[{"keyword":["Cellular and Molecular Neuroscience","Cognitive Neuroscience","Sensory Systems","Neuroscience (miscellaneous)"],"language":[{"iso":"eng"}],"file_date_updated":"2023-01-24T10:10:43Z","publication_identifier":{"issn":["1662-5110"]},"type":"journal_article","doi":"10.3389/fncir.2022.1028154","date_published":"2022-10-26T00:00:00Z","_id":"12149","month":"10","external_id":{"isi":["000886671400001"]},"quality_controlled":"1","publication_status":"published","intvolume":" 16","publication":"Frontiers in Neural Circuits","oa":1,"oa_version":"Published Version","author":[{"first_name":"Giuditta","full_name":"Gambino, Giuditta","last_name":"Gambino"},{"first_name":"Rebecca","last_name":"Bhik-Ghanie","full_name":"Bhik-Ghanie, Rebecca"},{"last_name":"Giglia","full_name":"Giglia, Giuseppe","first_name":"Giuseppe"},{"last_name":"Puig","full_name":"Puig, M. Victoria","first_name":"M. Victoria"},{"last_name":"Ramirez Villegas","full_name":"Ramirez Villegas, Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F"},{"first_name":"Daniel","last_name":"Zaldivar","full_name":"Zaldivar, Daniel"}],"file":[{"success":1,"content_type":"application/pdf","access_level":"open_access","checksum":"457aa00e1800847abb340853058531de","date_updated":"2023-01-24T10:10:43Z","file_name":"2022_FrontiersNeuralCircuits_Gambino.pdf","relation":"main_file","file_id":"12357","date_created":"2023-01-24T10:10:43Z","creator":"dernst","file_size":110031}],"department":[{"_id":"JoCs"}],"ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"isi":1,"day":"26","citation":{"mla":"Gambino, Giuditta, et al. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” Frontiers in Neural Circuits, vol. 16, 1028154, Frontiers Media, 2022, doi:10.3389/fncir.2022.1028154.","ieee":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M. V. Puig, J. F. Ramirez Villegas, and D. Zaldivar, “Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels,” Frontiers in Neural Circuits, vol. 16. Frontiers Media, 2022.","short":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M.V. Puig, J.F. Ramirez Villegas, D. Zaldivar, Frontiers in Neural Circuits 16 (2022).","apa":"Gambino, G., Bhik-Ghanie, R., Giglia, G., Puig, M. V., Ramirez Villegas, J. F., & Zaldivar, D. (2022). Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. Frontiers in Neural Circuits. Frontiers Media. https://doi.org/10.3389/fncir.2022.1028154","chicago":"Gambino, Giuditta, Rebecca Bhik-Ghanie, Giuseppe Giglia, M. Victoria Puig, Juan F Ramirez Villegas, and Daniel Zaldivar. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” Frontiers in Neural Circuits. Frontiers Media, 2022. https://doi.org/10.3389/fncir.2022.1028154.","ista":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. 2022. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. Frontiers in Neural Circuits. 16, 1028154.","ama":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. Frontiers in Neural Circuits. 2022;16. doi:10.3389/fncir.2022.1028154"},"license":"https://creativecommons.org/licenses/by/4.0/","abstract":[{"text":"Editorial on the Research Topic","lang":"eng"}],"has_accepted_license":"1","scopus_import":"1","volume":16,"acknowledgement":"This work was supported by a DFG grant ZA990/1 to DZ. This work was supported by the MSCA EU proposal 841301 - DREAM, European Commission; Horizon 2020 - Research and Innovation Framework Programme to JFRV.","date_created":"2023-01-12T12:07:39Z","year":"2022","article_type":"letter_note","status":"public","project":[{"name":"The Brainstem-Hippocampus Network Uncovered: Dynamics, Reactivation and Memory Consolidation","call_identifier":"H2020","_id":"26BAE2E4-B435-11E9-9278-68D0E5697425","grant_number":"841301"}],"article_number":"1028154","title":"Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels","article_processing_charge":"No","ddc":["570"],"publisher":"Frontiers Media","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:01:06Z"},{"scopus_import":"1","abstract":[{"text":"Methods inspired from machine learning have recently attracted great interest in the computational study of quantum many-particle systems. So far, however, it has proven challenging to deal with microscopic models in which the total number of particles is not conserved. To address this issue, we propose a variant of neural network states, which we term neural coherent states. Taking the Fröhlich impurity model as a case study, we show that neural coherent states can learn the ground state of nonadditive systems very well. In particular, we recover exact diagonalization in all regimes tested and observe substantial improvement over the standard coherent state estimates in the most challenging intermediate-coupling regime. Our approach is generic and does not assume specific details of the system, suggesting wide applications.","lang":"eng"}],"isi":1,"day":"15","citation":{"ista":"Rzadkowski W, Lemeshko M, Mentink JH. 2022. Artificial neural network states for nonadditive systems. Physical Review B. 106(15), 155127.","chicago":"Rzadkowski, Wojciech, Mikhail Lemeshko, and Johan H. Mentink. “Artificial Neural Network States for Nonadditive Systems.” Physical Review B. American Physical Society, 2022. https://doi.org/10.1103/physrevb.106.155127.","ama":"Rzadkowski W, Lemeshko M, Mentink JH. Artificial neural network states for nonadditive systems. Physical Review B. 2022;106(15). doi:10.1103/physrevb.106.155127","apa":"Rzadkowski, W., Lemeshko, M., & Mentink, J. H. (2022). Artificial neural network states for nonadditive systems. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.106.155127","short":"W. Rzadkowski, M. Lemeshko, J.H. Mentink, Physical Review B 106 (2022).","ieee":"W. Rzadkowski, M. Lemeshko, and J. H. Mentink, “Artificial neural network states for nonadditive systems,” Physical Review B, vol. 106, no. 15. American Physical Society, 2022.","mla":"Rzadkowski, Wojciech, et al. “Artificial Neural Network States for Nonadditive Systems.” Physical Review B, vol. 106, no. 15, 155127, American Physical Society, 2022, doi:10.1103/physrevb.106.155127."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","date_updated":"2023-08-04T09:01:48Z","article_number":"155127","article_processing_charge":"No","title":"Artificial neural network states for nonadditive systems","status":"public","project":[{"grant_number":"25681","_id":"05A235A0-7A3F-11EA-A408-12923DDC885E","name":"Analytic and machine learning approaches to composite quantum impurities"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2105.15193","open_access":"1"}],"article_type":"original","acknowledgement":"We acknowledge fruitful discussions with G. Bighin, G. Fabiani, A. Ghazaryan, C. Lampert, and A. Volosniev at various stages of this work. W.R. acknowledges support through a DOC Fellowship of the Austrian Academy of Sciences and has received funding from the EU Horizon 2020 programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. M.L. and J.H.M. acknowledge support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON) and Synergy Grant No. 856538 (3D-MAGiC), respectively. This work is part of the Shell-NWO/FOMinitiative “Computational sciences for energy research” of Shell and Chemical Sciences, Earth and Life Sciences, Physical Sciences, FOM and STW. ","volume":106,"year":"2022","date_created":"2023-01-12T12:07:49Z","publication_status":"published","quality_controlled":"1","oa":1,"intvolume":" 106","publication":"Physical Review B","_id":"12150","date_published":"2022-10-15T00:00:00Z","doi":"10.1103/physrevb.106.155127","arxiv":1,"external_id":{"isi":["000875189100005"],"arxiv":["2105.15193"]},"month":"10","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"issue":"15","type":"journal_article","ec_funded":1,"department":[{"_id":"MiLe"}],"author":[{"id":"48C55298-F248-11E8-B48F-1D18A9856A87","first_name":"Wojciech","last_name":"Rzadkowski","orcid":"0000-0002-1106-4419","full_name":"Rzadkowski, Wojciech"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"first_name":"Johan H.","last_name":"Mentink","full_name":"Mentink, Johan H."}],"oa_version":"Preprint"},{"author":[{"first_name":"Xiuyun","full_name":"Jiang, Xiuyun","last_name":"Jiang"},{"first_name":"Lena","full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck"},{"full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina","first_name":"Anna-Katharina"},{"full_name":"Lominadze, Elene","last_name":"Lominadze","first_name":"Elene"},{"first_name":"Aurélien","full_name":"Roux, Aurélien","last_name":"Roux"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"}],"oa_version":"Published Version","department":[{"_id":"AnSa"}],"ec_funded":1,"file":[{"creator":"dernst","file_size":2641067,"file_id":"12359","relation":"main_file","date_created":"2023-01-24T10:45:01Z","content_type":"application/pdf","access_level":"open_access","checksum":"bada6a7865e470cf42bbdfa67dd471d2","success":1,"date_updated":"2023-01-24T10:45:01Z","file_name":"2022_PLoSCompBio_Jiang.pdf"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"type":"journal_article","issue":"10","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"file_date_updated":"2023-01-24T10:45:01Z","month":"10","external_id":{"isi":["000924885500005"]},"date_published":"2022-10-17T00:00:00Z","doi":"10.1371/journal.pcbi.1010586","_id":"12152","oa":1,"publication":"PLOS Computational Biology","intvolume":" 18","quality_controlled":"1","publication_status":"published","date_created":"2023-01-12T12:08:10Z","year":"2022","volume":18,"acknowledgement":"A.S . received an award from European Research Council (https://erc.europa.eu, “NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org, UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open, Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation, Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc, MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research (https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and an award from the European Research Council\r\nConsolidator (https://erc.europa.eu, 311536). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","article_type":"original","project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","grant_number":"96752","name":"The evolution of trafficking: from archaea to eukaryotes"}],"status":"public","title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","article_processing_charge":"No","article_number":"e1010586","date_updated":"2023-08-04T09:03:21Z","publisher":"Public Library of Science","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"citation":{"ieee":"X. Jiang et al., “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” PLOS Computational Biology, vol. 18, no. 10. Public Library of Science, 2022.","mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” PLOS Computational Biology, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010586.","ista":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.","chicago":"Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010586.","apa":"Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K., Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010586","ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 2022;18(10). doi:10.1371/journal.pcbi.1010586","short":"X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E. Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022)."},"isi":1,"day":"17","abstract":[{"text":"ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.","lang":"eng"}],"scopus_import":"1","related_material":{"link":[{"url":"https://github.com/sharonJXY/3-filament-model","relation":"software"}]},"has_accepted_license":"1"},{"quality_controlled":"1","publication_status":"published","intvolume":" 14","publication":"Symmetry","oa":1,"date_published":"2022-10-17T00:00:00Z","doi":"10.3390/sym14102182","_id":"12154","month":"10","external_id":{"isi":["000875039200001"]},"keyword":["Physics and Astronomy (miscellaneous)","General Mathematics","Chemistry (miscellaneous)","Computer Science (miscellaneous)"],"language":[{"iso":"eng"}],"file_date_updated":"2023-01-24T10:56:12Z","publication_identifier":{"issn":["2073-8994"]},"type":"journal_article","issue":"10","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file":[{"creator":"dernst","file_size":843723,"relation":"main_file","date_created":"2023-01-24T10:56:12Z","file_id":"12361","content_type":"application/pdf","access_level":"open_access","checksum":"9b6bd0e484834dd76d7b26e3c5fba8bd","success":1,"file_name":"2022_Symmetry_Salsnich.pdf","date_updated":"2023-01-24T10:56:12Z"}],"department":[{"_id":"MiLe"}],"oa_version":"Published Version","author":[{"last_name":"Salasnich","full_name":"Salasnich, Luca","first_name":"Luca"},{"orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","last_name":"Cappellaro","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660"},{"full_name":"Furutani, Koichiro","last_name":"Furutani","first_name":"Koichiro"},{"first_name":"Andrea","last_name":"Tononi","full_name":"Tononi, Andrea"},{"last_name":"Bighin","orcid":"0000-0001-8823-9777","full_name":"Bighin, Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo"}],"has_accepted_license":"1","scopus_import":"1","abstract":[{"text":"We review our theoretical results of the sound propagation in two-dimensional (2D) systems of ultracold fermionic and bosonic atoms. In the superfluid phase, characterized by the spontaneous symmetry breaking of the U(1) symmetry, there is the coexistence of first and second sound. In the case of weakly-interacting repulsive bosons, we model the recent measurements of the sound velocities of 39K atoms in 2D obtained in the weakly-interacting regime and around the Berezinskii–Kosterlitz–Thouless (BKT) superfluid-to-normal transition temperature. In particular, we perform a quite accurate computation of the superfluid density and show that it is reasonably consistent with the experimental results. For superfluid attractive fermions, we calculate the first and second sound velocities across the whole BCS-BEC crossover. In the low-temperature regime, we reproduce the recent measurements of first-sound speed with 6Li atoms. We also predict that there is mixing between sound modes only in the finite-temperature BEC regime.","lang":"eng"}],"isi":1,"day":"17","citation":{"short":"L. Salasnich, A. Cappellaro, K. Furutani, A. Tononi, G. Bighin, Symmetry 14 (2022).","chicago":"Salasnich, Luca, Alberto Cappellaro, Koichiro Furutani, Andrea Tononi, and Giacomo Bighin. “First and Second Sound in Two-Dimensional Bosonic and Fermionic Superfluids.” Symmetry. MDPI, 2022. https://doi.org/10.3390/sym14102182.","ista":"Salasnich L, Cappellaro A, Furutani K, Tononi A, Bighin G. 2022. First and second sound in two-dimensional bosonic and fermionic superfluids. Symmetry. 14(10), 2182.","ama":"Salasnich L, Cappellaro A, Furutani K, Tononi A, Bighin G. First and second sound in two-dimensional bosonic and fermionic superfluids. Symmetry. 2022;14(10). doi:10.3390/sym14102182","apa":"Salasnich, L., Cappellaro, A., Furutani, K., Tononi, A., & Bighin, G. (2022). First and second sound in two-dimensional bosonic and fermionic superfluids. Symmetry. MDPI. https://doi.org/10.3390/sym14102182","mla":"Salasnich, Luca, et al. “First and Second Sound in Two-Dimensional Bosonic and Fermionic Superfluids.” Symmetry, vol. 14, no. 10, 2182, MDPI, 2022, doi:10.3390/sym14102182.","ieee":"L. Salasnich, A. Cappellaro, K. Furutani, A. Tononi, and G. Bighin, “First and second sound in two-dimensional bosonic and fermionic superfluids,” Symmetry, vol. 14, no. 10. MDPI, 2022."},"ddc":["530"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-08-09T10:13:17Z","publisher":"MDPI","article_number":"2182","title":"First and second sound in two-dimensional bosonic and fermionic superfluids","article_processing_charge":"Yes","article_type":"original","status":"public","volume":14,"acknowledgement":"This research is partially supported by University of Padova, BIRD grant “Ultracold atoms\r\nin curved geometries”. KF is supported by Fondazione CARIPARO with a PhD fellowship. AT is\r\npartially supported by French National Research Agency ANR Grant Droplets N. ANR-19-CE30-0003-02. LS thanks Herwig Ott and Sandro Wimberger for their kind invitation to the\r\nInternational Workshop “Quantum Transport with ultracold atoms” (2022).","date_created":"2023-01-12T12:08:31Z","year":"2022"},{"author":[{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"},{"full_name":"Tkačik, Gašper","orcid":"1","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","file":[{"file_name":"2022_CurrentBiology_Zoller.pdf","date_updated":"2023-01-24T12:14:10Z","checksum":"97ef01e0cc60cdc84f45640a0f248fb0","content_type":"application/pdf","access_level":"open_access","success":1,"creator":"dernst","file_size":2214944,"relation":"main_file","file_id":"12362","date_created":"2023-01-24T12:14:10Z"}],"department":[{"_id":"GaTk"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file_date_updated":"2023-01-24T12:14:10Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2452-3100"]},"keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"issue":"9","type":"journal_article","_id":"12156","date_published":"2022-09-01T00:00:00Z","doi":"10.1016/j.coisb.2022.100435","month":"09","publication_status":"published","quality_controlled":"1","oa":1,"publication":"Current Opinion in Systems Biology","intvolume":" 31","acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","volume":31,"year":"2022","date_created":"2023-01-12T12:08:51Z","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"status":"public","article_type":"original","article_number":"100435","article_processing_charge":"Yes (via OA deal)","title":"Eukaryotic gene regulation at equilibrium, or non?","ddc":["570"],"date_updated":"2023-02-13T09:20:34Z","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier, 2022. https://doi.org/10.1016/j.coisb.2022.100435.","apa":"Zoller, B., Gregor, T., & Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2022.100435","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022, doi:10.1016/j.coisb.2022.100435.","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier, 2022."},"abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"has_accepted_license":"1","scopus_import":"1"},{"type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"file_date_updated":"2023-01-24T12:21:32Z","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"intvolume":" 11","oa":1,"publication":"eLife","quality_controlled":"1","publication_status":"published","month":"09","external_id":{"isi":["000890735600001"]},"doi":"10.7554/elife.66697","date_published":"2022-09-26T00:00:00Z","_id":"12157","author":[{"first_name":"Laura","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","full_name":"Hayward, Laura","last_name":"Hayward"},{"last_name":"Sella","full_name":"Sella, Guy","first_name":"Guy"}],"oa_version":"Published Version","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"department":[{"_id":"NiBa"}],"file":[{"date_updated":"2023-01-24T12:21:32Z","file_name":"2022_eLife_Hayward.pdf","success":1,"checksum":"28de155b231ac1c8d4501c98b2fb359a","access_level":"open_access","content_type":"application/pdf","file_size":18935612,"creator":"dernst","date_created":"2023-01-24T12:21:32Z","relation":"main_file","file_id":"12363"}],"abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}],"citation":{"mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife, vol. 11, 66697, eLife Sciences Publications, 2022, doi:10.7554/elife.66697.","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” eLife, vol. 11. eLife Sciences Publications, 2022.","short":"L. Hayward, G. Sella, ELife 11 (2022).","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. eLife. 2022;11. doi:10.7554/elife.66697","apa":"Hayward, L., & Sella, G. (2022). Polygenic adaptation after a sudden change in environment. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.66697","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.66697.","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697."