[{"article_processing_charge":"Yes","author":[{"first_name":"Keiko","full_name":"Nomura, Keiko","last_name":"Nomura"},{"last_name":"Rella","full_name":"Rella, Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","first_name":"Simon"},{"first_name":"Haily","full_name":"Merritt, Haily","last_name":"Merritt"},{"full_name":"Baltussen, Mathieu","last_name":"Baltussen","first_name":"Mathieu"},{"full_name":"Bird, Darcy","last_name":"Bird","first_name":"Darcy"},{"first_name":"Annika","full_name":"Tjuka, Annika","last_name":"Tjuka"},{"last_name":"Falk","full_name":"Falk, Dan","first_name":"Dan"}],"title":"Tipping points of space debris in low earth orbit","citation":{"chicago":"Nomura, Keiko, Simon Rella, Haily Merritt, Mathieu Baltussen, Darcy Bird, Annika Tjuka, and Dan Falk. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons. Ubiquity Press, 2024. https://doi.org/10.5334/ijc.1275.","ista":"Nomura K, Rella S, Merritt H, Baltussen M, Bird D, Tjuka A, Falk D. 2024. Tipping points of space debris in low earth orbit. International Journal of the Commons. 18(1).","mla":"Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.” International Journal of the Commons, vol. 18, no. 1, Ubiquity Press, 2024, doi:10.5334/ijc.1275.","apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., & Falk, D. (2024). Tipping points of space debris in low earth orbit. International Journal of the Commons. Ubiquity Press. https://doi.org/10.5334/ijc.1275","ama":"Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low earth orbit. International Journal of the Commons. 2024;18(1). doi:10.5334/ijc.1275","ieee":"K. Nomura et al., “Tipping points of space debris in low earth orbit,” International Journal of the Commons, vol. 18, no. 1. Ubiquity Press, 2024.","short":"K. Nomura, S. Rella, H. Merritt, M. Baltussen, D. Bird, A. Tjuka, D. Falk, International Journal of the Commons 18 (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2024-01-30T11:58:02Z","date_published":"2024-01-11T00:00:00Z","doi":"10.5334/ijc.1275","year":"2024","has_accepted_license":"1","publication":"International Journal of the Commons","day":"11","oa":1,"publisher":"Ubiquity Press","quality_controlled":"1","acknowledgement":"The authors would like to thank the special issue co-editors, Marco Janssen and Xiao-Shan Yap, and the anonymous reviewers for their comments that helped improve the manuscript. The paper also benefited from suggestions by other author participants in this special issue. We would also like to thank the 2022 Santa Fe Institute Complex Systems Summer School for providing space to initiate this study.","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"file_date_updated":"2024-02-05T10:06:35Z","date_updated":"2024-02-05T10:10:27Z","ddc":["550"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["Sociology and Political Science"],"status":"public","_id":"14901","license":"https://creativecommons.org/licenses/by/4.0/","volume":18,"issue":"1","publication_status":"published","publication_identifier":{"issn":["1875-0281"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1305786,"date_updated":"2024-02-05T10:06:35Z","file_name":"2023_IntJourCommons_Nomura.pdf","date_created":"2024-02-05T10:06:35Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14939","checksum":"b80ebc889033c365d8f8c05a0c655382"}],"scopus_import":"1","intvolume":" 18","month":"01","abstract":[{"lang":"eng","text":"Global services like navigation, communication, and Earth observation have increased dramatically in the 21st century due to advances in outer space industries. But as orbits become increasingly crowded with both satellites and inevitable space debris pollution, continued operations become endangered by the heightened risks of debris collisions in orbit. Kessler Syndrome is the term for when a critical threshold of orbiting debris triggers a runaway positive feedback loop of debris collisions, creating debris congestion that can render orbits unusable. As this potential tipping point becomes more widely recognized, there have been renewed calls for debris mitigation and removal. Here, we combine complex systems and social-ecological systems approaches to study how these efforts may affect space debris accumulation and the likelihood of reaching Kessler Syndrome. Specifically, we model how debris levels are affected by future launch rates, cleanup activities, and collisions between extant debris. We contextualize and interpret our dynamic model within a discussion of existing space debris governance and other social, economic, and geopolitical factors that may influence effective collective management of the orbital commons. In line with previous studies, our model finds that debris congestion may be reached in less than 200 years, though a holistic management strategy combining removal and mitigation actions can avoid such outcomes while continuing space activities. Moreover, although active debris removal may be particularly effective, the current lack of market and governance support may impede its implementation. Research into these critical dynamics and the multi-faceted variables that influence debris outcomes can support policymakers in curating impactful governance strategies and realistic transition pathways to sustaining debris-free orbits. Overall, our study is useful for communicating about space debris sustainability in policy and education settings by providing an exploration of policy portfolio options supported by a simple and clear social-ecological modeling approach."