[{"issue":"1","author":[{"full_name":"Nomura, Keiko","last_name":"Nomura","first_name":"Keiko"},{"last_name":"Rella","first_name":"Simon","full_name":"Rella, Simon","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425"},{"full_name":"Merritt, Haily","last_name":"Merritt","first_name":"Haily"},{"full_name":"Baltussen, Mathieu","last_name":"Baltussen","first_name":"Mathieu"},{"full_name":"Bird, Darcy","first_name":"Darcy","last_name":"Bird"},{"full_name":"Tjuka, Annika","last_name":"Tjuka","first_name":"Annika"},{"last_name":"Falk","first_name":"Dan","full_name":"Falk, Dan"}],"scopus_import":"1","_id":"14901","intvolume":"        18","title":"Tipping points of space debris in low earth orbit","date_created":"2024-01-30T11:58:02Z","department":[{"_id":"GradSch"},{"_id":"GaTk"}],"article_processing_charge":"Yes","publication_status":"published","file_date_updated":"2024-02-05T10:06:35Z","quality_controlled":"1","article_type":"original","publisher":"Ubiquity Press","citation":{"apa":"Nomura, K., Rella, S., Merritt, H., Baltussen, M., Bird, D., Tjuka, A., &#38; Falk, D. (2024). Tipping points of space debris in low earth orbit. <i>International Journal of the Commons</i>. Ubiquity Press. <a href=\"https://doi.org/10.5334/ijc.1275\">https://doi.org/10.5334/ijc.1275</a>","ama":"Nomura K, Rella S, Merritt H, et al. Tipping points of space debris in low earth orbit. <i>International Journal of the Commons</i>. 2024;18(1). doi:<a href=\"https://doi.org/10.5334/ijc.1275\">10.5334/ijc.1275</a>","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.” <i>International Journal of the Commons</i>. Ubiquity Press, 2024. <a href=\"https://doi.org/10.5334/ijc.1275\">https://doi.org/10.5334/ijc.1275</a>.","ieee":"K. Nomura <i>et al.</i>, “Tipping points of space debris in low earth orbit,” <i>International Journal of the Commons</i>, 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).","mla":"Nomura, Keiko, et al. “Tipping Points of Space Debris in Low Earth Orbit.” <i>International Journal of the Commons</i>, vol. 18, no. 1, Ubiquity Press, 2024, doi:<a href=\"https://doi.org/10.5334/ijc.1275\">10.5334/ijc.1275</a>.","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)."},"year":"2024","date_updated":"2024-02-05T10:10:27Z","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."}],"day":"11","doi":"10.5334/ijc.1275","ddc":["550"],"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.","volume":18,"has_accepted_license":"1","publication":"International Journal of the Commons","month":"01","oa_version":"Published Version","keyword":["Sociology and Political Science"],"language":[{"iso":"eng"}],"type":"journal_article","date_published":"2024-01-11T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["1875-0281"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2024-02-05T10:06:35Z","file_name":"2023_IntJourCommons_Nomura.pdf","content_type":"application/pdf","date_created":"2024-02-05T10:06:35Z","file_size":1305786,"checksum":"b80ebc889033c365d8f8c05a0c655382","file_id":"14939","creator":"dernst","access_level":"open_access","relation":"main_file","success":1}]},{"ddc":["576","519"],"year":"2024","citation":{"ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>.","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. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>.","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>"},"date_updated":"2025-06-30T13:21:09Z","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"}],"day":"23","doi":"10.15479/at:ista:15020","file_date_updated":"2024-02-23T14:20:16Z","ec_funded":1,"page":"158","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Hledik, Michal","first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87"}],"_id":"15020","title":"Genetic information and biological optimization","alternative_title":["ISTA Thesis"],"date_created":"2024-02-23T14:02:04Z","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"article_processing_charge":"No","publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"7553","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"7606","status":"public"},{"id":"12081","relation":"part_of_dissertation","status":"public"}]},"file":[{"date_created":"2024-02-23T13:50:53Z","file_size":7102089,"checksum":"b2d3da47c98d481577a4baf68944fe41","date_updated":"2024-02-23T13:50:53Z","file_name":"hledik thesis pdfa 2b.pdf","content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","file_id":"15021","creator":"mhledik"},{"date_updated":"2024-02-23T14:20:16Z","file_name":"hledik thesis source.zip","content_type":"application/zip","date_created":"2024-02-23T13:50:54Z","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_size":14014790,"file_id":"15022","creator":"mhledik","relation":"source_file","access_level":"closed"}],"type":"dissertation","date_published":"2024-02-23T00:00:00Z","oa":1,"supervisor":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663 - 337X"]},"keyword":["Theoretical biology","Optimality","Evolution","Information"],"language":[{"iso":"eng"}],"has_accepted_license":"1","month":"02","project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327","name":"Understanding the evolution of continuous genomes"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version"},{"language":[{"iso":"eng"}],"publication":"Cell Reports","has_accepted_license":"1","month":"10","article_number":"113162","oa_version":"Published Version","project":[{"grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"file_id":"14914","creator":"dernst","success":1,"relation":"main_file","access_level":"open_access","date_updated":"2024-01-30T14:07:08Z","file_name":"2023_CellReports_Lombardi.pdf","content_type":"application/pdf","date_created":"2024-01-30T14:07:08Z","checksum":"9c71eb2a03aa160415f01ad95f49ceb5","file_size":5599007}],"date_published":"2023-10-31T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2211-1247"]},"file_date_updated":"2024-01-30T14:07:08Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Elsevier","author":[{"orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"full_name":"Herrmann, Hans J.","last_name":"Herrmann","first_name":"Hans J."