37:54Z","date_updated":"2023-02-28T12:37:54Z","checksum":"3f20365fb9515bdba3a111d912c8d8b4","success":1},{"file_size":455925,"content_type":"video/mp4","creator":"ggrosjea","file_name":"Suppl_vid2.mp4","access_level":"open_access","date_updated":"2023-02-28T12:37:54Z","date_created":"2023-02-28T12:37:54Z","checksum":"90cecacbe0e2f9dea11f91a4ba20c32e","success":1,"relation":"main_file","file_id":"12701"}],"oa_version":"Preprint"},{"file":[{"access_level":"open_access","file_name":"thesis_pdfa.pdf","creator":"cchlebak","file_size":18688376,"content_type":"application/pdf","file_id":"13176","relation":"main_file","success":1,"checksum":"7d03f1a5a5258ee43dfc3323dea4e08f","date_created":"2023-06-30T08:17:25Z","date_updated":"2023-06-30T08:17:25Z"},{"relation":"source_file","file_id":"13196","checksum":"c3b45317ae58e0527533f98c202d81b7","date_created":"2023-07-06T11:35:15Z","date_updated":"2023-07-06T11:35:15Z","access_level":"closed","file_name":"thesis.zip","file_size":37847025,"content_type":"application/x-zip-compressed","creator":"cchlebak"}],"oa_version":"Published Version","ddc":["537","535","539"],"status":"public","title":"Cavity quantum electrooptics","_id":"13175","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"text":"About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. \r\n\r\nQuantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. \r\n\r\nTill date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. \r\n\r\nAfter decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. \r\n\r\nOptical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. \r\n\r\nIn this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. \r\nWith this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2023-05-05T00:00:00Z","page":"202","citation":{"chicago":"Sahu, Rishabh. “Cavity Quantum Electrooptics.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13175.","short":"R. Sahu, Cavity Quantum Electrooptics, Institute of Science and Technology Austria, 2023.","mla":"Sahu, Rishabh. Cavity Quantum Electrooptics. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13175.","ieee":"R. Sahu, “Cavity quantum electrooptics,” Institute of Science and Technology Austria, 2023.","apa":"Sahu, R. (2023). Cavity quantum electrooptics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13175","ista":"Sahu R. 2023. Cavity quantum electrooptics. Institute of Science and Technology Austria.","ama":"Sahu R. Cavity quantum electrooptics. 2023. doi:10.15479/at:ista:13175"},"day":"05","article_processing_charge":"No","has_accepted_license":"1","keyword":["quantum optics","electrooptics","quantum networks","quantum communication","transduction"],"date_created":"2023-06-30T08:07:43Z","date_updated":"2023-08-24T11:16:35Z","author":[{"last_name":"Sahu","first_name":"Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh"}],"related_material":{"record":[{"id":"12900","status":"public","relation":"old_edition"},{"id":"10924","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"9114"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoFi"}],"publisher":"Institute of Science and Technology Austria","year":"2023","file_date_updated":"2023-07-06T11:35:15Z","ec_funded":1,"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"SSU"},{"_id":"NanoFab"}],"supervisor":[{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:13175","project":[{"_id":"26336814-B435-11E9-9278-68D0E5697425","grant_number":"758053","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Quantum Local Area Networks with Superconducting Qubits"},{"_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"month":"05","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-030-5"]}},{"abstract":[{"text":"We study the problem of training and certifying adversarially robust quantized neural networks (QNNs). Quantization is a technique for making neural networks more efficient by running them using low-bit integer arithmetic and is therefore commonly adopted in industry. Recent work has shown that floating-point neural networks that have been verified to be robust can become vulnerable to adversarial attacks after quantization, and certification of the quantized representation is necessary to guarantee robustness. In this work, we present quantization-aware interval bound propagation (QA-IBP), a novel method for training robust QNNs. Inspired by advances in robust learning of non-quantized networks, our training algorithm computes the gradient of an abstract representation of the actual network. Unlike existing approaches, our method can handle the discrete semantics of QNNs. Based on QA-IBP, we also develop a complete verification procedure for verifying the adversarial robustness of