}],"oa_version":"Published Version"},{"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/at:ista:15020","date_published":"2024-02-23T00:00:00Z","date_created":"2024-02-23T14:02:04Z","page":"158","day":"23","has_accepted_license":"1","year":"2024","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"title":"Genetic information and biological optimization","author":[{"first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","full_name":"Hledik, Michal"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria."},"month":"02","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"status":"public","id":"7553","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12081","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7606"}]},"ec_funded":1,"file":[{"date_created":"2024-02-23T13:50:53Z","file_name":"hledik thesis pdfa 2b.pdf","creator":"mhledik","date_updated":"2024-02-23T13:50:53Z","file_size":7102089,"file_id":"15021","checksum":"b2d3da47c98d481577a4baf68944fe41","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"15022","checksum":"eda9b9430da2610fee7ce1c1419a479a","date_updated":"2024-02-23T14:20:16Z","file_size":14014790,"creator":"mhledik","date_created":"2024-02-23T13:50:54Z","file_name":"hledik thesis source.zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","keyword":["Theoretical biology","Optimality","Evolution","Information"],"type":"dissertation","_id":"15020","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2024-02-23T14:20:16Z","ddc":["576","519"],"supervisor":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-06T14:22:52Z"},{"_id":"13127","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-08-07T13:09:09Z","ddc":["570"],"department":[{"_id":"SyCr"},{"_id":"GaTk"}],"file_date_updated":"2023-06-13T08:05:46Z","abstract":[{"text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense.","lang":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 14","month":"06","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-06-13T08:05:46Z","file_size":2358167,"creator":"dernst","date_created":"2023-06-13T08:05:46Z","file_name":"2023_NatureComm_CasillasPerez.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13132","checksum":"4af0393e3ed47b3fc46e68b81c3c1007","success":1}],"ec_funded":1,"volume":14,"related_material":{"record":[{"status":"public","id":"12945","relation":"research_data"}]},"article_number":"3232","project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771402","name":"Epidemics in ant societies on a chip"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012"}],"citation":{"apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., & Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-38947-y","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 2023;14. doi:10.1038/s41467-023-38947-y","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications, vol. 14, 3232, Springer Nature, 2023, doi:10.1038/s41467-023-38947-y.","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-38947-y."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"isi":["001002562700005"],"pmid":["37270641"]},"author":[{"last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7214-0171","full_name":"Bod'Ová, Katarína","last_name":"Bod'Ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V","last_name":"Grasse"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","year":"2023","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"03","date_created":"2023-06-11T22:00:40Z","date_published":"2023-06-03T00:00:00Z","doi":"10.1038/s41467-023-38947-y"},{"citation":{"mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science, vol. 3, Springer Nature, 2023, pp. 254–63, doi:10.1038/s43588-023-00410-9.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. Springer Nature. https://doi.org/10.1038/s43588-023-00410-9","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 2023;3:254-263. doi:10.1038/s43588-023-00410-9","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” Nature Computational Science, vol. 3. Springer Nature, pp. 254–263, 2023.","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” Nature Computational Science. Springer Nature, 2023. https://doi.org/10.1038/s43588-023-00410-9.