[{"publication":"iScience","issue":"10","day":"20","abstract":[{"lang":"eng","text":"Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis."}],"ddc":["570"],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318"}],"ec_funded":1,"oa_version":"Published Version","has_accepted_license":"1","publication_status":"published","scopus_import":"1","file":[{"access_level":"open_access","relation":"main_file","date_updated":"2023-10-09T07:23:46Z","date_created":"2023-10-09T07:23:46Z","checksum":"f499836af172ecc9865de4bb41fa99d1","creator":"dernst","file_id":"14412","success":1,"file_name":"2023_iScience_Scarpetta.pdf","file_size":4872708,"content_type":"application/pdf"}],"department":[{"_id":"GaTk"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","author":[{"last_name":"Scarpetta","full_name":"Scarpetta, Silvia","first_name":"Silvia"},{"full_name":"Morrisi, Niccolò","first_name":"Niccolò","last_name":"Morrisi"},{"full_name":"Mutti, Carlotta","last_name":"Mutti","first_name":"Carlotta"},{"first_name":"Nicoletta","full_name":"Azzi, Nicoletta","last_name":"Azzi"},{"last_name":"Trippi","first_name":"Irene","full_name":"Trippi, Irene"},{"last_name":"Ciliento","full_name":"Ciliento, Rosario","first_name":"Rosario"},{"first_name":"Ilenia","full_name":"Apicella, Ilenia","last_name":"Apicella"},{"last_name":"Messuti","full_name":"Messuti, Giovanni","first_name":"Giovanni"},{"last_name":"Angiolelli","full_name":"Angiolelli, Marianna","first_name":"Marianna"},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249"},{"full_name":"Parrino, Liborio","last_name":"Parrino","first_name":"Liborio"},{"last_name":"Vaudano","full_name":"Vaudano, Anna Elisabetta","first_name":"Anna Elisabetta"}],"license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"isi":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12487","page":"107840","pmid":1,"year":"2023","doi":"10.1016/j.isci.2023.107840","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411, and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318. IA acknowledges financial support from the MIUR PRIN 2017WZFTZP.","date_updated":"2025-04-14T07:44:00Z","status":"public","type":"journal_article","publisher":"Elsevier","intvolume":" 26","oa":1,"article_processing_charge":"Yes","month":"10","volume":26,"citation":{"ama":"Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 2023;26(10):107840. doi:10.1016/j.isci.2023.107840","chicago":"Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107840.","ieee":"S. Scarpetta et al., “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” iScience, vol. 26, no. 10. Elsevier, p. 107840, 2023.","mla":"Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:10.1016/j.isci.2023.107840.","apa":"Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R., … Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107840","short":"S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.","ista":"Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I, Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 26(10), 107840."},"file_date_updated":"2023-10-09T07:23:46Z","date_published":"2023-10-20T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2589-0042"]},"quality_controlled":"1","date_created":"2023-02-02T10:50:17Z"},{"ddc":["572"],"abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"day":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","contributor":[{"last_name":"Berbon","contributor_type":"researcher","first_name":"Mélanie"},{"last_name":"Vallet","first_name":"Alicia","contributor_type":"researcher"},{"last_name":"Grelard","first_name":"Axelle","contributor_type":"researcher"},{"last_name":"Morvan","contributor_type":"researcher","first_name":"Estelle"},{"last_name":"Bardiaux","first_name":"Benjamin","contributor_type":"researcher"},{"first_name":"Roman","last_name":"Lichtenecker","contributor_type":"researcher"},{"contributor_type":"researcher","last_name":"Ernst","first_name":"Matthias"},{"first_name":"Antoine","last_name":"Loquet","contributor_type":"researcher"},{"contributor_type":"contact_person","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606"},{"orcid":"0000-0002-6401-5151","contributor_type":"researcher","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","first_name":"Lea Marie"}],"_id":"12497","oa_version":"Published Version","year":"2023","doi":"10.15479/AT:ISTA:12497","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12675"}]},"has_accepted_license":"1","date_updated":"2024-10-21T06:01:38Z","type":"research_data","corr_author":"1","publisher":"Institute of Science and Technology Austria","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"status":"public","file":[{"file_name":"Research_Data.zip","checksum":"fd9a28620a81a82991fb70f4fd6591d9","creator":"lbecker","file_id":"12743","date_created":"2023-03-23T10:03:16Z","access_level":"open_access","relation":"main_file","date_updated":"2023-03-24T09:34:20Z","content_type":"application/zip","file_size":87018103},{"file_size":747,"content_type":"text/plain","file_name":"README.txt","date_updated":"2023-03-24T09:42:03Z","relation":"main_file","access_level":"open_access","date_created":"2023-03-24T07:13:55Z","file_id":"12755","checksum":"30ebdfb600af118fcf8518b6efe0b7e9","creator":"dernst"}],"oa":1,"month":"03","article_processing_charge":"No","citation":{"ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.","mla":"Becker, Lea Marie, and Paul Schanda. Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12497.","apa":"Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497","chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:10.15479/AT:ISTA:12497","short":"L.M. Becker, P. Schanda, (2023).","ista":"Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497."},"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"file_date_updated":"2023-03-24T09:42:03Z","title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","date_published":"2023-03-23T00:00:00Z","author":[{"full_name":"Becker, Lea Marie","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","orcid":"0000-0002-6401-5151"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2023-02-03T08:08:02Z"},{"_id":"12514","page":"318-328","year":"2023","pmid":1,"isi":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T12:58:30Z","status":"public","publisher":"Oxford University Press","type":"journal_article","intvolume":" 77","acknowledgement":"The authors of this article were supported by LMU Munich (J.B.W.W.), a James S. McDonnell Foundation postdoctoral fellowship (A.K.H.). P.N. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant agreement No. 770826 EE-Dynamics).\r\nWe thank participants in the 2019 Gordon Conference on Speciation for the extensive conversation on this topic. Thanks to Dan Funk for providing permission to use data from Funk et al. 2006, and for comments on the manuscript.","doi":"10.1093/evolut/qpac004","date_published":"2023-01-01T00:00:00Z","oa":1,"volume":77,"month":"01","article_processing_charge":"No","citation":{"ista":"Bolnick DI, Hund AK, Nosil P, Peng F, Ravinet M, Stankowski S, Subramanian S, Wolf JBW, Yukilevich R. 2023. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 77(1), 318–328.","short":"D.I. Bolnick, A.K. Hund, P. Nosil, F. Peng, M. Ravinet, S. Stankowski, S. Subramanian, J.B.W. Wolf, R. Yukilevich, Evolution: International Journal of Organic Evolution 77 (2023) 318–328.","apa":"Bolnick, D. I., Hund, A. K., Nosil, P., Peng, F., Ravinet, M., Stankowski, S., … Yukilevich, R. (2023). A multivariate view of the speciation continuum. Evolution: International Journal of Organic Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpac004","mla":"Bolnick, Daniel I., et al. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution, vol. 77, no. 1, Oxford University Press, 2023, pp. 318–28, doi:10.1093/evolut/qpac004.","ieee":"D. I. Bolnick et al., “A multivariate view of the speciation continuum,” Evolution: International journal of organic evolution, vol. 77, no. 1. Oxford University Press, pp. 318–328, 2023.","ama":"Bolnick DI, Hund AK, Nosil P, et al. A multivariate view of the speciation continuum. Evolution: International journal of organic evolution. 2023;77(1):318-328. doi:10.1093/evolut/qpac004","chicago":"Bolnick, Daniel I., Amanda K. Hund, Patrik Nosil, Foen Peng, Mark Ravinet, Sean Stankowski, Swapna Subramanian, Jochen B.W. Wolf, and Roman Yukilevich. “A Multivariate View of the Speciation Continuum.” Evolution: International Journal of Organic Evolution. Oxford University Press, 2023. https://doi.org/10.1093/evolut/qpac004."},"date_created":"2023-02-05T23:00:59Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1558-5646"]},"oa_version":"Published Version","publication":"Evolution: International journal of organic evolution","issue":"1","day":"01","abstract":[{"text":"The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.","lang":"eng"}],"publication_status":"published","scopus_import":"1","title":"A multivariate view of the speciation continuum","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/evolut/qpac004"}],"department":[{"_id":"NiBa"}],"external_id":{"isi":["001021686300024"],"pmid":["36622661"]},"author":[{"last_name":"Bolnick","full_name":"Bolnick, Daniel I.","first_name":"Daniel I."