QNNs, which is guaranteed to terminate and produce a correct answer. Compared to existing approaches, the key advantage of our verification procedure is that it runs entirely on GPU or other accelerator devices. We demonstrate experimentally that our approach significantly outperforms existing methods and establish the new state-of-the-art for training and certifying the robustness of QNNs.","lang":"eng"}],"issue":"12","type":"conference","oa_version":"Preprint","_id":"14242","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Quantization-aware interval bound propagation for training certifiably robust quantized neural networks","intvolume":" 37","day":"26","article_processing_charge":"No","scopus_import":"1","date_published":"2023-06-26T00:00:00Z","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","citation":{"chicago":"Lechner, Mathias, Dorde Zikelic, Krishnendu Chatterjee, Thomas A Henzinger, and Daniela Rus. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:14964–73. Association for the Advancement of Artificial Intelligence, 2023. https://doi.org/10.1609/aaai.v37i12.26747.","short":"M. Lechner, D. Zikelic, K. Chatterjee, T.A. Henzinger, D. Rus, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–14973.","mla":"Lechner, Mathias, et al. “Quantization-Aware Interval Bound Propagation for Training Certifiably Robust Quantized Neural Networks.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 12, Association for the Advancement of Artificial Intelligence, 2023, pp. 14964–73, doi:10.1609/aaai.v37i12.26747.","ieee":"M. Lechner, D. Zikelic, K. Chatterjee, T. A. Henzinger, and D. Rus, “Quantization-aware interval bound propagation for training certifiably robust quantized neural networks,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 12, pp. 14964–14973.","apa":"Lechner, M., Zikelic, D., Chatterjee, K., Henzinger, T. A., & Rus, D. (2023). Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 14964–14973). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v37i12.26747","ista":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. 2023. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 14964–14973.","ama":"Lechner M, Zikelic D, Chatterjee K, Henzinger TA, Rus D. Quantization-aware interval bound propagation for training certifiably robust quantized neural networks. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:14964-14973. doi:10.1609/aaai.v37i12.26747"},"page":"14964-14973","ec_funded":1,"author":[{"last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Rus","first_name":"Daniela","full_name":"Rus, Daniela"}],"date_created":"2023-08-27T22:01:17Z","date_updated":"2023-09-05T07:06:14Z","volume":37,"year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. Research was sponsored by the United\r\nStates Air Force Research Laboratory and the United States Air Force Artificial Intelligence Accelerator and was accomplished under Cooperative Agreement Number FA8750-19-2-\r\n1000. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied,\r\nof the United States Air Force or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright\r\nnotation herein. The research was also funded in part by the AI2050 program at Schmidt Futures (Grant G-22-63172) and Capgemini SE.","publication_status":"published","publisher":"Association for the Advancement of Artificial Intelligence","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"month":"06","publication_identifier":{"isbn":["9781577358800"]},"conference":{"end_date":"2023-02-14","start_date":"2023-02-07","location":"Washington, DC, United States","name":"AAAI: Conference on Artificial Intelligence"},"doi":"10.1609/aaai.v37i12.26747","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2211.16187"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.16187"}],"quality_controlled":"1","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"ec_funded":1,"year":"2023","acknowledgement":"This research was supported in part by ISF grant no.1679/21, by the ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"full_name":"Jecker, Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425","first_name":"Ismael R","last_name":"Jecker"},{"full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699"}],"volume":37,"date_updated":"2023-09-05T08:37:00Z","date_created":"2023-08-27T22:01:18Z","publication_identifier":{"isbn":["9781577358800"]},"month":"06","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1609/aaai.v37i5.25679"}],"external_id":{"arxiv":["2211.13626"]},"oa":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"quality_controlled":"1","doi":"10.1609/aaai.v37i5.25679","conference":{"name":"AAAI: Conference on Artificial Intelligence","location":"Washington, DC, United