[{"date_updated":"2025-04-23T08:57:12Z","month":"06","abstract":[{"lang":"eng","text":"Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death."}],"volume":618,"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"oa_version":"Published Version","has_accepted_license":"1","citation":{"ama":"Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. <i>Nature</i>. 2023;618:1065-1071. doi:<a href=\"https://doi.org/10.1038/s41586-023-05991-z\">10.1038/s41586-023-05991-z</a>","apa":"Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius, G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture in cell death. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-05991-z\">https://doi.org/10.1038/s41586-023-05991-z</a>","short":"M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius, E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier, C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.","ista":"Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 618, 1065–1071.","chicago":"Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-05991-z\">https://doi.org/10.1038/s41586-023-05991-z</a>.","ieee":"M. Degen <i>et al.</i>, “Structural basis of NINJ1-mediated plasma membrane rupture in cell death,” <i>Nature</i>, vol. 618. Springer Nature, pp. 1065–1071, 2023.","mla":"Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” <i>Nature</i>, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:<a href=\"https://doi.org/10.1038/s41586-023-05991-z\">10.1038/s41586-023-05991-z</a>."},"article_processing_charge":"Yes (via OA deal)","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"type":"journal_article","_id":"13096","status":"public","page":"1065-1071","publication_status":"published","file":[{"date_updated":"2023-11-14T11:48:18Z","creator":"dernst","relation":"main_file","success":1,"checksum":"0fab69252453bff1de7f0e2eceb76d34","file_id":"14533","content_type":"application/pdf","access_level":"open_access","file_name":"2023_Nature_Degen.pdf","date_created":"2023-11-14T11:48:18Z","file_size":12292188}],"publication":"Nature","pmid":1,"quality_controlled":"1","title":"Structural basis of NINJ1-mediated plasma membrane rupture in cell death","author":[{"full_name":"Degen, Morris","last_name":"Degen","first_name":"Morris"},{"last_name":"Santos","full_name":"Santos, José Carlos","first_name":"José Carlos"},{"first_name":"Kristyna","last_name":"Pluhackova","full_name":"Pluhackova, Kristyna"},{"first_name":"Gonzalo","last_name":"Cebrero","full_name":"Cebrero, Gonzalo"},{"last_name":"Ramos","full_name":"Ramos, Saray","first_name":"Saray"},{"full_name":"Jankevicius, Gytis","last_name":"Jankevicius","first_name":"Gytis"},{"first_name":"Ella","last_name":"Hartenian","full_name":"Hartenian, Ella"},{"id":"bb74f472-ae54-11eb-9835-bc9c22fb1183","first_name":"Undina","last_name":"Guillerm","full_name":"Guillerm, Undina"},{"first_name":"Stefania A.","last_name":"Mari","full_name":"Mari, Stefania A."},{"last_name":"Kohl","full_name":"Kohl, Bastian","first_name":"Bastian"},{"full_name":"Müller, Daniel J.","last_name":"Müller","first_name":"Daniel J."},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Maier","full_name":"Maier, Timm","first_name":"Timm"},{"full_name":"Perez, Camilo","last_name":"Perez","first_name":"Camilo"},{"last_name":"Sieben","full_name":"Sieben, Christian","first_name":"Christian"},{"first_name":"Petr","full_name":"Broz, Petr","last_name":"Broz"},{"first_name":"Sebastian","last_name":"Hiller","full_name":"Hiller, Sebastian"}],"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"date_published":"2023-06-29T00:00:00Z","scopus_import":"1","ddc":["570"],"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H. and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H. and by the Scientific Service Units of IST Austria through resources provided by the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were performed on the HoreKa supercomputer funded by the Ministry of Science, Research and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research. The authors thank the BioEM Lab of the Biozentrum, University of Basel for support; V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P. Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created with BioRender.com.\r\nOpen access funding provided by University of Basel.","publisher":"Springer Nature","doi":"10.1038/s41586-023-05991-z","day":"29","year":"2023","intvolume":"       618","department":[{"_id":"PaSc"}],"file_date_updated":"2023-11-14T11:48:18Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-05-28T22:01:04Z","external_id":{"isi":["000991386800011"],"pmid":["37198476"]},"language":[{"iso":"eng"}]},{"acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","scopus_import":"1","doi":"10.1126/science.adg3812","arxiv":1,"publisher":"American Association for the Advancement of Science","day":"18","ec_funded":1,"project":[{"grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"call_identifier":"H2020","grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"},{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644"},{"name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies","_id":"2671EB66-B435-11E9-9278-68D0E5697425"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"intvolume":"       380","year":"2023","department":[{"_id":"JoFi"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.03315"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-05-31T11:39:24Z","oa":1,"external_id":{"pmid":["37200415"],"isi":["000996515200004"],"arxiv":["2301.03315"]},"language":[{"iso":"eng"}],"corr_author":"1","related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/","relation":"press_release"}],"record":[{"relation":"research_data","status":"public","id":"13122"}]},"article_type":"original","keyword":["Multidisciplinary"],"date_updated":"2026-04-15T06:39:33Z","issue":"6646","month":"05","volume":380,"abstract":[{"text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification.","lang":"eng"}],"oa_version":"Preprint","isi":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"type":"journal_article","citation":{"mla":"Sahu, Rishabh, et al. “Entangling Microwaves with Light.” <i>Science</i>, vol. 380, no. 6646, American Association for the Advancement of Science, 2023, pp. 718–21, doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>.","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adg3812\">https://doi.org/10.1126/science.adg3812</a>.","ieee":"R. Sahu <i>et al.</i>, “Entangling microwaves with light,” <i>Science</i>, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023.","ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. Science. 380(6646), 718–721.","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721.","apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., &#38; Fink, J. M. (2023). Entangling microwaves with light. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg3812\">https://doi.org/10.1126/science.adg3812</a>","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. <i>Science</i>. 