[{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Public Library of Science","title":"Uncovering the organization of neural circuits with Generalized Phase Locking Analysis","isi":1,"author":[{"first_name":"Shervin","last_name":"Safavi","full_name":"Safavi, Shervin"},{"full_name":"Panagiotaropoulos, Theofanis I.","first_name":"Theofanis I.","last_name":"Panagiotaropoulos"},{"first_name":"Vishal","last_name":"Kapoor","full_name":"Kapoor, Vishal"},{"first_name":"Juan F","last_name":"Ramirez Villegas","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","full_name":"Ramirez Villegas, Juan F"},{"full_name":"Logothetis, Nikos K.","last_name":"Logothetis","first_name":"Nikos K."},{"last_name":"Besserve","first_name":"Michel","full_name":"Besserve, Michel"}],"file":[{"file_id":"12867","creator":"dernst","checksum":"edeb9d09f3e41ba7c0251308b9e372e7","access_level":"open_access","file_name":"2023_PLoSCompBio_Safavi.pdf","date_updated":"2023-04-25T08:59:18Z","date_created":"2023-04-25T08:59:18Z","relation":"main_file","content_type":"application/pdf","success":1,"file_size":4737671}],"acknowledgement":"We thank Britni Crocker for help with preprocessing of the data and spike sorting; Joachim Werner and Michael Schnabel for their excellent IT support; Andreas Tolias for help with the initial implantation’s of the Utah arrays.\r\nAll authors were supported by the Max Planck Society. M.B. was supported by the German\r\nFederal Ministry of Education and Research (BMBF) through the funding scheme received by\r\nthe Tübingen AI Center, FKZ: 01IS18039B. N.K.L. and V.K. acknowledge the support from the\r\nShanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","quality_controlled":"1","volume":19,"external_id":{"isi":["000962668700002"]},"related_material":{"link":[{"relation":"software","url":"https://github.com/shervinsafavi/gpla.git"}]},"article_processing_charge":"No","article_type":"original","type":"journal_article","department":[{"_id":"JoCs"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"PLoS Computational Biology","date_created":"2023-04-23T22:01:03Z","month":"04","status":"public","publication_identifier":{"eissn":["1553-7358"]},"oa":1,"article_number":"e1010983","_id":"12862","issue":"4","abstract":[{"lang":"eng","text":"Despite the considerable progress of in vivo neural recording techniques, inferring the biophysical mechanisms underlying large scale coordination of brain activity from neural data remains challenging. One obstacle is the difficulty to link high dimensional functional connectivity measures to mechanistic models of network activity. We address this issue by investigating spike-field coupling (SFC) measurements, which quantify the synchronization between, on the one hand, the action potentials produced by neurons, and on the other hand mesoscopic “field” signals, reflecting subthreshold activities at possibly multiple recording sites. As the number of recording sites gets large, the amount of pairwise SFC measurements becomes overwhelmingly challenging to interpret. We develop Generalized Phase Locking Analysis (GPLA) as an interpretable dimensionality reduction of this multivariate SFC. GPLA describes the dominant coupling between field activity and neural ensembles across space and frequencies. We show that GPLA features are biophysically interpretable when used in conjunction with appropriate network models, such that we can identify the influence of underlying circuit properties on these features. We demonstrate the statistical benefits and interpretability of this approach in various computational models and Utah array recordings. The results suggest that GPLA, used jointly with biophysical modeling, can help uncover the contribution of recurrent microcircuits to the spatio-temporal dynamics observed in multi-channel experimental recordings."}],"date_updated":"2023-08-01T14:15:16Z","year":"2023","citation":{"chicago":"Safavi, Shervin, Theofanis I. Panagiotaropoulos, Vishal Kapoor, Juan F Ramirez Villegas, Nikos K. Logothetis, and Michel Besserve. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” <i>PLoS Computational Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">https://doi.org/10.1371/journal.pcbi.1010983</a>.","apa":"Safavi, S., Panagiotaropoulos, T. I., Kapoor, V., Ramirez Villegas, J. F., Logothetis, N. K., &#38; Besserve, M. (2023). Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">https://doi.org/10.1371/journal.pcbi.1010983</a>","ista":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. 2023. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. PLoS Computational Biology. 