States","start_date":"2023-02-07","end_date":"2023-02-14"},"language":[{"iso":"eng"}],"type":"conference","issue":"5","abstract":[{"lang":"eng","text":"Two-player zero-sum \"graph games\" are central in logic, verification, and multi-agent systems. The game proceeds by placing a token on a vertex of a graph, and allowing the players to move it to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In \"bidding games\", however, the players have budgets and in each turn, an auction (bidding) determines which player moves the token. So far, bidding games have only been studied as full-information games. In this work we initiate the study of partial-information bidding games: we study bidding games in which a player's initial budget is drawn from a known probability distribution. We show that while for some bidding mechanisms and objectives, it is straightforward to adapt the results from the full-information setting to the partial-information setting, for others, the analysis is significantly more challenging, requires new techniques, and gives rise to interesting results. Specifically, we study games with \"mean-payoff\" objectives in combination with \"poorman\" bidding. We construct optimal strategies for a partially-informed player who plays against a fully-informed adversary. We show that, somewhat surprisingly, the \"value\" under pure strategies does not necessarily exist in such games."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14243","intvolume":" 37","status":"public","title":"Bidding graph games with partially-observable budgets","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"27","citation":{"ama":"Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable budgets. In: Proceedings of the 37th AAAI Conference on Artificial Intelligence. Vol 37. ; 2023:5464-5471. doi:10.1609/aaai.v37i5.25679","apa":"Avni, G., Jecker, I. R., & Zikelic, D. (2023). Bidding graph games with partially-observable budgets. In Proceedings of the 37th AAAI Conference on Artificial Intelligence (Vol. 37, pp. 5464–5471). Washington, DC, United States. https://doi.org/10.1609/aaai.v37i5.25679","ieee":"G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable budgets,” in Proceedings of the 37th AAAI Conference on Artificial Intelligence, Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.","ista":"Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 5464–5471.","short":"G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, 2023, pp. 5464–5471.","mla":"Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.” Proceedings of the 37th AAAI Conference on Artificial Intelligence, vol. 37, no. 5, 2023, pp. 5464–71, doi:10.1609/aaai.v37i5.25679.","chicago":"Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with Partially-Observable Budgets.” In Proceedings of the 37th AAAI Conference on Artificial Intelligence, 37:5464–71, 2023. https://doi.org/10.1609/aaai.v37i5.25679."},"publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","page":"5464-5471","date_published":"2023-06-27T00:00:00Z"},{"month":"07","publication_identifier":{"isbn":["9798400701597"]},"quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2305.05944","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2305.05944"]},"language":[{"iso":"eng"}],"conference":{"start_date":"2023-08-06","location":"Los Angeles, CA, United States","end_date":"2023-08-10","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"},"doi":"10.1145/3588432.3591542","article_number":"20","publication_status":"published","publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"year":"2023","acknowledgement":"The authors would like to thank Yuki Koyama and Takeo Igarashi for early discussions, and Yuta Yaguchi for support in 3D printing. This research is partially supported by the Israel Science Foundation grant number 1390/19.\r\n","date_created":"2023-08-27T22:01:17Z","date_updated":"2023-09-05T07:22:03Z","author":[{"last_name":"Tojo","first_name":"Kenji","full_name":"Tojo, Kenji"},{"first_name":"Ariel","last_name":"Shamir","full_name":"Shamir, Ariel"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"},{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"}],"scopus_import":"1","day":"23","article_processing_charge":"No","publication":"SIGGRAPH 2023 Conference Proceedings","citation":{"apa":"Tojo, K., Shamir, A., Bickel, B., & Umetani, N. (2023). Stealth shaper: Reflectivity optimization as surface stylization. In SIGGRAPH 2023 Conference Proceedings. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3588432.3591542","ieee":"K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Stealth shaper: Reflectivity optimization as surface stylization,” in SIGGRAPH 2023 Conference Proceedings, Los Angeles, CA, United States, 2023.","ista":"Tojo K, Shamir A, Bickel B, Umetani N. 2023. Stealth shaper: Reflectivity optimization as surface stylization. SIGGRAPH 2023 Conference Proceedings. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 20.","ama":"Tojo K, Shamir A, Bickel B, Umetani N. Stealth shaper: Reflectivity optimization as surface stylization. In: SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery; 2023. doi:10.1145/3588432.3591542","chicago":"Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” In SIGGRAPH 2023 Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591542.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH 2023 Conference Proceedings, Association for Computing Machinery, 2023.","mla":"Tojo, Kenji, et al. “Stealth Shaper: Reflectivity Optimization as Surface Stylization.” SIGGRAPH 2023 Conference Proceedings, 20, Association for Computing Machinery, 2023, doi:10.1145/3588432.3591542."},"date_published":"2023-07-23T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We present a technique to optimize the reflectivity of a surface while preserving its overall shape. The naïve optimization of the mesh vertices using the gradients of reflectivity simulations results in undesirable distortion. In contrast, our robust formulation optimizes the surface normal as an independent variable that bridges the reflectivity term with differential rendering, and the regularization term with as-rigid-as-possible elastic energy. We further adaptively subdivide the input mesh to improve the convergence. Consequently, our method can minimize the retroreflectivity of a wide range of input shapes, resulting in sharply creased shapes ubiquitous among stealth aircraft and Sci-Fi vehicles. Furthermore, by changing the reward for the direction of the outgoing light directions, our method can be applied to other reflectivity design tasks, such as the optimization of architectural walls to concentrate light in a specific region. We have tested the proposed method using light-transport simulations and real-world 3D-printed objects."}],"title":"Stealth shaper: Reflectivity optimization as surface stylization","status":"public","_id":"14241","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"_id":"13310","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["000"],"status":"public","title":"Monitoring algorithmic fairness","intvolume":" 13965","file":[{"file_id":"13327","relation":"main_file","success":1,"checksum":"ccaf94bf7d658ba012c016e11869b54c","date_created":"2023-07-31T08:11:20Z","date_updated":"2023-07-31T08:11:20Z","access_level":"open_access","file_name":"2023_LNCS_CAV_HenzingerT.pdf","creator":"dernst","content_type":"application/pdf","file_size":647760}],"oa_version":"Published Version","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Machine-learned systems are in widespread use for making decisions about humans, and it is important that they are fair, i.e., not biased against individuals based on sensitive attributes. We present runtime verification of algorithmic fairness for systems whose models are unknown, but are assumed to have a Markov chain structure. We introduce a specification language that can model many common algorithmic fairness properties, such as demographic parity, equal opportunity, and social burden. We build monitors that observe a long sequence of events as generated by a given system, and output, after each observation, a quantitative estimate of how fair or biased the system was on that run until that point in time. The estimate is proven to be correct modulo a variable error bound and a given confidence level, where the error bound gets tighter as the observed sequence gets longer. Our monitors are of two types, and use, respectively, frequentist and Bayesian statistical inference techniques. While the frequentist monitors compute estimates that are objectively correct with respect to the ground truth, the Bayesian monitors compute estimates that are correct subject to a given prior belief about the system’s model. Using a prototype implementation, we show how we can monitor if a bank is fair in giving loans to applicants from different social backgrounds, and if a college is fair in admitting students while maintaining a reasonable financial burden on the society. Although they exhibit different theoretical complexities in certain cases, in our experiments, both frequentist and Bayesian monitors took less than a millisecond to update their verdicts after each observation."}],"publication":"Computer Aided Verification","citation":{"ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Monitoring algorithmic fairness. Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13965, 358–382.","apa":"Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Monitoring algorithmic fairness. In Computer Aided Verification (Vol. 13965, pp. 358–382). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37703-7_17","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Monitoring algorithmic fairness,” in Computer Aided Verification, Paris, France, 2023, vol. 13965, pp. 358–382.","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Monitoring algorithmic fairness. In: Computer Aided Verification. Vol 13965. Springer Nature; 2023:358–382. doi:10.1007/978-3-031-37703-7_17","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Monitoring Algorithmic Fairness.” In Computer Aided Verification, 13965:358–382. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37703-7_17.","mla":"Henzinger, Thomas A., et al. “Monitoring Algorithmic Fairness.” Computer Aided Verification, vol. 13965, Springer Nature, 2023, pp. 358–382, doi:10.1007/978-3-031-37703-7_17.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, Computer Aided Verification, Springer Nature, 2023, pp. 358–382."},"page":"358–382","date_published":"2023-07-18T00:00:00Z","day":"18","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","acknowledgement":"This work is supported by the European Research Council under Grant No.: ERC-2020-AdG101020093.","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"author":[{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Karimi, Mahyar","last_name":"Karimi","first_name":"Mahyar","orcid":"0009-0005-0820-1696","id":"f1dedef5-2f78-11ee-989a-c4c97bccf506"},{"full_name":"Kueffner, Konstantin","orcid":"0000-0001-8974-2542","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","last_name":"Kueffner","first_name":"Konstantin"},{"last_name":"Mallik","first_name":"Kaushik","orcid":"0000-0001-9864-7475","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","full_name":"Mallik, Kaushik"}],"date_created":"2023-07-25T18:32:40Z","date_updated":"2023-09-05T15:14:00Z","volume":13965,"file_date_updated":"2023-07-31T08:11:20Z","ec_funded":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2305.15979"]},"quality_controlled":"1","project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"conference":{"end_date":"2023-07-22","start_date":"2023-07-17","location":"Paris, France","name":"CAV: Computer Aided Verification"},"doi":"10.1007/978-3-031-37703-7_17","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377020"],"eisbn":["9783031377037"],"issn":["0302-9743"]}},{"file_date_updated":"2023-02-02T13:01:20Z","volume":30,"date_updated":"2023-09-05T15:18:37Z","date_created":"2023-01-16T09:44:36Z","related_material":{"record":[{"status":"public","relation":"other","id":"12115"}]},"author":[{"full_name":"Glajzer, Jacek","first_name":"Jacek","last_name":"Glajzer"},{"full_name":"Castillo-Tong, Dan Cacsire","first_name":"Dan Cacsire","last_name":"Castillo-Tong"},{"full_name":"Richter, Rolf","last_name":"Richter","first_name":"Rolf"},{"full_name":"Vergote, Ignace","last_name":"Vergote","first_name":"Ignace"},{"last_name":"Kulbe","first_name":"Hagen","full_name":"Kulbe, Hagen"},{"full_name":"Vanderstichele, Adriaan","last_name":"Vanderstichele","first_name":"Adriaan"},{"last_name":"Ruscito","first_name":"Ilary","full_name":"Ruscito, Ilary"},{"last_name":"Trillsch","first_name":"Fabian","full_name":"Trillsch, Fabian"},{"first_name":"Alexander","last_name":"Mustea","full_name":"Mustea, Alexander"},{"full_name":"Kreuzinger, Caroline","first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Charlie","last_name":"Gourley","full_name":"Gourley, Charlie"},{"full_name":"Gabra, Hani","last_name":"Gabra","first_name":"Hani"},{"first_name":"Eliane T.","last_name":"Taube","full_name":"Taube, Eliane T."},{"last_name":"Dorigo","first_name":"Oliver","full_name":"Dorigo, Oliver"},{"full_name":"Horst, David","first_name":"David","last_name":"Horst"},{"first_name":"Carlotta","last_name":"Keunecke","full_name":"Keunecke, Carlotta"},{"full_name":"Baum, Joanna","last_name":"Baum","first_name":"Joanna"},{"full_name":"Angelotti, Timothy","first_name":"Timothy","last_name":"Angelotti"},{"full_name":"Sehouli, Jalid","last_name":"Sehouli","first_name":"Jalid"},{"full_name":"Braicu, Elena Ioana","first_name":"Elena Ioana","last_name":"Braicu"}],"publisher":"Springer Nature","department":[{"_id":"JoDa"}],"publication_status":"published","acknowledgement":"E.I.B. is a Feodor Lynen fellow of the Humboldt Foundation and a participant of the Charité Clinical Scientist Program funded by the Charité Universitätsmedizin Berlin and the Berlin Institute of Health. This work was supported by European Commission’s Seventh Framework Programme under grant agreement no. 279113 (OCTIPS; www.octips.eu).