2023;380(6646):718-721. doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>"},"article_processing_charge":"No","_id":"13106","status":"public","page":"718-721","publication_status":"published","pmid":1,"quality_controlled":"1","publication":"Science","title":"Entangling microwaves with light","author":[{"first_name":"Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","full_name":"Sahu, Rishabh","last_name":"Sahu","orcid":"0000-0001-6264-2162"},{"orcid":"0000-0003-4345-4267","last_name":"Qiu","full_name":"Qiu, Liu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac","first_name":"Liu"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Hease","orcid":"0000-0001-9868-2166","full_name":"Hease, William J"},{"full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","last_name":"Arnold","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Minoguchi","full_name":"Minoguchi, Y.","first_name":"Y."},{"full_name":"Rabl, P.","last_name":"Rabl","first_name":"P."},{"orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"date_published":"2023-05-18T00:00:00Z"},{"page":"147","publication_status":"published","file":[{"creator":"lknaus","relation":"source_file","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","date_updated":"2023-06-01T13:48:41Z","date_created":"2023-06-01T13:48:41Z","file_size":12991551,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"13112","file_name":"Thesis_Lisa Knaus_approved_final.docx"},{"date_created":"2023-06-02T09:47:29Z","file_size":9309015,"file_id":"13114","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","access_level":"open_access","content_type":"application/pdf","checksum":"6903d152aa01181d87a696085af31c83","creator":"lknaus","relation":"main_file","date_updated":"2023-06-07T08:41:49Z"}],"title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival","date_published":"2023-05-31T00:00:00Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"author":[{"full_name":"Knaus, Lisa","last_name":"Knaus","first_name":"Lisa","id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87"}],"month":"05","abstract":[{"lang":"eng","text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans."}],"date_updated":"2026-04-14T08:34:36Z","related_material":{"record":[{"relation":"part_of_dissertation","id":"12802","status":"public"}]},"has_accepted_license":"1","oa_version":"Published Version","article_processing_charge":"No","citation":{"ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","mla":"Knaus, Lisa. <i>The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>.","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>.","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>","apa":"Knaus, L. (2023). <i>The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>"},"type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"_id":"13107","supervisor":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"status":"public","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"year":"2023","project":[{"call_identifier":"H2020","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425"},{"name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","call_identifier":"FWF"}],"ec_funded":1,"oa":1,"file_date_updated":"2023-06-07T08:41:49Z","degree_awarded":"PhD","date_created":"2023-06-01T09:05:24Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","OA_place":"publisher","corr_author":"1","language":[{"iso":"eng"}],"ddc":["570"],"publisher":"Institute of Science and Technology Austria","doi":"10.15479/at:ista:13107","alternative_title":["ISTA Thesis"],"day":"31"},{"ddc":["539"],"acknowledgement":"This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M.  was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). ","day":"26","doi":"10.15479/AT:ISTA:13116","publisher":"Institute of Science and Technology Austria","ec_funded":1,"project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","grant_number":"679239"},{"grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","name":"In vitro reconstitution of bacterial cell division"},{"grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d","name":"Motile active matter models of migrating cells and chiral filaments"}],"year":"2023","department":[{"_id":"MaLo"},{"_id":"EdHa"},{"_id":"JoDa"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-06-02T12:30:40Z","file_date_updated":"2023-08-08T11:17:28Z","oa":1,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"related_material":{"record":[{"id":"13314","status":"public","relation":"used_in_publication"},{"id":"21423","status":"public","relation":"used_in_publication"}]},"date_updated":"2026-03-17T12:02:11Z","month":"07","abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. "}],"status":"public","_id":"13116","type":"research_data","citation":{"mla":"Dunajova, Zuzana, et al. <i>Chiral and Nematic Phases of Flexible Active Filaments</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">https://doi.org/10.15479/AT:ISTA:13116</a>.","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>.","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023).","apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">https://doi.org/10.15479/AT:ISTA:13116</a>","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. 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Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance in the final stages of the experiment. We acknowledge funding from the European Research Council under the European Union Horizon 2020 Research and Innovation Programme (Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654). F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone Project P 35891-N).","ddc":["530"],"scopus_import":"1","external_id":{"pmid":["37225993"],"isi":["001001139300008"]},"language":[{"iso":"eng"}],"date_created":"2023-06-04T22:01:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2023-11-14T13:00:19Z","oa":1,"intvolume":"       618","year":"2023","department":[{"_id":"GeKa"}],"status":"public","_id":"13119","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"type":"journal_article","citation":{"ieee":"V. Helson <i>et al.</i>, “Density-wave ordering in a unitary Fermi gas with photon-mediated interactions,” <i>Nature</i>, vol. 618. Springer Nature, pp. 716–720, 2023.","chicago":"Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06018-3\">https://doi.org/10.1038/s41586-023-06018-3</a>.","mla":"Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” <i>Nature</i>, vol. 618, Springer Nature, 2023, pp. 716–20, doi:<a href=\"https://doi.org/10.1038/s41586-023-06018-3\">10.1038/s41586-023-06018-3</a>.","short":"V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi, H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720.","ista":"Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H, Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 618, 716–720.","apa":"Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi, H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06018-3\">https://doi.org/10.1038/s41586-023-06018-3</a>","ama":"Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. <i>Nature</i>. 2023;618:716-720. doi:<a href=\"https://doi.org/10.1038/s41586-023-06018-3\">10.1038/s41586-023-06018-3</a>"},"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","isi":1,"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_type":"original","date_updated":"2025-04-23T08:58:21Z","month":"06","volume":618,"abstract":[{"lang":"eng","text":"A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order."