},{"last_name":"Hund","full_name":"Hund, Amanda K.","first_name":"Amanda K."},{"last_name":"Nosil","full_name":"Nosil, Patrik","first_name":"Patrik"},{"last_name":"Peng","first_name":"Foen","full_name":"Peng, Foen"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean"},{"full_name":"Subramanian, Swapna","last_name":"Subramanian","first_name":"Swapna"},{"last_name":"Wolf","full_name":"Wolf, Jochen B.W.","first_name":"Jochen B.W."},{"first_name":"Roman","last_name":"Yukilevich","full_name":"Yukilevich, Roman"}]},{"oa":1,"month":"01","volume":16,"article_processing_charge":"No","citation":{"ama":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, et al. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 2023;16. doi:10.3389/fnana.2022.1097467","chicago":"Ortiz-Leal, Irene, Mateo V. Torres, Victor M Vargas Barroso, Luis Eusebio Fidalgo, Ana María López-Beceiro, Jorge A. Larriva-Sahd, and Pablo Sánchez-Quinteiro. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy. Frontiers, 2023. https://doi.org/10.3389/fnana.2022.1097467.","apa":"Ortiz-Leal, I., Torres, M. V., Vargas Barroso, V. M., Fidalgo, L. E., López-Beceiro, A. M., Larriva-Sahd, J. A., & Sánchez-Quinteiro, P. (2023). The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. Frontiers. https://doi.org/10.3389/fnana.2022.1097467","mla":"Ortiz-Leal, Irene, et al. “The Olfactory Limbus of the Red Fox (Vulpes Vulpes). New Insights Regarding a Noncanonical Olfactory Bulb Pathway.” Frontiers in Neuroanatomy, vol. 16, 1097467, Frontiers, 2023, doi:10.3389/fnana.2022.1097467.","ieee":"I. Ortiz-Leal et al., “The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway,” Frontiers in Neuroanatomy, vol. 16. Frontiers, 2023.","ista":"Ortiz-Leal I, Torres MV, Vargas Barroso VM, Fidalgo LE, López-Beceiro AM, Larriva-Sahd JA, Sánchez-Quinteiro P. 2023. The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway. Frontiers in Neuroanatomy. 16, 1097467.","short":"I. Ortiz-Leal, M.V. Torres, V.M. Vargas Barroso, L.E. Fidalgo, A.M. López-Beceiro, J.A. Larriva-Sahd, P. Sánchez-Quinteiro, Frontiers in Neuroanatomy 16 (2023)."},"file_date_updated":"2023-02-06T07:56:14Z","date_published":"2023-01-10T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1662-5129"]},"date_created":"2023-02-05T23:01:00Z","isi":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12515","pmid":1,"year":"2023","acknowledgement":"This work was partially supported by a grant from “Consello Social Universidade de Santiago de Compostela” 2022-PU004.We would like to show special gratitude to Prof. Ludwig Wagner (Medical University, Vienna) for kindly providing us with the secretagogin antibody. We thank the Wildlife Recovery Centres of Galicia, Dirección Xeral de Patrimonio Natural (Xunta de Galicia, Spain), and Federación Galega de Caza for providing the red foxes used in this study.","doi":"10.3389/fnana.2022.1097467","date_updated":"2023-08-16T11:37:52Z","type":"journal_article","publisher":"Frontiers","status":"public","intvolume":" 16","file":[{"content_type":"application/pdf","file_size":21943473,"file_id":"12518","creator":"dernst","checksum":"49cd40f3bda6f267079427042e7d15e3","date_created":"2023-02-06T07:56:14Z","relation":"main_file","access_level":"open_access","date_updated":"2023-02-06T07:56:14Z","file_name":"2022_FrontiersNeuroanatomy_OrtizLeal.pdf","success":1}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"PeJo"}],"title":"The olfactory limbus of the red fox (Vulpes vulpes). New insights regarding a noncanonical olfactory bulb pathway","author":[{"full_name":"Ortiz-Leal, Irene","last_name":"Ortiz-Leal","first_name":"Irene"},{"full_name":"Torres, Mateo V.","first_name":"Mateo V.","last_name":"Torres"},{"id":"2F55A9DE-F248-11E8-B48F-1D18A9856A87","full_name":"Vargas Barroso, Victor M","first_name":"Victor M","last_name":"Vargas Barroso"},{"full_name":"Fidalgo, Luis Eusebio","first_name":"Luis Eusebio","last_name":"Fidalgo"},{"last_name":"López-Beceiro","full_name":"López-Beceiro, Ana María","first_name":"Ana María"},{"full_name":"Larriva-Sahd, Jorge A.","last_name":"Larriva-Sahd","first_name":"Jorge A."},{"full_name":"Sánchez-Quinteiro, Pablo","last_name":"Sánchez-Quinteiro","first_name":"Pablo"}],"external_id":{"pmid":["36704406"],"isi":["000919786900001"]},"publication":"Frontiers in Neuroanatomy","abstract":[{"lang":"eng","text":"Introduction: The olfactory system in most mammals is divided into several subsystems based on the anatomical locations of the neuroreceptor cells involved and the receptor families that are expressed. In addition to the main olfactory system and the vomeronasal system, a range of olfactory subsystems converge onto the transition zone located between the main olfactory bulb (MOB) and the accessory olfactory bulb (AOB), which has been termed the olfactory limbus (OL). The OL contains specialized glomeruli that receive noncanonical sensory afferences and which interact with the MOB and AOB. Little is known regarding the olfactory subsystems of mammals other than laboratory rodents.\r\nMethods: We have focused on characterizing the OL in the red fox by performing general and specific histological stainings on serial sections, using both single and double immunohistochemical and lectin-histochemical labeling techniques.\r\nResults: As a result, we have been able to determine that the OL of the red fox (Vulpes vulpes) displays an uncommonly high degree of development and complexity.\r\nDiscussion: This makes this species a novel mammalian model, the study of which could improve our understanding of the noncanonical pathways involved in the processing of chemosensory cues."}],"day":"10","ddc":["570"],"oa_version":"Published Version","article_number":"1097467","has_accepted_license":"1","publication_status":"published","scopus_import":"1"},{"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2643-1564"]},"date_created":"2023-02-10T09:02:26Z","oa":1,"month":"01","volume":5,"article_processing_charge":"No","citation":{"ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1). doi:10.1103/physrevresearch.5.013029","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029.","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:10.1103/physrevresearch.5.013029.","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023."},"file_date_updated":"2023-02-13T10:38:10Z","date_published":"2023-01-20T00:00:00Z","doi":"10.1103/physrevresearch.5.013029","acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","date_updated":"2025-04-14T07:48:54Z","status":"public","publisher":"American Physical Society","type":"journal_article","intvolume":" 5","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12534","year":"2023","author":[{"orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto","full_name":"Cappellaro, Alberto","last_name":"Cappellaro","orcid":"0000-0001-6110-2359"},{"orcid":"0000-0002-6990-7802","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem","last_name":"Volosniev"}],"file":[{"content_type":"application/pdf","file_size":865150,"file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","success":1,"checksum":"6068b62874c0099628a108bb9c5c6bd2","creator":"dernst","file_id":"12546","date_created":"2023-02-13T10:38:10Z","date_updated":"2023-02-13T10:38:10Z","relation":"main_file","access_level":"open_access"}],"department":[{"_id":"MiLe"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"title":"Dissipative dynamics of an impurity with spin-orbit coupling","article_number":"013029","has_accepted_license":"1","publication_status":"published","corr_author":"1","scopus_import":"1","issue":"1","publication":"Physical Review Research","day":"20","abstract":[{"text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics.","lang":"eng"}],"ddc":["530"],"project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"ec_funded":1,"oa_version":"Published Version"},{"external_id":{"pmid":["36731425"],"isi":["000994473300001"]},"author":[{"orcid":"0000-0002-5615-5277","last_name":"Villalba Requena","full_name":"Villalba Requena, Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247","first_name":"Ana"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"}],"title":"Going back in time with TEMPO","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2023.01.006","open_access":"1"}],"department":[{"_id":"SiHi"}],"publication_status":"published","corr_author":"1","scopus_import":"1","OA_place":"publisher","oa_version":"Published Version","issue":"3","publication":"Neuron","abstract":[{"text":"In this issue of Neuron, Espinosa-Medina et al.1 present the TEMPO (Temporal Encoding and Manipulation in a Predefined Order) system, which enables the marking and genetic manipulation of sequentially generated cell lineages in vertebrate species in vivo.","lang":"eng"}],"day":"01","date_created":"2023-02-12T23:00:58Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1097-4199"]},"date_published":"2023-02-01T00:00:00Z","volume":111,"month":"02","article_processing_charge":"No","oa":1,"citation":{"ista":"Villalba Requena A, Hippenmeyer S. 2023. Going back in time with TEMPO. Neuron. 111(3), 291–293.","short":"A. Villalba Requena, S. Hippenmeyer, Neuron 111 (2023) 291–293.","ama":"Villalba Requena A, Hippenmeyer S. Going back in time with TEMPO. Neuron. 