--- _id: '14841' abstract: - lang: eng text: De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium (K+) channel subunit Kv3.2 are a recently described cause of developmental and epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr) was identified via exome sequencing in a patient with DEE. Relative to wild-type Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing shift in the voltage dependence of activation, accelerated activation, and delayed deactivation consistent with a relative stabilization of the open conformation, along with increased current density. Leveraging the cryogenic electron microscopy (cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong π-π stacking interaction between the variant Tyr125 and Tyr156 in the α-6 helix of the T1 domain promotes a relative stabilization of the open conformation of the channel, which underlies the observed gain of function. A multicompartment computational model of a Kv3-expressing parvalbumin-positive cerebral cortex fast-spiking γ-aminobutyric acidergic (GABAergic) interneuron (PV-IN) demonstrates how the Kv3.2-Cys125Tyr variant impairs neuronal excitability and dysregulates inhibition in cerebral cortex circuits to explain the resulting epilepsy. acknowledgement: This work was supported by an ERC Consolidator Grant (SYNAPSEEK) to T.P.V., the NOMIS Foundation through the NOMIS Fellowships program at IST Austria to C.B.C., a Jefferson Synaptic Biology Center Pilot Project Grant to M.C., NIH NINDS U54 NS108874 (PI, Alfred L. George), and NIH NINDS R01 NS122887 to E.M.G. The computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at the PDC Center for High-Performance Computing, KTH Royal Institute of Technology, partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank Akshay Sridhar for the fruitful discussion of the project. article_number: e2307776121 article_processing_charge: No article_type: original author: - first_name: Jerome full_name: Clatot, Jerome last_name: Clatot - first_name: Christopher full_name: Currin, Christopher id: e8321fc5-3091-11eb-8a53-83f309a11ac9 last_name: Currin orcid: 0000-0002-4809-5059 - first_name: Qiansheng full_name: Liang, Qiansheng last_name: Liang - first_name: Tanadet full_name: Pipatpolkai, Tanadet last_name: Pipatpolkai - first_name: Shavonne L. full_name: Massey, Shavonne L. last_name: Massey - first_name: Ingo full_name: Helbig, Ingo last_name: Helbig - first_name: Lucie full_name: Delemotte, Lucie last_name: Delemotte - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Manuel full_name: Covarrubias, Manuel last_name: Covarrubias - first_name: Ethan M. full_name: Goldberg, Ethan M. last_name: Goldberg citation: ama: Clatot J, Currin C, Liang Q, et al. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(3). doi:10.1073/pnas.2307776121 apa: Clatot, J., Currin, C., Liang, Q., Pipatpolkai, T., Massey, S. L., Helbig, I., … Goldberg, E. M. (2024). A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2307776121 chicago: Clatot, Jerome, Christopher Currin, Qiansheng Liang, Tanadet Pipatpolkai, Shavonne L. Massey, Ingo Helbig, Lucie Delemotte, Tim P Vogels, Manuel Covarrubias, and Ethan M. Goldberg. “A Structurally Precise Mechanism Links an Epilepsy-Associated KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2307776121. ieee: J. Clatot et al., “A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 3. Proceedings of the National Academy of Sciences, 2024. ista: Clatot J, Currin C, Liang Q, Pipatpolkai T, Massey SL, Helbig I, Delemotte L, Vogels TP, Covarrubias M, Goldberg EM. 2024. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. 121(3), e2307776121. mla: Clatot, Jerome, et al. “A Structurally Precise Mechanism Links an Epilepsy-Associated KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 3, e2307776121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2307776121. short: J. Clatot, C. Currin, Q. Liang, T. Pipatpolkai, S.L. Massey, I. Helbig, L. Delemotte, T.P. Vogels, M. Covarrubias, E.M. Goldberg, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). date_created: 2024-01-21T23:00:56Z date_published: 2024-01-16T00:00:00Z date_updated: 2024-01-23T10:20:40Z day: '16' department: - _id: TiVo doi: 10.1073/pnas.2307776121 ec_funded: 1 external_id: pmid: - '38194456' intvolume: ' 121' issue: '3' language: - iso: eng month: '01' oa_version: None pmid: 1 project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: 'https://github.com/ChrisCurrin/pv-kcnc2 ' scopus_import: '1' status: public title: A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2024' ... --- _id: '14887' abstract: - lang: eng text: 'Episodic memories are encoded by experience-activated neuronal ensembles that remain necessary and sufficient for recall. However, the temporal evolution of memory engrams after initial encoding is unclear. In this study, we employed computational and experimental approaches to examine how the neural composition and selectivity of engrams change with memory consolidation. Our spiking neural network model yielded testable predictions: memories transition from unselective to selective as neurons drop out of and drop into engrams; inhibitory activity during recall is essential for memory selectivity; and inhibitory synaptic plasticity during memory consolidation is critical for engrams to become selective. Using activity-dependent labeling, longitudinal calcium imaging and a combination of optogenetic and chemogenetic manipulations in mouse dentate gyrus, we conducted contextual fear conditioning experiments that supported our model’s predictions. Our results reveal that memory engrams are dynamic and that changes in engram composition mediated by inhibitory plasticity are crucial for the emergence of memory selectivity.' acknowledgement: We thank S. Erisken from Inscopix for helping us establish in vivo one-photon calcium imaging for this work. We thank K. Su at Tsinghua University for assistance with this work. This work was funded by the President’s PhD Scholarship from Imperial College London (D.F.T.), the Wellcome Trust (225412/Z/22/Z) (S.S.), the Biotechnology and Biological Sciences Research Council (BB/N013956/1 and BB/N019008/1) (C.C.), the Wellcome Trust (200790/Z/16/Z) (C.C.), the Simons Foundation (564408) (C.C.) and the Engineering and Physical Sciences Research Council (EP/R035806/1) (CC). The School of Life Sciences and the IDG/McGovern Institute for Brain Research supported Y.Z. The Warren Alpert Distinguished Scholar Award and National Institutes of Health 1K99NS125131-01 supported D.S.R. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Douglas full_name: Feitosa Tomé, Douglas id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2 last_name: Feitosa Tomé - first_name: Ying full_name: Zhang, Ying last_name: Zhang - first_name: Tomomi full_name: Aida, Tomomi last_name: Aida - first_name: Olivia full_name: Mosto, Olivia last_name: Mosto - first_name: Yifeng full_name: Lu, Yifeng last_name: Lu - first_name: Mandy full_name: Chen, Mandy last_name: Chen - first_name: Sadra full_name: Sadeh, Sadra last_name: Sadeh - first_name: Dheeraj S. full_name: Roy, Dheeraj S. last_name: Roy - first_name: Claudia full_name: Clopath, Claudia last_name: Clopath citation: ama: Feitosa Tomé D, Zhang Y, Aida T, et al. Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience. 2024. doi:10.1038/s41593-023-01551-w apa: Feitosa Tomé, D., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., … Clopath, C. (2024). Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-023-01551-w chicago: Feitosa Tomé, Douglas, Ying Zhang, Tomomi Aida, Olivia Mosto, Yifeng Lu, Mandy Chen, Sadra Sadeh, Dheeraj S. Roy, and Claudia Clopath. “Dynamic and Selective Engrams Emerge with Memory Consolidation.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-023-01551-w. ieee: D. Feitosa Tomé et al., “Dynamic and selective engrams emerge with memory consolidation,” Nature Neuroscience. Springer Nature, 2024. ista: Feitosa Tomé D, Zhang Y, Aida T, Mosto O, Lu Y, Chen M, Sadeh S, Roy DS, Clopath C. 2024. Dynamic and selective engrams emerge with memory consolidation. Nature Neuroscience. mla: Feitosa Tomé, Douglas, et al. “Dynamic and Selective Engrams Emerge with Memory Consolidation.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-023-01551-w. short: D. Feitosa Tomé, Y. Zhang, T. Aida, O. Mosto, Y. Lu, M. Chen, S. Sadeh, D.S. Roy, C. Clopath, Nature Neuroscience (2024). date_created: 2024-01-28T23:01:43Z date_published: 2024-01-19T00:00:00Z date_updated: 2024-01-29T09:22:00Z day: '19' department: - _id: TiVo doi: 10.1038/s41593-023-01551-w external_id: isi: - '001145442300001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41593-023-01551-w month: '01' oa: 1 oa_version: Published Version publication: Nature Neuroscience publication_identifier: eissn: - 1546-1726 issn: - 1097-6256 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14892' relation: research_data status: public scopus_import: '1' status: public title: Dynamic and selective engrams emerge with memory consolidation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '15171' abstract: - lang: eng text: The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena. acknowledgement: We thank C. Currin, B. Podlaski and the members of the Vogels group for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. Open access funding provided by University of Basel. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Everton J. full_name: Agnes, Everton J. last_name: Agnes - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. 2024. doi:10.1038/s41593-024-01597-4 apa: Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4 chicago: Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4. ieee: E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks,” Nature Neuroscience. Springer Nature, 2024. ista: Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. mla: Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-024-01597-4. short: E.J. Agnes, T.P. Vogels, Nature Neuroscience (2024). date_created: 2024-03-24T23:01:00Z date_published: 2024-03-20T00:00:00Z date_updated: 2024-03-25T07:04:05Z day: '20' department: - _id: TiVo doi: 10.1038/s41593-024-01597-4 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41593-024-01597-4 month: '03' oa: 1 oa_version: Published Version project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: Nature Neuroscience publication_identifier: eissn: - 1546-1726 issn: - 1097-6256 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '15169' abstract: - lang: eng text: Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results. acknowledgement: 'The Python implementation of kCSD was started by Grzegorz Parka during Google Summer of Code project through the International Neuroinformatics Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class. This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691 to DKW; 2015/17/B/ST7/04123 to DKW). ' article_number: e1011941 article_processing_charge: Yes article_type: original author: - first_name: Chaitanya full_name: Chintaluri, Chaitanya id: E4EDB536-3485-11EA-98D2-20AF3DDC885E last_name: Chintaluri - first_name: Marta full_name: Bejtka, Marta last_name: Bejtka - first_name: Wladyslaw full_name: Sredniawa, Wladyslaw last_name: Sredniawa - first_name: Michal full_name: Czerwinski, Michal last_name: Czerwinski - first_name: Jakub M. full_name: Dzik, Jakub M. last_name: Dzik - first_name: Joanna full_name: Jedrzejewska-Szmek, Joanna last_name: Jedrzejewska-Szmek - first_name: Daniel K. full_name: Wojciki, Daniel K. last_name: Wojciki citation: ama: Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 2024;20(3). doi:10.1371/journal.pcbi.1011941 apa: Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek, J., & Wojciki, D. K. (2024). kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011941 chicago: Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011941. ieee: C. Chintaluri et al., “kCSD-python, reliable current source density estimation with quality control,” PLoS Computational Biology, vol. 20, no. 3. Public Library of Science, 2024. ista: Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 20(3), e1011941. mla: Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology, vol. 20, no. 3, e1011941, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011941. short: C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek, D.K. Wojciki, PLoS Computational Biology 20 (2024). date_created: 2024-03-24T23:00:59Z date_published: 2024-03-14T00:00:00Z date_updated: 2024-03-25T07:54:23Z day: '14' department: - _id: TiVo doi: 10.1371/journal.pcbi.1011941 intvolume: ' 20' issue: '3' language: - iso: eng month: '03' oa_version: Published Version publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 issn: - 1553-734X publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: link: - relation: software url: https://github.com/Neuroinflab/kCSD-python scopus_import: '1' status: public title: kCSD-python, reliable current source density estimation with quality control type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2024' ... --- _id: '12866' abstract: - lang: eng text: "Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain." alternative_title: - 'Vol. 1: Biological Development and Physical Health' article_processing_charge: No author: - first_name: Christopher full_name: Currin, Christopher id: e8321fc5-3091-11eb-8a53-83f309a11ac9 last_name: Currin orcid: 0000-0002-4809-5059 - first_name: Chad full_name: Beyer, Chad last_name: Beyer citation: ama: 'Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. Encyclopedia of Child and Adolescent Health. 1st ed. Elsevier; 2023:86-98. doi:10.1016/b978-0-12-818872-9.00129-1' apa: Currin, C., & Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health (1st ed., pp. 86–98). Elsevier. https://doi.org/10.1016/b978-0-12-818872-9.00129-1 chicago: Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-818872-9.00129-1. ieee: C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in Encyclopedia of Child and Adolescent Health, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98. ista: 'Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98.' mla: Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:10.1016/b978-0-12-818872-9.00129-1. short: C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98. date_created: 2023-04-25T07:52:43Z date_published: 2023-02-01T00:00:00Z date_updated: 2023-04-25T09:25:40Z day: '01' department: - _id: TiVo doi: 10.1016/b978-0-12-818872-9.00129-1 edition: '1' editor: - first_name: Bonnie full_name: Halpern-Felsher, Bonnie last_name: Halpern-Felsher language: - iso: eng month: '02' oa_version: None page: 86-98 publication: Encyclopedia of Child and Adolescent Health publication_identifier: isbn: - '9780128188736' publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Altered childhood brain development in autism and epilepsy type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14422' abstract: - lang: eng text: "Animals exhibit a remarkable ability to learn and remember new behaviors, skills, and associations throughout their lifetime. These capabilities are made possible thanks to a variety of\r\nchanges in the brain throughout adulthood, regrouped under the term \"plasticity\". Some cells\r\nin the brain —neurons— and specifically changes in the connections between neurons, the\r\nsynapses, were shown to be crucial for the formation, selection, and consolidation of memories\r\nfrom past experiences. These ongoing changes of synapses across time are called synaptic\r\nplasticity. Understanding how a myriad of biochemical processes operating at individual\r\nsynapses can somehow work in concert to give rise to meaningful changes in behavior is a\r\nfascinating problem and an active area of research.\r\nHowever, the experimental search for the precise plasticity mechanisms at play in the brain\r\nis daunting, as it is difficult to control and observe synapses during learning. Theoretical\r\napproaches have thus been the default method to probe the plasticity-behavior connection. Such\r\nstudies attempt to extract unifying principles across synapses and model all observed synaptic\r\nchanges using plasticity rules: equations that govern the evolution of synaptic strengths across\r\ntime in neuronal network models. These rules can use many relevant quantities to determine\r\nthe magnitude of synaptic changes, such as the precise timings of pre- and postsynaptic\r\naction potentials, the recent neuronal activity levels, the state of neighboring synapses, etc.\r\nHowever, analytical studies rely heavily on human intuition and are forced to make simplifying\r\nassumptions about plasticity rules.\r\nIn this thesis, we aim to assist and augment human intuition in this search for plasticity rules.\r\nWe explore whether a numerical approach could automatically discover the plasticity rules\r\nthat elicit desired behaviors in large networks of interconnected neurons. This approach is\r\ndubbed meta-learning synaptic plasticity: learning plasticity rules which themselves will make\r\nneuronal networks learn how to solve a desired task. We first write all the potential plasticity\r\nmechanisms to consider using a single expression with adjustable parameters. We then optimize\r\nthese plasticity parameters using evolutionary strategies or Bayesian inference on tasks known\r\nto involve synaptic plasticity, such as familiarity detection and network stabilization.\r\nWe show that these automated approaches are powerful tools, able to complement established\r\nanalytical methods. By comprehensively screening plasticity rules at all synapse types in\r\nrealistic, spiking neuronal network models, we discover entire sets of degenerate plausible\r\nplasticity rules that reliably elicit memory-related behaviors. Our approaches allow for more\r\nrobust experimental predictions, by abstracting out the idiosyncrasies of individual plasticity\r\nrules, and provide fresh insights on synaptic plasticity in spiking network models.