},{"last_name":"Parrino","first_name":"Liborio","full_name":"Parrino, Liborio"},{"full_name":"Plenz, Dietmar","first_name":"Dietmar","last_name":"Plenz"},{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"first_name":"Anna Elisabetta","last_name":"Vaudano","full_name":"Vaudano, Anna Elisabetta"},{"full_name":"De Arcangelis, Lucilla","last_name":"De Arcangelis","first_name":"Lucilla"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"}],"issue":"10","pmid":1,"_id":"14402","scopus_import":"1","title":"Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state","intvolume":"        42","publication_status":"published","date_created":"2023-10-08T22:01:15Z","article_processing_charge":"Yes","department":[{"_id":"GaTk"}],"ddc":["570"],"volume":42,"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.).","isi":1,"external_id":{"pmid":["37777965"],"isi":["001086695500001"]},"date_updated":"2024-01-30T14:07:40Z","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.","mla":"Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” <i>Cell Reports</i>, vol. 42, no. 10, 113162, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">10.1016/j.celrep.2023.113162</a>.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).","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.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">https://doi.org/10.1016/j.celrep.2023.113162</a>.","ieee":"F. Lombardi <i>et al.</i>, “Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state,” <i>Cell Reports</i>, 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. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">https://doi.org/10.1016/j.celrep.2023.113162</a>","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. <i>Cell Reports</i>. 2023;42(10). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">10.1016/j.celrep.2023.113162</a>"},"year":"2023","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"}],"doi":"10.1016/j.celrep.2023.113162","day":"31"},{"oa":1,"publication_identifier":{"eissn":["2160-3308"]},"date_published":"2023-10-26T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-11-13T09:00:19Z","content_type":"application/pdf","file_name":"2023_PhysReviewX_Reinhardt.pdf","date_created":"2023-11-13T09:00:19Z","checksum":"32574aeebcca7347a4152c611b66b3d5","file_size":1595223,"file_id":"14522","creator":"dernst","access_level":"open_access","relation":"main_file","success":1}],"month":"10","article_number":"041017","oa_version":"Published Version","publication":"Physical Review X","has_accepted_license":"1","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"doi":"10.1103/PhysRevX.13.041017","arxiv":1,"day":"26","external_id":{"arxiv":["2203.03461"]},"date_updated":"2023-11-13T09:03:30Z","citation":{"mla":"Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” <i>Physical Review X</i>, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">10.1103/PhysRevX.13.041017</a>.","short":"M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).","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.","apa":"Reinhardt, M., Tkačik, G., &#38; Ten Wolde, P. R. (2023). Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">https://doi.org/10.1103/PhysRevX.13.041017</a>","ama":"Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. <i>Physical Review X</i>. 2023;13(4). doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">10.1103/PhysRevX.13.041017</a>","ieee":"M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” <i>Physical Review X</i>, vol. 13, no. 4. American Physical Society, 2023.","chicago":"Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” <i>Physical Review X</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">https://doi.org/10.1103/PhysRevX.13.041017</a>."},"year":"2023","ddc":["530"],"volume":13,"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).","title":"Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories","intvolume":"        13","publication_status":"published","article_processing_charge":"Yes","date_created":"2023-11-12T23:00:55Z","department":[{"_id":"GaTk"}],"author":[{"first_name":"Manuel","last_name":"Reinhardt","full_name":"Reinhardt, Manuel"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"full_name":"Ten Wolde, Pieter Rein","last_name":"Ten Wolde","first_name":"Pieter Rein"}],"issue":"4","_id":"14515","scopus_import":"1","article_type":"original","publisher":"American Physical Society","file_date_updated":"2023-11-13T09:00:19Z","quality_controlled":"1"},{"external_id":{"pmid":["37758476"]},"date_updated":"2023-12-11T11:37:20Z","year":"2023","citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. 2023;43(48):8140-8156. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. Society of Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>. Society of Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>The Journal of Neuroscience</i>, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","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."},"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."}],"doi":"10.1523/JNEUROSCI.0194-23.2023","day":"29","ddc":["570"],"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.","volume":43,"author":[{"last_name":"Nardin","first_name":"Michele","full_name":"Nardin, Michele","orcid":"0000-0001-8849-6570","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina","first_name":"Cristina","last_name":"Savin"}],"issue":"48","pmid":1,"_id":"14656","scopus_import":"1","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","intvolume":"        43","publication_status":"published","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2023-12-10T23:00:58Z","file_date_updated":"2023-12-11T11:30:37Z","page":"8140-8156","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"Society of Neuroscience","date_published":"2023-11-29T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["1529-2401"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023"}],"file":[{"file_name":"2023_JourNeuroscience_Nardin.pdf","content_type":"application/pdf","date_updated":"2023-12-11T11:30:37Z","file_size":2280632,"checksum":"e2503c8f84be1050e28f64320f1d5bd2","embargo_to":"open_access","embargo":"2024-06-01","date_created":"2023-12-11T11:30:37Z","creator":"dernst","file_id":"14674","access_level":"closed","relation":"main_file"}],"publication":"The