},"isi":1,"day":"26","scopus_import":"1","has_accepted_license":"1","article_type":"original","status":"public","date_created":"2023-01-12T12:09:00Z","year":"2022","volume":11,"acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","date_updated":"2023-08-04T09:04:58Z","publisher":"eLife Sciences Publications","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Polygenic adaptation after a sudden change in environment","article_processing_charge":"No","article_number":"66697"},{"publisher":"Institute of Electrical and Electronics Engineers","date_updated":"2023-08-04T09:06:02Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Hierarchical consensus: A horizontal scaling framework for blockchains","article_processing_charge":"No","status":"public","page":"45-52","date_created":"2023-01-12T12:09:28Z","year":"2022","volume":2022,"scopus_import":"1","abstract":[{"text":"We present the Filecoin Hierarchical Consensus framework, which aims to overcome the throughput challenges of blockchain consensus by horizontally scaling the network. Unlike traditional sharding designs, based on partitioning the state of the network, our solution centers on the concept of subnets -which are organized hierarchically- and can be spawned on-demand to manage new state. Child sub nets are firewalled from parent subnets, have their own specific policies, and run a different consensus algorithm, increasing the network capacity and enabling new applications. Moreover, they benefit from the security of parent subnets by periodically checkpointing state. In this paper, we introduce the overall system architecture, our detailed designs for cross-net transaction handling, and the open questions that we are still exploring.","lang":"eng"}],"citation":{"short":"A. De la Rocha, E. Kokoris Kogias, J.M. Soares, M. Vukolic, in:, 42nd International Conference on Distributed Computing Systems Workshops, Institute of Electrical and Electronics Engineers, 2022, pp. 45–52.","chicago":"De la Rocha, Alfonso, Eleftherios Kokoris Kogias, Jorge M. Soares, and Marko Vukolic. “Hierarchical Consensus: A Horizontal Scaling Framework for Blockchains.” In 42nd International Conference on Distributed Computing Systems Workshops, 2022:45–52. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/icdcsw56584.2022.00018.","ista":"De la Rocha A, Kokoris Kogias E, Soares JM, Vukolic M. 2022. Hierarchical consensus: A horizontal scaling framework for blockchains. 42nd International Conference on Distributed Computing Systems Workshops. ICDCSW: International Conference on Distributed Computing Systems Workshop vol. 2022, 45–52.","apa":"De la Rocha, A., Kokoris Kogias, E., Soares, J. M., & Vukolic, M. (2022). Hierarchical consensus: A horizontal scaling framework for blockchains. In 42nd International Conference on Distributed Computing Systems Workshops (Vol. 2022, pp. 45–52). Bologna, Italy: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdcsw56584.2022.00018","ama":"De la Rocha A, Kokoris Kogias E, Soares JM, Vukolic M. Hierarchical consensus: A horizontal scaling framework for blockchains. In: 42nd International Conference on Distributed Computing Systems Workshops. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:45-52. doi:10.1109/icdcsw56584.2022.00018","mla":"De la Rocha, Alfonso, et al. “Hierarchical Consensus: A Horizontal Scaling Framework for Blockchains.” 42nd International Conference on Distributed Computing Systems Workshops, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 45–52, doi:10.1109/icdcsw56584.2022.00018.","ieee":"A. De la Rocha, E. Kokoris Kogias, J. M. Soares, and M. Vukolic, “Hierarchical consensus: A horizontal scaling framework for blockchains,” in 42nd International Conference on Distributed Computing Systems Workshops, Bologna, Italy, 2022, vol. 2022, pp. 45–52."},"day":"29","isi":1,"department":[{"_id":"ElKo"}],"author":[{"first_name":"Alfonso","full_name":"De la Rocha, Alfonso","last_name":"De la Rocha"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"first_name":"Jorge M.","full_name":"Soares, Jorge M.","last_name":"Soares"},{"first_name":"Marko","full_name":"Vukolic, Marko","last_name":"Vukolic"}],"oa_version":"None","publication":"42nd International Conference on Distributed Computing Systems Workshops","intvolume":" 2022","quality_controlled":"1","publication_status":"published","month":"11","external_id":{"isi":["000895984800009"]},"conference":{"start_date":"2022-07-10","name":"ICDCSW: International Conference on Distributed Computing Systems Workshop","location":"Bologna, Italy","end_date":"2022-07-10"},"date_published":"2022-11-29T00:00:00Z","doi":"10.1109/icdcsw56584.2022.00018","_id":"12160","type":"conference","publication_identifier":{"eissn":["2332-5666"],"eisbn":["9781665488792"]},"language":[{"iso":"eng"}]},{"scopus_import":"1","abstract":[{"text":"We introduce LIMES, a new method for learning with non-stationary streaming data, inspired by the recent success of meta-learning. The main idea is not to attempt to learn a single classifier that would have to work well across all occurring data distributions, nor many separate classifiers, but to exploit a hybrid strategy: we learn a single set of model parameters from which a specific classifier for any specific data distribution is derived via classifier adaptation. Assuming a multiclass classification setting with class-prior shift, the adaptation step can be performed analytically with only the classifier’s bias terms being affected. Another contribution of our work is an extrapolation step that predicts suitable adaptation parameters for future time steps based on the previous data. In combination, we obtain a lightweight procedure for learning from streaming data with varying class distribution that adds no trainable parameters and almost no memory or computational overhead compared to training a single model. Experiments on a set of exemplary tasks using Twitter data show that LIMES achieves higher accuracy than alternative approaches, especially with respect to the relevant real-world metric of lowest within-day accuracy.","lang":"eng"}],"citation":{"ieee":"P. Tomaszewska and C. Lampert, “Lightweight conditional model extrapolation for streaming data under class-prior shift,” in 26th International Conference on Pattern Recognition, Montreal, Canada, 2022, vol. 2022, pp. 2128–2134.","mla":"Tomaszewska, Paulina, and Christoph Lampert. “Lightweight Conditional Model Extrapolation for Streaming Data under Class-Prior Shift.” 26th International Conference on Pattern Recognition, vol. 2022, Institute of Electrical and Electronics Engineers, 2022, pp. 2128–34, doi:10.1109/icpr56361.2022.9956195.","chicago":"Tomaszewska, Paulina, and Christoph Lampert. “Lightweight Conditional Model Extrapolation for Streaming Data under Class-Prior Shift.” In 26th International Conference on Pattern Recognition, 2022:2128–34. Institute of Electrical and Electronics Engineers, 2022. https://doi.org/10.1109/icpr56361.2022.9956195.","ista":"Tomaszewska P, Lampert C. 2022. Lightweight conditional model extrapolation for streaming data under class-prior shift. 26th International Conference on Pattern Recognition. ICPR: International Conference on Pattern Recognition vol. 2022, 2128–2134.","ama":"Tomaszewska P, Lampert C. Lightweight conditional model extrapolation for streaming data under class-prior shift. In: 26th International Conference on Pattern Recognition. Vol 2022. Institute of Electrical and Electronics Engineers; 2022:2128-2134. doi:10.1109/icpr56361.2022.9956195","apa":"Tomaszewska, P., & Lampert, C. (2022). Lightweight conditional model extrapolation for streaming data under class-prior shift. In 26th International Conference on Pattern Recognition (Vol. 2022, pp. 2128–2134). Montreal, Canada: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icpr56361.2022.9956195","short":"P. Tomaszewska, C. Lampert, in:, 26th International Conference on Pattern Recognition, Institute of Electrical and Electronics Engineers, 2022, pp. 2128–2134."},"day":"29","isi":1,"publisher":"Institute of Electrical and Electronics Engineers","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:06:34Z","article_processing_charge":"No","title":"Lightweight conditional model extrapolation for streaming data under class-prior shift","status":"public","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2206.05181","open_access":"1"}],"page":"2128-2134","year":"2022","date_created":"2023-01-12T12:09:38Z","volume":2022,"publication":"26th International Conference on Pattern Recognition","intvolume":" 2022","oa":1,"publication_status":"published","quality_controlled":"1","arxiv":1,"external_id":{"arxiv":["2206.05181"],"isi":["000897707602018"]},"conference":{"start_date":"2022-08-21","name":"ICPR: International Conference on Pattern Recognition","location":"Montreal, Canada","end_date":"2022-08-25"},"month":"11","_id":"12161","date_published":"2022-11-29T00:00:00Z","doi":"10.1109/icpr56361.2022.9956195","type":"conference","publication_identifier":{"eisbn":["9781665490627"],"eissn":["2831-7475"]},"language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"author":[{"last_name":"Tomaszewska","full_name":"Tomaszewska, Paulina","first_name":"Paulina"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint"},{"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"intvolume":" 32","publication":"Molecular Ecology","oa":1,"publication_status":"published","quality_controlled":"1","external_id":{"isi":["000892168800001"]},"month":"11","_id":"12166","doi":"10.1111/mec.16779","date_published":"2022-11-28T00:00:00Z","author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"oa_version":"Published Version","department":[{"_id":"NiBa"}],"abstract":[{"text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings.","lang":"eng"}],"citation":{"mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” Molecular Ecology, vol. 32, no. 1, Wiley, 2022, pp. 26–29, doi:10.1111/mec.16779.","ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” Molecular Ecology, vol. 32, no. 1. Wiley, pp. 26–29, 2022.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.","ista":"Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","apa":"Westram, A. M., & Butlin, R. (2022). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16779","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 2022;32(1):26-29. doi:10.1111/mec.16779","chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” Molecular Ecology. Wiley, 2022. https://doi.org/10.1111/mec.16779."