19(4), e1010983.","mla":"Safavi, Shervin, et al. “Uncovering the Organization of Neural Circuits with Generalized Phase Locking Analysis.” <i>PLoS Computational Biology</i>, vol. 19, no. 4, e1010983, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">10.1371/journal.pcbi.1010983</a>.","ieee":"S. Safavi, T. I. Panagiotaropoulos, V. Kapoor, J. F. Ramirez Villegas, N. K. Logothetis, and M. Besserve, “Uncovering the organization of neural circuits with Generalized Phase Locking Analysis,” <i>PLoS Computational Biology</i>, vol. 19, no. 4. Public Library of Science, 2023.","ama":"Safavi S, Panagiotaropoulos TI, Kapoor V, Ramirez Villegas JF, Logothetis NK, Besserve M. Uncovering the organization of neural circuits with Generalized Phase Locking Analysis. <i>PLoS Computational Biology</i>. 2023;19(4). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010983\">10.1371/journal.pcbi.1010983</a>","short":"S. Safavi, T.I. Panagiotaropoulos, V. Kapoor, J.F. Ramirez Villegas, N.K. Logothetis, M. Besserve, PLoS Computational Biology 19 (2023)."},"intvolume":"        19","file_date_updated":"2023-04-25T08:59:18Z","scopus_import":"1","ddc":["570"],"oa_version":"Published Version","date_published":"2023-04-01T00:00:00Z","doi":"10.1371/journal.pcbi.1010983","publication_status":"published"},{"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JoCs"}],"has_accepted_license":"1","date_created":"2023-01-12T12:07:39Z","publication":"Frontiers in Neural Circuits","external_id":{"isi":["000886671400001"]},"volume":16,"quality_controlled":"1","keyword":["Cellular and Molecular Neuroscience","Cognitive Neuroscience","Sensory Systems","Neuroscience (miscellaneous)"],"article_processing_charge":"No","article_type":"letter_note","project":[{"grant_number":"841301","_id":"26BAE2E4-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"The Brainstem-Hippocampus Network Uncovered: Dynamics, Reactivation and Memory Consolidation"}],"isi":1,"author":[{"full_name":"Gambino, Giuditta","first_name":"Giuditta","last_name":"Gambino"},{"last_name":"Bhik-Ghanie","first_name":"Rebecca","full_name":"Bhik-Ghanie, Rebecca"},{"full_name":"Giglia, Giuseppe","last_name":"Giglia","first_name":"Giuseppe"},{"full_name":"Puig, M. Victoria","last_name":"Puig","first_name":"M. Victoria"},{"full_name":"Ramirez Villegas, Juan F","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","last_name":"Ramirez Villegas","first_name":"Juan F"},{"full_name":"Zaldivar, Daniel","first_name":"Daniel","last_name":"Zaldivar"}],"file":[{"content_type":"application/pdf","relation":"main_file","success":1,"file_size":110031,"checksum":"457aa00e1800847abb340853058531de","creator":"dernst","file_id":"12357","access_level":"open_access","file_name":"2022_FrontiersNeuralCircuits_Gambino.pdf","date_updated":"2023-01-24T10:10:43Z","date_created":"2023-01-24T10:10:43Z"}],"acknowledgement":"This work was supported by a DFG grant ZA990/1 to DZ. This work was supported by the MSCA EU proposal 841301 - DREAM, European Commission; Horizon 2020 - Research and Innovation Framework Programme to JFRV.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"26","publisher":"Frontiers Media","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels","oa_version":"Published Version","date_published":"2022-10-26T00:00:00Z","publication_status":"published","doi":"10.3389/fncir.2022.1028154","intvolume":"        16","citation":{"ieee":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M. V. Puig, J. F. Ramirez Villegas, and D. Zaldivar, “Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels,” <i>Frontiers in Neural Circuits</i>, vol. 16. Frontiers Media, 2022.","ama":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. <i>Frontiers in Neural Circuits</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fncir.2022.1028154\">10.3389/fncir.2022.1028154</a>","short":"G. Gambino, R. Bhik-Ghanie, G. Giglia, M.V. Puig, J.F. Ramirez Villegas, D. Zaldivar, Frontiers in Neural Circuits 16 (2022).","ista":"Gambino G, Bhik-Ghanie R, Giglia G, Puig MV, Ramirez Villegas JF, Zaldivar D. 2022. Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. Frontiers in Neural Circuits. 16, 1028154.","mla":"Gambino, Giuditta, et al. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” <i>Frontiers in Neural Circuits</i>, vol. 16, 1028154, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fncir.2022.1028154\">10.3389/fncir.2022.1028154</a>.","apa":"Gambino, G., Bhik-Ghanie, R., Giglia, G., Puig, M. V., Ramirez Villegas, J. F., &#38; Zaldivar, D. (2022). Editorial: Neuromodulatory ascending systems: Their influence at the microscopic and macroscopic levels. <i>Frontiers in Neural Circuits</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncir.2022.1028154\">https://doi.org/10.3389/fncir.2022.1028154</a>","chicago":"Gambino, Giuditta, Rebecca Bhik-Ghanie, Giuseppe Giglia, M. Victoria Puig, Juan F Ramirez Villegas, and Daniel Zaldivar. “Editorial: Neuromodulatory Ascending Systems: Their Influence at the Microscopic and Macroscopic Levels.” <i>Frontiers in Neural Circuits</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fncir.2022.1028154\">https://doi.org/10.3389/fncir.2022.1028154</a>."