Journal of Neuroscience","has_accepted_license":"1","month":"11","oa_version":"Published Version","project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}]},{"file":[{"creator":"dernst","file_id":"14882","access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"2023_EurJourPublicHealth_Rella.pdf","date_updated":"2024-01-24T11:12:33Z","file_size":71057,"checksum":"98706755bb4cc5d553818ade7660a7d2","date_created":"2024-01-24T11:12:33Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"type":"conference_abstract","date_published":"2023-10-01T00:00:00Z","publication_identifier":{"eissn":["1464-360X"],"issn":["1101-1262"]},"oa":1,"keyword":["Public Health","Environmental and Occupational Health"],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"European Journal of Public Health","oa_version":"Published Version","article_number":"ckad160.597","month":"10","volume":33,"ddc":["570"],"year":"2023","citation":{"apa":"Rella, S., Kulikova, Y., Minnegalieva, A., &#38; Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In <i>European Journal of Public Health</i> (Vol. 33). Oxford University Press. <a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">https://doi.org/10.1093/eurpub/ckad160.597</a>","ama":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: <i>European Journal of Public Health</i>. Vol 33. Oxford University Press; 2023. doi:<a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">10.1093/eurpub/ckad160.597</a>","chicago":"Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In <i>European Journal of Public Health</i>, Vol. 33. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">https://doi.org/10.1093/eurpub/ckad160.597</a>.","ieee":"S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in <i>European Journal of Public Health</i>, 2023, vol. 33, no. Supplement_2.","mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” <i>European Journal of Public Health</i>, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">10.1093/eurpub/ckad160.597</a>.","short":"S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.","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."},"date_updated":"2024-01-24T11:16:09Z","day":"01","doi":"10.1093/eurpub/ckad160.597","quality_controlled":"1","file_date_updated":"2024-01-24T11:12:33Z","publisher":"Oxford University Press","_id":"14862","issue":"Supplement_2","author":[{"id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon","last_name":"Rella","first_name":"Simon"},{"last_name":"Kulikova","first_name":"Y","full_name":"Kulikova, Y"},{"full_name":"Minnegalieva, Aygul","last_name":"Minnegalieva","first_name":"Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E"},{"last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-01-22T12:02:28Z","article_processing_charge":"No","department":[{"_id":"GaTk"}],"publication_status":"published","intvolume":"        33","title":"Complex vaccination strategies prevent the emergence of vaccine resistance"},{"quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-06-13T08:05:46Z","publisher":"Springer Nature","article_type":"original","scopus_import":"1","_id":"13127","pmid":1,"author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'Ová, Katarína","orcid":"0000-0002-7214-0171","last_name":"Bod'Ová","first_name":"Katarína"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse"},{"orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2023-06-11T22:00:40Z","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"article_processing_charge":"Yes","publication_status":"published","intvolume":"        14","title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","volume":14,"acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","ddc":["570"],"year":"2023","citation":{"ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>, vol. 14, 3232, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>.","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>.","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., &#38; Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>"},"date_updated":"2023-08-07T13:09:09Z","external_id":{"pmid":["37270641"],"isi":["001002562700005"]},"isi":1,"day":"03","doi":"10.1038/s41467-023-38947-y","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"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Nature Communications","project":[{"call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","grant_number":"771402","name":"Epidemics in ant societies on a chip"},{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"oa_version":"Published Version","article_number":"3232","month":"06","file":[{"checksum":"4af0393e3ed47b3fc46e68b81c3c1007","file_size":2358167,"date_created":"2023-06-13T08:05:46Z","content_type":"application/pdf","file_name":"2023_NatureComm_CasillasPerez.pdf","date_updated":"2023-06-13T08:05:46Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"13132"}],"related_material":{"record":[{"status":"public","id":"12945","relation":"research_data"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2023-06-03T00:00:00Z","publication_identifier":{"eissn":["2041-1723"]},"oa":1},{"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.","volume":26,"ddc":["570"],"doi":"10.1016/j.isci.2023.107840","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.</jats:p><jats:sec><jats:title>Significance statement</jats:title><jats:p>We 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."}],"date_updated":"2023-12-13T11:11:24Z","year":"2023","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. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107840\">https://doi.org/10.1016/j.isci.2023.107840</a>","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. <i>iScience</i>. 2023;26(10):107840. doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107840\">10.1016/j.isci.2023.107840</a>","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.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107840\">https://doi.org/10.1016/j.isci.2023.107840</a>.","ieee":"S. Scarpetta <i>et al.