},"isi":1,"day":"28","scopus_import":"1","status":"public","article_type":"letter_note","main_file_link":[{"url":"https://doi.org/10.1111/mec.16779","open_access":"1"}],"page":"26-29","year":"2022","date_created":"2023-01-12T12:10:28Z","volume":32,"date_updated":"2023-08-04T09:09:15Z","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize"},{"volume":13411,"date_created":"2023-01-12T12:10:38Z","year":"2022","page":"358-373","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2110.08848","open_access":"1"}],"status":"public","title":"Hide & Seek: Privacy-preserving rebalancing on payment channel networks","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","date_updated":"2023-09-05T15:10:57Z","day":"22","citation":{"chicago":"Avarikioti, Georgia, Krzysztof Z Pietrzak, Iosif Salem, Stefan Schmid, Samarth Tiwari, and Michelle X Yeo. “Hide & Seek: Privacy-Preserving Rebalancing on Payment Channel Networks.” In Financial Cryptography and Data Security, 13411:358–73. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-18283-9_17.","ama":"Avarikioti G, Pietrzak KZ, Salem I, Schmid S, Tiwari S, Yeo MX. Hide & Seek: Privacy-preserving rebalancing on payment channel networks. In: Financial Cryptography and Data Security. Vol 13411. Springer Nature; 2022:358-373. doi:10.1007/978-3-031-18283-9_17","ista":"Avarikioti G, Pietrzak KZ, Salem I, Schmid S, Tiwari S, Yeo MX. 2022. Hide & Seek: Privacy-preserving rebalancing on payment channel networks. Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13411, 358–373.","apa":"Avarikioti, G., Pietrzak, K. Z., Salem, I., Schmid, S., Tiwari, S., & Yeo, M. X. (2022). Hide & Seek: Privacy-preserving rebalancing on payment channel networks. In Financial Cryptography and Data Security (Vol. 13411, pp. 358–373). Grenada: Springer Nature. https://doi.org/10.1007/978-3-031-18283-9_17","short":"G. Avarikioti, K.Z. Pietrzak, I. Salem, S. Schmid, S. Tiwari, M.X. Yeo, in:, Financial Cryptography and Data Security, Springer Nature, 2022, pp. 358–373.","ieee":"G. Avarikioti, K. Z. Pietrzak, I. Salem, S. Schmid, S. Tiwari, and M. X. Yeo, “Hide & Seek: Privacy-preserving rebalancing on payment channel networks,” in Financial Cryptography and Data Security, Grenada, 2022, vol. 13411, pp. 358–373.","mla":"Avarikioti, Georgia, et al. “Hide & Seek: Privacy-Preserving Rebalancing on Payment Channel Networks.” Financial Cryptography and Data Security, vol. 13411, Springer Nature, 2022, pp. 358–73, doi:10.1007/978-3-031-18283-9_17."},"abstract":[{"text":"Payment channels effectively move the transaction load off-chain thereby successfully addressing the inherent scalability problem most cryptocurrencies face. A major drawback of payment channels is the need to “top up” funds on-chain when a channel is depleted. Rebalancing was proposed to alleviate this issue, where parties with depleting channels move their funds along a cycle to replenish their channels off-chain. Protocols for rebalancing so far either introduce local solutions or compromise privacy.\r\nIn this work, we present an opt-in rebalancing protocol that is both private and globally optimal, meaning our protocol maximizes the total amount of rebalanced funds. We study rebalancing from the framework of linear programming. To obtain full privacy guarantees, we leverage multi-party computation in solving the linear program, which is executed by selected participants to maintain efficiency. Finally, we efficiently decompose the rebalancing solution into incentive-compatible cycles which conserve user balances when executed atomically.","lang":"eng"}],"scopus_import":"1","author":[{"full_name":"Avarikioti, Georgia","last_name":"Avarikioti","first_name":"Georgia","id":"c20482a0-3b89-11eb-9862-88cf6404b88c"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"first_name":"Iosif","last_name":"Salem","full_name":"Salem, Iosif"},{"first_name":"Stefan","full_name":"Schmid, Stefan","last_name":"Schmid"},{"last_name":"Tiwari","full_name":"Tiwari, Samarth","first_name":"Samarth"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","department":[{"_id":"KrPi"}],"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783031182822"],"eisbn":["9783031182839"],"eissn":["1611-3349"],"issn":["0302-9743"]},"type":"conference","doi":"10.1007/978-3-031-18283-9_17","date_published":"2022-10-22T00:00:00Z","_id":"12167","month":"10","arxiv":1,"conference":{"location":"Grenada","end_date":"2022-05-06","name":"FC: Financial Cryptography and Data Security","start_date":"2022-05-02"},"external_id":{"arxiv":["2110.08848"]},"quality_controlled":"1","publication_status":"published","intvolume":" 13411","publication":"Financial Cryptography and Data Security","oa":1},{"publication":"International Conference on Financial Cryptography and Data Security","intvolume":" 13411","oa":1,"quality_controlled":"1","publication_status":"published","month":"10","arxiv":1,"external_id":{"arxiv":["2110.00960"]},"conference":{"name":"FC: Financial Cryptography and Data Security","start_date":"2022-05-02","location":"Grenada","end_date":"2022-05-06"},"date_published":"2022-10-22T00:00:00Z","doi":"10.1007/978-3-031-18283-9_13","_id":"12168","type":"conference","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783031182839"],"isbn":["9783031182822"],"issn":["0302-9743"],"eissn":["1611-3349"]},"alternative_title":["LNCS"],"department":[{"_id":"ElKo"}],"oa_version":"Preprint","author":[{"first_name":"Shir","full_name":"Cohen, Shir","last_name":"Cohen"},{"last_name":"Gelashvili","full_name":"Gelashvili, Rati","first_name":"Rati"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Li","full_name":"Li, Zekun","first_name":"Zekun"},{"first_name":"Dahlia","last_name":"Malkhi","full_name":"Malkhi, Dahlia"},{"first_name":"Alberto","full_name":"Sonnino, Alberto","last_name":"Sonnino"},{"full_name":"Spiegelman, Alexander","last_name":"Spiegelman","first_name":"Alexander"}],"scopus_import":"1","abstract":[{"text":"Advances in blockchains have influenced the State-Machine-Replication (SMR) world and many state-of-the-art blockchain-SMR solutions are based on two pillars: Chaining and Leader-rotation. A predetermined round-robin mechanism used for Leader-rotation, however, has an undesirable behavior: crashed parties become designated leaders infinitely often, slowing down overall system performance. In this paper, we provide a new Leader-Aware SMR framework that, among other desirable properties, formalizes a Leader-utilization requirement that bounds the number of rounds whose leaders are faulty in crash-only executions.\r\nWe introduce Carousel, a novel, reputation-based Leader-rotation solution to achieve Leader-Aware SMR. The challenge in adaptive Leader-rotation is that it cannot rely on consensus to determine a leader, since consensus itself needs a leader. Carousel uses the available on-chain information to determine a leader locally and achieves Liveness despite this difficulty. A HotStuff implementation fitted with Carousel demonstrates drastic performance improvements: it increases throughput over 2x in faultless settings and provided a 20x throughput increase and 5x latency reduction in the presence of faults.","lang":"eng"}],"citation":{"short":"S. Cohen, R. Gelashvili, E. Kokoris Kogias, Z. Li, D. Malkhi, A. Sonnino, A. Spiegelman, in:, International Conference on Financial Cryptography and Data Security, Springer Nature, 2022, pp. 279–295.","apa":"Cohen, S., Gelashvili, R., Kokoris Kogias, E., Li, Z., Malkhi, D., Sonnino, A., & Spiegelman, A. (2022). Be aware of your leaders. In International Conference on Financial Cryptography and Data Security (Vol. 13411, pp. 279–295). Grenada: Springer Nature. https://doi.org/10.1007/978-3-031-18283-9_13","ama":"Cohen S, Gelashvili R, Kokoris Kogias E, et al. Be aware of your leaders. In: International Conference on Financial Cryptography and Data Security. Vol 13411. Springer Nature; 2022:279-295. doi:10.1007/978-3-031-18283-9_13","ista":"Cohen S, Gelashvili R, Kokoris Kogias E, Li Z, Malkhi D, Sonnino A, Spiegelman A. 2022. Be aware of your leaders. International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13411, 279–295.","chicago":"Cohen, Shir, Rati Gelashvili, Eleftherios Kokoris Kogias, Zekun Li, Dahlia Malkhi, Alberto Sonnino, and Alexander Spiegelman. “Be Aware of Your Leaders.” In International Conference on Financial Cryptography and Data Security, 13411:279–95. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-18283-9_13.","mla":"Cohen, Shir, et al. “Be Aware of Your Leaders.” International Conference on Financial Cryptography and Data Security, vol. 13411, Springer Nature, 2022, pp. 279–95, doi:10.1007/978-3-031-18283-9_13.","ieee":"S. Cohen et al., “Be aware of your leaders,” in International Conference on Financial Cryptography and Data Security, Grenada, 2022, vol. 13411, pp. 279–295."},"day":"22","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","date_updated":"2023-09-05T15:11:35Z","title":"Be aware of your leaders","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2110.00960"}],"status":"public","page":"279-295","date_created":"2023-01-12T12:10:49Z","year":"2022","volume":13411},{"intvolume":" 13505","publication":"20th International Symposium on Automated Technology for Verification and Analysis","quality_controlled":"1","publication_status":"published","month":"10","conference":{"end_date":"2022-10-28","location":"Virtual","start_date":"2022-10-25","name":"ATVA: Automated Technology for Verification and Analysis"},"doi":"10.1007/978-3-031-19992-9_20","date_published":"2022-10-21T00:00:00Z","_id":"12170","type":"conference","publication_identifier":{"isbn":["9783031199912"],"eisbn":["9783031199929"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"department":[{"_id":"KrCh"}],"oa_version":"None","author":[{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer"}],"scopus_import":"1","abstract":[{"text":"We present PET, a specialized and highly optimized framework for partial exploration on probabilistic systems. Over the last decade, several significant advances in the analysis of Markov decision processes employed partial exploration. In a nutshell, this idea allows to focus computation on specific parts of the system, guided by heuristics, while maintaining correctness. In particular, only relevant parts of the system are constructed on demand, which in turn potentially allows to omit constructing large parts of the system. Depending on the model, this leads to dramatic speed-ups, in extreme cases even up to an arbitrary factor. PET unifies several previous implementations and provides a flexible framework to easily implement partial exploration for many further problems. Our experimental evaluation shows significant improvements compared to the previous implementations while vastly reducing the overhead required to add support for additional properties.","lang":"eng"}],"citation":{"ieee":"T. Meggendorfer, “PET – A partial exploration tool for probabilistic verification,” in 20th International Symposium on Automated Technology for Verification and Analysis, Virtual, 2022, vol. 13505, pp. 320–326.","mla":"Meggendorfer, Tobias. “PET – A Partial Exploration Tool for Probabilistic Verification.” 