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249"},{"last_name":"Pepic","full_name":"Pepic, Selver","first_name":"Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"first_name":"Oren","full_name":"Shriki, Oren","last_name":"Shriki"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"arxiv":["2108.06686"]},"title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"has_accepted_license":"1","year":"2023","day":"20","publication":"Nature Computational Science","page":"254-263","doi":"10.1038/s43588-023-00410-9","date_published":"2023-03-20T00:00:00Z","date_created":"2023-03-26T22:01:08Z","acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"date_updated":"2023-08-16T12:41:53Z","ddc":["570"],"department":[{"_id":"GaTk"},{"_id":"GradSch"}],"file_date_updated":"2023-08-16T12:39:57Z","_id":"12762","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["2662-8457"]},"publication_status":"published","file":[{"file_name":"2023_NatureCompScience_Lombardi.pdf","date_created":"2023-08-16T12:39:57Z","creator":"dernst","file_size":4474284,"date_updated":"2023-08-16T12:39:57Z","success":1,"file_id":"14073","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":3,"ec_funded":1,"abstract":[{"text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 3"},{"day":"26","publication":"Physical Review X","has_accepted_license":"1","year":"2023","date_published":"2023-10-26T00:00:00Z","doi":"10.1103/PhysRevX.13.041017","date_created":"2023-11-12T23:00:55Z","acknowledgement":"We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis, and Daan Frenkel for useful discussions and a careful reading of the manuscript, and we thank Age Tjalma for support with obtaining the Gaussian approximation of the chemotaxis system. This work is part of the Dutch Research Council (NWO) and was performed at the research institute AMOLF. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant (024.003.019).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 2023;13(4). doi:10.1103/PhysRevX.13.041017","apa":"Reinhardt, M., Tkačik, G., & Ten Wolde, P. R. (2023). Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.13.041017","ieee":"M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” Physical Review X, vol. 13, no. 4. American Physical Society, 2023.","short":"M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).","mla":"Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:10.1103/PhysRevX.13.041017.","ista":"Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 13(4), 041017.","chicago":"Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” Physical Review X. American Physical Society, 2023. https://doi.org/10.1103/PhysRevX.13.041017."},"title":"Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories","author":[{"first_name":"Manuel","last_name":"Reinhardt","full_name":"Reinhardt, Manuel"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"},{"last_name":"Ten Wolde","full_name":"Ten Wolde, Pieter Rein","first_name":"Pieter Rein"}],"external_id":{"arxiv":["2203.03461"]},"article_processing_charge":"Yes","article_number":"041017","file":[{"creator":"dernst","date_updated":"2023-11-13T09:00:19Z","file_size":1595223,"date_created":"2023-11-13T09:00:19Z","file_name":"2023_PhysReviewX_Reinhardt.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"32574aeebcca7347a4152c611b66b3d5","file_id":"14522","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2160-3308"]},"publication_status":"published","issue":"4","volume":13,"oa_version":"Published Version","abstract":[{"text":"Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger.","lang":"eng"}],"month":"10","intvolume":" 13","scopus_import":"1","ddc":["530"],"date_updated":"2023-11-13T09:03:30Z","file_date_updated":"2023-11-13T09:00:19Z","department":[{"_id":"GaTk"}],"_id":"14515","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"14656","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"file_date_updated":"2023-12-11T11:30:37Z","date_updated":"2023-12-11T11:37:20Z","ddc":["570"],"main_file_link":[{"url":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023","open_access":"1"}],"scopus_import":"1","intvolume":" 43","month":"11","abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"pmid":1,"oa_version":"Published Version","ec_funded":1,"issue":"48","volume":43,"publication_status":"published","publication_identifier":{"eissn":["1529-2401"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf","embargo":"2024-06-01","checksum":"e2503c8f84be1050e28f64320f1d5bd2","file_id":"14674","creator":"dernst","file_size":2280632,"date_updated":"2023-12-11T11:30:37Z","file_name":"2023_JourNeuroscience_Nardin.pdf","date_created":"2023-12-11T11:30:37Z"}],"project":[{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"external_id":{"pmid":["37758476"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Nardin","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele"},{"last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","citation":{"ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. Society of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Society of Neuroscience","acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","page":"8140-8156","date_created":"2023-12-10T23:00:58Z","date_published":"2023-11-29T00:00:00Z","doi":"10.1523/JNEUROSCI.0194-23.2023","year":"2023","has_accepted_license":"1","publication":"The Journal of Neuroscience","day":"29"},{"date_updated":"2023-12-13T11:11:24Z","ddc":["570"],"file_date_updated":"2023-10-09T07:23:46Z","department":[{"_id":"GaTk"}],"_id":"12487","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["2589-0042"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_iScience_Scarpetta.pdf","date_created":"2023-10-09T07:23:46Z","file_size":4872708,"date_updated":"2023-10-09T07:23:46Z","creator":"dernst","success":1,"file_id":"14412","checksum":"f499836af172ecc9865de4bb41fa99d1","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"ec_funded":1,"issue":"10","volume":26,"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."