}],"author":[{"last_name":"Helson","full_name":"Helson, Victor","first_name":"Victor"},{"first_name":"Timo","full_name":"Zwettler, Timo","last_name":"Zwettler"},{"full_name":"Mivehvar, Farokh","last_name":"Mivehvar","first_name":"Farokh"},{"first_name":"Elvia","last_name":"Colella","full_name":"Colella, Elvia"},{"first_name":"Kevin Etienne Robert","id":"53f93ea2-803f-11ed-ab7e-b283135794ef","full_name":"Roux, Kevin Etienne Robert","last_name":"Roux"},{"first_name":"Hideki","last_name":"Konishi","full_name":"Konishi, Hideki"},{"full_name":"Ritsch, Helmut","last_name":"Ritsch","first_name":"Helmut"},{"first_name":"Jean Philippe","full_name":"Brantut, Jean Philippe","last_name":"Brantut"}],"date_published":"2023-06-22T00:00:00Z","title":"Density-wave ordering in a unitary Fermi gas with photon-mediated interactions","pmid":1,"quality_controlled":"1","file":[{"date_updated":"2023-11-14T13:00:19Z","success":1,"checksum":"4887a296e3b6f54e8c0b946cbfd24f49","creator":"dernst","relation":"main_file","file_name":"2023_Nature_Helson.pdf","content_type":"application/pdf","file_id":"14534","access_level":"open_access","file_size":8156497,"date_created":"2023-11-14T13:00:19Z"}],"publication":"Nature","publication_status":"published","page":"716-720"},{"year":"2023","department":[{"_id":"JoFi"}],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7789418","open_access":"1"}],"oa":1,"title":"Entangling microwaves with light","date_created":"2023-06-06T06:46:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-03-31T00:00:00Z","author":[{"orcid":"0000-0001-6264-2162","last_name":"Sahu","full_name":"Sahu, Rishabh","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","first_name":"Rishabh"}],"corr_author":"1","abstract":[{"text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1","lang":"eng"}],"month":"03","date_updated":"2026-04-15T06:39:32Z","related_material":{"record":[{"id":"13106","status":"public","relation":"used_in_publication"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","publisher":"Zenodo","article_processing_charge":"No","citation":{"mla":"Sahu, Rishabh. <i>Entangling Microwaves with Light</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>.","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","short":"R. Sahu, (2023).","apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>","ama":"Sahu R. Entangling microwaves with light. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>"},"type":"research_data_reference","doi":"10.5281/ZENODO.7789417","_id":"13122","day":"31","status":"public"},{"date_updated":"2026-06-03T07:16:05Z","month":"04","abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request."}],"related_material":{"record":[{"status":"public","id":"13117","relation":"used_in_publication"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","ddc":["530"],"citation":{"mla":"Redchenko, Elena, et al. <i>Tunable Directional Photon Scattering from a Pair of Superconducting Qubits</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>.","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., &#38; Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>"},"publisher":"Zenodo","article_processing_charge":"No","doi":"10.5281/ZENODO.7858567","type":"research_data_reference","day":"28","_id":"13124","status":"public","department":[{"_id":"JoFi"}],"year":"2023","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7858567","open_access":"1"}],"oa":1,"date_created":"2023-06-06T07:36:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Tunable directional photon scattering from a pair of superconducting qubits","corr_author":"1","author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Poshakinskiy","full_name":"Poshakinskiy, Alexander","first_name":"Alexander"},{"full_name":"Sett, Riya","orcid":"0000-0001-7641-8348","last_name":"Sett","first_name":"Riya","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zemlicka, Martin","orcid":"0009-0005-0878-3032","last_name":"Zemlicka","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Poddubny","full_name":"Poddubny, Alexander"},{"last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"date_published":"2023-04-28T00:00:00Z"},{"has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"related_material":{"record":[{"id":"14257","status":"public","relation":"used_in_publication"}],"link":[{"description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. 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It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"date_updated":"2026-04-14T08:34:35Z","status":"public","_id":"13126","type":"research_data","article_processing_charge":"No","citation":{"apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>","mla":"Danzl, Johann G. <i>Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>.","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","short":"J.G. 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We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 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Communications","file":[{"date_updated":"2023-06-13T08:05:46Z","checksum":"4af0393e3ed47b3fc46e68b81c3c1007","success":1,"relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"13132","content_type":"application/pdf","file_name":"2023_NatureComm_CasillasPerez.pdf","file_size":2358167,"date_created":"2023-06-13T08:05:46Z"}],"pmid":1,"quality_controlled":"1","publication_status":"published","_id":"13127","status":"public","citation":{"apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., &#38; Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>.","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>, vol. 14, 3232, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>.","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232."},"article_processing_charge":"Yes","publication_identifier":{"eissn":["2041-1723"]},"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"isi":1,"oa_version":"Published Version","has_accepted_license":"1","date_updated":"2025-04-14T07:47:53Z","month":"06","abstract":[{"text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense.","lang":"eng"}],"volume":14,"related_material":{"record":[{"relation":"research_data","id":"12945","status":"public"}]},"article_type":"original","corr_author":"1","external_id":{"isi":["001002562700005"],"pmid":["37270641"]},"language":[{"iso":"eng"}],"file_date_updated":"2023-06-13T08:05:46Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-06-11T22:00:40Z","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012"}],"department":[{"_id":"SyCr"},{"_id":"GaTk"}],"intvolume":"        14","year":"2023","ec_funded":1,"day":"03","publisher":"Springer Nature","doi":"10.1038/s41467-023-38947-y","scopus_import":"1","acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","ddc":["570"]},{"status":"public","_id":"13128","citation":{"short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295.","chicago":"Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>.","ieee":"A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023.","mla":"Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>.","ama":"Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. 2023;66(4):1280-1295. doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>","apa":"Mohammadi, A., Pham, T., &#38; Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. Cambridge University Press. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>"},"article_processing_charge":"No","publication_identifier":{"eissn":["1496-4287"],"issn":["0008-4395"]},"type":"journal_article","oa_version":"Preprint","isi":1,"date_updated":"2026-04-08T13:04:49Z","issue":"4","volume":66,"month":"12","abstract":[{"text":"Given 𝐴 ⊆𝐺⁡𝐿2⁡(𝔽𝑞), we prove that there exist disjoint subsets 𝐵,𝐶 ⊆𝐴 such that 𝐴 =𝐵 ⊔𝐶 and their additive and multiplicative energies satisfying\r\nmax⁡{𝐸+⁡(𝐵),𝐸×⁡(𝐶)}≪|𝐴|3/𝑀⁡(|𝐴|), where\r\n𝑀⁡(|𝐴|)=min⁡{𝑞4/3/|𝐴|1/3⁢(log⁡|𝐴|)2/3, |𝐴|4/5/𝑞13/5⁢(log⁡|𝐴|)27/10}.