2023;111(3):291-293. doi:10.1016/j.neuron.2023.01.006","chicago":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron. Elsevier, 2023. https://doi.org/10.1016/j.neuron.2023.01.006.","apa":"Villalba Requena, A., & Hippenmeyer, S. (2023). Going back in time with TEMPO. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.01.006","mla":"Villalba Requena, Ana, and Simon Hippenmeyer. “Going Back in Time with TEMPO.” Neuron, vol. 111, no. 3, Elsevier, 2023, pp. 291–93, doi:10.1016/j.neuron.2023.01.006.","ieee":"A. Villalba Requena and S. Hippenmeyer, “Going back in time with TEMPO,” Neuron, vol. 111, no. 3. Elsevier, pp. 291–293, 2023."},"status":"public","publisher":"Elsevier","type":"journal_article","date_updated":"2025-06-25T06:24:25Z","intvolume":" 111","doi":"10.1016/j.neuron.2023.01.006","page":"291-293","_id":"12542","pmid":1,"year":"2023","article_type":"letter_note","OA_type":"free access","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":" 7","date_updated":"2025-04-14T07:47:53Z","type":"journal_article","publisher":"Springer Nature","status":"public","acknowledgement":"We thank B. M. Steinwender, N. V. Meyling and J. Eilenberg for the fungal strains; J. Anaya-Rojas for statistical advice; the Social Immunity team at ISTA for ant collection and experimental help, in particular H. Leitner, and the ISTA Lab Support Facility for general laboratory support; D. Ebert, H. Schulenburg and J. Heinze for continued project discussion; and M. Sixt, R. Roemhild and the Social Immunity team for comments on the manuscript. The study was funded by the German Research Foundation (CR118/3-1) within the Framework of the Priority Program SPP 1399, and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP), both to S.C.","doi":"10.1038/s41559-023-01981-6","year":"2023","pmid":1,"_id":"12543","acknowledged_ssus":[{"_id":"LifeSc"}],"page":"450-460","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","date_created":"2023-02-12T23:00:59Z","publication_identifier":{"eissn":["2397-334X"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2023-03-01T00:00:00Z","file_date_updated":"2023-08-16T11:54:59Z","citation":{"chicago":"Stock, Miriam, Barbara Milutinovic, Michaela Hönigsberger, Anna V Grasse, Florian Wiesenhofer, Niklas Kampleitner, Madhumitha Narasimhan, Thomas Schmitt, and Sylvia Cremer. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1038/s41559-023-01981-6.","ama":"Stock M, Milutinovic B, Hönigsberger M, et al. Pathogen evasion of social immunity. Nature Ecology and Evolution. 2023;7:450-460. doi:10.1038/s41559-023-01981-6","mla":"Stock, Miriam, et al. “Pathogen Evasion of Social Immunity.” Nature Ecology and Evolution, vol. 7, Springer Nature, 2023, pp. 450–60, doi:10.1038/s41559-023-01981-6.","ieee":"M. Stock et al., “Pathogen evasion of social immunity,” Nature Ecology and Evolution, vol. 7. Springer Nature, pp. 450–460, 2023.","apa":"Stock, M., Milutinovic, B., Hönigsberger, M., Grasse, A. V., Wiesenhofer, F., Kampleitner, N., … Cremer, S. (2023). Pathogen evasion of social immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-023-01981-6","short":"M. Stock, B. Milutinovic, M. Hönigsberger, A.V. Grasse, F. Wiesenhofer, N. Kampleitner, M. Narasimhan, T. Schmitt, S. Cremer, Nature Ecology and Evolution 7 (2023) 450–460.","ista":"Stock M, Milutinovic B, Hönigsberger M, Grasse AV, Wiesenhofer F, Kampleitner N, Narasimhan M, Schmitt T, Cremer S. 2023. Pathogen evasion of social immunity. Nature Ecology and Evolution. 7, 450–460."},"oa":1,"month":"03","volume":7,"article_processing_charge":"No","scopus_import":"1","publication_status":"published","corr_author":"1","has_accepted_license":"1","related_material":{"link":[{"description":"News on ISTA website","url":"https://ista.ac.at/en/news/how-sneaky-germs-hide-from-ants/","relation":"press_release"}]},"oa_version":"Published Version","ec_funded":1,"abstract":[{"lang":"eng","text":"Treating sick group members is a hallmark of collective disease defence in vertebrates and invertebrates alike. Despite substantial effects on pathogen fitness and epidemiology, it is still largely unknown how pathogens react to the selection pressure imposed by care intervention. Using social insects and pathogenic fungi, we here performed a serial passage experiment in the presence or absence of colony members, which provide social immunity by grooming off infectious spores from exposed individuals. We found specific effects on pathogen diversity, virulence and transmission. Under selection of social immunity, pathogens invested into higher spore production, but spores were less virulent. Notably, they also elicited a lower grooming response in colony members, compared with spores from the individual host selection lines. Chemical spore analysis suggested that the spores from social selection lines escaped the caregivers’ detection by containing lower levels of ergosterol, a key fungal membrane component. Experimental application of chemically pure ergosterol indeed induced sanitary grooming, supporting its role as a microbe-associated cue triggering host social immunity against fungal pathogens. By reducing this detection cue, pathogens were able to evade the otherwise very effective collective disease defences of their social hosts."}],"ddc":["570"],"day":"01","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","grant_number":"771402"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"publication":"Nature Ecology and Evolution","external_id":{"pmid":["36732670"],"isi":["000924572800001"]},"author":[{"full_name":"Stock, Miriam","last_name":"Stock","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8214-4758","last_name":"Milutinovic","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","full_name":"Milutinovic, Barbara"},{"last_name":"Hönigsberger","full_name":"Hönigsberger, Michaela","id":"953894f3-25bd-11ec-8556-f70a9d38ef60","first_name":"Michaela"},{"first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"first_name":"Florian","full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer","id":"39523C54-F248-11E8-B48F-1D18A9856A87"},{"id":"2AC57FAC-F248-11E8-B48F-1D18A9856A87","full_name":"Kampleitner, Niklas","last_name":"Kampleitner","first_name":"Niklas"},{"first_name":"Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","full_name":"Narasimhan, Madhumitha","last_name":"Narasimhan","orcid":"0000-0002-8600-0671"},{"first_name":"Thomas","full_name":"Schmitt, Thomas","last_name":"Schmitt"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"title":"Pathogen evasion of social immunity","department":[{"_id":"SyCr"},{"_id":"LifeSc"},{"_id":"JiFr"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"creator":"dernst","checksum":"8244f4650a0e7aeea488d1bcd4a31702","file_id":"14069","date_created":"2023-08-16T11:54:59Z","date_updated":"2023-08-16T11:54:59Z","access_level":"open_access","relation":"main_file","success":1,"file_name":"2023_NatureEcoEvo_Stock.pdf","content_type":"application/pdf","file_size":1600499}]},{"ec_funded":1,"oa_version":"Published Version","issue":"3","publication":"Journal of Chemical Information and Modeling","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"name":"Mathematics, Computer Science","call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35"}],"abstract":[{"text":"Geometry is crucial in our efforts to comprehend the structures and dynamics of biomolecules. For example, volume, surface area, and integrated mean and Gaussian curvature of the union of balls representing a molecule are used to quantify its interactions with the water surrounding it in the morphometric implicit solvent models. The Alpha Shape theory provides an accurate and reliable method for computing these geometric measures. In this paper, we derive homogeneous formulas for the expressions of these measures and their derivatives with respect to the atomic coordinates, and we provide algorithms that implement them into a new software package, AlphaMol. The only variables in these formulas are the interatomic distances, making them insensitive to translations and rotations. AlphaMol includes a sequential algorithm and a parallel algorithm. In the parallel version, we partition the atoms of the molecule of interest into 3D rectangular blocks, using a kd-tree algorithm. We then apply the sequential algorithm of AlphaMol to each block, augmented by a buffer zone to account for atoms whose ball representations may partially cover the block. The current parallel version of AlphaMol leads to a 20-fold speed-up compared to an independent serial implementation when using 32 processors. For instance, it takes 31 s to compute the geometric measures and derivatives of each atom in a viral capsid with more than 26 million atoms on 32 Intel processors running at 2.7 GHz. The presence of the buffer zones, however, leads to redundant computations, which ultimately limit the impact of using multiple processors. AlphaMol is available as an OpenSource software.","lang":"eng"}],"day":"13","ddc":["510","540"],"publication_status":"published","corr_author":"1","scopus_import":"1","has_accepted_license":"1","title":"Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives","file":[{"content_type":"application/pdf","file_size":8069223,"success":1,"file_name":"2023_JCIM_Koehl.pdf","file_id":"14070","checksum":"7d20562269edff1e31b9d6019d4983b0","creator":"dernst","access_level":"open_access","relation":"main_file","date_updated":"2023-08-16T12:21:13Z","date_created":"2023-08-16T12:21:13Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"HeEd"}],"external_id":{"isi":["000920370700001"],"pmid":["36638318"]},"author":[{"full_name":"Koehl, Patrice","first_name":"Patrice","last_name":"Koehl"},{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X"},{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"page":"973-985","_id":"12544","year":"2023","pmid":1,"article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"American Chemical Society","type":"journal_article","date_updated":"2025-04-15T07:16:52Z","intvolume":" 63","doi":"10.1021/acs.jcim.2c01346","acknowledgement":"P.K. acknowledges support from the University of California Multicampus Research Programs and Initiatives (Grant No. M21PR3267) and from the NSF (Grant No.1760485). H.E. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.\r\nOpen Access is funded by the Austrian Science Fund (FWF).","file_date_updated":"2023-08-16T12:21:13Z","date_published":"2023-02-13T00:00:00Z","article_processing_charge":"No","month":"02","volume":63,"oa":1,"citation":{"mla":"Koehl, Patrice, et al. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling, vol. 63, no. 3, American Chemical Society, 2023, pp. 973–85, doi:10.1021/acs.jcim.2c01346.","ieee":"P. Koehl, A. Akopyan, and H. Edelsbrunner, “Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives,” Journal of Chemical Information and Modeling, vol. 63, no. 3. American Chemical Society, pp. 973–985, 2023.","apa":"Koehl, P., Akopyan, A., & Edelsbrunner, H. (2023). Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. American Chemical Society. https://doi.org/10.1021/acs.jcim.2c01346","chicago":"Koehl, Patrice, Arseniy Akopyan, and Herbert Edelsbrunner. “Computing the Volume, Surface Area, Mean, and Gaussian Curvatures of Molecules and Their Derivatives.” Journal of Chemical Information and Modeling. American Chemical Society, 2023. https://doi.org/10.1021/acs.jcim.2c01346.","ama":"Koehl P, Akopyan A, Edelsbrunner H. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 2023;63(3):973-985. doi:10.1021/acs.jcim.2c01346","short":"P. Koehl, A. Akopyan, H. Edelsbrunner, Journal of Chemical Information and Modeling 63 (2023) 973–985.","ista":"Koehl P, Akopyan A, Edelsbrunner H. 2023. Computing the volume, surface area, mean, and Gaussian curvatures of molecules and their derivatives. Journal of Chemical Information and Modeling. 63(3), 973–985."},"date_created":"2023-02-12T23:00:59Z","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1549-960X"],"issn":["1549-9596"]},"quality_controlled":"1"},{"external_id":{"arxiv":["2301.01856"],"pmid":["36797971"],"isi":["000963909800006"]},"author":[{"first_name":"Mauricio Nicolas","full_name":"Rojas Vega, Mauricio Nicolas","last_name":"Rojas Vega","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d"},{"first_name":"Pablo","full_name":"De Castro, Pablo","last_name":"De Castro"},{"first_name":"Rodrigo","full_name":"Soto, Rodrigo","last_name":"Soto"}],"title":"Wetting dynamics by mixtures of fast and slow self-propelled particles","department":[{"_id":"GradSch"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.01856","open_access":"1"}],"scopus_import":"1","publication_status":"published","article_number":"014608","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We study active surface wetting using a minimal model of bacteria that takes into account the intrinsic motility diversity of living matter. A mixture of “fast” and “slow” self-propelled Brownian particles is considered in the presence of a wall. The evolution of the wetting layer thickness shows an overshoot before stationarity and its composition evolves in two stages, equilibrating after a slow elimination of excess particles. Nonmonotonic evolutions are shown to arise from delayed avalanches towards the dilute phase combined with the emergence of a transient particle front."}],"day":"24","issue":"1","publication":"Physical Review E","date_created":"2023-02-12T23:00:59Z","arxiv":1,"quality_controlled":"1","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"language":[{"iso":"eng"}],"date_published":"2023-01-24T00:00:00Z","citation":{"chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E. American Physical Society, 2023. https://doi.org/10.1103/PhysRevE.107.014608.","ama":"Rojas Vega MN, De Castro P, Soto R. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 2023;107(1). doi:10.1103/PhysRevE.107.014608","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Wetting dynamics by mixtures of fast and slow self-propelled particles,” Physical Review E, vol. 107, no. 1. American Physical Society, 2023.","mla":"Rojas Vega, Mauricio Nicolas, et al. “Wetting Dynamics by Mixtures of Fast and Slow Self-Propelled Particles.” Physical Review E, vol. 107, no. 1, 014608, American Physical Society, 2023, doi:10.1103/PhysRevE.107.014608.","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.107.014608","short":"M.N. Rojas Vega, P. De Castro, R. Soto, Physical Review E 107 (2023).","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Wetting dynamics by mixtures of fast and slow self-propelled particles. Physical Review E. 107(1), 014608."},"article_processing_charge":"No","month":"01","volume":107,"oa":1,"intvolume":" 107","status":"public","type":"journal_article","publisher":"American Physical Society","date_updated":"2025-03-06T14:01:47Z","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and ANID – Millennium Science Initiative Program – NCN19 170D, Chile. PdC is supported by grant #2021/10139-2, Sao Paulo Research Foundation (FAPESP), Brazil.","doi":"10.1103/PhysRevE.107.014608","pmid":1,"year":"2023","_id":"12545","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","isi":1},{"year":"2023","_id":"12548","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"date_updated":"2024-10-21T06:01:25Z","status":"public","type":"conference","publisher":"Institute of Electrical and Electronics Engineers","doi":"10.1109/icdmw58026.2022.00093","date_published":"2023-02-08T00:00:00Z","file_date_updated":"2023-02-14T07:58:26Z","citation":{"apa":"Forghani, M., Claramunt, C., Karimipour, F., & Heiler, G. (2023). Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In 2022 IEEE International Conference on Data Mining Workshops. Orlando, FL, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/icdmw58026.2022.00093","ieee":"M. Forghani, C. Claramunt, F. Karimipour, and G. Heiler, “Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic,” in 2022 IEEE International Conference on Data Mining Workshops, Orlando, FL, United States, 2023.","mla":"Forghani, Mohammad, et al. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” 2022 IEEE International Conference on Data Mining Workshops, 00093, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/icdmw58026.2022.00093.","ama":"Forghani M, Claramunt C, Karimipour F, Heiler G. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. In: 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/icdmw58026.2022.00093","chicago":"Forghani, Mohammad, Christophe Claramunt, Farid Karimipour, and Georg Heiler. “Visual Analytics of Mobility Network Changes Observed Using Mobile Phone Data during COVID-19 Pandemic.” In 2022 IEEE International Conference on Data Mining Workshops. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/icdmw58026.2022.00093.","ista":"Forghani M, Claramunt C, Karimipour F, Heiler G. 2023. Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic. 2022 IEEE International Conference on Data Mining Workshops. ICDMW: Conference on Data Mining Workshops, 00093.","short":"M. Forghani, C. Claramunt, F. Karimipour, G. Heiler, in:, 2022 IEEE International Conference on Data Mining Workshops, Institute of Electrical and Electronics Engineers, 2023."