</i>, “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” <i>iScience</i>, vol. 26, no. 10. Elsevier, p. 107840, 2023.","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.","mla":"Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” <i>IScience</i>, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107840\">10.1016/j.isci.2023.107840</a>.","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."},"isi":1,"external_id":{"isi":["001082331200001"],"pmid":["37766992"]},"publisher":"Elsevier","article_type":"original","page":"107840","quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-10-09T07:23:46Z","publication_status":"published","date_created":"2023-02-02T10:50:17Z","article_processing_charge":"Yes","department":[{"_id":"GaTk"}],"title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","intvolume":"        26","_id":"12487","pmid":1,"scopus_import":"1","author":[{"last_name":"Scarpetta","first_name":"Silvia","full_name":"Scarpetta, Silvia"},{"last_name":"Morrisi","first_name":"Niccolò","full_name":"Morrisi, Niccolò"},{"full_name":"Mutti, Carlotta","last_name":"Mutti","first_name":"Carlotta"},{"full_name":"Azzi, Nicoletta","last_name":"Azzi","first_name":"Nicoletta"},{"first_name":"Irene","last_name":"Trippi","full_name":"Trippi, Irene"},{"full_name":"Ciliento, Rosario","last_name":"Ciliento","first_name":"Rosario"},{"full_name":"Apicella, Ilenia","last_name":"Apicella","first_name":"Ilenia"},{"last_name":"Messuti","first_name":"Giovanni","full_name":"Messuti, Giovanni"},{"last_name":"Angiolelli","first_name":"Marianna","full_name":"Angiolelli, Marianna"},{"full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"last_name":"Parrino","first_name":"Liborio","full_name":"Parrino, Liborio"},{"last_name":"Vaudano","first_name":"Anna Elisabetta","full_name":"Vaudano, Anna Elisabetta"}],"issue":"10","file":[{"access_level":"open_access","success":1,"relation":"main_file","file_id":"14412","creator":"dernst","date_created":"2023-10-09T07:23:46Z","checksum":"f499836af172ecc9865de4bb41fa99d1","file_size":4872708,"date_updated":"2023-10-09T07:23:46Z","content_type":"application/pdf","file_name":"2023_iScience_Scarpetta.pdf"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2589-0042"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2023-10-20T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"}],"month":"10","publication":"iScience","has_accepted_license":"1"},{"title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","intvolume":"         3","publication_status":"published","date_created":"2023-03-26T22:01:08Z","article_processing_charge":"No","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"author":[{"last_name":"Lombardi","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"last_name":"Pepic","first_name":"Selver","full_name":"Pepic, Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"last_name":"Shriki","first_name":"Oren","full_name":"Shriki, Oren"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"_id":"12762","scopus_import":"1","article_type":"original","publisher":"Springer Nature","file_date_updated":"2023-08-16T12:39:57Z","page":"254-263","quality_controlled":"1","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"}],"doi":"10.1038/s43588-023-00410-9","arxiv":1,"day":"20","external_id":{"arxiv":["2108.06686"]},"date_updated":"2023-08-16T12:41:53Z","year":"2023","citation":{"short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263.","mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>, vol. 3, Springer Nature, 2023, pp. 254–63, doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263.","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. 2023;3:254-263. doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., &#38; De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>","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.” <i>Nature Computational Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>.","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,” <i>Nature Computational Science</i>, vol. 3. Springer Nature, pp. 254–263, 2023."},"ddc":["570"],"volume":3,"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.).","month":"03","oa_version":"Published Version","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"publication":"Nature Computational Science","has_accepted_license":"1","language":[{"iso":"eng"}],"oa":1,"publication_identifier":{"eissn":["2662-8457"]},"date_published":"2023-03-20T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","success":1,"access_level":"open_access","file_id":"14073","creator":"dernst","date_created":"2023-08-16T12:39:57Z","file_size":4474284,"checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","date_updated":"2023-08-16T12:39:57Z","file_name":"2023_NatureCompScience_Lombardi.pdf","content_type":"application/pdf"}]},{"date_published":"2022-01-26T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"eissn":["2050-084X"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"relation":"main_file","access_level":"open_access","creator":"cchlebak","file_id":"10739","file_size":5604343,"checksum":"decdcdf600ff51e9a9703b49ca114170","date_created":"2022-02-07T07:14:09Z","content_type":"application/pdf","file_name":"2022_ELife_Lagator.pdf","date_updated":"2022-02-07T07:14:09Z"}],"publication":"eLife","has_accepted_license":"1","month":"01","article_number":"e64543","oa_version":"Published Version","project":[{"name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"isi":1,"external_id":{"isi":["000751104400001"],"pmid":["35080492"]},"date_updated":"2023-08-02T14:09:02Z","citation":{"apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., &#38; Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>","ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>","ieee":"M. Lagator <i>et al.</i>, “Predicting bacterial promoter function and evolution from random sequences,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>, vol. 11, e64543, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>.","ista":"Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543."},"year":"2022","abstract":[{"lang":"eng","text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought."}],"doi":"10.7554/eLife.64543","day":"26","ddc":["576"],"acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","volume":11,"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","last_name":"Sarikas","first_name":"Srdjan","full_name":"Sarikas, Srdjan"},{"last_name":"Steinrueck","first_name":"Magdalena","full_name":"Steinrueck, Magdalena"},{"full_name":"Toledo-Aparicio, David","last_name":"Toledo-Aparicio","first_name":"David"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"_id":"10736","scopus_import":"1","title":"Predicting bacterial promoter function and evolution from random sequences","intvolume":"        11","publication_status":"published","date_created":"2022-02-06T23:01:32Z","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"article_processing_charge":"No","file_date_updated":"2022-02-07T07:14:09Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"eLife Sciences Publications"},{"language":[{"iso":"eng"}],"page":"25","ec_funded":1,"publisher":"Cold Spring Harbor Laboratory","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi","first_name":"Fabrizio"},{"full_name":"Herrmann, Hans J.","last_name":"Herrmann","first_name":"Hans J."},{"last_name":"Parrino","first_name":"Liborio","full_name":"Parrino, Liborio"},{"full_name":"Plenz, Dietmar","first_name":"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"},{"first_name":"Lucilla","last_name":"de Arcangelis","full_name":"de Arcangelis, Lucilla"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"}],"publication":"bioRxiv","_id":"10821","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","month":"03","oa_version":"Preprint","publication_status":"published","department":[{"_id":"GaTk"}],"date_created":"2022-03-04T22:20:59Z","article_processing_charge":"No","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.03.482657","open_access":"1"}],"date_published":"2022-03-04T00:00:00Z","type":"preprint","date_updated":"2022-03-07T07:28:34Z","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, <a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022).","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2022, doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","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.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2022. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>.","ieee":"F. Lombardi <i>et al.</i>, “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2022.","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. 2022. doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>","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. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>"},"year":"2022","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."}],"oa":1,"doi":"10.1101/2022.03.03.482657","day":"04"},{"publication":"Physical Review Research","has_accepted_license":"1","month":"06","article_number":"023240","oa_version":"Published Version","language":[{"iso":"eng"}],"date_published":"2022-06-24T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2643-1564"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2022-07-25T07:47:23Z","content_type":"application/pdf","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","date_created":"2022-07-25T07:47:23Z","file_size":1379683,"checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","file_id":"11644","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file"}],"author":[{"full_name":"Ngampruetikorn, Vudtiwat","first_name":"Vudtiwat","last_name":"Ngampruetikorn"},{"full_name":"Sachdeva, Vedant","first_name":"Vedant","last_name":"Sachdeva"},{"full_name":"Torrence, Johanna","first_name":"Johanna","last_name":"Torrence"},{"full_name":"Humplik, Jan","last_name":"Humplik","first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David J.","last_name":"Schwab","full_name":"Schwab, David J."},{"last_name":"Palmer","first_name":"Stephanie E.","full_name":"Palmer, Stephanie E."}],"issue":"2","_id":"11638","scopus_import":"1","title":"Inferring couplings in networks across order-disorder phase transitions","intvolume":"         4","publication_status":"published","date_created":"2022-07-24T22:01:42Z","department":[{"_id":"GaTk"}],"article_processing_charge":"No","file_date_updated":"2022-07-25T07:47:23Z","quality_controlled":"1","article_type":"original","publisher":"American Physical Society","external_id":{"arxiv":["2106.02349"]},"date_updated":"2022-07-25T07:52:35Z","citation":{"chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” <i>Physical Review Research</i>, vol. 4, no. 2. American Physical Society, 2022.","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022)."},"year":"2022","abstract":[{"text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data.","lang":"eng"}],"arxiv":1,"doi":"10.1103/PhysRevResearch.4.023240","day":"24","funded_apc":"1","ddc":["530"],"volume":4,"acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030)."},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","date_published":"2022-01-04T00:00:00Z","publication_identifier":{"issn":["0006-3495"]},"oa":1,"file":[{"creator":"dernst","file_id":"11697","access_level":"open_access","relation":"main_file","success":1,"file_name":"2022_BiophysicalJour_Zisis.pdf","content_type":"application/pdf","date_updated":"2022-07-29T10:17:10Z","file_size":4475504,"checksum":"1aa7c3478e0c8256b973b632efd1f6b4","date_created":"2022-07-29T10:17:10Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","publication":"Biophysical Journal","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"oa_version":"Published Version","month":"01","keyword":["Biophysics"],"language":[{"iso":"eng"}],"citation":{"ieee":"T. Zisis <i>et al.</i>, “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” <i>Biophysical Journal</i>, vol. 121, no. 1. Elsevier, pp. P44-60, 2022.","chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>.","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. 2022;121(1):P44-60. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>.","short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60."