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Basile J full_name: Confavreux, Basile J id: C7610134-B532-11EA-BD9F-F5753DDC885E last_name: Confavreux citation: ama: 'Confavreux BJ. Synapseek: Meta-learning synaptic plasticity rules. 2023. doi:10.15479/at:ista:14422' apa: 'Confavreux, B. J. (2023). Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14422' chicago: 'Confavreux, Basile J. “Synapseek: Meta-Learning Synaptic Plasticity Rules.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14422.' ieee: 'B. J. Confavreux, “Synapseek: Meta-learning synaptic plasticity rules,” Institute of Science and Technology Austria, 2023.' ista: 'Confavreux BJ. 2023. Synapseek: Meta-learning synaptic plasticity rules. Institute of Science and Technology Austria.' mla: 'Confavreux, Basile J. Synapseek: Meta-Learning Synaptic Plasticity Rules. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14422.' short: 'B.J. Confavreux, Synapseek: Meta-Learning Synaptic Plasticity Rules, Institute of Science and Technology Austria, 2023.' date_created: 2023-10-12T14:13:25Z date_published: 2023-10-12T00:00:00Z date_updated: 2023-10-18T09:20:56Z day: '12' ddc: - '610' degree_awarded: PhD department: - _id: GradSch - _id: TiVo doi: 10.15479/at:ista:14422 ec_funded: 1 file: - access_level: closed checksum: 7f636555eae7803323df287672fd13ed content_type: application/pdf creator: cchlebak date_created: 2023-10-12T14:53:50Z date_updated: 2023-10-12T14:54:52Z embargo: 2024-10-12 embargo_to: open_access file_id: '14424' file_name: Confavreux_Thesis_2A.pdf file_size: 30599717 relation: main_file - access_level: closed checksum: 725e85946db92290a4583a0de9779e1b content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-10-18T07:38:34Z date_updated: 2023-10-18T07:56:08Z file_id: '14440' file_name: Confavreux Thesis.zip file_size: 68406739 relation: source_file file_date_updated: 2023-10-18T07:56:08Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '10' oa_version: Published Version page: '148' project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '9633' relation: part_of_dissertation status: public status: public supervisor: - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 title: 'Synapseek: Meta-learning synaptic plasticity rules' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14666' abstract: - lang: eng text: So-called spontaneous activity is a central hallmark of most nervous systems. Such non-causal firing is contrary to the tenet of spikes as a means of communication, and its purpose remains unclear. We propose that self-initiated firing can serve as a release valve to protect neurons from the toxic conditions arising in mitochondria from lower-than-baseline energy consumption. To demonstrate the viability of our hypothesis, we built a set of models that incorporate recent experimental results indicating homeostatic control of metabolic products—Adenosine triphosphate (ATP), adenosine diphosphate (ADP), and reactive oxygen species (ROS)—by changes in firing. We explore the relationship of metabolic cost of spiking with its effect on the temporal patterning of spikes and reproduce experimentally observed changes in intrinsic firing in the fruitfly dorsal fan-shaped body neuron in a model with ROS-modulated potassium channels. We also show that metabolic spiking homeostasis can produce indefinitely sustained avalanche dynamics in cortical circuits. Our theory can account for key features of neuronal activity observed in many studies ranging from ion channel function all the way to resting state dynamics. We finish with a set of experimental predictions that would confirm an integrated, crucial role for metabolically regulated spiking and firmly link metabolic homeostasis and neuronal function. acknowledgement: We thank Prof. C. Nazaret and Prof. J.-P. Mazat for sharing the code of their mitochondrial model. We also thank G. Miesenböck, E. Marder, L. Abbott, A. Kempf, P. Hasenhuetl, W. Podlaski, F. Zenke, E. Agnes, P. Bozelos, J. Watson, B. Confavreux, and G. Christodoulou, and the rest of the Vogels Lab for their feedback. This work was funded by Wellcome Trust and Royal Society Sir Henry Dale Research Fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and a UK Research and Innovation, Biotechnology and Biological Sciences Research Council grant (UKRI-BBSRC BB/N019512/1). article_number: e2306525120 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Chaitanya full_name: Chintaluri, Chaitanya id: E4EDB536-3485-11EA-98D2-20AF3DDC885E last_name: Chintaluri - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Chintaluri C, Vogels TP. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(48). doi:10.1073/pnas.2306525120 apa: Chintaluri, C., & Vogels, T. P. (2023). Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2306525120 chicago: Chintaluri, Chaitanya, and Tim P Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2023. https://doi.org/10.1073/pnas.2306525120. ieee: C. Chintaluri and T. P. Vogels, “Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species,” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48. National Academy of Sciences, 2023. ista: Chintaluri C, Vogels TP. 2023. Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species. Proceedings of the National Academy of Sciences of the United States of America. 120(48), e2306525120. mla: Chintaluri, Chaitanya, and Tim P. Vogels. “Metabolically Regulated Spiking Could Serve Neuronal Energy Homeostasis and Protect from Reactive Oxygen Species.” Proceedings of the National Academy of Sciences of the United States of America, vol. 120, no. 48, e2306525120, National Academy of Sciences, 2023, doi:10.1073/pnas.2306525120. short: C. Chintaluri, T.P. Vogels, Proceedings of the National Academy of Sciences of the United States of America 120 (2023). date_created: 2023-12-10T23:01:00Z date_published: 2023-11-21T00:00:00Z date_updated: 2023-12-11T12:47:41Z day: '21' ddc: - '570' department: - _id: TiVo doi: 10.1073/pnas.2306525120 external_id: pmid: - '37988463' file: - access_level: open_access checksum: bf4ec38602a70dae4338077a5a4d497f content_type: application/pdf creator: dernst date_created: 2023-12-11T12:45:12Z date_updated: 2023-12-11T12:45:12Z file_id: '14678' file_name: 2023_PNAS_Chintaluri.pdf file_size: 16891602 relation: main_file success: 1 file_date_updated: 2023-12-11T12:45:12Z has_accepted_license: '1' intvolume: ' 120' issue: '48' language: - iso: eng month: '11' oa: 1 oa_version: None pmid: 1 project: - _id: c084a126-5a5b-11eb-8a69-d75314a70a87 grant_number: 214316/Z/18/Z name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks. publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/ccluri/metabolic_spiking scopus_import: '1' status: public title: Metabolically regulated spiking could serve neuronal energy homeostasis and protect from reactive oxygen species tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 120 year: '2023' ... --- _id: '14892' abstract: - lang: eng text: 'Code and data necessary to reproduce the simulations and data analyses reported in our manuscript: Tomé, D.F., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., Sadeh, S., Roy, D. S., Clopath, C. Dynamic and selective engrams emerge with memory consolidation. 2023.' article_processing_charge: No author: - first_name: Douglas full_name: Feitosa Tomé, Douglas id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2 last_name: Feitosa Tomé citation: ama: 'Feitosa Tomé D. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. 2023. doi:10.5281/ZENODO.10251087' apa: 'Feitosa Tomé, D. (2023). douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. Zenodo. https://doi.org/10.5281/ZENODO.10251087' chicago: 'Feitosa Tomé, Douglas. “Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.10251087.' ieee: 'D. Feitosa Tomé, “douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation.” Zenodo, 2023.' ista: 'Feitosa Tomé D. 2023. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation, Zenodo, 10.5281/ZENODO.10251087.' mla: 'Feitosa Tomé, Douglas. Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation. Zenodo, 2023, doi:10.5281/ZENODO.10251087.' short: D. Feitosa Tomé, (2023). date_created: 2024-01-29T09:06:43Z date_published: 2023-12-02T00:00:00Z date_updated: 2024-01-29T09:22:01Z day: '02' ddc: - '570' department: - _id: TiVo doi: 10.5281/ZENODO.10251087 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.10251087 month: '12' oa: 1 oa_version: None publisher: Zenodo related_material: record: - id: '14887' relation: used_in_publication status: public status: public title: 'douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14993' abstract: - lang: eng text: "Traditional top-down approaches for global health have historically failed to achieve social progress (Hoffman et al., 2015; Hoffman & Røttingen, 2015). Recently, however, a more holistic, multi-level approach termed One Health (OH) (Osterhaus et al., 2020) is being adopted. Several sets of challenges have been identified for the implementation of OH (dos S. Ribeiro et al., 2019), including policy and funding, education and training, and multi-actor, multi-domain, and multi-level collaborations. These exist despite the increasing accessibility to\r\nknowledge and digital collaborative research tools through the internet. To address some of these challenges, we propose a general framework for grassroots community-based means of participatory research. Additionally, we present a specific roadmap to create a Machine Learning for Global Health community in Africa. The proposed framework aims to enable any small group of individuals with scarce resources to build and sustain an online community within approximately two years. We provide a discussion on the potential impact of the proposed framework for global health research collaborations." acknowledgement: "Houcemeddine Turki’s contributions to this final output have been funded through the Adapting\r\nWikidata to support clinical practice using Data Science, Semantic Web and Machine Learning\r\nproject, which is part of the Wikimedia Research Fund maintained by the Wikimedia Foundation in San Francisco, California, United States of America." article_processing_charge: No author: - first_name: Christopher full_name: Currin, Christopher id: e8321fc5-3091-11eb-8a53-83f309a11ac9 last_name: Currin orcid: 0000-0002-4809-5059 - first_name: Mercy Nyamewaa full_name: Asiedu , Mercy Nyamewaa last_name: 'Asiedu ' - first_name: Chris full_name: Fourie, Chris last_name: Fourie - first_name: Benjamin full_name: Rosman, Benjamin last_name: Rosman - first_name: Houcemeddine full_name: Turki, Houcemeddine last_name: Turki - first_name: Atnafu full_name: Lambebo Tonja, Atnafu last_name: Lambebo Tonja - first_name: Jade full_name: Abbott, Jade last_name: Abbott - first_name: Marvellous full_name: Ajala, Marvellous last_name: Ajala - first_name: Sadiq Adewale full_name: Adedayo, Sadiq Adewale last_name: Adedayo - first_name: Chris Chinenye full_name: Emezue, Chris Chinenye last_name: Emezue - first_name: Daphne full_name: Machangara, Daphne last_name: Machangara citation: ama: 'Currin C, Asiedu MN, Fourie C, et al. A framework for grassroots research collaboration in machine learning and global health. In: 1st Workshop on Machine Learning & Global Health. OpenReview; 2023.' apa: 'Currin, C., Asiedu , M. N., Fourie, C., Rosman, B., Turki, H., Lambebo Tonja, A., … Machangara, D. (2023). A framework for grassroots research collaboration in machine learning and global health. In 1st Workshop on Machine Learning & Global Health. Kigali, Rwanda: OpenReview.' chicago: Currin, Christopher, Mercy Nyamewaa Asiedu , Chris Fourie, Benjamin Rosman, Houcemeddine Turki, Atnafu Lambebo Tonja, Jade Abbott, et al. “A Framework for Grassroots Research Collaboration in Machine Learning and Global Health.” In 1st Workshop on Machine Learning & Global Health. OpenReview, 2023. ieee: C. Currin et al., “A framework for grassroots research collaboration in machine learning and global health,” in 1st Workshop on Machine Learning & Global Health, Kigali, Rwanda, 2023. ista: 'Currin C, Asiedu MN, Fourie C, Rosman B, Turki H, Lambebo Tonja A, Abbott J, Ajala M, Adedayo SA, Emezue CC, Machangara D. 2023. A framework for grassroots research collaboration in machine learning and global health. 1st Workshop on Machine Learning & Global Health. ICLR: International Conference on Learning Representations.' mla: Currin, Christopher, et al. “A Framework for Grassroots Research Collaboration in Machine Learning and Global Health.” 1st Workshop on Machine Learning & Global Health, OpenReview, 2023. short: C. Currin, M.N. Asiedu , C. Fourie, B. Rosman, H. Turki, A. Lambebo Tonja, J. Abbott, M. Ajala, S.A. Adedayo, C.C. Emezue, D. Machangara, in:, 1st Workshop on Machine Learning & Global Health, OpenReview, 2023. conference: end_date: 2023-05-05 location: Kigali, Rwanda name: 'ICLR: International Conference on Learning Representations' start_date: 2023-05-05 date_created: 2024-02-14T15:11:48Z date_published: 2023-03-02T00:00:00Z date_updated: 2024-02-28T12:12:00Z day: '02' department: - _id: TiVo language: - iso: eng main_file_link: - open_access: '1' url: https://openreview.net/forum?id=jHY_G91R880 month: '03' oa: 1 oa_version: Published Version publication: 1st Workshop on Machine Learning & Global Health publication_status: published publisher: OpenReview quality_controlled: '1' status: public title: A framework for grassroots research collaboration in machine learning and global health type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13239' abstract: - lang: eng text: Brains are thought to engage in predictive learning - learning to predict upcoming stimuli - to construct an internal model of their environment. This is especially notable for spatial navigation, as first described by Tolman’s latent learning tasks. However, predictive learning has also been observed in sensory cortex, in settings unrelated to spatial navigation. Apart from normative frameworks such as active inference or efficient coding, what could be the utility of learning to predict the patterns of occurrence of correlated stimuli? Here we show that prediction, and thereby the construction of an internal model of sequential stimuli, can bootstrap the learning process of a working memory task in a recurrent neural network. We implemented predictive learning alongside working memory match-tasks, and networks emerged to solve the prediction task first by encoding information across time to predict upcoming stimuli, and then eavesdropped on this solution to solve the matching task. Eavesdropping was most beneficial when neural resources were limited. Hence, predictive learning acts as a general neural mechanism to learn to store sensory information that can later be essential for working memory tasks. acknowledgement: "The authors would like to thank members of the Vogels lab and Manohar lab, as well as Adam Packer, Andrew Saxe, Stefano Sarao Mannelli and Jacob Bakermans for fruitful discussions and comments on earlier versions of the manuscript.\r\nTLvdP was supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) [grant number BB/M011224/1]. TPV was supported by an ERC Consolidator Grant (SYNAPSEEK). SGM was funded by a MRC Clinician Scientist Fellowship MR/P00878X and Leverhulme Grant RPG-2018-310." article_processing_charge: No author: - first_name: Thijs L. full_name: Van Der Plas, Thijs L. last_name: Van Der Plas - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Sanjay G. full_name: Manohar, Sanjay G. last_name: Manohar citation: ama: 'Van Der Plas TL, Vogels TP, Manohar SG. Predictive learning enables neural networks to learn complex working memory tasks. In: Proceedings of Machine Learning Research. Vol 199. ML Research Press; 2022:518-531.' apa: Van Der Plas, T. L., Vogels, T. P., & Manohar, S. G. (2022). Predictive learning enables neural networks to learn complex working memory tasks. In Proceedings of Machine Learning Research (Vol. 199, pp. 518–531). ML Research Press. chicago: Van Der Plas, Thijs L., Tim P Vogels, and Sanjay G. Manohar. “Predictive Learning Enables Neural Networks to Learn Complex Working Memory Tasks.” In Proceedings of Machine Learning Research, 199:518–31. ML Research Press, 2022. ieee: T. L. Van Der Plas, T. P. Vogels, and S. G. Manohar, “Predictive learning enables neural networks to learn complex working memory tasks,” in Proceedings of Machine Learning Research, 2022, vol. 199, pp. 518–531. ista: Van Der Plas TL, Vogels TP, Manohar SG. 2022. Predictive learning enables neural networks to learn complex working memory tasks. Proceedings of Machine Learning Research. vol. 199, 518–531. mla: Van Der Plas, Thijs L., et al. “Predictive Learning Enables Neural Networks to Learn Complex Working Memory Tasks.” Proceedings of Machine Learning Research, vol. 199, ML Research Press, 2022, pp. 518–31. short: T.L. Van Der Plas, T.P. Vogels, S.G. Manohar, in:, Proceedings of Machine Learning Research, ML Research Press, 2022, pp. 518–531. date_created: 2023-07-16T22:01:12Z date_published: 2022-12-01T00:00:00Z date_updated: 2023-07-18T06:36:28Z day: '01' ddc: - '000' department: - _id: TiVo ec_funded: 1 file: - access_level: open_access checksum: 7530a93ef42e10b4db1e5e4b69796e93 content_type: application/pdf creator: dernst date_created: 2023-07-18T06:32:38Z date_updated: 2023-07-18T06:32:38Z file_id: '13243' file_name: 2022_PMLR_vanderPlas.pdf file_size: 585135 relation: main_file success: 1 file_date_updated: 2023-07-18T06:32:38Z has_accepted_license: '1' intvolume: ' 199' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 518-531 project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: Proceedings of Machine Learning Research publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Predictive learning enables neural networks to learn complex working memory tasks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 199 year: '2022' ... --- _id: '11143' abstract: - lang: eng text: 'Dravet syndrome is a neurodevelopmental disorder characterized by epilepsy, intellectual disability, and sudden death due to pathogenic variants in SCN1A with loss of function of the sodium channel subunit Nav1.1. Nav1.1-expressing parvalbumin GABAergic interneurons (PV-INs) from young Scn1a+/− mice show impaired action potential generation. An approach assessing PV-IN function in the same mice at two time points shows impaired spike generation in all Scn1a+/− mice at postnatal days (P) 16–21, whether deceased prior or surviving to P35, with normalization by P35 in surviving mice. However, PV-IN synaptic transmission is dysfunctional in young Scn1a+/− mice that did not survive and in Scn1a+/− mice ≥ P35. Modeling confirms that PV-IN axonal propagation is more sensitive to decreased sodium conductance than spike generation. These results demonstrate dynamic dysfunction in Dravet syndrome: combined abnormalities of PV-IN spike generation and propagation drives early disease severity, while ongoing dysfunction of synaptic transmission contributes to chronic pathology.' acknowledgement: We would like to thank Bernardo Rudy, Joanna Mattis, and Laura Mcgarry for comments on a previous version of the manuscript; Xiaohong Zhang for expert technical support and mouse colony maintenance; Melody Cheng for assistance with generation of the graphical abstract; and Jennifer Kearney for the gift of Scn1a+/− mice. This work was supported by the National Institute of Neurological Disorders and Stroke of the National Institutes of Health under F31NS111803 (to K.M.G.) and K08NS097633 and R01NS110869 (to E.M.G.), the Dravet Syndrome Foundation (to A.S.), an ERC Consolidator Grant (SYNAPSEEK) (to T.P.V.), and the NOMIS Foundation through the NOMIS Fellowships program at IST Austria (to C.C.). The graphical abstract was prepared using BioRender software (BioRender.com). article_number: '110580' article_processing_charge: No article_type: original author: - first_name: Keisuke full_name: Kaneko, Keisuke last_name: Kaneko - first_name: Christopher full_name: Currin, Christopher id: e8321fc5-3091-11eb-8a53-83f309a11ac9 last_name: Currin orcid: 0000-0002-4809-5059 - first_name: Kevin M. full_name: Goff, Kevin M. last_name: Goff - first_name: Eric R. full_name: Wengert, Eric R. last_name: Wengert - first_name: Ala full_name: Somarowthu, Ala last_name: Somarowthu - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Ethan M. full_name: Goldberg, Ethan M. last_name: Goldberg citation: ama: Kaneko K, Currin C, Goff KM, et al. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. 2022;38(13). doi:10.1016/j.celrep.2022.110580 apa: Kaneko, K., Currin, C., Goff, K. M., Wengert, E. R., Somarowthu, A., Vogels, T. P., & Goldberg, E. M. (2022). Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2022.110580 chicago: Kaneko, Keisuke, Christopher Currin, Kevin M. Goff, Eric R. Wengert, Ala Somarowthu, Tim P Vogels, and Ethan M. Goldberg. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” Cell Reports. Elsevier, 2022. https://doi.org/10.1016/j.celrep.2022.110580. ieee: K. Kaneko et al., “Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome,” Cell Reports, vol. 38, no. 13. Elsevier, 2022. ista: Kaneko K, Currin C, Goff KM, Wengert ER, Somarowthu A, Vogels TP, Goldberg EM. 2022. Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome. Cell Reports. 38(13), 110580. mla: Kaneko, Keisuke, et al. “Developmentally Regulated Impairment of Parvalbumin Interneuron Synaptic Transmission in an Experimental Model of Dravet Syndrome.” Cell Reports, vol. 38, no. 13, 110580, Elsevier, 2022, doi:10.1016/j.celrep.2022.110580. short: K. Kaneko, C. Currin, K.M. Goff, E.R. Wengert, A. Somarowthu, T.P. Vogels, E.M. Goldberg, Cell Reports 38 (2022). date_created: 2022-04-10T22:01:39Z date_published: 2022-03-29T00:00:00Z date_updated: 2023-08-03T06:32:55Z day: '29' ddc: - '570' department: - _id: TiVo doi: 10.1016/j.celrep.2022.110580 ec_funded: 1 external_id: isi: - '000779794000001' file: - access_level: open_access checksum: 49105c6c27c9af0f37f50a8bbb4d380d content_type: application/pdf creator: dernst date_created: 2022-04-15T11:00:58Z date_updated: 2022-04-15T11:00:58Z file_id: '11172' file_name: 2022_CellReports_Kaneko.pdf file_size: 4774216 relation: main_file success: 1 file_date_updated: 2022-04-15T11:00:58Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '13' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. - _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A name: NOMIS Fellowship Program publication: Cell Reports publication_identifier: eissn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2022' ... --- _id: '12009' abstract: - lang: eng text: Changes in the short-term dynamics of excitatory synapses over development have been observed throughout cortex, but their purpose and consequences remain unclear. Here, we propose that developmental changes in synaptic dynamics buffer the effect of slow inhibitory long-term plasticity, allowing for continuously stable neural activity. Using computational modeling we demonstrate that early in development excitatory short-term depression quickly stabilises neural activity, even in the face of strong, unbalanced excitation. We introduce a model of the commonly observed developmental shift from depression to facilitation and show that neural activity remains stable throughout development, while inhibitory synaptic plasticity slowly balances excitation, consistent with experimental observations. Our model predicts changes in the input responses from phasic to phasic-and-tonic and more precise spike timings. We also observe a gradual emergence of short-lasting memory traces governed by short-term plasticity development. We conclude that the developmental depression-to-facilitation shift may control excitation-inhibition balance throughout development with important functional consequences. acknowledgement: We would like to thank the Vogels Lab for feedback on an earlier version of this manuscript. D.W.J. was supported by a Marshall Scholarship and a Clarendon Scholarship. R.P.C. and T.P.V. were supported by a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (WT 100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and an ERC Consolidator Grant (SYNAPSEEK). article_number: '873' article_processing_charge: No article_type: original author: - first_name: David W. full_name: Jia, David W. last_name: Jia - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Rui Ponte full_name: Costa, Rui Ponte last_name: Costa citation: ama: Jia DW, Vogels TP, Costa RP. Developmental depression-to-facilitation shift controls excitation-inhibition balance. Communications biology. 2022;5. doi:10.1038/s42003-022-03801-2 apa: Jia, D. W., Vogels, T. P., & Costa, R. P. (2022). Developmental depression-to-facilitation shift controls excitation-inhibition balance. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-022-03801-2 chicago: Jia, David W., Tim P Vogels, and Rui Ponte Costa. “Developmental Depression-to-Facilitation Shift Controls Excitation-Inhibition Balance.” Communications Biology. Springer Nature, 2022. https://doi.org/10.1038/s42003-022-03801-2. ieee: D. W. Jia, T. P. Vogels, and R. P. Costa, “Developmental depression-to-facilitation shift controls excitation-inhibition balance,” Communications biology, vol. 5. Springer Nature, 2022. ista: Jia DW, Vogels TP, Costa RP. 2022. Developmental depression-to-facilitation shift controls excitation-inhibition balance. Communications biology. 