},"oa":1,"month":"02","article_processing_charge":"No","conference":{"end_date":"2022-12-01","name":"ICDMW: Conference on Data Mining Workshops","location":"Orlando, FL, United States","start_date":"2022-11-28"},"date_created":"2023-02-14T07:56:21Z","quality_controlled":"1","publication_identifier":{"eissn":["2375-9259"],"eisbn":["9798350346091"]},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","abstract":[{"text":"The limited exchange between human communities is a key factor in preventing the spread of COVID-19. This paper introduces a digital framework that combines an integration of real mobility data at the country scale with a series of modeling techniques and visual capabilities that highlight mobility patterns before and during the pandemic. The findings not only significantly exhibit mobility trends and different degrees of similarities at regional and local levels but also provide potential insight into the emergence of a pandemic on human behavior patterns and their likely socio-economic impacts.","lang":"eng"}],"day":"08","ddc":["600"],"publication":"2022 IEEE International Conference on Data Mining Workshops","scopus_import":"1","publication_status":"published","has_accepted_license":"1","article_number":"00093","title":"Visual analytics of mobility network changes observed using mobile phone data during COVID-19 pandemic","department":[{"_id":"HeEd"}],"file":[{"file_size":1183339,"content_type":"application/pdf","file_name":"Visual Analysis_Mobility_COVID19 - SocDM2022.pdf","success":1,"date_updated":"2023-02-14T07:58:26Z","relation":"main_file","access_level":"open_access","date_created":"2023-02-14T07:58:26Z","creator":"fkarimip","checksum":"c253bee25e6dfe484f96662daa119cb6","file_id":"12549"}],"external_id":{"isi":["000971492200145"]},"author":[{"first_name":"Mohammad","full_name":"Forghani, Mohammad","last_name":"Forghani"},{"first_name":"Christophe","last_name":"Claramunt","full_name":"Claramunt, Christophe"},{"id":"2A2BCDC4-CF62-11E9-BE5E-3B1EE6697425","first_name":"Farid","last_name":"Karimipour","full_name":"Karimipour, Farid","orcid":"0000-0001-6746-4174"},{"first_name":"Georg","last_name":"Heiler","full_name":"Heiler, Georg"}]},{"department":[{"_id":"SiHi"}],"title":"Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons","author":[{"first_name":"David R.","full_name":"Ladle, David R.","last_name":"Ladle"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"external_id":{"isi":["000957721600001"],"pmid":["36695533"]},"abstract":[{"lang":"eng","text":"Presynaptic inputs determine the pattern of activation of postsynaptic neurons in a neural circuit. Molecular and genetic pathways that regulate the selective formation of subsets of presynaptic inputs are largely unknown, despite significant understanding of the general process of synaptogenesis. In this study, we have begun to identify such factors using the spinal monosynaptic stretch reflex circuit as a model system. In this neuronal circuit, Ia proprioceptive afferents establish monosynaptic connections with spinal motor neurons that project to the same muscle (termed homonymous connections) or muscles with related or synergistic function. However, monosynaptic connections are not formed with motor neurons innervating muscles with antagonistic functions. The ETS transcription factor ER81 (also known as ETV1) is expressed by all proprioceptive afferents, but only a small set of motor neuron pools in the lumbar spinal cord of the mouse. Here we use conditional mouse genetic techniques to eliminate Er81 expression selectively from motor neurons. We find that ablation of Er81 in motor neurons reduces synaptic inputs from proprioceptive afferents conveying information from homonymous and synergistic muscles, with no change observed in the connectivity pattern from antagonistic proprioceptive afferents. In summary, these findings suggest a role for ER81 in defined motor neuron pools to control the assembly of specific presynaptic inputs and thereby influence the profile of activation of these motor neurons."}],"day":"01","publication":"Journal of Neurophysiology","issue":"3","oa_version":"None","scopus_import":"1","publication_status":"published","citation":{"short":"D.R. Ladle, S. Hippenmeyer, Journal of Neurophysiology 129 (2023) 501–512.","ista":"Ladle DR, Hippenmeyer S. 2023. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 129(3), 501–512.","chicago":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology. American Physiological Society, 2023. https://doi.org/10.1152/jn.00172.2022.","ama":"Ladle DR, Hippenmeyer S. Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. 2023;129(3):501-512. doi:10.1152/jn.00172.2022","mla":"Ladle, David R., and Simon Hippenmeyer. “Loss of ETV1/ER81 in Motor Neurons Leads to Reduced Monosynaptic Inputs from Proprioceptive Sensory Neurons.” Journal of Neurophysiology, vol. 129, no. 3, American Physiological Society, 2023, pp. 501–12, doi:10.1152/jn.00172.2022.","ieee":"D. R. Ladle and S. Hippenmeyer, “Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons,” Journal of Neurophysiology, vol. 129, no. 3. American Physiological Society, pp. 501–512, 2023.","apa":"Ladle, D. R., & Hippenmeyer, S. (2023). Loss of ETV1/ER81 in motor neurons leads to reduced monosynaptic inputs from proprioceptive sensory neurons. Journal of Neurophysiology. American Physiological Society. https://doi.org/10.1152/jn.00172.2022"},"article_processing_charge":"No","month":"03","volume":129,"date_published":"2023-03-01T00:00:00Z","quality_controlled":"1","publication_identifier":{"issn":["0022-3077"],"eissn":["1522-1598"]},"language":[{"iso":"eng"}],"date_created":"2023-02-15T14:46:14Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","isi":1,"pmid":1,"year":"2023","page":"501-512","_id":"12562","acknowledgement":"The authors gratefully thank Dr. Silvia Arber, University of Basel and Friedrich Miescher Institute for Biomedical Research, for support and in whose lab the data were collected. For advice on statistical analysis, we thank Michael Bottomley from the Statistical Consulting Center, College of Science and Mathematics, Wright State University.","doi":"10.1152/jn.00172.2022","intvolume":" 129","status":"public","publisher":"American Physiological Society","keyword":["Physiology","General Neuroscience"],"type":"journal_article","date_updated":"2024-10-21T06:01:28Z"},{"ec_funded":1,"oa_version":"Preprint","publication":"SIAM Journal on Computing","issue":"1","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"day":"01","abstract":[{"lang":"eng","text":"he approximate graph coloring problem, whose complexity is unresolved in most cases, concerns finding a c-coloring of a graph that is promised to be k-colorable, where c≥k. This problem naturally generalizes to promise graph homomorphism problems and further to promise constraint satisfaction problems. The complexity of these problems has recently been studied through an algebraic approach. In this paper, we introduce two new techniques to analyze the complexity of promise CSPs: one is based on topology and the other on adjunction. We apply these techniques, together with the previously introduced algebraic approach, to obtain new unconditional NP-hardness results for a significant class of approximate graph coloring and promise graph homomorphism problems."}],"publication_status":"published","scopus_import":"1","title":"Topology and adjunction in promise constraint satisfaction","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2003.11351"}],"department":[{"_id":"UlWa"}],"external_id":{"arxiv":["2003.11351"],"isi":["000955000000001"]},"author":[{"full_name":"Krokhin, Andrei","first_name":"Andrei","last_name":"Krokhin"},{"first_name":"Jakub","last_name":"Opršal","id":"ec596741-c539-11ec-b829-c79322a91242","full_name":"Opršal, Jakub","orcid":"0000-0003-1245-3456"},{"first_name":"Marcin","full_name":"Wrochna, Marcin","last_name":"Wrochna"},{"first_name":"Stanislav","last_name":"Živný","full_name":"Živný, Stanislav"}],"page":"38-79","_id":"12563","year":"2023","article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics","status":"public","type":"journal_article","keyword":["General Mathematics","General Computer Science"],"date_updated":"2025-05-14T10:51:32Z","intvolume":" 52","doi":"10.1137/20m1378223","acknowledgement":"Andrei Krokhin and Jakub Opršal were supported by the UK EPSRC grant EP/R034516/1. Jakub Opršal has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Stanislav Živný was supported by a Royal Society University Research Fellowship. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 714532). The paper re\u001eects only the authors’ views and not the views of the ERC or the European Commission. ","date_published":"2023-01-01T00:00:00Z","article_processing_charge":"No","month":"01","volume":52,"oa":1,"citation":{"apa":"Krokhin, A., Opršal, J., Wrochna, M., & Živný, S. (2023). Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20m1378223","ieee":"A. Krokhin, J. Opršal, M. Wrochna, and S. Živný, “Topology and adjunction in promise constraint satisfaction,” SIAM Journal on Computing, vol. 52, no. 1. Society for Industrial and Applied Mathematics, pp. 38–79, 2023.","mla":"Krokhin, Andrei, et al. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing, vol. 52, no. 1, Society for Industrial and Applied Mathematics, 2023, pp. 38–79, doi:10.1137/20m1378223.","chicago":"Krokhin, Andrei, Jakub Opršal, Marcin Wrochna, and Stanislav Živný. “Topology and Adjunction in Promise Constraint Satisfaction.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/20m1378223.","ama":"Krokhin A, Opršal J, Wrochna M, Živný S. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 2023;52(1):38-79. doi:10.1137/20m1378223","ista":"Krokhin A, Opršal J, Wrochna M, Živný S. 2023. Topology and adjunction in promise constraint satisfaction. SIAM Journal on Computing. 52(1), 38–79.","short":"A. Krokhin, J. Opršal, M. Wrochna, S. Živný, SIAM Journal on Computing 52 (2023) 38–79."},"date_created":"2023-02-16T07:03:52Z","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]}},{"oa":1,"volume":948,"article_processing_charge":"Yes (via OA deal)","month":"02","citation":{"apa":"Alistarh, D.-A., Ellen, F., & Rybicki, J. (2023). Wait-free approximate agreement on graphs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.113733","ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” Theoretical Computer Science, vol. 948, no. 2. Elsevier, 2023.","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science, vol. 948, no. 2, 113733, Elsevier, 2023, doi:10.1016/j.tcs.2023.113733.