},"year":"2022","date_updated":"2023-08-02T13:34:25Z","external_id":{"isi":["000740815400007"]},"isi":1,"day":"04","doi":"10.1016/j.bpj.2021.12.006","abstract":[{"text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n","lang":"eng"}],"acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","volume":121,"ddc":["570"],"_id":"10530","issue":"1","author":[{"full_name":"Zisis, Themistoklis","last_name":"Zisis","first_name":"Themistoklis"},{"last_name":"Brückner","first_name":"David","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"last_name":"Brandstätter","first_name":"Tom","full_name":"Brandstätter, Tom"},{"full_name":"Siow, Wei Xiong","first_name":"Wei Xiong","last_name":"Siow"},{"first_name":"Joseph","last_name":"d’Alessandro","full_name":"d’Alessandro, Joseph"},{"full_name":"Vollmar, Angelika M.","last_name":"Vollmar","first_name":"Angelika M."},{"first_name":"Chase P.","last_name":"Broedersz","full_name":"Broedersz, Chase P."},{"full_name":"Zahler, Stefan","last_name":"Zahler","first_name":"Stefan"}],"date_created":"2021-12-10T09:48:19Z","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"article_processing_charge":"No","publication_status":"published","intvolume":"       121","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","quality_controlled":"1","page":"P44-60","file_date_updated":"2022-07-29T10:17:10Z","publisher":"Elsevier","article_type":"original"},{"publisher":"Proceedings of the National Academy of Sciences","article_type":"original","ec_funded":1,"quality_controlled":"1","file_date_updated":"2022-09-12T08:08:12Z","publication_status":"published","date_created":"2022-09-11T22:01:55Z","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"title":"Accumulation and maintenance of information in evolution","intvolume":"       119","pmid":1,"_id":"12081","scopus_import":"1","author":[{"full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"1","last_name":"Tkačik","first_name":"Gašper"}],"issue":"36","volume":119,"acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","ddc":["570"],"doi":"10.1073/pnas.2123152119","day":"29","abstract":[{"text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.","lang":"eng"}],"date_updated":"2025-06-30T13:21:05Z","year":"2022","citation":{"chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>.","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences</i>. 2022;119(36). doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>","apa":"Hledik, M., Barton, N. H., &#38; Tkačik, G. (2022). Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences</i>, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022)."},"isi":1,"external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"month":"08","article_number":"e2123152119","publication":"Proceedings of the National Academy of Sciences","has_accepted_license":"1","file":[{"file_id":"12091","creator":"dernst","access_level":"open_access","success":1,"relation":"main_file","date_updated":"2022-09-12T08:08:12Z","file_name":"2022_PNAS_Hledik.pdf","content_type":"application/pdf","date_created":"2022-09-12T08:08:12Z","file_size":2165752,"checksum":"6dec51f6567da9039982a571508a8e4d"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"15020","status":"public"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-08-29T00:00:00Z","type":"journal_article"},{"has_accepted_license":"1","publication":"Current Opinion in Systems Biology","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"Published Version","article_number":"100435","month":"09","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-09-01T00:00:00Z","publication_identifier":{"issn":["2452-3100"]},"oa":1,"file":[{"file_size":2214944,"checksum":"97ef01e0cc60cdc84f45640a0f248fb0","date_created":"2023-01-24T12:14:10Z","file_name":"2022_CurrentBiology_Zoller.pdf","content_type":"application/pdf","date_updated":"2023-01-24T12:14:10Z","access_level":"open_access","relation":"main_file","success":1,"creator":"dernst","file_id":"12362"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","_id":"12156","issue":"9","author":[{"full_name":"Zoller, Benjamin","first_name":"Benjamin","last_name":"Zoller"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"1","last_name":"Tkačik","first_name":"Gašper"}],"date_created":"2023-01-12T12:08:51Z","department":[{"_id":"GaTk"}],"article_processing_charge":"Yes (via OA deal)","publication_status":"published","intvolume":"        31","title":"Eukaryotic gene regulation at equilibrium, or non?","quality_controlled":"1","file_date_updated":"2023-01-24T12:14:10Z","publisher":"Elsevier","article_type":"original","year":"2022","citation":{"apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022.","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435."},"date_updated":"2023-02-13T09:20:34Z","day":"01","doi":"10.1016/j.coisb.2022.100435","abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"volume":31,"acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","ddc":["570"]},{"acknowledgement":"We thank Robbe Goris for generously providing figures from his work and Ann M. Hermundstad for helpful discussions.\r\nGT & WM were supported by the Austrian Science Fund Standalone Grant P 34015 \"Efficient Coding with Biophysical Realism\" (https://pf.fwf.ac.at/) WM was additionally supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (https://ec.europa.eu/research/mariecurieactions/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","volume":20,"ddc":["570"],"citation":{"ista":"Mlynarski WF, Tkačik G. 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 20(12), e3001889.","short":"W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.","mla":"Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>.","ieee":"W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional modulation,” <i>PLoS Biology</i>, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.","chicago":"Mlynarski, Wiktor F, and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>.","apa":"Mlynarski, W. F., &#38; Tkačik, G. (2022). Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>","ama":"Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. 2022;20(12):e3001889. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>"},"year":"2022","date_updated":"2023-08-03T14:23:49Z","external_id":{"isi":["000925192000001"]},"isi":1,"day":"21","doi":"10.1371/journal.pbio.3001889","abstract":[{"lang":"eng","text":"Activity of sensory neurons is driven not only by external stimuli but also by feedback signals from higher brain areas. Attention is one particularly important internal signal whose presumed role is to modulate sensory representations such that they only encode information currently relevant to the organism at minimal cost. This hypothesis has, however, not yet been expressed in a normative computational framework. Here, by building on normative principles of probabilistic inference and efficient coding, we developed a model of dynamic population coding in the visual cortex. By continuously adapting the sensory code to changing demands of the perceptual observer, an attention-like modulation emerges. This modulation can dramatically reduce the amount of neural activity without deteriorating the accuracy of task-specific inferences. Our results suggest that a range of seemingly disparate cortical phenomena such as intrinsic gain modulation, attention-related tuning modulation, and response variability could be manifestations of the same underlying principles, which combine efficient sensory coding with optimal probabilistic inference in dynamic environments."}],"quality_controlled":"1","ec_funded":1,"page":"e3001889","file_date_updated":"2023-01-23T08:46:40Z","publisher":"Public Library of Science","article_type":"original","scopus_import":"1","_id":"12332","issue":"12","author":[{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","first_name":"Wiktor F","full_name":"Mlynarski, Wiktor F"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"1"}],"article_processing_charge":"No","date_created":"2023-01-22T23:00:55Z","department":[{"_id":"GaTk"}],"publication_status":"published","intvolume":"        20","title":"Efficient coding theory of dynamic attentional modulation","file":[{"creator":"dernst","file_id":"12337","relation":"main_file","success":1,"access_level":"open_access","content_type":"application/pdf","file_name":"2022_PloSBiology_Mlynarski.pdf","date_updated":"2023-01-23T08:46:40Z","file_size":4248838,"checksum":"5d7f1111a87e5f2c1bf92f8886738894","date_created":"2023-01-23T08:46:40Z"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-12-21T00:00:00Z","publication_identifier":{"eissn":["1545-7885"]},"oa":1,"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"PLoS Biology","project":[{"name":"Efficient coding with biophysical realism","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"oa_version":"Published Version","month":"12"},{"publisher":"arXiv","ec_funded":1,"page":"37","language":[{"iso":"eng"}],"date_created":"2022-03-21T11:41:28Z","department":[{"_id":"GaTk"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015","name":"Efficient coding with biophysical realism"}],"article_processing_charge":"No","publication_status":"submitted","oa_version":"Preprint","month":"08","title":"Quantifying the coexistence of neuronal oscillations and avalanches","_id":"10912","author":[{"first_name":"Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425","full_name":"Pepic, Selver","first_name":"Selver","last_name":"Pepic"},{"last_name":"Shriki","first_name":"Oren","full_name":"Shriki, Oren"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2108.06686"}],"acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. GT\r\nacknowledges the support of the Austrian Science Fund (FWF) under Stand-Alone Grant\r\nNo. P34015.","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"day":"17","doi":"10.48550/ARXIV.2108.06686","arxiv":1,"oa":1,"abstract":[{"text":"Brain dynamics display collective phenomena as diverse as neuronal oscillations and avalanches. Oscillations are rhythmic, with fluctuations occurring at a characteristic scale, whereas avalanches are scale-free cascades of neural activity. Here we show that such antithetic features can coexist in a very generic class of adaptive neural networks. In the most simple yet fully microscopic model from this class we 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 fluctuations, collective behaviors of nearly-synchronous extreme events on multiple sensors, to neuronal avalanches unfolding over multiple sensors across multiple time-bins. Importantly, the inferred parameters correlate with model-independent signatures of \"closeness to criticality\", suggesting that the coexistence of scale-specific (neural oscillations) and scale-free (neuronal avalanches) dynamics in brain activity occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.","lang":"eng"}],"citation":{"ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. doi:<a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">10.48550/ARXIV.2108.06686</a>","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., &#38; De Martino, D. (n.d.). Quantifying the coexistence of neuronal oscillations and avalanches. arXiv. <a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">https://doi.org/10.48550/ARXIV.2108.06686</a>","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.” arXiv, n.d. <a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">https://doi.org/10.48550/ARXIV.2108.06686</a>.","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv.","mla":"Lombardi, Fabrizio, et al. <i>Quantifying the Coexistence of Neuronal Oscillations and Avalanches</i>. arXiv, doi:<a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">10.48550/ARXIV.2108.06686</a>.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.).","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. <a href=\"https://doi.org/10.48550/ARXIV.2108.06686\">10.48550/ARXIV.2108.06686</a>."