5, 873. mla: Jia, David W., et al. “Developmental Depression-to-Facilitation Shift Controls Excitation-Inhibition Balance.” Communications Biology, vol. 5, 873, Springer Nature, 2022, doi:10.1038/s42003-022-03801-2. short: D.W. Jia, T.P. Vogels, R.P. Costa, Communications Biology 5 (2022). date_created: 2022-09-04T22:02:02Z date_published: 2022-08-25T00:00:00Z date_updated: 2023-08-03T13:22:42Z day: '25' ddc: - '570' department: - _id: TiVo doi: 10.1038/s42003-022-03801-2 ec_funded: 1 external_id: isi: - '000844814800007' file: - access_level: open_access checksum: 3ec724c4f6d3440028c217305e32915f content_type: application/pdf creator: dernst date_created: 2022-09-05T08:55:11Z date_updated: 2022-09-05T08:55:11Z file_id: '12022' file_name: 2022_CommBiology_Jia.pdf file_size: 2491191 relation: main_file success: 1 file_date_updated: 2022-09-05T08:55:11Z has_accepted_license: '1' intvolume: ' 5' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: c084a126-5a5b-11eb-8a69-d75314a70a87 grant_number: 214316/Z/18/Z name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks. - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: Communications biology publication_identifier: eissn: - 2399-3642 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Developmental depression-to-facilitation shift controls excitation-inhibition balance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2022' ... --- _id: '12084' abstract: - lang: eng text: Neuronal networks encode information through patterns of activity that define the networks’ function. The neurons’ activity relies on specific connectivity structures, yet the link between structure and function is not fully understood. Here, we tackle this structure-function problem with a new conceptual approach. Instead of manipulating the connectivity directly, we focus on upper triangular matrices, which represent the network dynamics in a given orthonormal basis obtained by the Schur decomposition. This abstraction allows us to independently manipulate the eigenspectrum and feedforward structures of a connectivity matrix. Using this method, we describe a diverse repertoire of non-normal transient amplification, and to complement the analysis of the dynamical regimes, we quantify the geometry of output trajectories through the effective rank of both the eigenvector and the dynamics matrices. Counter-intuitively, we find that shrinking the eigenspectrum’s imaginary distribution leads to highly amplifying regimes in linear and long-lasting dynamics in nonlinear networks. We also find a trade-off between amplification and dimensionality of neuronal dynamics, i.e., trajectories in neuronal state-space. Networks that can amplify a large number of orthogonal initial conditions produce neuronal trajectories that lie in the same subspace of the neuronal state-space. Finally, we examine networks of excitatory and inhibitory neurons. We find that the strength of global inhibition is directly linked with the amplitude of amplification, such that weakening inhibitory weights also decreases amplification, and that the eigenspectrum’s imaginary distribution grows with an increase in the ratio between excitatory-to-inhibitory and excitatory-to-excitatory connectivity strengths. Consequently, the strength of global inhibition reveals itself as a strong signature for amplification and a potential control mechanism to switch dynamical regimes. Our results shed a light on how biological networks, i.e., networks constrained by Dale’s law, may be optimised for specific dynamical regimes. acknowledgement: 'We thank Friedemann Zenke for his comments, especially on the effect of the self loops on the spectrum. We also thank Ken Miller and Bill Podlaski for helpful comments. This research was funded by a Wellcome Trust and Royal Society Henry Dale Research Fellowship (WT100000; TPV), a Wellcome Senior Research Fellowship (214316/Z/18/Z; GC, EJA, and TPV), and a Research Project Grant by the Leverhulme Trust (RPG-2016-446; EJA and TPV). ' article_number: e1010365 article_processing_charge: No article_type: original author: - first_name: Georgia full_name: Christodoulou, Georgia last_name: Christodoulou - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Everton J. full_name: Agnes, Everton J. last_name: Agnes citation: ama: Christodoulou G, Vogels TP, Agnes EJ. Regimes and mechanisms of transient amplification in abstract and biological neural networks. PLoS Computational Biology. 2022;18(8). doi:10.1371/journal.pcbi.1010365 apa: Christodoulou, G., Vogels, T. P., & Agnes, E. J. (2022). Regimes and mechanisms of transient amplification in abstract and biological neural networks. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010365 chicago: Christodoulou, Georgia, Tim P Vogels, and Everton J. Agnes. “Regimes and Mechanisms of Transient Amplification in Abstract and Biological Neural Networks.” PLoS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010365. ieee: G. Christodoulou, T. P. Vogels, and E. J. Agnes, “Regimes and mechanisms of transient amplification in abstract and biological neural networks,” PLoS Computational Biology, vol. 18, no. 8. Public Library of Science, 2022. ista: Christodoulou G, Vogels TP, Agnes EJ. 2022. Regimes and mechanisms of transient amplification in abstract and biological neural networks. PLoS Computational Biology. 18(8), e1010365. mla: Christodoulou, Georgia, et al. “Regimes and Mechanisms of Transient Amplification in Abstract and Biological Neural Networks.” PLoS Computational Biology, vol. 18, no. 8, e1010365, Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010365. short: G. Christodoulou, T.P. Vogels, E.J. Agnes, PLoS Computational Biology 18 (2022). date_created: 2022-09-11T22:01:56Z date_published: 2022-08-15T00:00:00Z date_updated: 2023-08-03T14:06:29Z day: '15' ddc: - '570' department: - _id: TiVo doi: 10.1371/journal.pcbi.1010365 external_id: isi: - '000937227700001' file: - access_level: open_access checksum: 8a81ab29f837991ee0ea770817c4a50e content_type: application/pdf creator: dernst date_created: 2022-09-12T07:47:55Z date_updated: 2022-09-12T07:47:55Z file_id: '12090' file_name: 2022_PLoSCompBio_Christodoulou.pdf file_size: 2867337 relation: main_file success: 1 file_date_updated: 2022-09-12T07:47:55Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: c084a126-5a5b-11eb-8a69-d75314a70a87 grant_number: 214316/Z/18/Z name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks. publication: PLoS Computational Biology publication_identifier: eissn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Regimes and mechanisms of transient amplification in abstract and biological neural networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 18 year: '2022' ... --- _id: '12225' abstract: - lang: eng text: In social networks, users often engage with like-minded peers. This selective exposure to opinions might result in echo chambers, i.e., political fragmentation and social polarization of user interactions. When echo chambers form, opinions have a bimodal distribution with two peaks on opposite sides. In certain issues, where either extreme positions contain a degree of misinformation, neutral consensus is preferable for promoting discourse. In this paper, we use an opinion dynamics model that naturally forms echo chambers in order to find a feedback mechanism that bridges these communities and leads to a neutral consensus. We introduce the random dynamical nudge (RDN), which presents each agent with input from a random selection of other agents’ opinions and does not require surveillance of every person’s opinions. Our computational results in two different models suggest that the RDN leads to a unimodal distribution of opinions centered around the neutral consensus. Furthermore, the RDN is effective both for preventing the formation of echo chambers and also for depolarizing existing echo chambers. Due to the simple and robust nature of the RDN, social media networks might be able to implement a version of this self-feedback mechanism, when appropriate, to prevent the segregation of online communities on complex social issues. acknowledgement: CBC and AKN would like to thank Neuromatch Academy https://www.neuromatchacademy.org for introducing the authors to each other. We thank Dr. Krešimir Josic (University of Houston) , Fabian Baumann (Humboldt University) and Dr. Igor M. Sokolov (Humboldt University) for carefully reading the early versions of the manuscript and providing constructive feedback. CBC is supported by the German Deutscher Akademischer Austauschdienst (DAAD, https://daad.de), the South African National Research Foundation (NRF, https://nrf.ac.za), the University of Cape Town (UCT, https://uct.ac.za), and the NOMIS Foundation through the NOMIS Fellowships at IST Austria program (https://nomisfoundation.ch). SVV appreciate the generosity of Tecnológico de Monterrey for covering the publication fee. article_number: '9234' article_processing_charge: No article_type: original author: - first_name: Christopher full_name: Currin, Christopher id: e8321fc5-3091-11eb-8a53-83f309a11ac9 last_name: Currin orcid: 0000-0002-4809-5059 - first_name: Sebastián Vallejo full_name: Vera, Sebastián Vallejo last_name: Vera - first_name: Ali full_name: Khaledi-Nasab, Ali last_name: Khaledi-Nasab citation: ama: Currin C, Vera SV, Khaledi-Nasab A. Depolarization of echo chambers by random dynamical nudge. Scientific Reports. 2022;12. doi:10.1038/s41598-022-12494-w apa: Currin, C., Vera, S. V., & Khaledi-Nasab, A. (2022). Depolarization of echo chambers by random dynamical nudge. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-12494-w chicago: Currin, Christopher, Sebastián Vallejo Vera, and Ali Khaledi-Nasab. “Depolarization of Echo Chambers by Random Dynamical Nudge.” Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-12494-w. ieee: C. Currin, S. V. Vera, and A. Khaledi-Nasab, “Depolarization of echo chambers by random dynamical nudge,” Scientific Reports, vol. 12. Springer Nature, 2022. ista: Currin C, Vera SV, Khaledi-Nasab A. 2022. Depolarization of echo chambers by random dynamical nudge. Scientific Reports. 