20th International Symposium on Automated Technology for Verification and Analysis, vol. 13505, Springer Nature, 2022, pp. 320–26, doi:10.1007/978-3-031-19992-9_20.","ama":"Meggendorfer T. PET – A partial exploration tool for probabilistic verification. In: 20th International Symposium on Automated Technology for Verification and Analysis. Vol 13505. Springer Nature; 2022:320-326. doi:10.1007/978-3-031-19992-9_20","ista":"Meggendorfer T. 2022. PET – A partial exploration tool for probabilistic verification. 20th International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 13505, 320–326.","chicago":"Meggendorfer, Tobias. “PET – A Partial Exploration Tool for Probabilistic Verification.” In 20th International Symposium on Automated Technology for Verification and Analysis, 13505:320–26. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-19992-9_20.","apa":"Meggendorfer, T. (2022). PET – A partial exploration tool for probabilistic verification. In 20th International Symposium on Automated Technology for Verification and Analysis (Vol. 13505, pp. 320–326). Virtual: Springer Nature. https://doi.org/10.1007/978-3-031-19992-9_20","short":"T. Meggendorfer, in:, 20th International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2022, pp. 320–326."},"day":"21","publisher":"Springer Nature","date_updated":"2023-09-05T15:11:51Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"PET – A partial exploration tool for probabilistic verification","article_processing_charge":"No","status":"public","page":"320-326","date_created":"2023-01-12T12:11:07Z","year":"2022","volume":13505,"acknowledgement":"We thank Pranav Ashok and Maximilian Weininger for their contributions to spiritual predecessors of PET as well as motivating the initial development of this tool."},{"oa_version":"Preprint","author":[{"id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Garcia Soto","orcid":"0000-0003-2936-5719","full_name":"Garcia Soto, Miriam"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"last_name":"Schilling","full_name":"Schilling, Christian","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"ec_funded":1,"department":[{"_id":"ToHe"}],"publication_identifier":{"eisbn":["9783031199929"],"isbn":["9783031199912"],"issn":["0302-9743"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"publication_status":"published","quality_controlled":"1","publication":"20th International Symposium on Automated Technology for Verification and Analysis","oa":1,"intvolume":" 13505","_id":"12171","doi":"10.1007/978-3-031-19992-9_22","date_published":"2022-10-21T00:00:00Z","external_id":{"arxiv":["2208.06383"]},"arxiv":1,"conference":{"location":"Virtual","end_date":"2022-10-28","start_date":"2022-10-25","name":"ATVA: Automated Technology for Verification and Analysis"},"month":"10","page":"337-353","status":"public","project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.06383"}],"acknowledgement":"This work was supported in part by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 847635, by the ERC-2020-AdG 101020093, by DIREC - Digital Research Centre Denmark, and by the Villum Investigator Grant S4OS.","volume":13505,"year":"2022","date_created":"2023-01-12T12:11:16Z","date_updated":"2023-02-13T09:27:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","article_processing_charge":"No","title":"Synthesis of parametric hybrid automata from time series","abstract":[{"text":"We propose an algorithmic approach for synthesizing linear hybrid automata from time-series data. Unlike existing approaches, our approach provides a whole family of models with the same discrete structure but different dynamics. Each model in the family is guaranteed to capture the input data up to a precision error ε, in the following sense: For each time series, the model contains an execution that is ε-close to the data points. Our construction allows to effectively choose a model from this family with minimal precision error ε. We demonstrate the algorithm’s efficiency and its ability to find precise models in two case studies.","lang":"eng"}],"day":"21","citation":{"short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, in:, 20th International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2022, pp. 337–353.","ama":"Garcia Soto M, Henzinger TA, Schilling C. Synthesis of parametric hybrid automata from time series. In: 20th International Symposium on Automated Technology for Verification and Analysis. Vol 13505. Springer Nature; 2022:337-353. doi:10.1007/978-3-031-19992-9_22","ista":"Garcia Soto M, Henzinger TA, Schilling C. 2022. Synthesis of parametric hybrid automata from time series. 20th International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 13505, 337–353.","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, and Christian Schilling. “Synthesis of Parametric Hybrid Automata from Time Series.” In 20th International Symposium on Automated Technology for Verification and Analysis, 13505:337–53. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-19992-9_22.","apa":"Garcia Soto, M., Henzinger, T. A., & Schilling, C. (2022). Synthesis of parametric hybrid automata from time series. In 20th International Symposium on Automated Technology for Verification and Analysis (Vol. 13505, pp. 337–353). Virtual: Springer Nature. https://doi.org/10.1007/978-3-031-19992-9_22","mla":"Garcia Soto, Miriam, et al. “Synthesis of Parametric Hybrid Automata from Time Series.” 20th International Symposium on Automated Technology for Verification and Analysis, vol. 13505, Springer Nature, 2022, pp. 337–53, doi:10.1007/978-3-031-19992-9_22.","ieee":"M. Garcia Soto, T. A. Henzinger, and C. Schilling, “Synthesis of parametric hybrid automata from time series,” in 20th International Symposium on Automated Technology for Verification and Analysis, Virtual, 2022, vol. 13505, pp. 337–353."},"scopus_import":"1"},{"acknowledgement":"We would like to acknowledge Anita Krnjic, Christina Gmainer, Marion Nehr, Helga Mock, and Sena Ecin for technical support in conducting the experiments.\r\nThis study was supported by the Austrian Science Fund (P 32302) and the Vienna Science and Technology Fund (LS18- 053; Austrian Science Fund (FWF)) [P 32302].","volume":14,"year":"2022","date_created":"2023-01-12T12:11:36Z","status":"public","article_type":"original","article_number":"e2143218","article_processing_charge":"No","title":"Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis","ddc":["570"],"date_updated":"2023-08-04T09:10:18Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Taylor & Francis","day":"22","isi":1,"citation":{"mla":"Baumgartner, Maximilian, et al. “Atypical Enteropathogenic E. Coli Are Associated with Disease Activity in Ulcerative Colitis.” Gut Microbes, vol. 14, no. 1, e2143218, Taylor & Francis, 2022, doi:10.1080/19490976.2022.2143218.","ieee":"M. Baumgartner et al., “Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis,” Gut Microbes, vol. 14, no. 1. Taylor & Francis, 2022.","short":"M. Baumgartner, R. Zirnbauer, S. Schlager, D. Mertens, N. Gasche, B. Sladek, C. Herbold, O. Bochkareva, V. Emelianenko, H. Vogelsang, M. Lang, A. Klotz, B. Moik, A. Makristathis, D. Berry, S. Dabsch, V. Khare, C. Gasche, Gut Microbes 14 (2022).","chicago":"Baumgartner, Maximilian, Rebecca Zirnbauer, Sabine Schlager, Daniel Mertens, Nikolaus Gasche, Barbara Sladek, Craig Herbold, et al. “Atypical Enteropathogenic E. Coli Are Associated with Disease Activity in Ulcerative Colitis.” Gut Microbes. Taylor & Francis, 2022. https://doi.org/10.1080/19490976.2022.2143218.","apa":"Baumgartner, M., Zirnbauer, R., Schlager, S., Mertens, D., Gasche, N., Sladek, B., … Gasche, C. (2022). Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes. Taylor & Francis. https://doi.org/10.1080/19490976.2022.2143218","ama":"Baumgartner M, Zirnbauer R, Schlager S, et al. Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes. 2022;14(1). doi:10.1080/19490976.2022.2143218","ista":"Baumgartner M, Zirnbauer R, Schlager S, Mertens D, Gasche N, Sladek B, Herbold C, Bochkareva O, Emelianenko V, Vogelsang H, Lang M, Klotz A, Moik B, Makristathis A, Berry D, Dabsch S, Khare V, Gasche C. 2022. Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis. Gut Microbes. 14(1), e2143218."},"abstract":[{"lang":"eng","text":"With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic E. coli (aEPEC) with IBD disease activity. The presence of diarrheagenic E. coli was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins espV and espG2 distinguish aEPEC cultured from UC and Crohn’s disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune–microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro."}],"has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","author":[{"last_name":"Baumgartner","full_name":"Baumgartner, Maximilian","first_name":"Maximilian"},{"last_name":"Zirnbauer","full_name":"Zirnbauer, Rebecca","first_name":"Rebecca"},{"first_name":"Sabine","full_name":"Schlager, Sabine","last_name":"Schlager"},{"last_name":"Mertens","full_name":"Mertens, Daniel","first_name":"Daniel"},{"full_name":"Gasche, Nikolaus","last_name":"Gasche","first_name":"Nikolaus"},{"full_name":"Sladek, Barbara","last_name":"Sladek","first_name":"Barbara"},{"full_name":"Herbold, Craig","last_name":"Herbold","first_name":"Craig"},{"first_name":"Olga","last_name":"Bochkareva","full_name":"Bochkareva, Olga"},{"full_name":"Emelianenko, Vera","last_name":"Emelianenko","first_name":"Vera","id":"20152b9d-927a-11ed-8107-be36d740812d"},{"full_name":"Vogelsang, Harald","last_name":"Vogelsang","first_name":"Harald"},{"first_name":"Michaela","full_name":"Lang, Michaela","last_name":"Lang"},{"first_name":"Anton","last_name":"Klotz","full_name":"Klotz, Anton"},{"first_name":"Birgit","full_name":"Moik, Birgit","last_name":"Moik"},{"last_name":"Makristathis","full_name":"Makristathis, Athanasios","first_name":"Athanasios"},{"first_name":"David","last_name":"Berry","full_name":"Berry, David"},{"first_name":"Stefanie","full_name":"Dabsch, Stefanie","last_name":"Dabsch"},{"first_name":"Vineeta","last_name":"Khare","full_name":"Khare, Vineeta"},{"last_name":"Gasche","full_name":"Gasche, Christoph","first_name":"Christoph"}],"file":[{"creator":"dernst","file_size":4075251,"relation":"main_file","date_created":"2023-01-26T10:56:51Z","file_id":"12400","checksum":"ee7681a17ae27645e9b5c1df61c15429","content_type":"application/pdf","access_level":"open_access","success":1,"date_updated":"2023-01-26T10:56:51Z","file_name":"2022_GutMicrobes_Baumgartner.pdf"}],"department":[{"_id":"FyKo"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"file_date_updated":"2023-01-26T10:56:51Z","publication_identifier":{"eissn":["1949-0984"],"issn":["1949-0976"]},"language":[{"iso":"eng"}],"keyword":["Infectious Diseases","Microbiology (medical)","Gastroenterology","Microbiology"],"issue":"1","type":"journal_article","_id":"12173","date_published":"2022-11-22T00:00:00Z","doi":"10.1080/19490976.2022.2143218","external_id":{"isi":["000889180100001"]},"month":"11","publication_status":"published","quality_controlled":"1","publication":"Gut Microbes","oa":1,"intvolume":" 14"},{"author":[{"first_name":"Renzo","last_name":"Guerrini","full_name":"Guerrini, Renzo"},{"full_name":"Mei, Davide","last_name":"Mei","first_name":"Davide"},{"full_name":"Szigeti, Margit Katalin","orcid":"0000-0001-9500-8758","last_name":"Szigeti","first_name":"Margit Katalin","id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pepe, Sara","last_name":"Pepe","first_name":"Sara"},{"first_name":"Mary Kay","full_name":"Koenig, Mary Kay","last_name":"Koenig"},{"first_name":"Gretchen","last_name":"Von Allmen","full_name":"Von Allmen, Gretchen"},{"full_name":"Cho, Megan T","last_name":"Cho","first_name":"Megan T"},{"last_name":"McDonald","full_name":"McDonald, Kimberly","first_name":"Kimberly"},{"last_name":"Baker","full_name":"Baker, Janice","first_name":"Janice"},{"last_name":"Bhambhani","full_name":"Bhambhani, Vikas","first_name":"Vikas"},{"full_name":"Powis, Zöe","last_name":"Powis","first_name":"Zöe"},{"full_name":"Rodan, Lance","last_name":"Rodan","first_name":"Lance"},{"full_name":"Nabbout, Rima","last_name":"Nabbout","first_name":"Rima"},{"first_name":"Giulia","full_name":"Barcia, Giulia","last_name":"Barcia"},{"full_name":"Rosenfeld, Jill A","last_name":"Rosenfeld","first_name":"Jill A"},{"last_name":"Bacino","full_name":"Bacino, Carlos A","first_name":"Carlos A"},{"first_name":"Cyril","full_name":"Mignot, Cyril","last_name":"Mignot"},{"last_name":"Power","full_name":"Power, Lillian H","first_name":"Lillian H"},{"first_name":"Catharine J","full_name":"Harris, Catharine J","last_name":"Harris"},{"first_name":"Dragan","full_name":"Marjanovic, Dragan","last_name":"Marjanovic"},{"first_name":"Rikke S","last_name":"Møller","full_name":"Møller, Rikke S"},{"first_name":"Trine B","full_name":"Hammer, Trine B","last_name":"Hammer"},{"first_name":"Riikka","last_name":"Keski Filppula","full_name":"Keski Filppula, Riikka"},{"full_name":"Vieira, Päivi","last_name":"Vieira","first_name":"Päivi"},{"last_name":"Hildebrandt","full_name":"Hildebrandt, Clara","first_name":"Clara"},{"full_name":"Sacharow, Stephanie","last_name":"Sacharow","first_name":"Stephanie"},{"first_name":"Luca","last_name":"Maragliano","full_name":"Maragliano, Luca"},{"first_name":"Fabio","last_name":"Benfenati","full_name":"Benfenati, Fabio"},{"first_name":"Katherine","full_name":"Lachlan, Katherine","last_name":"Lachlan"},{"first_name":"Andreas","last_name":"Benneche","full_name":"Benneche, Andreas"},{"first_name":"Florence","last_name":"Petit","full_name":"Petit, Florence"},{"full_name":"de Sainte Agathe, Jean Madeleine","last_name":"de Sainte Agathe","first_name":"Jean Madeleine"},{"first_name":"Barbara","last_name":"Hallinan","full_name":"Hallinan, Barbara"},{"first_name":"Yue","last_name":"Si","full_name":"Si, Yue"},{"full_name":"Wentzensen, Ingrid M","last_name":"Wentzensen","first_name":"Ingrid M"},{"first_name":"Fanggeng","last_name":"Zou","full_name":"Zou, Fanggeng"},{"first_name":"Vinodh","last_name":"Narayanan","full_name":"Narayanan, Vinodh"},{"first_name":"Naomichi","last_name":"Matsumoto","full_name":"Matsumoto, Naomichi"},{"first_name":"Alessandra","last_name":"Boncristiano","full_name":"Boncristiano, Alessandra"},{"last_name":"la Marca","full_name":"la Marca, Giancarlo","first_name":"Giancarlo"},{"last_name":"Kato","full_name":"Kato, Mitsuhiro","first_name":"Mitsuhiro"},{"last_name":"Anderson","full_name":"Anderson, Kristin","first_name":"Kristin"},{"first_name":"Carmen","last_name":"Barba","full_name":"Barba, Carmen"},{"last_name":"Sturiale","full_name":"Sturiale, Luisa","first_name":"Luisa"},{"first_name":"Domenico","last_name":"Garozzo","full_name":"Garozzo, Domenico"},{"first_name":"Roberto","full_name":"Bei, Roberto","last_name":"Bei"},{"first_name":"Laura","full_name":"Masuelli, Laura","last_name":"Masuelli"},{"first_name":"Valerio","last_name":"Conti","full_name":"Conti, Valerio"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"first_name":"Anna","last_name":"Fassio","full_name":"Fassio, Anna"}],"oa_version":"Published Version","ec_funded":1,"department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0006-8950"],"eissn":["1460-2156"]},"keyword":["Neurology (clinical)"],"issue":"8","type":"journal_article","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"publication_status":"published","quality_controlled":"1","oa":1,"intvolume":" 145","publication":"Brain","_id":"12174","date_published":"2022-08-01T00:00:00Z","doi":"10.1093/brain/awac145","external_id":{"isi":["000807770000001"]},"month":"08","page":"2687-2703","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"status":"public","article_type":"original","main_file_link":[{"url":"https://doi.org/10.1093/brain/awac145","open_access":"1"}],"acknowledgement":"We thank all patients and family members for their participation in this study. We thank Melanie Pieraks and Eva Reinthaler (Neurolentech, Austria) for generating the human iPSC lines and\r\nfor performing quality checks. We thank Vanessa Zheden and Daniel Gütl for their excellent technical support in the specimen preparation for transmission electron microscopy and Flavia Leite for preparing the lentiviruses. The support from Electron Microscopy Facility and Molecular Biology Services at IST Austria is greatly acknowledged. We would like to thank Doctors Jane Hurst and Richard Scott for their help in retrieving the detailed clinical information of Patient 17. The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. See Supplementary Material for Undiagnosed Disease Network consortium details. Genetic information on Patient 23 was made available through access to the data and findings generated by the 100 000 Genomes\r\nProject; www.genomicsengland.co.uk (to K.L.). \r\nThis work was supported by the EU 7th Framework Programme (FP7) under the project DESIRE grant N602531 (to R.G.); the Regione Toscana under the Call for Health 2018 (grant\r\nDECODE-EE) (to R.G.); the ‘Brain Project’ by Fondazione Cassa di Risparmio di Firenze (to R.G.); IRCCS Ospedale Policlinico San Martino 5×1000 and Ricerca Corrente (to A.F. and F.B.). The European Reference Network (ERN) for rare and complex epilepsies (EpiCARE) provided financial support for meetings organization. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant number HICF-1009-003), a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute (grant number WT098051). The views expressed in this publication\r\nare those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). This study makes use of DECIPHER (https://www.deciphergenomics.org), which is funded by Wellcome. K.K.-S. was supported by the ISTplus fellowship. ","volume":145,"year":"2022","date_created":"2023-01-12T12:11:45Z","publisher":"Oxford University Press","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:13:08Z","article_processing_charge":"No","title":"Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis","abstract":[{"text":"Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease.\r\nHere we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs.\r\n Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes.\r\nATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants.","lang":"eng"}],"day":"01","isi":1,"citation":{"ieee":"R. Guerrini et al., “Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis,” Brain, vol. 145, no. 8. Oxford University Press, pp. 2687–2703, 2022.","mla":"Guerrini, Renzo, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” Brain, vol. 145, no. 8, Oxford University Press, 2022, pp. 2687–703, doi:10.1093/brain/awac145.","apa":"Guerrini, R., Mei, D., Szigeti, M. K., Pepe, S., Koenig, M. K., Von Allmen, G., … Fassio, A. (2022). Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. Oxford University Press. https://doi.org/10.1093/brain/awac145","ama":"Guerrini R, Mei D, Szigeti MK, et al. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 2022;145(8):2687-2703. doi:10.1093/brain/awac145","chicago":"Guerrini, Renzo, Davide Mei, Margit Katalin Szigeti, Sara Pepe, Mary Kay Koenig, Gretchen Von Allmen, Megan T Cho, et al. “Phenotypic and Genetic Spectrum of ATP6V1A Encephalopathy: A Disorder of Lysosomal Homeostasis.” Brain. Oxford University Press, 2022. https://doi.org/10.1093/brain/awac145.","ista":"Guerrini R, Mei D, Szigeti MK, Pepe S, Koenig MK, Von Allmen G, Cho MT, McDonald K, Baker J, Bhambhani V, Powis Z, Rodan L, Nabbout R, Barcia G, Rosenfeld JA, Bacino CA, Mignot C, Power LH, Harris CJ, Marjanovic D, Møller RS, Hammer TB, Keski Filppula R, Vieira P, Hildebrandt C, Sacharow S, Maragliano L, Benfenati F, Lachlan K, Benneche A, Petit F, de Sainte Agathe JM, Hallinan B, Si Y, Wentzensen IM, Zou F, Narayanan V, Matsumoto N, Boncristiano A, la Marca G, Kato M, Anderson K, Barba C, Sturiale L, Garozzo D, Bei R, Masuelli L, Conti V, Novarino G, Fassio A. 2022. Phenotypic and genetic spectrum of ATP6V1A encephalopathy: A disorder of lysosomal homeostasis. Brain. 