},"year":"2021","date_updated":"2022-03-22T07:53:18Z","type":"preprint","external_id":{"arxiv":["2108.06686"]},"date_published":"2021-08-17T00:00:00Z"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","related_material":{"record":[{"status":"public","id":"7673","relation":"earlier_version"},{"relation":"research_data","id":"8930","status":"public"}]},"file":[{"file_id":"9092","creator":"dernst","success":1,"access_level":"open_access","relation":"main_file","date_updated":"2021-02-04T12:30:48Z","file_name":"2021_PlosComBio_Kavcic.pdf","content_type":"application/pdf","date_created":"2021-02-04T12:30:48Z","file_size":3690053,"checksum":"e29f2b42651bef8e034781de8781ffac"}],"oa":1,"publication_identifier":{"issn":["1553-7358"]},"date_published":"2021-01-07T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"month":"01","article_number":"e1008529","oa_version":"Published Version","project":[{"call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"publication":"PLOS Computational Biology","has_accepted_license":"1","ddc":["570"],"acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","volume":17,"abstract":[{"lang":"eng","text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems."}],"doi":"10.1371/journal.pcbi.1008529","day":"07","isi":1,"external_id":{"isi":["000608045000010"]},"date_updated":"2024-02-21T12:41:41Z","citation":{"ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. 2021;17. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” <i>PLOS Computational Biology</i>, vol. 17. Public Library of Science, 2021.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">https://doi.org/10.1371/journal.pcbi.1008529</a>.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” <i>PLOS Computational Biology</i>, vol. 17, e1008529, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1008529\">10.1371/journal.pcbi.1008529</a>.","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529."},"year":"2021","article_type":"original","publisher":"Public Library of Science","file_date_updated":"2021-02-04T12:30:48Z","quality_controlled":"1","title":"Minimal biophysical model of combined antibiotic action","intvolume":"        17","publication_status":"published","department":[{"_id":"GaTk"}],"date_created":"2021-01-08T07:16:18Z","article_processing_charge":"Yes","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor","last_name":"Kavcic","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik"},{"full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"_id":"8997"},{"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.03.930966"}],"date_published":"2021-05-13T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"issn":["0925-2312"],"eissn":["1872-8286"]},"language":[{"iso":"eng"}],"publication":"Neurocomputing","month":"05","oa_version":"Preprint","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"volume":461,"acknowledgement":"LdA would like to acknowledge the financial support from MIUR-PRIN2017 WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies CAPES and FUNCAP for financial support.","isi":1,"external_id":{"isi":["000704086300015"]},"date_updated":"2023-08-04T10:46:29Z","citation":{"apa":"Lombardi, F., Shriki, O., Herrmann, H. J., &#38; de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>","ama":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. <i>Neurocomputing</i>. 2021;461:657-666. doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>","chicago":"Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">https://doi.org/10.1016/j.neucom.2020.05.126</a>.","ieee":"F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” <i>Neurocomputing</i>, vol. 461. Elsevier, pp. 657–666, 2021.","mla":"Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” <i>Neurocomputing</i>, vol. 461, Elsevier, 2021, pp. 657–66, doi:<a href=\"https://doi.org/10.1016/j.neucom.2020.05.126\">10.1016/j.neucom.2020.05.126</a>.","short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.","ista":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 461, 657–666."},"year":"2021","abstract":[{"lang":"eng","text":"Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms."}],"doi":"10.1016/j.neucom.2020.05.126","day":"13","page":"657-666","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Elsevier","author":[{"first_name":"Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"},{"full_name":"Herrmann, Hans J","first_name":"Hans J","last_name":"Herrmann"},{"last_name":"de Arcangelis","first_name":"Lucilla","full_name":"de Arcangelis, Lucilla"}],"_id":"7463","scopus_import":"1","title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","intvolume":"       461","publication_status":"published","date_created":"2020-02-06T16:09:14Z","department":[{"_id":"GaTk"}],"article_processing_charge":"No"},{"volume":109,"acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","external_id":{"isi":["000637809600006"]},"isi":1,"year":"2021","citation":{"mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. <i>Neuron</i>. 2021;109(7):1227-1241.e5. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">10.1016/j.neuron.2021.01.020</a>","apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2021). Statistical analysis and optimality of neural systems. <i>Neuron</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>","chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” <i>Neuron</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.01.020\">https://doi.org/10.1016/j.neuron.2021.01.020</a>.","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” <i>Neuron</i>, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021."},"date_updated":"2025-06-30T13:21:05Z","abstract":[{"text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems.","lang":"eng"}],"day":"07","doi":"10.1016/j.neuron.2021.01.020","quality_controlled":"1","ec_funded":1,"page":"1227-1241.e5","publisher":"Cell Press","issue":"7","author":[{"first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal"},{"last_name":"Sokolowski","first_name":"Thomas R","full_name":"Sokolowski, Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"7553","intvolume":"       109","title":"Statistical analysis and optimality of neural systems","department":[{"_id":"GaTk"}],"article_processing_charge":"No","date_created":"2020-02-28T11:00:12Z","publication_status":"published","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15020"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/848374"}],"type":"journal_article","date_published":"2021-04-07T00:00:00Z","oa":1,"language":[{"iso":"eng"}],"publication":"Neuron","month":"04","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"oa_version":"Preprint"}]