\r\nOpen Access funding enabled and organized by Projekt DEAL.","year":"2023","publication_identifier":{"eissn":["1534-4681"],"issn":["1068-9265"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1245/s10434-022-12459-3","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000852125500006"]},"oa":1,"abstract":[{"lang":"eng","text":"Background: This study seeks to evaluate the impact of breast cancer (BRCA) gene status on tumor dissemination pattern, surgical outcome and survival in a multicenter cohort of paired primary ovarian cancer (pOC) and recurrent ovarian cancer (rOC).\r\n\r\nPatients and Methods: Medical records and follow-up data from 190 patients were gathered retrospectively. All patients had surgery at pOC and at least one further rOC surgery at four European high-volume centers. Patients were divided into one cohort with confirmed mutation for BRCA1 and/or BRCA2 (BRCAmut) and a second cohort with BRCA wild type or unknown (BRCAwt). Patterns of tumor presentation, surgical outcome and survival data were analyzed between the two groups.\r\n\r\nResults: Patients with BRCAmut disease were on average 4 years younger and had significantly more tumor involvement upon diagnosis. Patients with BRCAmut disease showed higher debulking rates at all stages. Multivariate analysis showed that only patient age had significant predictive value for complete tumor resection in pOC. At rOC, however, only BRCAmut status significantly correlated with optimal debulking. Patients with BRCAmut disease showed significantly prolonged overall survival (OS) by 24.3 months. Progression-free survival (PFS) was prolonged in the BRCAmut group at all stages as well, reaching statistical significance during recurrence.\r\n\r\nConclusions: Patients with BRCAmut disease showed a more aggressive course of disease with earlier onset and more extensive tumor dissemination at pOC. However, surgical outcome and OS were significantly better in patients with BRCAmut disease compared with patients with BRCAwt disease. We therefore propose to consider BRCAmut status in regard to patient selection for cytoreductive surgery, especially in rOC."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2023-02-02T13:01:20Z","date_created":"2023-02-02T13:01:20Z","checksum":"36a1200e1011f4b2155a8041d0308f34","success":1,"relation":"main_file","file_id":"12490","file_size":365865,"content_type":"application/pdf","creator":"dernst","file_name":"2023_AnnalsSurgicalOncology_Glajzer.pdf","access_level":"open_access"}],"intvolume":" 30","ddc":["610"],"status":"public","title":"Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"12205","has_accepted_license":"1","article_processing_charge":"No","day":"01","keyword":["Oncology","Surgery"],"scopus_import":"1","date_published":"2023-01-01T00:00:00Z","page":"35-45","article_type":"original","citation":{"chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12459-3.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 35–45.","mla":"Glajzer, Jacek, et al. “Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer: A Multicenter Retrospective Study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 35–45, doi:10.1245/s10434-022-12459-3.","ieee":"J. Glajzer et al., “Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 35–45, 2023.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12459-3","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 35–45.","ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome and patient survival in primary and recurrent high-grade serous ovarian cancer: A multicenter retrospective study by the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:35-45. doi:10.1245/s10434-022-12459-3"},"publication":"Annals of Surgical Oncology"},{"keyword":["Oncology","Surgery"],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"46-47","article_type":"original","citation":{"ama":"Glajzer J, Castillo-Tong DC, Richter R, et al. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 2023;30:46-47. doi:10.1245/s10434-022-12681-z","ista":"Glajzer J, Castillo-Tong DC, Richter R, Vergote I, Kulbe H, Vanderstichele A, Ruscito I, Trillsch F, Mustea A, Kreuzinger C, Gourley C, Gabra H, Taube ET, Dorigo O, Horst D, Keunecke C, Baum J, Angelotti T, Sehouli J, Braicu EI. 2023. ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. 30, 46–47.","ieee":"J. Glajzer et al., “ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium,” Annals of Surgical Oncology, vol. 30. Springer Nature, pp. 46–47, 2023.","apa":"Glajzer, J., Castillo-Tong, D. C., Richter, R., Vergote, I., Kulbe, H., Vanderstichele, A., … Braicu, E. I. (2023). ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium. Annals of Surgical Oncology. Springer Nature. https://doi.org/10.1245/s10434-022-12681-z","mla":"Glajzer, Jacek, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology, vol. 30, Springer Nature, 2023, pp. 46–47, doi:10.1245/s10434-022-12681-z.","short":"J. Glajzer, D.C. Castillo-Tong, R. Richter, I. Vergote, H. Kulbe, A. Vanderstichele, I. Ruscito, F. Trillsch, A. Mustea, C. Kreuzinger, C. Gourley, H. Gabra, E.T. Taube, O. Dorigo, D. Horst, C. Keunecke, J. Baum, T. Angelotti, J. Sehouli, E.I. Braicu, Annals of Surgical Oncology 30 (2023) 46–47.","chicago":"Glajzer, Jacek, Dan Cacsire Castillo-Tong, Rolf Richter, Ignace Vergote, Hagen Kulbe, Adriaan Vanderstichele, Ilary Ruscito, et al. “ASO Visual Abstract: Impact of BRCA Mutation Status on Tumor Dissemination Pattern, Surgical Outcome, and Patient Survival in Primary and Recurrent High-Grade Serous Ovarian Cancer (HGSOC). A Multicenter, Retrospective Study of the Ovarian Cancer Therapy—Innovative Models Prolong Survival (OCTIPS) Consortium.” Annals of Surgical Oncology. Springer Nature, 2023. https://doi.org/10.1245/s10434-022-12681-z."},"publication":"Annals of Surgical Oncology","date_published":"2023-01-01T00:00:00Z","type":"journal_article","intvolume":" 30","status":"public","title":"ASO Visual Abstract: Impact of BRCA mutation status on tumor dissemination pattern, surgical outcome, and patient survival in primary and recurrent high-grade serous ovarian cancer (HGSOC). A multicenter, retrospective study of the ovarian cancer therapy—innovative models prolong survival (OCTIPS) consortium","_id":"12115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","publication_identifier":{"issn":["1068-9265"],"eissn":["1534-4681"]},"month":"01","isi":1,"quality_controlled":"1","external_id":{"isi":["000879151800001"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1245/s10434-022-12681-z","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1245/s10434-022-12681-z","publisher":"Springer Nature","department":[{"_id":"JoDa"}],"publication_status":"published","acknowledgement":"This work was supported by European Commission’s Seventh Framework Programme under Grant Agreement No. 279113 (OCTIPS; www.octips.eu).","year":"2023","volume":30,"date_created":"2023-01-12T11:56:22Z","date_updated":"2023-09-05T15:18:36Z","related_material":{"record":[{"id":"12205","status":"public","relation":"other"}]},"author":[{"last_name":"Glajzer","first_name":"Jacek","full_name":"Glajzer, Jacek"},{"first_name":"Dan Cacsire","last_name":"Castillo-Tong","full_name":"Castillo-Tong, Dan Cacsire"},{"first_name":"Rolf","last_name":"Richter","full_name":"Richter, Rolf"},{"full_name":"Vergote, Ignace","last_name":"Vergote","first_name":"Ignace"},{"first_name":"Hagen","last_name":"Kulbe","full_name":"Kulbe, Hagen"},{"full_name":"Vanderstichele, Adriaan","first_name":"Adriaan","last_name":"Vanderstichele"},{"full_name":"Ruscito, Ilary","last_name":"Ruscito","first_name":"Ilary"},{"full_name":"Trillsch, Fabian","first_name":"Fabian","last_name":"Trillsch"},{"first_name":"Alexander","last_name":"Mustea","full_name":"Mustea, Alexander"},{"full_name":"Kreuzinger, Caroline","first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Charlie","last_name":"Gourley","full_name":"Gourley, Charlie"},{"full_name":"Gabra, Hani","first_name":"Hani","last_name":"Gabra"},{"full_name":"Taube, Eliane T.","last_name":"Taube","first_name":"Eliane T."},{"full_name":"Dorigo, Oliver","last_name":"Dorigo","first_name":"Oliver"},{"last_name":"Horst","first_name":"David","full_name":"Horst, David"},{"first_name":"Carlotta","last_name":"Keunecke","full_name":"Keunecke, Carlotta"},{"full_name":"Baum, Joanna","last_name":"Baum","first_name":"Joanna"},{"last_name":"Angelotti","first_name":"Timothy","full_name":"Angelotti, Timothy"},{"full_name":"Sehouli, Jalid","last_name":"Sehouli","first_name":"Jalid"},{"full_name":"Braicu, Elena Ioana","last_name":"Braicu","first_name":"Elena Ioana"}]},{"quality_controlled":"1","external_id":{"pmid":["37633939"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-023-40930-6","month":"08","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Springer Nature","year":"2023","acknowledgement":"We thank Kayla Templeton and Peter Turcanu for technical assistance, Michelle Salemi for assistance with LC-MS data acquisition and analysis, Dr. Belvin Gong for advice on monoclonal antibody generation, Drs. Maria Casas Prat and Eamonn Dickson for assistance with super-resolution TIRF microscopy, Dr. Oscar Cerda for assistance with the design of TAT-FFAT peptides, Dr. Fernando Santana for helpful discussions, and Dr. Jodi Nunnari for a careful reading of our manuscript. We also thank Dr. Alan Howe, Dr. Sohum Mehta, and Dr. Jin Zhang for providing plasmids used in this study. This project was funded by NIH Grants R01NS114210 and R21NS101648 (J.S.T.), and F32NS108519 (N.C.V.).","pmid":1,"date_created":"2023-09-03T22:01:14Z","date_updated":"2023-09-06T06:53:32Z","volume":14,"author":[{"full_name":"Vierra, Nicholas C.","last_name":"Vierra","first_name":"Nicholas C."