145(8), 2687–2703.","short":"R. Guerrini, D. Mei, M.K. Szigeti, S. Pepe, M.K. Koenig, G. Von Allmen, M.T. Cho, K. McDonald, J. Baker, V. Bhambhani, Z. Powis, L. Rodan, R. Nabbout, G. Barcia, J.A. Rosenfeld, C.A. Bacino, C. Mignot, L.H. Power, C.J. Harris, D. Marjanovic, R.S. Møller, T.B. Hammer, R. Keski Filppula, P. Vieira, C. Hildebrandt, S. Sacharow, L. Maragliano, F. Benfenati, K. Lachlan, A. Benneche, F. Petit, J.M. de Sainte Agathe, B. Hallinan, Y. Si, I.M. Wentzensen, F. Zou, V. Narayanan, N. Matsumoto, A. Boncristiano, G. la Marca, M. Kato, K. Anderson, C. Barba, L. Sturiale, D. Garozzo, R. Bei, L. Masuelli, V. Conti, G. Novarino, A. Fassio, Brain 145 (2022) 2687–2703."},"scopus_import":"1"},{"publisher":"Springer Nature","date_updated":"2023-09-05T15:12:08Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"History-deterministic timed automata are not determinizable","page":"67-76","status":"public","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"main_file_link":[{"open_access":"1","url":"https://hal.science/hal-03849398/"}],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, the EPSRC project EP/V025848/1, and the EPSRC project EP/X017796/1.","volume":13608,"year":"2022","date_created":"2023-01-12T12:11:57Z","scopus_import":"1","abstract":[{"text":"An automaton is history-deterministic (HD) if one can safely resolve its non-deterministic choices on the fly. In a recent paper, Henzinger, Lehtinen and Totzke studied this in the context of Timed Automata [9], where it was conjectured that the class of timed ω-languages recognised by HD-timed automata strictly extends that of deterministic ones. We provide a proof for this fact.","lang":"eng"}],"day":"12","citation":{"apa":"Bose, S., Henzinger, T. A., Lehtinen, K., Schewe, S., & Totzke, P. (2022). History-deterministic timed automata are not determinizable. In 16th International Conference on Reachability Problems (Vol. 13608, pp. 67–76). Kaiserslautern, Germany: Springer Nature. https://doi.org/10.1007/978-3-031-19135-0_5","ama":"Bose S, Henzinger TA, Lehtinen K, Schewe S, Totzke P. History-deterministic timed automata are not determinizable. In: 16th International Conference on Reachability Problems. Vol 13608. Springer Nature; 2022:67-76. doi:10.1007/978-3-031-19135-0_5","chicago":"Bose, Sougata, Thomas A Henzinger, Karoliina Lehtinen, Sven Schewe, and Patrick Totzke. “History-Deterministic Timed Automata Are Not Determinizable.” In 16th International Conference on Reachability Problems, 13608:67–76. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-19135-0_5.","ista":"Bose S, Henzinger TA, Lehtinen K, Schewe S, Totzke P. 2022. History-deterministic timed automata are not determinizable. 16th International Conference on Reachability Problems. RC: Reachability Problems, LNCS, vol. 13608, 67–76.","short":"S. Bose, T.A. Henzinger, K. Lehtinen, S. Schewe, P. Totzke, in:, 16th International Conference on Reachability Problems, Springer Nature, 2022, pp. 67–76.","ieee":"S. Bose, T. A. Henzinger, K. Lehtinen, S. Schewe, and P. Totzke, “History-deterministic timed automata are not determinizable,” in 16th International Conference on Reachability Problems, Kaiserslautern, Germany, 2022, vol. 13608, pp. 67–76.","mla":"Bose, Sougata, et al. “History-Deterministic Timed Automata Are Not Determinizable.” 16th International Conference on Reachability Problems, vol. 13608, Springer Nature, 2022, pp. 67–76, doi:10.1007/978-3-031-19135-0_5."},"ec_funded":1,"department":[{"_id":"ToHe"}],"oa_version":"Preprint","author":[{"full_name":"Bose, Sougata","last_name":"Bose","first_name":"Sougata"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"last_name":"Lehtinen","full_name":"Lehtinen, Karoliina","first_name":"Karoliina"},{"first_name":"Sven","full_name":"Schewe, Sven","last_name":"Schewe"},{"first_name":"Patrick","last_name":"Totzke","full_name":"Totzke, Patrick"}],"publication_status":"published","quality_controlled":"1","intvolume":" 13608","publication":"16th International Conference on Reachability Problems","oa":1,"_id":"12175","date_published":"2022-10-12T00:00:00Z","doi":"10.1007/978-3-031-19135-0_5","conference":{"end_date":"2022-10-21","location":"Kaiserslautern, Germany","name":"RC: Reachability Problems","start_date":"2022-10-17"},"month":"10","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783031191343"],"eisbn":["9783031191350"],"eissn":["1611-3349"],"issn":["0302-9743"]},"type":"conference","alternative_title":["LNCS"]},{"quality_controlled":"1","publication_status":"published","intvolume":" 13508","oa":1,"publication":"Advances in Cryptology – CRYPTO 2022","doi":"10.1007/978-3-031-15979-4_13","date_published":"2022-10-13T00:00:00Z","_id":"12176","month":"10","external_id":{"isi":["000886792700013"]},"conference":{"end_date":"2022-08-18","location":"Santa Barbara, CA, United States","start_date":"2022-08-15","name":"CRYYPTO: International Cryptology Conference"},"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783031159794"],"isbn":["9783031159787"],"issn":["0302-9743"],"eissn":["1611-3349"]},"type":"conference","alternative_title":["LNCS"],"department":[{"_id":"KrPi"}],"oa_version":"Preprint","author":[{"last_name":"Hoffmann","orcid":"0000-0003-2027-5549","full_name":"Hoffmann, Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","first_name":"Charlotte"},{"first_name":"Pavel","last_name":"Hubáček","full_name":"Hubáček, Pavel"},{"full_name":"Kamath, Chethan","last_name":"Kamath","first_name":"Chethan"},{"full_name":"Klein, Karen","last_name":"Klein","first_name":"Karen"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"scopus_import":"1","abstract":[{"text":"A proof of exponentiation (PoE) in a group G of unknown order allows a prover to convince a verifier that a tuple (x,q,T,y)∈G×N×N×G satisfies xqT=y. This primitive has recently found exciting applications in the constructions of verifiable delay functions and succinct arguments of knowledge. The most practical PoEs only achieve soundness either under computational assumptions, i.e., they are arguments (Wesolowski, Journal of Cryptology 2020), or in groups that come with the promise of not having any small subgroups (Pietrzak, ITCS 2019). The only statistically-sound PoE in general groups of unknown order is due to Block et al. (CRYPTO 2021), and can be seen as an elaborate parallel repetition of Pietrzak’s PoE: to achieve λ bits of security, say λ=80, the number of repetitions required (and thus the blow-up in communication) is as large as λ.\r\n\r\nIn this work, we propose a statistically-sound PoE for the case where the exponent q is the product of all primes up to some bound B. We show that, in this case, it suffices to run only λ/log(B) parallel instances of Pietrzak’s PoE, which reduces the concrete proof-size compared to Block et al. by an order of magnitude. Furthermore, we show that in the known applications where PoEs are used as a building block such structured exponents are viable. Finally, we also discuss batching of our PoE, showing that many proofs (for the same G and q but different x and T) can be batched by adding only a single element to the proof per additional statement.","lang":"eng"}],"isi":1,"day":"13","citation":{"ama":"Hoffmann C, Hubáček P, Kamath C, Klein K, Pietrzak KZ. Practical statistically-sound proofs of exponentiation in any group. In: Advances in Cryptology – CRYPTO 2022. Vol 13508. Springer Nature; 2022:370-399. doi:10.1007/978-3-031-15979-4_13","ista":"Hoffmann C, Hubáček P, Kamath C, Klein K, Pietrzak KZ. 2022. Practical statistically-sound proofs of exponentiation in any group. Advances in Cryptology – CRYPTO 2022. CRYYPTO: International Cryptology Conference, LNCS, vol. 13508, 370–399.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., Klein, K., & Pietrzak, K. Z. (2022). Practical statistically-sound proofs of exponentiation in any group. In Advances in Cryptology – CRYPTO 2022 (Vol. 13508, pp. 370–399). Santa Barbara, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-15979-4_13","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, Karen Klein, and Krzysztof Z Pietrzak. “Practical Statistically-Sound Proofs of Exponentiation in Any Group.” In Advances in Cryptology – CRYPTO 2022, 13508:370–99. Springer Nature, 2022. https://doi.org/10.1007/978-3-031-15979-4_13.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K. Klein, K.Z. Pietrzak, in:, Advances in Cryptology – CRYPTO 2022, Springer Nature, 2022, pp. 370–399.","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, K. Klein, and K. Z. Pietrzak, “Practical statistically-sound proofs of exponentiation in any group,” in Advances in Cryptology – CRYPTO 2022, Santa Barbara, CA, United States, 2022, vol. 13508, pp. 370–399.","mla":"Hoffmann, Charlotte, et al. “Practical Statistically-Sound Proofs of Exponentiation in Any Group.” Advances in Cryptology – CRYPTO 2022, vol. 13508, Springer Nature, 2022, pp. 370–99, doi:10.1007/978-3-031-15979-4_13."