},"file_date_updated":"2023-01-24T10:10:43Z","scopus_import":"1","ddc":["570"],"article_number":"1028154","_id":"12149","date_updated":"2023-08-04T09:01:06Z","abstract":[{"text":"Editorial on the Research Topic","lang":"eng"}],"year":"2022","month":"10","ec_funded":1,"status":"public","oa":1,"publication_identifier":{"issn":["1662-5110"]}},{"acknowledgement":"We thank O. Eschenko and M. Constantinou for providing feedback on earlier versions of this work, and J. Werner and M. Schnabel for technical support during the development of this study. This research was supported by the Max Planck Society.","pmid":1,"day":"07","author":[{"full_name":"Ramirez Villegas, Juan F","last_name":"Ramirez Villegas","id":"44B06F76-F248-11E8-B48F-1D18A9856A87","first_name":"Juan F"},{"first_name":"Michel","last_name":"Besserve","full_name":"Besserve, Michel"},{"full_name":"Murayama, Yusuke","first_name":"Yusuke","last_name":"Murayama"},{"full_name":"Evrard, Henry C.","first_name":"Henry C.","last_name":"Evrard"},{"full_name":"Oeltermann, Axel","last_name":"Oeltermann","first_name":"Axel"},{"full_name":"Logothetis, Nikos K.","last_name":"Logothetis","first_name":"Nikos K."}],"isi":1,"publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Coupling of hippocampal theta and ripples with pontogeniculooccipital waves","date_created":"2020-11-29T23:01:19Z","page":"96-102","publication":"Nature","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JoCs"}],"article_processing_charge":"No","article_type":"original","external_id":{"isi":["000591047800005"],"pmid":["33208951"]},"quality_controlled":"1","volume":589,"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-020-03068-9","relation":"erratum"}]},"date_updated":"2023-08-04T11:13:08Z","issue":"7840","abstract":[{"text":"The hippocampus has a major role in encoding and consolidating long-term memories, and undergoes plastic changes during sleep1. These changes require precise homeostatic control by subcortical neuromodulatory structures2. The underlying mechanisms of this phenomenon, however, remain unknown. Here, using multi-structure recordings in macaque monkeys, we show that the brainstem transiently modulates hippocampal network events through phasic pontine waves known as pontogeniculooccipital waves (PGO waves). Two physiologically distinct types of PGO wave appear to occur sequentially, selectively influencing high-frequency ripples and low-frequency theta events, respectively. The two types of PGO wave are associated with opposite hippocampal spike-field coupling, prompting periods of high neural synchrony of neural populations during periods of ripple and theta instances. The coupling between PGO waves and ripples, classically associated with distinct sleep stages, supports the notion that a global coordination mechanism of hippocampal sleep dynamics by cholinergic pontine transients may promote systems and synaptic memory consolidation as well as synaptic homeostasis.","lang":"eng"}],"year":"2021","_id":"8818","status":"public","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"month":"01","publication_status":"published","doi":"10.1038/s41586-020-2914-4","oa_version":"None","date_published":"2021-01-07T00:00:00Z","scopus_import":"1","intvolume":"       589","citation":{"apa":"Ramirez Villegas, J. F., Besserve, M., Murayama, Y., Evrard, H. C., Oeltermann, A., &#38; Logothetis, N. K. (2021). Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-020-2914-4\">https://doi.org/10.1038/s41586-020-2914-4</a>","ista":"Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. 2021. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. Nature. 589(7840), 96–102.","mla":"Ramirez Villegas, Juan F., et al. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” <i>Nature</i>, vol. 589, no. 7840, Springer Nature, 2021, pp. 96–102, doi:<a href=\"https://doi.org/10.1038/s41586-020-2914-4\">10.1038/s41586-020-2914-4</a>.","chicago":"Ramirez Villegas, Juan F, Michel Besserve, Yusuke Murayama, Henry C. Evrard, Axel Oeltermann, and Nikos K. Logothetis. “Coupling of Hippocampal Theta and Ripples with Pontogeniculooccipital Waves.” <i>Nature</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41586-020-2914-4\">https://doi.org/10.1038/s41586-020-2914-4</a>.","ama":"Ramirez Villegas JF, Besserve M, Murayama Y, Evrard HC, Oeltermann A, Logothetis NK. Coupling of hippocampal theta and ripples with pontogeniculooccipital waves. <i>Nature</i>. 2021;589(7840):96-102. doi:<a href=\"https://doi.org/10.1038/s41586-020-2914-4\">10.1038/s41586-020-2914-4</a>","ieee":"J. F. Ramirez Villegas, M. Besserve, Y. Murayama, H. C. Evrard, A. Oeltermann, and N. K. Logothetis, “Coupling of hippocampal theta and ripples with pontogeniculooccipital waves,” <i>Nature</i>, vol. 589, no. 7840. Springer Nature, pp. 96–102, 2021.","short":"J.F. Ramirez Villegas, M. Besserve, Y. Murayama, H.C. Evrard, A. Oeltermann, N.K. Logothetis, Nature 589 (2021) 96–102."}}]