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. Theoretical Computer Science. 2023;948(2). doi:10.1016/j.tcs.2023.113733","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.113733.","ista":"Alistarh D-A, Ellen F, Rybicki J. 2023. Wait-free approximate agreement on graphs. Theoretical Computer Science. 948(2), 113733.","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, Theoretical Computer Science 948 (2023)."},"file_date_updated":"2023-02-20T07:30:20Z","date_published":"2023-02-28T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0304-3975"]},"date_created":"2023-02-19T23:00:55Z","isi":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12566","year":"2023","doi":"10.1016/j.tcs.2023.113733","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 805223 ScaleML) and under the Marie Skłodowska-Curie grant agreement No. 840605 and from the Natural Sciences and Engineering Research Council of Canada grant RGPIN-2020-04178. Part of this work was done while Faith Ellen was visiting IST Austria.","date_updated":"2025-04-14T07:49:16Z","status":"public","publisher":"Elsevier","type":"journal_article","intvolume":" 948","file":[{"creator":"dernst","checksum":"b27c5290f2f1500c403494364ee39c9f","file_id":"12570","date_updated":"2023-02-20T07:30:20Z","relation":"main_file","access_level":"open_access","date_created":"2023-02-20T07:30:20Z","file_name":"2023_TheoreticalCompScience_Alistarh.pdf","success":1,"content_type":"application/pdf","file_size":602333}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"DaAl"}],"title":"Wait-free approximate agreement on graphs","author":[{"first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"orcid":"0000-0002-6432-6646","last_name":"Rybicki","full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"}],"external_id":{"isi":["000934262700001"]},"publication":"Theoretical Computer Science","issue":"2","abstract":[{"lang":"eng","text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a node of the graph as input and, if non-faulty, must output a node such that\r\n– all the outputs are within distance 1 of one another, and\r\n– each output value lies on a shortest path between two input values.\r\nFrom prior work, it is known that there is no wait-free algorithm among processes for this problem on any cycle of length , by reduction from 2-set agreement (Castañeda et al., 2018).\r\n\r\nIn this work, we investigate the solvability of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length , via a generalisation of Sperner's Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a different class of graphs, which properly contains the class of chordal graphs."}],"day":"28","ddc":["000"],"project":[{"grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425"},{"name":"Coordination in constrained and natural distributed systems","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","grant_number":"840605"}],"ec_funded":1,"oa_version":"Published Version","article_number":"113733","has_accepted_license":"1","corr_author":"1","publication_status":"published","scopus_import":"1"},{"title":"Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation","department":[{"_id":"PeJo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"file_id":"12569","checksum":"69a35dcd3e0249f902ab881b06ee2e58","creator":"dernst","relation":"main_file","date_updated":"2023-02-20T07:09:27Z","access_level":"open_access","date_created":"2023-02-20T07:09:27Z","file_name":"2023_IJMS_Mrestani.pdf","success":1,"content_type":"application/pdf","file_size":2823025}],"external_id":{"pmid":["36768451"],"isi":["000930324700001"]},"author":[{"full_name":"Mrestani, Achmed","last_name":"Mrestani","first_name":"Achmed"},{"first_name":"Katharina","full_name":"Lichter, Katharina","id":"39302e62-fcfc-11ec-8196-8b01447dbd3d","last_name":"Lichter","orcid":"0000-0002-1485-0351"},{"full_name":"Sirén, Anna Leena","first_name":"Anna Leena","last_name":"Sirén"},{"first_name":"Manfred","full_name":"Heckmann, Manfred","last_name":"Heckmann"},{"full_name":"Paul, Mila M.","first_name":"Mila M.","last_name":"Paul"},{"first_name":"Martin","full_name":"Pauli, Martin","last_name":"Pauli"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Single-molecule localization microscopy (SMLM) greatly advances structural studies of diverse biological tissues. For example, presynaptic active zone (AZ) nanotopology is resolved in increasing detail. Immunofluorescence imaging of AZ proteins usually relies on epitope preservation using aldehyde-based immunocompetent fixation. Cryofixation techniques, such as high-pressure freezing (HPF) and freeze substitution (FS), are widely used for ultrastructural studies of presynaptic architecture in electron microscopy (EM). HPF/FS demonstrated nearer-to-native preservation of AZ ultrastructure, e.g., by facilitating single filamentous structures. Here, we present a protocol combining the advantages of HPF/FS and direct stochastic optical reconstruction microscopy (dSTORM) to quantify nanotopology of the AZ scaffold protein Bruchpilot (Brp) at neuromuscular junctions (NMJs) of Drosophila melanogaster. Using this standardized model, we tested for preservation of Brp clusters in different FS protocols compared to classical aldehyde fixation. In HPF/FS samples, presynaptic boutons were structurally well preserved with ~22% smaller Brp clusters that allowed quantification of subcluster topology. In summary, we established a standardized near-to-native preparation and immunohistochemistry protocol for SMLM analyses of AZ protein clusters in a defined model synapse. Our protocol could be adapted to study protein arrangements at single-molecule resolution in other intact tissue preparations."}],"day":"21","ddc":["570"],"issue":"3","publication":"International Journal of Molecular Sciences","scopus_import":"1","publication_status":"published","has_accepted_license":"1","article_number":"2128","date_published":"2023-01-21T00:00:00Z","file_date_updated":"2023-02-20T07:09:27Z","citation":{"ista":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. 2023. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 24(3), 2128.","short":"A. Mrestani, K. Lichter, A.L. Sirén, M. Heckmann, M.M. Paul, M. Pauli, International Journal of Molecular Sciences 24 (2023).","apa":"Mrestani, A., Lichter, K., Sirén, A. L., Heckmann, M., Paul, M. M., & Pauli, M. (2023). Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms24032128","ieee":"A. Mrestani, K. Lichter, A. L. Sirén, M. Heckmann, M. M. Paul, and M. Pauli, “Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation,” International Journal of Molecular Sciences, vol. 24, no. 3. MDPI, 2023.","mla":"Mrestani, Achmed, et al. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences, vol. 24, no. 3, 2128, MDPI, 2023, doi:10.3390/ijms24032128.","chicago":"Mrestani, Achmed, Katharina Lichter, Anna Leena Sirén, Manfred Heckmann, Mila M. Paul, and Martin Pauli. “Single-Molecule Localization Microscopy of Presynaptic Active Zones in Drosophila Melanogaster after Rapid Cryofixation.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms24032128.","ama":"Mrestani A, Lichter K, Sirén AL, Heckmann M, Paul MM, Pauli M. Single-molecule localization microscopy of presynaptic active zones in Drosophila melanogaster after rapid cryofixation. International Journal of Molecular Sciences. 2023;24(3). doi:10.3390/ijms24032128"},"oa":1,"article_processing_charge":"No","month":"01","volume":24,"date_created":"2023-02-19T23:00:56Z","quality_controlled":"1","publication_identifier":{"eissn":["1422-0067"]},"language":[{"iso":"eng"}],"pmid":1,"year":"2023","_id":"12567","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","intvolume":" 24","date_updated":"2025-04-23T08:48:27Z","publisher":"MDPI","type":"journal_article","status":"public","doi":"10.3390/ijms24032128","acknowledgement":"This work has been supported by funding of the German Research Foundation (Deutsche Forschungsgemeinschaft [DFG], CRC 166, Project B06 to M.H. and A.-L.S., FOR 3004 SYNABS P1 to M.H.) and by the Interdisciplinary Clinical Research Center (IZKF) Würzburg (Z-3/69 to M.M.P., N-229 to M.H. and A.-L.S.). A.M. is funded by the University of Leipzig Clinician Scientist Program."},{"corr_author":"1","publication_status":"published","alternative_title":["TMLR"],"has_accepted_license":"1","OA_place":"repository","related_material":{"link":[{"url":"https://github.com/jonnyascott/xclp","relation":"software"}]},"oa_version":"Preprint","publication":"Transactions in Machine Learning","abstract":[{"lang":"eng","text":"We present Cross-Client Label Propagation(XCLP), a new method for transductive federated learning. XCLP estimates a data graph jointly from the data of multiple clients and computes labels for the unlabeled data by propagating label information across the graph. To avoid clients having to share their data with anyone, XCLP employs two cryptographically secure protocols: secure Hamming distance computation and secure summation. We demonstrate two distinct applications of XCLP within federated learning. In the first, we use it in a one-shot way to predict labels for unseen test points. In the second, we use it to repeatedly pseudo-label unlabeled training data in a federated semi-supervised setting. Experiments on both real federated and standard benchmark datasets show that in both applications XCLP achieves higher classification accuracy than alternative approaches."