\r\n \r\nWe also study some related questions on moderate expanders over matrix rings, namely, for 𝐴,𝐵,𝐶 ⊆𝐺⁡𝐿2⁡(𝔽𝑞), we have\r\n|𝐴⁢𝐵+𝐶|, |(𝐴+𝐵)⁢𝐶|≫𝑞4,\r\n whenever |𝐴|⁢|𝐵|⁢|𝐶| ≫𝑞10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, 𝐹⁡𝑜⁢𝑟⁢𝑢⁢𝑚⁢𝑀⁢𝑎⁢𝑡⁢ℎ., 31, 951–970).","lang":"eng"}],"article_type":"original","author":[{"last_name":"Mohammadi","full_name":"Mohammadi, Ali","first_name":"Ali"},{"first_name":"Thang","full_name":"Pham, Thang","last_name":"Pham"},{"full_name":"Wang, Yiting","last_name":"Wang","orcid":"0000-0002-2856-767X","first_name":"Yiting","id":"1917d194-076e-11ed-97cd-837255f88785"}],"date_published":"2023-12-01T00:00:00Z","title":"An energy decomposition theorem for matrices and related questions","publication":"Canadian Mathematical Bulletin","quality_controlled":"1","page":"1280-1295","publication_status":"published","day":"01","publisher":"Cambridge University Press","doi":"10.4153/S000843952300036X","arxiv":1,"scopus_import":"1","external_id":{"arxiv":["2106.07328"],"isi":["001011963000001"]},"language":[{"iso":"eng"}],"oa":1,"date_created":"2023-06-11T22:00:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.07328"}],"year":"2023","department":[{"_id":"GradSch"}],"intvolume":"        66"},{"title":"Discrete analytical objects in the body-centered cubic grid","date_published":"2023-10-01T00:00:00Z","article_number":"109693","author":[{"first_name":"Lidija","last_name":"Čomić","full_name":"Čomić, Lidija"},{"first_name":"Gaëlle","full_name":"Largeteau-Skapin, Gaëlle","last_name":"Largeteau-Skapin"},{"first_name":"Rita","last_name":"Zrour","full_name":"Zrour, Rita"},{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita"},{"full_name":"Andres, Eric","last_name":"Andres","first_name":"Eric"}],"publication_status":"published","publication":"Pattern Recognition","quality_controlled":"1","article_processing_charge":"No","citation":{"ama":"Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. Discrete analytical objects in the body-centered cubic grid. <i>Pattern Recognition</i>. 2023;142(10). doi:<a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">10.1016/j.patcog.2023.109693</a>","apa":"Čomić, L., Largeteau-Skapin, G., Zrour, R., Biswas, R., &#38; Andres, E. (2023). Discrete analytical objects in the body-centered cubic grid. <i>Pattern Recognition</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">https://doi.org/10.1016/j.patcog.2023.109693</a>","short":"L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, E. Andres, Pattern Recognition 142 (2023).","ista":"Čomić L, Largeteau-Skapin G, Zrour R, Biswas R, Andres E. 2023. Discrete analytical objects in the body-centered cubic grid. Pattern Recognition. 142(10), 109693.","chicago":"Čomić, Lidija, Gaëlle Largeteau-Skapin, Rita Zrour, Ranita Biswas, and Eric Andres. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” <i>Pattern Recognition</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">https://doi.org/10.1016/j.patcog.2023.109693</a>.","ieee":"L. Čomić, G. Largeteau-Skapin, R. Zrour, R. Biswas, and E. Andres, “Discrete analytical objects in the body-centered cubic grid,” <i>Pattern Recognition</i>, vol. 142, no. 10. Elsevier, 2023.","mla":"Čomić, Lidija, et al. “Discrete Analytical Objects in the Body-Centered Cubic Grid.” <i>Pattern Recognition</i>, vol. 142, no. 10, 109693, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.patcog.2023.109693\">10.1016/j.patcog.2023.109693</a>."},"type":"journal_article","publication_identifier":{"issn":["0031-3203"]},"_id":"13134","status":"public","abstract":[{"text":"We propose a characterization of discrete analytical spheres, planes and lines in the body-centered cubic (BCC) grid, both in the Cartesian and in the recently proposed alternative compact coordinate system, in which each integer triplet addresses some voxel in the grid. We define spheres and planes through double Diophantine inequalities and investigate their relevant topological features, such as functionality or the interrelation between the thickness of the objects and their connectivity and separation properties. We define lines as the intersection of planes. The number of the planes (up to six) is equal to the number of the pairs of faces of a BCC voxel that are parallel to the line.","lang":"eng"}],"volume":142,"month":"10","date_updated":"2025-04-15T07:45:32Z","issue":"10","article_type":"original","isi":1,"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-06-18T22:00:45Z","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001013526000001"]},"year":"2023","department":[{"_id":"HeEd"}],"intvolume":"       142","project":[{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"},{"name":"Persistent Homology, Algorithms and Stochastic Geometry","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"}],"publisher":"Elsevier","doi":"10.1016/j.patcog.2023.109693","day":"01","scopus_import":"1","acknowledgement":"The first author has been partially supported by the Ministry of Science, Technological Development and Innovation of the Republic of Serbia through the project no. 451-03-47/2023-01/200156. The fourth author is funded by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35."},{"ec_funded":1,"project":[{"name":"Bridging Scales in Random Materials","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","call_identifier":"H2020"}],"year":"2023","intvolume":"       368","department":[{"_id":"JuFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-06-18T22:00:45Z","file_date_updated":"2024-01-29T11:03:09Z","oa":1,"external_id":{"isi":["001019018700001"]},"language":[{"iso":"eng"}],"corr_author":"1","ddc":["510"],"acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 948819) Image 1. The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","scopus_import":"1","doi":"10.1016/j.jde.2023.05.038","publisher":"Elsevier","day":"25","page":"247-300","publication_status":"published","quality_controlled":"1","publication":"Journal of Differential Equations","file":[{"content_type":"application/pdf","file_name":"2023_JourDifferentialEquations_Agresti.pdf","file_id":"14895","access_level":"open_access","date_created":"2024-01-29T11:03:09Z","file_size":834638,"date_updated":"2024-01-29T11:03:09Z","creator":"dernst","relation":"main_file","success":1,"checksum":"246b703b091dfe047bfc79abf0891a63"}],"title":"Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity","author":[{"full_name":"Agresti, Antonio","orcid":"0000-0002-9573-2962","last_name":"Agresti","first_name":"Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72"},{"full_name":"Veraar, Mark","last_name":"Veraar","first_name":"Mark"}],"date_published":"2023-09-25T00:00:00Z","article_type":"original","date_updated":"2025-04-14T07:53:59Z","issue":"9","volume":368,"abstract":[{"text":"In this paper we consider a class of stochastic reaction-diffusion equations. We provide local well-posedness, regularity, blow-up criteria and positivity of solutions. The key novelties of this work are related to the use transport noise, critical spaces and the proof of higher order regularity of solutions – even in case of non-smooth initial data. Crucial tools are Lp(Lp)-theory, maximal regularity estimates and sharp blow-up criteria. We view the results of this paper as a general toolbox for establishing global well-posedness for a large class of reaction-diffusion systems of practical interest, of which many are completely open. In our follow-up work [8], the results of this paper are applied in the specific cases of the Lotka-Volterra equations and the Brusselator model.","lang":"eng"}],"month":"09","isi":1,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1090-2732"],"issn":["0022-0396"]},"type":"journal_article","citation":{"short":"A. Agresti, M. Veraar, Journal of Differential Equations 368 (2023) 247–300.","ista":"Agresti A, Veraar M. 2023. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. 368(9), 247–300.","ieee":"A. Agresti and M. Veraar, “Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity,” <i>Journal of Differential Equations</i>, vol. 368, no. 9. Elsevier, pp. 247–300, 2023.","chicago":"Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” <i>Journal of Differential Equations</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">https://doi.org/10.1016/j.jde.2023.05.038</a>.","mla":"Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” <i>Journal of Differential Equations</i>, vol. 368, no. 9, Elsevier, 2023, pp. 247–300, doi:<a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">10.1016/j.jde.2023.05.038</a>.","ama":"Agresti A, Veraar M. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. <i>Journal of Differential Equations</i>. 2023;368(9):247-300. doi:<a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">10.1016/j.jde.2023.05.038</a>","apa":"Agresti, A., &#38; Veraar, M. (2023). Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2023.05.038\">https://doi.org/10.1016/j.jde.2023.05.038</a>"},"article_processing_charge":"Yes (in subscription journal)","_id":"13135","status":"public"},{"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2023-06-18T22:00:46Z","external_id":{"isi":["001003686900004"],"arxiv":["2303.00729"]},"language":[{"iso":"eng"}],"year":"2023","intvolume":"       107","department":[{"_id":"GradSch"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.00729"}],"publisher":"American Physical Society","doi":"10.1103/PhysRevB.107.184312","arxiv":1,"day":"01","scopus_import":"1","acknowledgement":"The numerical computations in this work were performed using QuSpin [83, 84]. We acknowledge useful discussions with Igor Aleiner, Boris Altshuler, Jacopo de Nardis, Anatoli Polkovnikov, and Gora Shlyapnikov. We thank Piotr Sierant and Dario Rosa for drawing our attention to Refs. [31, 42, 46] and Ref. [47], respectively. We are grateful to an anonymous referee for very useful comments and for drawing our attention to Refs. [80, 81]. The work of VG is part of the DeltaITP consortium, a program of the Netherlands Organization for Scientific\r\nResearch (NWO) funded by the Dutch Ministry of Education, Culture and Science (OCW). VG is also partially supported by RSF 19-71-10092. The work of AT was supported by the ERC Starting Grant 101042293 (HEPIQ). RS acknowledges support from Slovenian Research Agency (ARRS) - research programme P1-0402. ","title":"Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain","author":[{"last_name":"Orlov","full_name":"Orlov, Pavel","first_name":"Pavel"},{"first_name":"Anastasiia","full_name":"Tiutiakina, Anastasiia","last_name":"Tiutiakina"},{"first_name":"Rustem","last_name":"Sharipov","full_name":"Sharipov, Rustem"},{"full_name":"Petrova, Elena","last_name":"Petrova","first_name":"Elena","id":"0ac84990-897b-11ed-a09c-f5abb56a4ede"},{"first_name":"Vladimir","last_name":"Gritsev","full_name":"Gritsev, Vladimir"},{"full_name":"Kurlov, Denis V.","last_name":"Kurlov","first_name":"Denis V."}],"article_number":"184312","date_published":"2023-05-01T00:00:00Z","publication_status":"published","publication":"Physical Review B","quality_controlled":"1","citation":{"ista":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. 2023. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. Physical Review B. 107(18), 184312.","short":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, D.V. Kurlov, Physical Review B 107 (2023).","mla":"Orlov, Pavel, et al. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” <i>Physical Review B</i>, vol. 107, no. 18, 184312, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">10.1103/PhysRevB.107.184312</a>.","ieee":"P. Orlov, A. Tiutiakina, R. Sharipov, E. Petrova, V. Gritsev, and D. V. Kurlov, “Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain,” <i>Physical Review B</i>, vol. 107, no. 18. American Physical Society, 2023.","chicago":"Orlov, Pavel, Anastasiia Tiutiakina, Rustem Sharipov, Elena Petrova, Vladimir Gritsev, and Denis V. Kurlov. “Adiabatic Eigenstate Deformations and Weak Integrability Breaking of Heisenberg Chain.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">https://doi.org/10.1103/PhysRevB.107.184312</a>.","ama":"Orlov P, Tiutiakina A, Sharipov R, Petrova E, Gritsev V, Kurlov DV. Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. <i>Physical Review B</i>. 2023;107(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">10.1103/PhysRevB.107.184312</a>","apa":"Orlov, P., Tiutiakina, A., Sharipov, R., Petrova, E., Gritsev, V., &#38; Kurlov, D. V. (2023). Adiabatic eigenstate deformations and weak integrability breaking of Heisenberg chain. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.107.184312\">https://doi.org/10.1103/PhysRevB.107.184312</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"type":"journal_article","status":"public","_id":"13138","issue":"18","date_updated":"2023-08-02T06:16:02Z","month":"05","abstract":[{"text":"We consider the spin-\r\n1\r\n2\r\n Heisenberg chain (XXX model) weakly perturbed away from integrability by an isotropic next-to-nearest neighbor exchange interaction. Recently, it was conjectured that this model possesses an infinite tower of quasiconserved integrals of motion (charges) [D. Kurlov et al., Phys. Rev. B 105, 104302 (2022)]. In this work we first test this conjecture by investigating how the norm of the adiabatic gauge potential (AGP) scales with the system size, which is known to be a remarkably accurate measure of chaos. We find that for the perturbed XXX chain the behavior of the AGP norm corresponds to neither an integrable nor a chaotic regime, which supports the conjectured quasi-integrability of the model. We then prove the conjecture and explicitly construct the infinite set of quasiconserved charges. Our proof relies on the fact that the XXX chain perturbed by next-to-nearest exchange interaction can be viewed as a truncation of an integrable long-range deformation of the Heisenberg spin chain.","lang":"eng"}],"volume":107,"article_type":"original","oa_version":"Preprint","isi":1},{"related_material":{"record":[{"relation":"research_data","id":"14990","status":"public"}]},"abstract":[{"text":"A classical problem for Markov chains is determining their stationary (or steady-state) distribution. This problem has an equally classical solution based on eigenvectors and linear equation systems. However, this approach does not scale to large instances, and iterative solutions are desirable. It turns out that a naive approach, as used by current model checkers, may yield completely wrong results. We present a new approach, which utilizes recent advances in partial exploration and mean payoff computation to obtain a correct, converging approximation.","lang":"eng"}],"volume":13993,"month":"04","date_updated":"2025-09-09T12:28:12Z","has_accepted_license":"1","oa_version":"Published Version","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"conference","publication_identifier":{"isbn":["9783031308222"],"eissn":["1611-3349"],"issn":["0302-9743"]},"article_processing_charge":"No","citation":{"apa":"Meggendorfer, T. (2023). Correct approximation of stationary distributions. In <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 13993, pp. 489–507). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_25\">https://doi.org/10.1007/978-3-031-30823-9_25</a>","ama":"Meggendorfer T. Correct approximation of stationary distributions. In: <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 13993. Springer Nature; 2023:489-507. doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_25\">10.1007/978-3-031-30823-9_25</a>","mla":"Meggendorfer, Tobias. “Correct Approximation of Stationary Distributions.” <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 13993, Springer Nature, 2023, pp. 489–507, doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_25\">10.1007/978-3-031-30823-9_25</a>.","chicago":"Meggendorfer, Tobias. “Correct Approximation of Stationary Distributions.” In <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, 13993:489–507. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_25\">https://doi.org/10.1007/978-3-031-30823-9_25</a>.","ieee":"T. Meggendorfer, “Correct approximation of stationary distributions,” in <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, Paris, France, 2023, vol. 13993, pp. 489–507.","ista":"Meggendorfer T. 2023. Correct approximation of stationary distributions. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 489–507.","short":"T. Meggendorfer, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 489–507."},"status":"public","_id":"13139","publication_status":"published","page":"489-507","quality_controlled":"1","publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","file":[{"file_size":521951,"date_created":"2023-06-19T07:18:40Z","file_id":"13148","access_level":"open_access","file_name":"2023_LNCS_Meggendorfer.pdf","content_type":"application/pdf","relation":"main_file","checksum":"59f707a3949c03793251b0d04c62542a","creator":"dernst","success":1,"date_updated":"2023-06-19T07:18:40Z"}],"title":"Correct approximation of stationary distributions","conference":{"start_date":"2023-04-22","location":"Paris, France","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"date_published":"2023-04-22T00:00:00Z","author":[{"full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","last_name":"Meggendorfer","first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"}],"ddc":["000"],"scopus_import":"1","arxiv":1,"doi":"10.1007/978-3-031-30823-9_25","publisher":"Springer Nature","alternative_title":["LNCS"],"day":"22","department":[{"_id":"KrCh"}],"year":"2023","intvolume":"     13993","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-06-18T22:00:46Z","oa":1,"file_date_updated":"2023-06-19T07:18:40Z","language":[{"iso":"eng"}],"external_id":{"isi":["001288688000025"],"arxiv":["2301.08137"]},"corr_author":"1"},{"status":"public","_id":"13141","type":"conference","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308192"],"issn":["0302-9743"]},"article_processing_charge":"No","citation":{"mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:<a href=\"https://doi.org/10.1007/978-3-031-30820-8_15\">10.1007/978-3-031-30820-8_15</a>.","chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, 13994:211–28. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30820-8_15\">https://doi.org/10.1007/978-3-031-30820-8_15</a>.","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>, Paris, France, 2023, vol. 13994, pp. 211–228.","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228.","short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228.","apa":"Anand, A., Mallik, K., Nayak, S. P., &#38; Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30820-8_15\">https://doi.org/10.1007/978-3-031-30820-8_15</a>","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: <i>TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 13994. Springer Nature; 2023:211-228. doi:<a href=\"https://doi.org/10.1007/978-3-031-30820-8_15\">10.1007/978-3-031-30820-8_15</a>"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"volume":13994,"month":"04","abstract":[{"lang":"eng","text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive."}],"date_updated":"2025-09-09T12:30:00Z","date_published":"2023-04-20T00:00:00Z","author":[{"last_name":"Anand","full_name":"Anand, Ashwani","first_name":"Ashwani"},{"orcid":"0000-0001-9864-7475","last_name":"Mallik","full_name":"Mallik, Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","first_name":"Kaushik"},{"first_name":"Satya Prakash","last_name":"Nayak","full_name":"Nayak, Satya Prakash"},{"last_name":"Schmuck","full_name":"Schmuck, Anne Kathrin","first_name":"Anne Kathrin"}],"title":"Computing adequately permissive assumptions for synthesis","conference":{"end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Paris, France","start_date":"2023-04-22"},"quality_controlled":"1","file":[{"date_updated":"2023-06-19T08:43:21Z","creator":"dernst","relation":"main_file","success":1,"checksum":"60dcafc1b4f6f070be43bad3fe877974","file_name":"2023_LNCS_Anand.pdf","content_type":"application/pdf","file_id":"13151","access_level":"open_access","date_created":"2023-06-19T08:43:21Z","file_size":521425}],"publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","publication_status":"published","page":"211-228","alternative_title":["LNCS"],"day":"20","doi":"10.1007/978-3-031-30820-8_15","publisher":"Springer Nature","ddc":["000"],"scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001288698100015"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-06-18T22:00:47Z","oa":1,"file_date_updated":"2023-06-19T08:43:21Z","year":"2023","intvolume":"     13994","department":[{"_id":"ToHe"}]},{"year":"2023","intvolume":"     13993","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"ec_funded":1,"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001288688000001"]},"oa":1,"file_date_updated":"2023-06-19T08:29:30Z","date_created":"2023-06-18T22:00:47Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","ddc":["000"],"alternative_title":["LNCS"],"day":"22","publisher":"Springer Nature","doi":"10.1007/978-3-031-30823-9_1","publication":"Tools and Algorithms for the Construction and Analysis of Systems ","file":[{"date_updated":"2023-06-19T08:29:30Z","relation":"main_file","creator":"dernst","success":1,"checksum":"3d8a8bb24d211bc83360dfc2fd744307","file_name":"2023_LNCS_Chatterjee.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"13150","date_created":"2023-06-19T08:29:30Z","file_size":528455}],"quality_controlled":"1","publication_status":"published","page":"3-25","date_published":"2023-04-22T00:00:00Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4681-1699","last_name":"Zikelic","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France"},"title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"month":"04","volume":13993,"abstract":[{"lang":"eng","text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions."}],"date_updated":"2025-09-09T12:29:26Z","_id":"13142","status":"public","article_processing_charge":"No","citation":{"apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., &#38; Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In <i>Tools and Algorithms for the Construction and Analysis of Systems </i> (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">https://doi.org/10.1007/978-3-031-30823-9_1</a>","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: <i>Tools and Algorithms for the Construction and Analysis of Systems </i>. Vol 13993. Springer Nature; 2023:3-25. doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">10.1007/978-3-031-30823-9_1</a>","mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, vol. 13993, Springer Nature, 2023, pp. 3–25, doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">10.1007/978-3-031-30823-9_1</a>.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, 13993:3–25. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">https://doi.org/10.1007/978-3-031-30823-9_1</a>.","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, Paris, France, 2023, vol. 13993, pp. 3–25.","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25."},"type":"conference","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031308222"],"issn":["0302-9743"]}},{"quality_controlled":"1","publication":"Public-Key Cryptography - PKC 2023","publication_status":"published","page":"530-553","author":[{"orcid":"0000-0003-2027-5549","last_name":"Hoffmann","full_name":"Hoffmann, Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7","first_name":"Charlotte"},{"full_name":"Hubáček, Pavel","last_name":"Hubáček","first_name":"Pavel"},{"first_name":"Chethan","last_name":"Kamath","full_name":"Kamath, Chethan"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"}],"date_published":"2023-05-02T00:00:00Z","title":"Certifying giant nonprimes","conference":{"end_date":"2023-05-10","name":"PKC: Public-Key Cryptography","location":"Atlanta, GA, United States","start_date":"2023-05-07"},"isi":1,"oa_version":"Submitted Version","related_material":{"record":[{"relation":"dissertation_contains","id":"20920","status":"public"},{"relation":"dissertation_contains","status":"public","id":"20556"}]},"date_updated":"2026-04-07T12:34:30Z","abstract":[{"lang":"eng","text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality."}],"month":"05","volume":13940,"status":"public","_id":"13143","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031313677"],"issn":["0302-9743"]},"type":"conference","citation":{"ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in <i>Public-Key Cryptography - PKC 2023</i>, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553.","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In <i>Public-Key Cryptography - PKC 2023</i>, 13940:530–53. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-31368-4_19\">https://doi.org/10.1007/978-3-031-31368-4_19</a>.","mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” <i>Public-Key Cryptography - PKC 2023</i>, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:<a href=\"https://doi.org/10.1007/978-3-031-31368-4_19\">10.1007/978-3-031-31368-4_19</a>.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553.","ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., &#38; Pietrzak, K. Z. (2023). Certifying giant nonprimes. In <i>Public-Key Cryptography - PKC 2023</i> (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-31368-4_19\">https://doi.org/10.1007/978-3-031-31368-4_19</a>","ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: <i>Public-Key Cryptography - PKC 2023</i>. Vol 13940. Springer Nature; 2023:530-553. doi:<a href=\"https://doi.org/10.1007/978-3-031-31368-4_19\">10.1007/978-3-031-31368-4_19</a>"},"article_processing_charge":"No","main_file_link":[{"url":"https://eprint.iacr.org/2023/238","open_access":"1"}],"year":"2023","intvolume":"     13940","department":[{"_id":"KrPi"}],"external_id":{"isi":["001276519300019"]},"language":[{"iso":"eng"}],"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2023-06-18T22:00:47Z","oa":1,"acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","scopus_import":"1","alternative_title":["LNCS"],"day":"02","doi":"10.1007/978-3-031-31368-4_19","publisher":"Springer Nature"},{"status":"public","_id":"13145","type":"journal_article","publication_identifier":{"eissn":["1083-589X"]},"article_processing_charge":"No","citation":{"apa":"Dello Schiavo, L., &#38; Lytvynov, E. (2023). A Mecke-type characterization of the Dirichlet–Ferguson measure. <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/23-ECP528\">https://doi.org/10.1214/23-ECP528</a>","ama":"Dello Schiavo L, Lytvynov E. A Mecke-type characterization of the Dirichlet–Ferguson measure. <i>Electronic Communications in Probability</i>. 2023;28:1-12. doi:<a href=\"https://doi.org/10.1214/23-ECP528\">10.1214/23-ECP528</a>","ieee":"L. Dello Schiavo and E. Lytvynov, “A Mecke-type characterization of the Dirichlet–Ferguson measure,” <i>Electronic Communications in Probability</i>, vol. 28. Institute of Mathematical Statistics, pp. 1–12, 2023.","chicago":"Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” <i>Electronic Communications in Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/23-ECP528\">https://doi.org/10.1214/23-ECP528</a>.","mla":"Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” <i>Electronic Communications in Probability</i>, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–12, doi:<a href=\"https://doi.org/10.1214/23-ECP528\">10.1214/23-ECP528</a>.","short":"L. Dello Schiavo, E. Lytvynov, Electronic Communications in Probability 28 (2023) 1–12.","ista":"Dello Schiavo L, Lytvynov E. 2023. A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. 28, 1–12."},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"article_type":"original","volume":28,"month":"05","abstract":[{"text":"We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes.","lang":"eng"}],"date_updated":"2025-04-14T12:59:08Z","date_published":"2023-05-05T00:00:00Z","author":[{"first_name":"Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo"},{"last_name":"Lytvynov","full_name":"Lytvynov, Eugene","first_name":"Eugene"}],"title":"A Mecke-type characterization of the Dirichlet–Ferguson measure","quality_controlled":"1","publication":"Electronic Communications in Probability","file":[{"success":1,"relation":"main_file","creator":"dernst","checksum":"4a543fe4b3f9e747cc52167c17bfb524","date_updated":"2023-06-19T09:37:40Z","file_size":271434,"date_created":"2023-06-19T09:37:40Z","access_level":"open_access","file_id":"13152","file_name":"2023_ElectronCommProbability_Schiavo.pdf","content_type":"application/pdf"}],"page":"1-12","publication_status":"published","day":"05","doi":"10.1214/23-ECP528","publisher":"Institute of Mathematical Statistics","acknowledgement":"Research supported by the Sfb 1060 The Mathematics of Emergent Effects (University of Bonn). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through project ESPRIT 208.","ddc":["510"],"scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001042025400001"]},"corr_author":"1","date_created":"2023-06-18T22:00:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2023-06-19T09:37:40Z","department":[{"_id":"JaMa"}],"year":"2023","intvolume":"        28","project":[{"grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"}]},{"title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries","article_number":"3506","date_published":"2023-06-14T00:00:00Z","author":[{"first_name":"Krista R.B.","full_name":"Gert, Krista R.B.","last_name":"Gert"},{"first_name":"Karin","last_name":"Panser","full_name":"Panser, Karin"},{"last_name":"Surm","full_name":"Surm, Joachim","first_name":"Joachim"},{"full_name":"Steinmetz, Benjamin S.","last_name":"Steinmetz","first_name":"Benjamin S."