},{"last_name":"Ribeiro-Silva","first_name":"Luisa","full_name":"Ribeiro-Silva, Luisa"},{"first_name":"Michael","last_name":"Kirmiz","full_name":"Kirmiz, Michael"},{"last_name":"Van Der List","first_name":"Deborah","full_name":"Van Der List, Deborah"},{"full_name":"Bhandari, Pradeep","last_name":"Bhandari","first_name":"Pradeep","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olivia A.","last_name":"Mack","full_name":"Mack, Olivia A."},{"first_name":"James","last_name":"Carroll","full_name":"Carroll, James"},{"full_name":"Le Monnier, Elodie","id":"3B59276A-F248-11E8-B48F-1D18A9856A87","first_name":"Elodie","last_name":"Le Monnier"},{"first_name":"Sue A.","last_name":"Aicher","full_name":"Aicher, Sue A."},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Trimmer, James S.","last_name":"Trimmer","first_name":"James S."}],"article_number":"5231","file_date_updated":"2023-09-06T06:50:07Z","article_type":"original","publication":"Nature Communications","citation":{"ama":"Vierra NC, Ribeiro-Silva L, Kirmiz M, et al. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 2023;14. doi:10.1038/s41467-023-40930-6","ista":"Vierra NC, Ribeiro-Silva L, Kirmiz M, Van Der List D, Bhandari P, Mack OA, Carroll J, Le Monnier E, Aicher SA, Shigemoto R, Trimmer JS. 2023. Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. 14, 5231.","apa":"Vierra, N. C., Ribeiro-Silva, L., Kirmiz, M., Van Der List, D., Bhandari, P., Mack, O. A., … Trimmer, J. S. (2023). Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40930-6","ieee":"N. C. Vierra et al., “Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Vierra, Nicholas C., et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications, vol. 14, 5231, Springer Nature, 2023, doi:10.1038/s41467-023-40930-6.","short":"N.C. Vierra, L. Ribeiro-Silva, M. Kirmiz, D. Van Der List, P. Bhandari, O.A. Mack, J. Carroll, E. Le Monnier, S.A. Aicher, R. Shigemoto, J.S. Trimmer, Nature Communications 14 (2023).","chicago":"Vierra, Nicholas C., Luisa Ribeiro-Silva, Michael Kirmiz, Deborah Van Der List, Pradeep Bhandari, Olivia A. Mack, James Carroll, et al. “Neuronal ER-Plasma Membrane Junctions Couple Excitation to Ca2+-Activated PKA Signaling.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40930-6."},"date_published":"2023-08-26T00:00:00Z","scopus_import":"1","day":"26","article_processing_charge":"Yes","has_accepted_license":"1","status":"public","title":"Neuronal ER-plasma membrane junctions couple excitation to Ca2+-activated PKA signaling","ddc":["570"],"intvolume":" 14","_id":"14253","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"2023_NatureComm_Vierra.pdf","access_level":"open_access","content_type":"application/pdf","file_size":9412549,"creator":"dernst","relation":"main_file","file_id":"14270","date_updated":"2023-09-06T06:50:07Z","date_created":"2023-09-06T06:50:07Z","checksum":"6ab8aab4e957f626a09a1c73db3388fb","success":1}],"type":"journal_article","abstract":[{"lang":"eng","text":"Junctions between the endoplasmic reticulum (ER) and the plasma membrane (PM) are specialized membrane contacts ubiquitous in eukaryotic cells. Concentration of intracellular signaling machinery near ER-PM junctions allows these domains to serve critical roles in lipid and Ca2+ signaling and homeostasis. Subcellular compartmentalization of protein kinase A (PKA) signaling also regulates essential cellular functions, however, no specific association between PKA and ER-PM junctional domains is known. Here, we show that in brain neurons type I PKA is directed to Kv2.1 channel-dependent ER-PM junctional domains via SPHKAP, a type I PKA-specific anchoring protein. SPHKAP association with type I PKA regulatory subunit RI and ER-resident VAP proteins results in the concentration of type I PKA between stacked ER cisternae associated with ER-PM junctions. This ER-associated PKA signalosome enables reciprocal regulation between PKA and Ca2+ signaling machinery to support Ca2+ influx and excitation-transcription coupling. These data reveal that neuronal ER-PM junctions support a receptor-independent form of PKA signaling driven by membrane depolarization and intracellular Ca2+, allowing conversion of information encoded in electrical signals into biochemical changes universally recognized throughout the cell."}]}]