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","date_updated":"2023-09-05T15:12:27Z","title":"Practical statistically-sound proofs of exponentiation in any group","article_processing_charge":"No","page":"370-399","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2022/1021"}],"status":"public","volume":13508,"acknowledgement":"We would like to thank the authors of [BHR+21] for clarifying several questions we had\r\nregarding their results. Pavel Hubá£ek was supported by the Grant Agency of the Czech\r\nRepublic under the grant agreement no. 19-27871X and by the Charles University project\r\nUNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship\r\nand ISF grants 484/18 and 1789/19. Karen Klein was supported in part by ERC CoG grant\r\n724307 and conducted part of this work at Institute of Science and Technology Austria.","date_created":"2023-01-12T12:12:07Z","year":"2022"},{"title":"Effective contraction of Skinning maps","article_processing_charge":"No","ddc":["510"],"date_updated":"2023-01-26T13:04:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Mathematical Society","volume":9,"acknowledgement":"The first author was partially supported by the National Science Foundation under Grant\r\nNo. DMS-1928930 while participating in a program hosted by the Mathematical Sciences Research Institute in Berkeley, California, during the Fall 2020 semester. The second author gratefully acknowledges funding by the Austrian Science Fund (FWF) through grants F65 and ESPRIT 208, by the European Research Council (ERC, grant No. 716117, awarded to Prof. Dr. Jan Maas), and by the Deutsche Forschungsgemeinschaft through the SPP 2265.","date_created":"2023-01-12T12:12:17Z","year":"2022","page":"445-459","article_type":"original","status":"public","project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"has_accepted_license":"1","scopus_import":"1","day":"02","citation":{"apa":"Cremaschi, T., & Dello Schiavo, L. (2022). Effective contraction of Skinning maps. Proceedings of the American Mathematical Society, Series B. American Mathematical Society. https://doi.org/10.1090/bproc/134","ama":"Cremaschi T, Dello Schiavo L. Effective contraction of Skinning maps. Proceedings of the American Mathematical Society, Series B. 2022;9(43):445-459. doi:10.1090/bproc/134","ista":"Cremaschi T, Dello Schiavo L. 2022. Effective contraction of Skinning maps. Proceedings of the American Mathematical Society, Series B. 9(43), 445–459.","chicago":"Cremaschi, Tommaso, and Lorenzo Dello Schiavo. “Effective Contraction of Skinning Maps.” Proceedings of the American Mathematical Society, Series B. American Mathematical Society, 2022. https://doi.org/10.1090/bproc/134.","short":"T. Cremaschi, L. Dello Schiavo, Proceedings of the American Mathematical Society, Series B 9 (2022) 445–459.","ieee":"T. Cremaschi and L. Dello Schiavo, “Effective contraction of Skinning maps,” Proceedings of the American Mathematical Society, Series B, vol. 9, no. 43. American Mathematical Society, pp. 445–459, 2022.","mla":"Cremaschi, Tommaso, and Lorenzo Dello Schiavo. “Effective Contraction of Skinning Maps.” Proceedings of the American Mathematical Society, Series B, vol. 9, no. 43, American Mathematical Society, 2022, pp. 445–59, doi:10.1090/bproc/134."},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","text":"Using elementary hyperbolic geometry, we give an explicit formula for the contraction constant of the skinning map over moduli spaces of relatively acylindrical hyperbolic manifolds."}],"file":[{"creator":"dernst","file_size":326471,"relation":"main_file","file_id":"12404","date_created":"2023-01-26T13:02:07Z","file_name":"2022_ProceedingsAMS_Cremaschi.pdf","date_updated":"2023-01-26T13:02:07Z","success":1,"checksum":"cb4a79937c1f60d4c329a10ee797f0d2","content_type":"application/pdf","access_level":"open_access"}],"department":[{"_id":"JaMa"}],"ec_funded":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"oa_version":"Published Version","author":[{"first_name":"Tommaso","full_name":"Cremaschi, Tommaso","last_name":"Cremaschi"},{"first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo"}],"date_published":"2022-11-02T00:00:00Z","doi":"10.1090/bproc/134","_id":"12177","month":"11","quality_controlled":"1","publication_status":"published","oa":1,"intvolume":" 9","publication":"Proceedings of the American Mathematical Society, Series B","file_date_updated":"2023-01-26T13:02:07Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2330-1511"]},"type":"journal_article","issue":"43"},{"external_id":{"isi":["000874389000001"]},"month":"10","_id":"12178","date_published":"2022-10-27T00:00:00Z","doi":"10.1007/s40072-022-00277-3","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","oa":1,"publication_status":"epub_ahead","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2194-041X"],"issn":["2194-0401"]},"keyword":["Applied Mathematics","Modeling and Simulation","Statistics and Probability"],"department":[{"_id":"JuFi"}],"oa_version":"Published Version","author":[{"first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962","last_name":"Agresti"},{"first_name":"Matthias","full_name":"Hieber, Matthias","last_name":"Hieber"},{"last_name":"Hussein","full_name":"Hussein, Amru","first_name":"Amru"},{"first_name":"Martin","full_name":"Saal, Martin","last_name":"Saal"}],"scopus_import":"1","citation":{"ieee":"A. Agresti, M. Hieber, A. Hussein, and M. Saal, “The stochastic primitive equations with transport noise and turbulent pressure,” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2022.","mla":"Agresti, Antonio, et al. “The Stochastic Primitive Equations with Transport Noise and Turbulent Pressure.” Stochastics and Partial Differential Equations: Analysis and Computations, Springer Nature, 2022, doi:10.1007/s40072-022-00277-3.","apa":"Agresti, A., Hieber, M., Hussein, A., & Saal, M. (2022). The stochastic primitive equations with transport noise and turbulent pressure. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-022-00277-3","chicago":"Agresti, Antonio, Matthias Hieber, Amru Hussein, and Martin Saal. “The Stochastic Primitive Equations with Transport Noise and Turbulent Pressure.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2022. https://doi.org/10.1007/s40072-022-00277-3.","ama":"Agresti A, Hieber M, Hussein A, Saal M. The stochastic primitive equations with transport noise and turbulent pressure. Stochastics and Partial Differential Equations: Analysis and Computations. 2022. doi:10.1007/s40072-022-00277-3","ista":"Agresti A, Hieber M, Hussein A, Saal M. 2022. The stochastic primitive equations with transport noise and turbulent pressure. Stochastics and Partial Differential Equations: Analysis and Computations.","short":"A. Agresti, M. Hieber, A. Hussein, M. Saal, Stochastics and Partial Differential Equations: Analysis and Computations (2022)."},"isi":1,"day":"27","abstract":[{"text":"In this paper we consider the stochastic primitive equation for geophysical flows subject to transport noise and turbulent pressure. Admitting very rough noise terms, the global existence and uniqueness of solutions to this stochastic partial differential equation are proven using stochastic maximal L² regularity, the theory of critical spaces for stochastic evolution equations, and global a priori bounds. Compared to other results in this direction, we do not need any smallness assumption on the transport noise which acts directly on the velocity field and we also allow rougher noise terms. The adaptation to Stratonovich type noise and, more generally, to variable viscosity and/or conductivity are discussed as well.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","title":"The stochastic primitive equations with transport noise and turbulent pressure","date_updated":"2023-08-16T09:11:38Z","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","date_created":"2023-01-12T12:12:29Z","acknowledgement":"The authors thank the anonymous referees for their helpful comments and suggestions. Open Access funding enabled and organized by Projekt DEAL.","status":"public","main_file_link":[{"url":"https://doi.org/10.1007/s40072-022-00277-3","open_access":"1"}],"article_type":"original"},{"intvolume":" 43","publication":"SIAM Journal on Matrix Analysis and Applications","oa":1,"quality_controlled":"1","publication_status":"published","month":"07","external_id":{"arxiv":["2105.13719"]},"arxiv":1,"date_published":"2022-07-01T00:00:00Z","doi":"10.1137/21m1424408","_id":"12179","type":"journal_article","issue":"3","keyword":["Analysis"],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1095-7162"],"issn":["0895-4798"]},"department":[{"_id":"LaEr"}],"author":[{"orcid":"0000-0002-4901-7992","full_name":"Cipolloni, Giorgio","last_name":"Cipolloni","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","last_name":"Schröder"}],"oa_version":"Preprint","scopus_import":"1","abstract":[{"lang":"eng","text":"We derive an accurate lower tail estimate on the lowest singular value σ1(X−z) of a real Gaussian (Ginibre) random matrix X shifted by a complex parameter z. Such shift effectively changes the upper tail behavior of the condition number κ(X−z) from the slower (κ(X−z)≥t)≲1/t decay typical for real Ginibre matrices to the faster 1/t2 decay seen for complex Ginibre matrices as long as z is away from the real axis. This sharpens and resolves a recent conjecture in [J. Banks et al., https://arxiv.org/abs/2005.08930, 2020] on the regularizing effect of the real Ginibre ensemble with a genuinely complex shift. As a consequence we obtain an improved upper bound on the eigenvalue condition numbers (known also as the eigenvector overlaps) for real Ginibre matrices. The main technical tool is a rigorous supersymmetric analysis from our earlier work [Probab. Math. Phys., 1 (2020), pp. 101--146]."}],"citation":{"ama":"Cipolloni G, Erdös L, Schröder DJ. On the condition number of the shifted real Ginibre ensemble. SIAM Journal on Matrix Analysis and Applications. 2022;43(3):1469-1487. doi:10.1137/21m1424408","ista":"Cipolloni G, Erdös L, Schröder DJ. 2022. On the condition number of the shifted real Ginibre ensemble. SIAM Journal on Matrix Analysis and Applications. 43(3), 1469–1487.","apa":"Cipolloni, G., Erdös, L., & Schröder, D. J. (2022). On the condition number of the shifted real Ginibre ensemble. SIAM Journal on Matrix Analysis and Applications. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/21m1424408","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “On the Condition Number of the Shifted Real Ginibre Ensemble.” SIAM Journal on Matrix Analysis and Applications. Society for Industrial and Applied Mathematics, 2022. https://doi.org/10.1137/21m1424408.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, SIAM Journal on Matrix Analysis and Applications 43 (2022) 1469–1487.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “On the condition number of the shifted real Ginibre ensemble,” SIAM Journal on Matrix Analysis and Applications, vol. 43, no. 3. Society for Industrial and Applied Mathematics, pp. 1469–1487, 2022.","mla":"Cipolloni, Giorgio, et al. “On the Condition Number of the Shifted Real Ginibre Ensemble.” SIAM Journal on Matrix Analysis and Applications, vol. 43, no. 3, Society for Industrial and Applied Mathematics, 2022, pp. 1469–87, doi:10.1137/21m1424408."},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics","date_updated":"2023-01-27T06:56:06Z","title":"On the condition number of the shifted real Ginibre ensemble","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.13719","open_access":"1"}],"article_type":"original","status":"public","page":"1469-1487","date_created":"2023-01-12T12:12:38Z","year":"2022","volume":43}]