},{"full_name":"Schleiffer, Alexander","last_name":"Schleiffer","first_name":"Alexander"},{"last_name":"Jovine","full_name":"Jovine, Luca","first_name":"Luca"},{"last_name":"Moran","full_name":"Moran, Yehu","first_name":"Yehu"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"full_name":"Pauli, Andrea","last_name":"Pauli","first_name":"Andrea"}],"publication_status":"published","file":[{"date_updated":"2023-06-26T10:26:04Z","creator":"dernst","success":1,"checksum":"d6165f41c7f1c2c04b04256ec9f003fb","relation":"main_file","file_name":"2023_NatureComm_Gert.pdf","content_type":"application/pdf","file_id":"13172","access_level":"open_access","file_size":1555006,"date_created":"2023-06-26T10:26:04Z"}],"publication":"Nature Communications","quality_controlled":"1","pmid":1,"article_processing_charge":"No","citation":{"short":"K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).","ista":"Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y, Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 14, 3506.","chicago":"Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39317-4\">https://doi.org/10.1038/s41467-023-39317-4</a>.","ieee":"K. R. B. Gert <i>et al.</i>, “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","mla":"Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” <i>Nature Communications</i>, vol. 14, 3506, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39317-4\">10.1038/s41467-023-39317-4</a>.","ama":"Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39317-4\">10.1038/s41467-023-39317-4</a>","apa":"Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39317-4\">https://doi.org/10.1038/s41467-023-39317-4</a>"},"type":"journal_article","publication_identifier":{"eissn":["2041-1723"]},"status":"public","_id":"13164","abstract":[{"lang":"eng","text":"Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization."}],"volume":14,"month":"06","date_updated":"2025-04-23T08:59:40Z","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"oa":1,"file_date_updated":"2023-06-26T10:26:04Z","date_created":"2023-06-25T22:00:45Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"external_id":{"isi":["001048208600023"],"pmid":["37316475"]},"intvolume":"        14","department":[{"_id":"FyKo"}],"year":"2023","publisher":"Springer Nature","doi":"10.1038/s41467-023-39317-4","day":"14","scopus_import":"1","acknowledgement":"We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis; Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award (RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","ddc":["570"]},{"date_published":"2023-10-01T00:00:00Z","article_number":"105776","author":[{"first_name":"Lixing","full_name":"Fang, Lixing","last_name":"Fang"},{"full_name":"Huang, Hao","last_name":"Huang","first_name":"Hao"},{"first_name":"János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","full_name":"Pach, János","last_name":"Pach"},{"first_name":"Gábor","full_name":"Tardos, Gábor","last_name":"Tardos"},{"first_name":"Junchi","full_name":"Zuo, Junchi","last_name":"Zuo"}],"title":"Successive vertex orderings of fully regular graphs","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2023_JourCombinatiorialTheory_Fang.pdf","file_id":"14902","access_level":"open_access","file_size":352555,"date_created":"2024-01-30T12:03:10Z","date_updated":"2024-01-30T12:03:10Z","creator":"dernst","relation":"main_file","checksum":"9eebc213b4182a66063a99083ff5bd04","success":1}],"publication":"Journal of Combinatorial Theory. Series A","publication_status":"published","_id":"13165","status":"public","type":"journal_article","publication_identifier":{"issn":["0097-3165"],"eissn":["1096-0899"]},"article_processing_charge":"Yes (in subscription journal)","citation":{"ama":"Fang L, Huang H, Pach J, Tardos G, Zuo J. Successive vertex orderings of fully regular graphs. <i>Journal of Combinatorial Theory Series A</i>. 2023;199(10). doi:<a href=\"https://doi.org/10.1016/j.jcta.2023.105776\">10.1016/j.jcta.2023.105776</a>","apa":"Fang, L., Huang, H., Pach, J., Tardos, G., &#38; Zuo, J. (2023). Successive vertex orderings of fully regular graphs. <i>Journal of Combinatorial Theory. Series A</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcta.2023.105776\">https://doi.org/10.1016/j.jcta.2023.105776</a>","ista":"Fang L, Huang H, Pach J, Tardos G, Zuo J. 2023. Successive vertex orderings of fully regular graphs. Journal of Combinatorial Theory. Series A. 199(10), 105776.","short":"L. Fang, H. Huang, J. Pach, G. Tardos, J. Zuo, Journal of Combinatorial Theory. Series A 199 (2023).","mla":"Fang, Lixing, et al. “Successive Vertex Orderings of Fully Regular Graphs.” <i>Journal of Combinatorial Theory. Series A</i>, vol. 199, no. 10, 105776, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jcta.2023.105776\">10.1016/j.jcta.2023.105776</a>.","ieee":"L. Fang, H. Huang, J. Pach, G. Tardos, and J. Zuo, “Successive vertex orderings of fully regular graphs,” <i>Journal of Combinatorial Theory. Series A</i>, vol. 199, no. 10. Elsevier, 2023.","chicago":"Fang, Lixing, Hao Huang, János Pach, Gábor Tardos, and Junchi Zuo. “Successive Vertex Orderings of Fully Regular Graphs.” <i>Journal of Combinatorial Theory. Series A</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jcta.2023.105776\">https://doi.org/10.1016/j.jcta.2023.105776</a>."},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"article_type":"original","volume":199,"month":"10","abstract":[{"lang":"eng","text":"A graph G=(V, E) is called fully regular if for every independent set I c V, the number of vertices in V\\I  that are not connected to any element of I depends only on the size of I. A linear ordering of the vertices of G is called successive if for every i, the first i vertices induce a connected subgraph of G. We give an explicit formula for the number of successive vertex orderings of a fully regular graph.\r\nAs an application of our results, we give alternative proofs of two theorems of Stanley and Gao & Peng, determining the number of linear edge orderings of complete graphs and complete bipartite graphs, respectively, with the property that the first i edges induce a connected subgraph.\r\nAs another application, we give a simple product formula for the number of linear orderings of the hyperedges of a complete 3-partite 3-uniform hypergraph such that, for every i, the first i hyperedges induce a connected subgraph. We found similar formulas for complete (non-partite) 3-uniform hypergraphs and in another closely related case, but we managed to verify them only when the number of vertices is small."}],"date_updated":"2025-09-09T12:30:39Z","issue":"10","language":[{"iso":"eng"}],"external_id":{"arxiv":["2206.13592"],"isi":["001144487800001"]},"corr_author":"1","date_created":"2023-06-25T22:00:45Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"file_date_updated":"2024-01-30T12:03:10Z","year":"2023","department":[{"_id":"HeEd"}],"intvolume":"       199","day":"01","arxiv":1,"doi":"10.1016/j.jcta.2023.105776","publisher":"Elsevier","ddc":["510"],"scopus_import":"1"}]