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 26","month":"10","citation":{"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","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","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"article_processing_charge":"Yes","author":[{"first_name":"Silvia","full_name":"Scarpetta, Silvia","last_name":"Scarpetta"},{"first_name":"Niccolò","full_name":"Morrisi, Niccolò","last_name":"Morrisi"},{"full_name":"Mutti, Carlotta","last_name":"Mutti","first_name":"Carlotta"},{"last_name":"Azzi","full_name":"Azzi, Nicoletta","first_name":"Nicoletta"},{"first_name":"Irene","full_name":"Trippi, Irene","last_name":"Trippi"},{"first_name":"Rosario","last_name":"Ciliento","full_name":"Ciliento, Rosario"},{"first_name":"Ilenia","full_name":"Apicella, Ilenia","last_name":"Apicella"},{"first_name":"Giovanni","full_name":"Messuti, Giovanni","last_name":"Messuti"},{"first_name":"Marianna","last_name":"Angiolelli","full_name":"Angiolelli, Marianna"},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi"},{"full_name":"Parrino, Liborio","last_name":"Parrino","first_name":"Liborio"},{"full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano","first_name":"Anna Elisabetta"}],"title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"}],"year":"2023","isi":1,"has_accepted_license":"1","publication":"iScience","day":"20","page":"107840","date_created":"2023-02-02T10:50:17Z","doi":"10.1016/j.isci.2023.107840","date_published":"2023-10-20T00:00:00Z","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.","oa":1,"quality_controlled":"1","publisher":"Elsevier"},{"article_number":"ckad160.597","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” European Journal of Public Health, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597.","short":"S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.","ieee":"S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. Supplement_2.","ama":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: European Journal of Public Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597","apa":"Rella, S., Kulikova, Y., Minnegalieva, A., & Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In European Journal of Public Health (Vol. 33). Oxford University Press. https://doi.org/10.1093/eurpub/ckad160.597","chicago":"Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597.","ista":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597."},"title":"Complex vaccination strategies prevent the emergence of vaccine resistance","author":[{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","first_name":"Simon","full_name":"Rella, Simon","last_name":"Rella"},{"full_name":"Kulikova, Y","last_name":"Kulikova","first_name":"Y"},{"first_name":"Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","full_name":"Minnegalieva, Aygul","last_name":"Minnegalieva"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"article_processing_charge":"No","quality_controlled":"1","publisher":"Oxford University Press","oa":1,"day":"01","publication":"European Journal of Public Health","has_accepted_license":"1","year":"2023","doi":"10.1093/eurpub/ckad160.597","date_published":"2023-10-01T00:00:00Z","date_created":"2024-01-22T12:02:28Z","_id":"14862","status":"public","keyword":["Public Health","Environmental and Occupational Health"],"type":"conference_abstract","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"ddc":["570"],"date_updated":"2024-01-24T11:16:09Z","department":[{"_id":"GaTk"}],"file_date_updated":"2024-01-24T11:12:33Z","oa_version":"Published Version","month":"10","intvolume":" 33","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14882","checksum":"98706755bb4cc5d553818ade7660a7d2","creator":"dernst","file_size":71057,"date_updated":"2024-01-24T11:12:33Z","file_name":"2023_EurJourPublicHealth_Rella.pdf","date_created":"2024-01-24T11:12:33Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1101-1262"],"eissn":["1464-360X"]},"publication_status":"published","volume":33,"issue":"Supplement_2","license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"article_number":"113162","project":[{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 42(10), 113162.","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113162.