}],"ddc":["004"],"day":"27","external_id":{"arxiv":["2210.06434"]},"author":[{"first_name":"Jonathan A","full_name":"Scott, Jonathan A","id":"e499926b-f6e0-11ea-865d-9c63db0031e8","last_name":"Scott"},{"first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X","orcid":"0009-0001-3676-4809"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"title":"Cross-client label propagation for transductive and semi-supervised federated learning","file":[{"access_level":"open_access","date_updated":"2025-02-04T08:30:05Z","relation":"main_file","date_created":"2025-02-04T08:30:05Z","creator":"dernst","checksum":"aa322ad91cbd229f5cafe6733a119bd1","file_id":"18990","success":1,"file_name":"2023_TMLR_Scott.pdf","file_size":553717,"content_type":"application/pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"ChLa"}],"type":"conference","publisher":"Curran Associates","status":"public","date_updated":"2025-02-04T08:32:19Z","_id":"12660","year":"2023","OA_type":"green","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-02-20T08:21:50Z","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2835-8856"]},"file_date_updated":"2025-02-04T08:30:05Z","date_published":"2023-11-27T00:00:00Z","month":"11","article_processing_charge":"No","oa":1,"citation":{"apa":"Scott, J. A., Yeo, M. X., & Lampert, C. (2023). Cross-client label propagation for transductive and semi-supervised federated learning. In Transactions in Machine Learning. Curran Associates.","ieee":"J. A. Scott, M. X. Yeo, and C. Lampert, “Cross-client label propagation for transductive and semi-supervised federated learning,” in Transactions in Machine Learning, 2023.","mla":"Scott, Jonathan A., et al. “Cross-Client Label Propagation for Transductive and Semi-Supervised Federated Learning.” Transactions in Machine Learning, Curran Associates, 2023.","chicago":"Scott, Jonathan A, Michelle X Yeo, and Christoph Lampert. “Cross-Client Label Propagation for Transductive and Semi-Supervised Federated Learning.” In Transactions in Machine Learning. Curran Associates, 2023.","ama":"Scott JA, Yeo MX, Lampert C. Cross-client label propagation for transductive and semi-supervised federated learning. In: Transactions in Machine Learning. Curran Associates; 2023.","ista":"Scott JA, Yeo MX, Lampert C. 2023. Cross-client label propagation for transductive and semi-supervised federated learning. Transactions in Machine Learning. , TMLR, .","short":"J.A. Scott, M.X. Yeo, C. Lampert, in:, Transactions in Machine Learning, Curran Associates, 2023."}},{"article_processing_charge":"No","volume":24,"month":"01","oa":1,"citation":{"ieee":"L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.","mla":"Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023, doi:10.1186/s13059-022-02844-2.","apa":"Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023). Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2","chicago":"Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang, Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.","ama":"Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2","short":"L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J. Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).","ista":"Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat. Genome Biology. 24, 7."},"date_published":"2023-01-13T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1474-760X"]},"quality_controlled":"1","date_created":"2023-02-23T09:13:49Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12668","year":"2023","pmid":1,"doi":"10.1186/s13059-022-02844-2","type":"journal_article","publisher":"Springer Nature","status":"public","date_updated":"2023-05-08T10:52:49Z","intvolume":" 24","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s13059-022-02844-2"}],"department":[{"_id":"XiFe"}],"title":"Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat","author":[{"full_name":"Zhao, Long","last_name":"Zhao","first_name":"Long"},{"full_name":"Yang, Yiman","first_name":"Yiman","last_name":"Yang"},{"last_name":"Chen","first_name":"Jinchao","full_name":"Chen, Jinchao"},{"full_name":"Lin, Xuelei","last_name":"Lin","first_name":"Xuelei"},{"last_name":"Zhang","full_name":"Zhang, Hao","first_name":"Hao"},{"full_name":"Wang, Hao","first_name":"Hao","last_name":"Wang"},{"first_name":"Hongzhe","full_name":"Wang, Hongzhe","last_name":"Wang"},{"full_name":"Bie, Xiaomin","first_name":"Xiaomin","last_name":"Bie"},{"first_name":"Jiafu","full_name":"Jiang, Jiafu","last_name":"Jiang"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"first_name":"Xiangdong","last_name":"Fu","full_name":"Fu, Xiangdong"},{"last_name":"Zhang","first_name":"Xiansheng","full_name":"Zhang, Xiansheng"},{"first_name":"Zhuo","full_name":"Du, Zhuo","last_name":"Du"},{"first_name":"Jun","last_name":"Xiao","full_name":"Xiao, Jun"}],"external_id":{"pmid":["36639687"]},"publication":"Genome Biology","day":"13","abstract":[{"lang":"eng","text":"Background: Plant and animal embryogenesis have conserved and distinct features. Cell fate transitions occur during embryogenesis in both plants and animals. The epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults: Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific and proximal–distal distinct chromatin accessibility and dynamics concordant with transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3, H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific epigenomic dynamics during zygotic genome activation. Polycomb repressive complex 2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to establish a permissive chromatin environment facilitating the access of transcription factors to cis-elements for fate patterning. Embryonic maturation is characterized by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates in restricting totipotency while preventing extensive organogenesis. Finally, epigenomic signatures are correlated with biased expression among homeolog triads and divergent expression after polyploidization, revealing an epigenomic contributor to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively, we present an invaluable resource for comparative and mechanistic analysis of the epigenomic regulation of crop embryogenesis."}],"oa_version":"Published Version","article_number":"7","publication_status":"published","extern":"1","scopus_import":"1"},{"doi":"10.1093/plcell/koac346","keyword":["Cell Biology","Plant Science"],"publisher":"Oxford University Press","status":"public","type":"journal_article","date_updated":"2023-10-04T09:48:43Z","intvolume":" 35","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12669","pmid":1,"year":"2023","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"date_created":"2023-02-23T09:14:59Z","volume":35,"month":"06","article_processing_charge":"No","oa":1,"citation":{"short":"P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth, K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J. Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).","ista":"Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 35(6), koac346.","mla":"Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” The Plant Cell, vol. 35, no. 6, koac346, Oxford University Press, 2023, doi:10.1093/plcell/koac346.","ieee":"P. A. Manavella et al., “Beyond transcription: compelling open questions in plant RNA biology,” The Plant Cell, vol. 35, no. 6. Oxford University Press, 2023.","apa":"Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth, L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koac346","ama":"Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling open questions in plant RNA biology. The Plant Cell. 2023;35(6). doi:10.1093/plcell/koac346","chicago":"Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson, Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription: Compelling Open Questions in Plant RNA Biology.” The Plant Cell. Oxford University Press, 2023. https://doi.org/10.1093/plcell/koac346."},"date_published":"2023-06-01T00:00:00Z","article_number":"koac346","extern":"1","publication_status":"published","scopus_import":"1","publication":"The Plant Cell","issue":"6","day":"01","abstract":[{"lang":"eng","text":"The study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader."}],"oa_version":"Published Version","author":[{"first_name":"Pablo A","last_name":"Manavella","full_name":"Manavella, Pablo A"},{"full_name":"Godoy Herz, Micaela A","first_name":"Micaela A","last_name":"Godoy Herz"},{"full_name":"Kornblihtt, Alberto R","first_name":"Alberto R","last_name":"Kornblihtt"},{"full_name":"Sorenson, Reed","first_name":"Reed","last_name":"Sorenson"},{"full_name":"Sieburth, Leslie E","first_name":"Leslie E","last_name":"Sieburth"},{"full_name":"Nakaminami, Kentaro","last_name":"Nakaminami","first_name":"Kentaro"},{"full_name":"Seki, Motoaki","last_name":"Seki","first_name":"Motoaki"},{"full_name":"Ding, Yiliang","last_name":"Ding","first_name":"Yiliang"},{"last_name":"Sun","first_name":"Qianwen","full_name":"Sun, Qianwen"},{"full_name":"Kang, Hunseung","last_name":"Kang","first_name":"Hunseung"},{"first_name":"Federico D","full_name":"Ariel, Federico D","last_name":"Ariel"},{"last_name":"Crespi","first_name":"Martin","full_name":"Crespi, Martin"},{"first_name":"Axel J","full_name":"Giudicatti, Axel J","last_name":"Giudicatti"},{"first_name":"Qiang","full_name":"Cai, Qiang","last_name":"Cai"},{"first_name":"Hailing","full_name":"Jin, Hailing","last_name":"Jin"},{"last_name":"Feng","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234"},{"first_name":"Yijun","full_name":"Qi, Yijun","last_name":"Qi"},{"full_name":"Pikaard, Craig S","first_name":"Craig S","last_name":"Pikaard"}],"external_id":{"pmid":["36477566"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plcell/koac346"}],"department":[{"_id":"XiFe"}],"title":"Beyond transcription: compelling open questions in plant RNA biology"},{"external_id":{"isi":["000944921600001"]},"author":[{"full_name":"Lyons, David B.","last_name":"Lyons","first_name":"David B."},{"first_name":"Amy","full_name":"Briffa, Amy","last_name":"Briffa"},{"full_name":"He, Shengbo","first_name":"Shengbo","last_name":"He"},{"first_name":"Jaemyung","full_name":"Choi, Jaemyung","last_name":"Choi"},{"full_name":"Hollwey, Elizabeth","first_name":"Elizabeth","last_name":"Hollwey","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"first_name":"Jack","full_name":"Colicchio, Jack","last_name":"Colicchio"},{"last_name":"Anderson","first_name":"Ian","full_name":"Anderson, Ian"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234"},{"full_name":"Howard, Martin","last_name":"Howard","first_name":"Martin"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman"}],"title":"Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"file":[{"date_updated":"2023-05-11T10:41:42Z","relation":"main_file","access_level":"open_access","date_created":"2023-05-11T10:41:42Z","creator":"kschuh","checksum":"6cbc44fdb18bf18834c9e2a5b9c67123","file_id":"12941","success":1,"file_name":"2023_CellReports_Lyons.pdf","file_size":8401261,"content_type":"application/pdf"}],"scopus_import":"1","corr_author":"1","publication_status":"published","has_accepted_license":"1","article_number":"112132","oa_version":"Published Version","ec_funded":1,"ddc":["580"],"day":"28","abstract":[{"lang":"eng","text":"Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited over many generations. Such inheritance is thought to be mediated by a semiconservative mechanism that produces binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is stably inherited across many generations and is quantitatively associated with transposon expression. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamic balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive de novo methylation."}],"project":[{"grant_number":"725746","_id":"62935a00-2b32-11ec-9570-eff30fa39068","call_identifier":"H2020","name":"Quantitative analysis of DNA methylation maintenance with chromatin"}],"issue":"3","publication":"Cell Reports","date_created":"2023-02-23T09:17:44Z","quality_controlled":"1","publication_identifier":{"eissn":["2211-1247"]},"language":[{"iso":"eng"}],"date_published":"2023-03-28T00:00:00Z","file_date_updated":"2023-05-11T10:41:42Z","citation":{"short":"D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson, X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).","ista":"Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3), 112132.","ama":"Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 2023;42(3). doi:10.1016/j.celrep.2023.112132","chicago":"Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey, Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.","ieee":"D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons,” Cell Reports, vol. 42, no. 3. Elsevier, 2023.","mla":"Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no. 3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132.","apa":"Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman, D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132"},"oa":1,"month":"03","article_processing_charge":"Yes","volume":42,"intvolume":" 42","date_updated":"2025-04-14T07:57:43Z","publisher":"Elsevier","status":"public","type":"journal_article","doi":"10.1016/j.celrep.2023.112132","acknowledgement":"The authors would like to thank Jasper Rine for advice and mentorship to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from the Helen Hay Whitney Foundation to D.B.L.","year":"2023","_id":"12672","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original"},{"publication_status":"published","corr_author":"1","scopus_import":"1","article_number":"e202219314","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/dancing-styles-of-atoms/","description":"News on ISTA website"}],"record":[{"relation":"research_data","status":"public","id":"12497"},{"relation":"other","status":"public","id":"14861"}]},"has_accepted_license":"1","oa_version":"Published Version","publication":"Angewandte Chemie International Edition","issue":"19","ddc":["540"],"abstract":[{"lang":"eng","text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture."}],"day":"01","external_id":{"pmid":["36738230"],"isi":["000956919900001"]},"author":[{"full_name":"Becker, Lea Marie","last_name":"Becker","first_name":"Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","orcid":"0000-0002-6401-5151"},{"full_name":"Berbon, Mélanie","first_name":"Mélanie","last_name":"Berbon"},{"full_name":"Vallet, Alicia","first_name":"Alicia","last_name":"Vallet"},{"last_name":"Grelard","full_name":"Grelard, Axelle","first_name":"Axelle"},{"full_name":"Morvan, Estelle","first_name":"Estelle","last_name":"Morvan"},{"full_name":"Bardiaux, Benjamin","last_name":"Bardiaux","first_name":"Benjamin"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"first_name":"Matthias","full_name":"Ernst, Matthias","last_name":"Ernst"},{"full_name":"Loquet, Antoine","first_name":"Antoine","last_name":"Loquet"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"title":"The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues","file":[{"file_size":1422445,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2023-08-16T12:33:31Z","date_created":"2023-08-16T12:33:31Z","checksum":"7dd083ed8850faa55c34e411ed390de9","file_id":"14072","creator":"dernst","success":1,"file_name":"2023_AngewChemInt_Becker.pdf"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"date_updated":"2024-10-21T06:01:38Z","type":"journal_article","publisher":"Wiley","keyword":["General Chemistry","Catalysis"],"status":"public","intvolume":" 62","acknowledgement":"We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University.","doi":"10.1002/anie.202219314","_id":"12675","year":"2023","pmid":1,"isi":1,"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-02-24T10:45:01Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"file_date_updated":"2023-08-16T12:33:31Z","date_published":"2023-05-01T00:00:00Z","oa":1,"volume":62,"month":"05","article_processing_charge":"Yes (via OA deal)","citation":{"chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202219314.","ama":"Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 2023;62(19). doi:10.1002/anie.202219314","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202219314","ieee":"L. M. Becker et al., “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” Angewandte Chemie International Edition, vol. 62, no. 19. Wiley, 2023.","mla":"Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202219314, Wiley, 2023, doi:10.1002/anie.202219314.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023)."}},{"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","last_name":"Meggendorfer","orcid":"0000-0002-1712-2165"},{"orcid":"0000-0001-5103-038X","last_name":"Saona Urmeneta","first_name":"Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","full_name":"Saona Urmeneta, Raimundo J"},{"last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267"}],"title":"Faster algorithm for turn-based stochastic games with bounded treewidth","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1137/1.9781611977554.ch173"}],"corr_author":"1","publication_status":"published","oa_version":"Published Version","ec_funded":1,"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth."}],"day":"01","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","conference":{"start_date":"2023-01-22","location":"Florence, Italy","name":"SODA: Symposium on Discrete Algorithms","end_date":"2023-01-25"},"date_created":"2023-02-24T12:20:47Z","publication_identifier":{"isbn":["9781611977554"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2023-02-01T00:00:00Z","citation":{"apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173.","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605.","short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605."},"article_processing_charge":"No","month":"02","oa":1,"type":"conference","publisher":"Society for Industrial and Applied Mathematics","status":"public","date_updated":"2025-04-14T07:52:47Z","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","doi":"10.1137/1.9781611977554.ch173","year":"2023","page":"4590-4605","_id":"12676","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]