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).","ieee":"F. Lombardi et al., “Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state,” Cell Reports, vol. 42, no. 10. Elsevier, 2023.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113162","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 2023;42(10). doi:10.1016/j.celrep.2023.113162","mla":"Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” Cell Reports, vol. 42, no. 10, 113162, Elsevier, 2023, doi:10.1016/j.celrep.2023.113162."},"title":"Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state","article_processing_charge":"Yes","external_id":{"pmid":["37777965"],"isi":["001086695500001"]},"author":[{"first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","last_name":"Lombardi"},{"first_name":"Hans J.","full_name":"Herrmann, Hans J.","last_name":"Herrmann"},{"last_name":"Parrino","full_name":"Parrino, Liborio","first_name":"Liborio"},{"full_name":"Plenz, Dietmar","last_name":"Plenz","first_name":"Dietmar"},{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano","first_name":"Anna Elisabetta"},{"full_name":"De Arcangelis, Lucilla","last_name":"De Arcangelis","first_name":"Lucilla"},{"first_name":"Oren","full_name":"Shriki, Oren","last_name":"Shriki"}],"acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP [brain criticality and information processing]). L.d.A. acknowledges support from the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU (NGEU) funded by the Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022). O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The work was supported in part by DIRP ZIAMH02797 (to D.P.).","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Cell Reports","day":"31","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-10-08T22:01:15Z","date_published":"2023-10-31T00:00:00Z","doi":"10.1016/j.celrep.2023.113162","_id":"14402","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"date_updated":"2024-01-30T14:07:40Z","department":[{"_id":"GaTk"}],"file_date_updated":"2024-01-30T14:07:08Z","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition).","lang":"eng"}],"intvolume":" 42","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2024-01-30T14:07:08Z","file_name":"2023_CellReports_Lombardi.pdf","creator":"dernst","date_updated":"2024-01-30T14:07:08Z","file_size":5599007,"checksum":"9c71eb2a03aa160415f01ad95f49ceb5","file_id":"14914","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2211-1247"]},"ec_funded":1,"volume":42,"issue":"10"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis L, Shriki O. 2022. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv, 10.1101/2022.03.03.482657.","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2022.03.03.482657.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2022). Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.03.03.482657","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv. 2022. doi:10.1101/2022.03.03.482657","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022).","ieee":"F. Lombardi et al., “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” bioRxiv. Cold Spring Harbor Laboratory, 2022.","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” BioRxiv, Cold Spring Harbor Laboratory, 2022, doi:10.1101/2022.03.03.482657."},"date_updated":"2022-03-07T07:28:34Z","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","department":[{"_id":"GaTk"}],"article_processing_charge":"No","author":[{"last_name":"Lombardi","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Hans J.","last_name":"Herrmann","full_name":"Herrmann, Hans J."},{"full_name":"Parrino, Liborio","last_name":"Parrino","first_name":"Liborio"},{"first_name":"Dietmar","full_name":"Plenz, Dietmar","last_name":"Plenz"},{"first_name":"Silvia","last_name":"Scarpetta","full_name":"Scarpetta, Silvia"},{"full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano","first_name":"Anna Elisabetta"},{"full_name":"de Arcangelis, Lucilla","last_name":"de Arcangelis","first_name":"Lucilla"},{"last_name":"Shriki","full_name":"Shriki, Oren","first_name":"Oren"}],"_id":"10821","status":"public","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"type":"preprint","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"04","year":"2022","publication_status":"published","date_created":"2022-03-04T22:20:59Z","ec_funded":1,"doi":"10.1101/2022.03.03.482657","date_published":"2022-03-04T00:00:00Z","page":"25","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and the project E-PASSION of the program VALERE 2019 funded by the University of Campania, Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation, Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the \"waxing and waning\" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the \"waxing and waning\" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales."}],"month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.03.482657"}],"oa":1,"publisher":"Cold Spring Harbor Laboratory"}]