12, 9234. mla: Currin, Christopher, et al. “Depolarization of Echo Chambers by Random Dynamical Nudge.” Scientific Reports, vol. 12, 9234, Springer Nature, 2022, doi:10.1038/s41598-022-12494-w. short: C. Currin, S.V. Vera, A. Khaledi-Nasab, Scientific Reports 12 (2022). date_created: 2023-01-16T09:48:30Z date_published: 2022-06-02T00:00:00Z date_updated: 2023-08-04T09:26:30Z day: '02' ddc: - '570' department: - _id: TiVo doi: 10.1038/s41598-022-12494-w external_id: isi: - '000805561200024' pmid: - '35654942' file: - access_level: open_access checksum: e024a75f14ce5667795a31e44a259c52 content_type: application/pdf creator: dernst date_created: 2023-01-27T08:56:18Z date_updated: 2023-01-27T08:56:18Z file_id: '12418' file_name: 2022_ScientificReports_Currin.pdf file_size: 3625627 relation: main_file success: 1 file_date_updated: 2023-01-27T08:56:18Z has_accepted_license: '1' intvolume: ' 12' isi: 1 keyword: - Multidisciplinary language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Reports publication_identifier: issn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Depolarization of echo chambers by random dynamical nudge tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2022' ... --- _id: '10753' abstract: - lang: eng text: This is a comment on "Meta-learning synaptic plasticity and memory addressing for continual familiarity detection." Neuron. 2022 Feb 2;110(3):544-557.e8. article_processing_charge: No article_type: letter_note author: - first_name: Basile J full_name: Confavreux, Basile J id: C7610134-B532-11EA-BD9F-F5753DDC885E last_name: Confavreux - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: 'Confavreux BJ, Vogels TP. A familiar thought: Machines that replace us? Neuron. 2022;110(3):361-362. doi:10.1016/j.neuron.2022.01.014' apa: 'Confavreux, B. J., & Vogels, T. P. (2022). A familiar thought: Machines that replace us? Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2022.01.014' chicago: 'Confavreux, Basile J, and Tim P Vogels. “A Familiar Thought: Machines That Replace Us?” Neuron. Elsevier, 2022. https://doi.org/10.1016/j.neuron.2022.01.014.' ieee: 'B. J. Confavreux and T. P. Vogels, “A familiar thought: Machines that replace us?,” Neuron, vol. 110, no. 3. Elsevier, pp. 361–362, 2022.' ista: 'Confavreux BJ, Vogels TP. 2022. A familiar thought: Machines that replace us? Neuron. 110(3), 361–362.' mla: 'Confavreux, Basile J., and Tim P. Vogels. “A Familiar Thought: Machines That Replace Us?” Neuron, vol. 110, no. 3, Elsevier, 2022, pp. 361–62, doi:10.1016/j.neuron.2022.01.014.' short: B.J. Confavreux, T.P. Vogels, Neuron 110 (2022) 361–362. date_created: 2022-02-13T23:01:34Z date_published: 2022-02-02T00:00:00Z date_updated: 2023-10-03T10:53:17Z day: '02' department: - _id: TiVo doi: 10.1016/j.neuron.2022.01.014 external_id: isi: - '000751819100005' pmid: - '35114107' intvolume: ' 110' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2022.01.014 month: '02' oa: 1 oa_version: Published Version page: 361-362 pmid: 1 publication: Neuron publication_identifier: eissn: - 1097-4199 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'A familiar thought: Machines that replace us?' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2022' ... --- _id: '8125' abstract: - lang: eng text: Context, such as behavioral state, is known to modulate memory formation and retrieval, but is usually ignored in associative memory models. Here, we propose several types of contextual modulation for associative memory networks that greatly increase their performance. In these networks, context inactivates specific neurons and connections, which modulates the effective connectivity of the network. Memories are stored only by the active components, thereby reducing interference from memories acquired in other contexts. Such networks exhibit several beneficial characteristics, including enhanced memory capacity, high robustness to noise, increased robustness to memory overloading, and better memory retention during continual learning. Furthermore, memories can be biased to have different relative strengths, or even gated on or off, according to contextual cues, providing a candidate model for cognitive control of memory and efficient memory search. An external context-encoding network can dynamically switch the memory network to a desired state, which we liken to experimentally observed contextual signals in prefrontal cortex and hippocampus. Overall, our work illustrates the benefits of organizing memory around context, and provides an important link between behavioral studies of memory and mechanistic details of neural circuits.SIGNIFICANCEMemory is context dependent — both encoding and recall vary in effectiveness and speed depending on factors like location and brain state during a task. We apply this idea to a simple computational model of associative memory through contextual gating of neurons and synaptic connections. Intriguingly, this results in several advantages, including vastly enhanced memory capacity, better robustness, and flexible memory gating. Our model helps to explain (i) how gating and inhibition contribute to memory processes, (ii) how memory access dynamically changes over time, and (iii) how context representations, such as those observed in hippocampus and prefrontal cortex, may interact with and control memory processes. article_processing_charge: No author: - first_name: William F. full_name: Podlaski, William F. last_name: Podlaski orcid: 0000-0001-6619-7502 - first_name: Everton J. full_name: Agnes, Everton J. last_name: Agnes orcid: 0000-0001-7184-7311 - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. bioRxiv. 2022. doi:10.1101/2020.01.08.898528 apa: Podlaski, W. F., Agnes, E. J., & Vogels, T. P. (2022). High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.08.898528 chicago: Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2020.01.08.898528. ieee: W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating,” bioRxiv. Cold Spring Harbor Laboratory, 2022. ista: Podlaski WF, Agnes EJ, Vogels TP. 2022. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. bioRxiv, 10.1101/2020.01.08.898528. mla: Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” BioRxiv, Cold Spring Harbor Laboratory, 2022, doi:10.1101/2020.01.08.898528. short: W.F. Podlaski, E.J. Agnes, T.P. Vogels, BioRxiv (2022). date_created: 2020-07-16T12:24:28Z date_published: 2022-12-21T00:00:00Z date_updated: 2024-03-06T12:03:59Z day: '21' department: - _id: TiVo doi: 10.1101/2020.01.08.898528 language: - iso: eng locked: '1' main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/2020.01.08.898528 ' month: '12' oa: 1 oa_version: Preprint publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory status: public title: High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11453' abstract: - lang: eng text: "Neuronal computations depend on synaptic connectivity and intrinsic electrophysiological properties. Synaptic connectivity determines which inputs from presynaptic neurons are integrated, while cellular properties determine how inputs are filtered over time. Unlike their biological counterparts, most computational approaches to learning in simulated neural networks are limited to changes in synaptic connectivity. However, if intrinsic parameters change, neural computations are altered drastically. Here, we include the parameters that determine the intrinsic properties,\r\ne.g., time constants and reset potential, into the learning paradigm. Using sparse feedback signals that indicate target spike times, and gradient-based parameter updates, we show that the intrinsic parameters can be learned along with the synaptic weights to produce specific input-output functions. Specifically, we use a teacher-student paradigm in which a randomly initialised leaky integrate-and-fire or resonate-and-fire neuron must recover the parameters of a teacher neuron. We show that complex temporal functions can be learned online and without backpropagation through time, relying on event-based updates only. Our results are a step towards online learning of neural computations from ungraded and unsigned sparse feedback signals with a biologically inspired learning mechanism." acknowledgement: We would like to thank Professor Dr. Henning Sprekeler for his valuable suggestions and Dr. Andrew Saxe, Milan Klöwer and Anna Wallis for their constructive feedback on the manuscript. Lukas Braun was supported by the Network of European Neuroscience Schools through their NENS Exchange Grant program, by the European Union through their European Community Action Scheme for the Mobility of University Students, the Woodward Scholarship awarded by Wadham College, Oxford and the Medical Research Council [MR/N013468/1]. Tim P. Vogels was supported by a Wellcome Trust Senior Research Fellowship [214316/Z/18/Z]. article_processing_charge: No author: - first_name: Lukas full_name: Braun, Lukas last_name: Braun - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: 'Braun L, Vogels TP. Online learning of neural computations from sparse temporal feedback. In: Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems. Vol 20. Neural Information Processing Systems Foundation; 2021:16437-16450.' apa: 'Braun, L., & Vogels, T. P. (2021). Online learning of neural computations from sparse temporal feedback. In Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems (Vol. 20, pp. 16437–16450). Virtual, Online: Neural Information Processing Systems Foundation.' chicago: Braun, Lukas, and Tim P Vogels. “Online Learning of Neural Computations from Sparse Temporal Feedback.” In Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems, 20:16437–50. Neural Information Processing Systems Foundation, 2021. ieee: L. Braun and T. P. Vogels, “Online learning of neural computations from sparse temporal feedback,” in Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems, Virtual, Online, 2021, vol. 20, pp. 16437–16450. ista: 'Braun L, Vogels TP. 2021. Online learning of neural computations from sparse temporal feedback. Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 20, 16437–16450.' mla: Braun, Lukas, and Tim P. Vogels. “Online Learning of Neural Computations from Sparse Temporal Feedback.” Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems, vol. 20, Neural Information Processing Systems Foundation, 2021, pp. 16437–50. short: L. Braun, T.P. Vogels, in:, Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 16437–16450. conference: end_date: 2021-12-14 location: Virtual, Online name: 'NeurIPS: Neural Information Processing Systems' start_date: 2021-12-06 date_created: 2022-06-19T22:01:59Z date_published: 2021-12-01T00:00:00Z date_updated: 2022-06-20T07:12:58Z day: '01' department: - _id: TiVo intvolume: ' 20' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.neurips.cc/paper/2021/file/88e1ce84f9feef5a08d0df0334c53468-Paper.pdf month: '12' oa: 1 oa_version: Published Version page: 16437-16450 project: - _id: c084a126-5a5b-11eb-8a69-d75314a70a87 grant_number: 214316/Z/18/Z name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks. publication: Advances in Neural Information Processing Systems - 35th Conference on Neural Information Processing Systems publication_identifier: isbn: - '9781713845393' issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' scopus_import: '1' status: public title: Online learning of neural computations from sparse temporal feedback type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2021' ... --- _id: '8253' abstract: - lang: eng text: Brains process information in spiking neural networks. Their intricate connections shape the diverse functions these networks perform. In comparison, the functional capabilities of models of spiking networks are still rudimentary. This shortcoming is mainly due to the lack of insight and practical algorithms to construct the necessary connectivity. Any such algorithm typically attempts to build networks by iteratively reducing the error compared to a desired output. But assigning credit to hidden units in multi-layered spiking networks has remained challenging due to the non-differentiable nonlinearity of spikes. To avoid this issue, one can employ surrogate gradients to discover the required connectivity in spiking network models. However, the choice of a surrogate is not unique, raising the question of how its implementation influences the effectiveness of the method. Here, we use numerical simulations to systematically study how essential design parameters of surrogate gradients impact learning performance on a range of classification problems. We show that surrogate gradient learning is robust to different shapes of underlying surrogate derivatives, but the choice of the derivative’s scale can substantially affect learning performance. When we combine surrogate gradients with a suitable activity regularization technique, robust information processing can be achieved in spiking networks even at the sparse activity limit. Our study provides a systematic account of the remarkable robustness of surrogate gradient learning and serves as a practical guide to model functional spiking neural networks. acknowledgement: F.Z. was supported by the Wellcome Trust (110124/Z/15/Z) and the Novartis Research Foundation. T.P.V. was supported by a Wellcome Trust Sir Henry Dale Research fellowship (WT100000), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z), and an ERC Consolidator Grant SYNAPSEEK. article_processing_charge: No article_type: original author: - first_name: Friedemann full_name: Zenke, Friedemann last_name: Zenke orcid: 0000-0003-1883-644X - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Zenke F, Vogels TP. The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. Neural Computation. 2021;33(4):899-925. doi:10.1162/neco_a_01367 apa: Zenke, F., & Vogels, T. P. (2021). The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. Neural Computation. MIT Press. https://doi.org/10.1162/neco_a_01367 chicago: Zenke, Friedemann, and Tim P Vogels. “The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks.” Neural Computation. MIT Press, 2021. https://doi.org/10.1162/neco_a_01367. ieee: F. Zenke and T. P. Vogels, “The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks,” Neural Computation, vol. 33, no. 4. MIT Press, pp. 899–925, 2021. ista: Zenke F, Vogels TP. 2021. The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks. Neural Computation. 33(4), 899–925. mla: Zenke, Friedemann, and Tim P. Vogels. “The Remarkable Robustness of Surrogate Gradient Learning for Instilling Complex Function in Spiking Neural Networks.” Neural Computation, vol. 33, no. 4, MIT Press, 2021, pp. 899–925, doi:10.1162/neco_a_01367. short: F. Zenke, T.P. Vogels, Neural Computation 33 (2021) 899–925. date_created: 2020-08-12T12:08:24Z date_published: 2021-03-01T00:00:00Z date_updated: 2023-08-04T10:53:14Z day: '01' ddc: - '000' - '570' department: - _id: TiVo doi: 10.1162/neco_a_01367 ec_funded: 1 external_id: isi: - '000663433900003' pmid: - '33513328' file: - access_level: open_access checksum: eac5a51c24c8989ae7cf9ae32ec3bc95 content_type: application/pdf creator: dernst date_created: 2022-04-08T06:05:39Z date_updated: 2022-04-08T06:05:39Z file_id: '11131' file_name: 2021_NeuralComputation_Zenke.pdf file_size: 1611614 relation: main_file success: 1 file_date_updated: 2022-04-08T06:05:39Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '4' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 899-925 pmid: 1 project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. - _id: c084a126-5a5b-11eb-8a69-d75314a70a87 grant_number: 214316/Z/18/Z name: What’s in a memory? Spatiotemporal dynamics in strongly coupled recurrent neuronal networks. publication: Neural Computation publication_identifier: eissn: - 1530-888X issn: - 0899-7667 publication_status: published publisher: MIT Press quality_controlled: '1' scopus_import: '1' status: public title: The remarkable robustness of surrogate gradient learning for instilling complex function in spiking neural networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 33 year: '2021' ... --- _id: '8757' abstract: - lang: eng text: Traditional scientific conferences and seminar events have been hugely disrupted by the COVID-19 pandemic, paving the way for virtual forms of scientific communication to take hold and be put to the test. article_processing_charge: No article_type: letter_note author: - first_name: Panagiotis full_name: Bozelos, Panagiotis id: 52e9c652-2982-11eb-81d4-b43d94c63700 last_name: Bozelos - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 citation: ama: Bozelos P, Vogels TP. Talking science, online. Nature Reviews Neuroscience. 2021;22(1):1-2. doi:10.1038/s41583-020-00408-6 apa: Bozelos, P., & Vogels, T. P. (2021). Talking science, online. Nature Reviews Neuroscience. Springer Nature. https://doi.org/10.1038/s41583-020-00408-6 chicago: Bozelos, Panagiotis, and Tim P Vogels. “Talking Science, Online.” Nature Reviews Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41583-020-00408-6. ieee: P. Bozelos and T. P. Vogels, “Talking science, online,” Nature Reviews Neuroscience, vol. 22, no. 1. Springer Nature, pp. 1–2, 2021. ista: Bozelos P, Vogels TP. 2021. Talking science, online. Nature Reviews Neuroscience. 22(1), 1–2. mla: Bozelos, Panagiotis, and Tim P. Vogels. “Talking Science, Online.” Nature Reviews Neuroscience, vol. 22, no. 1, Springer Nature, 2021, pp. 1–2, doi:10.1038/s41583-020-00408-6. short: P. Bozelos, T.P. Vogels, Nature Reviews Neuroscience 22 (2021) 1–2. date_created: 2020-11-15T23:01:18Z date_published: 2021-01-01T00:00:00Z date_updated: 2023-08-04T11:10:20Z day: '01' ddc: - '570' department: - _id: TiVo doi: 10.1038/s41583-020-00408-6 external_id: isi: - '000588256300001' pmid: - '33173190' file: - access_level: open_access checksum: 7985d7dff94c086e35b94a911d78d9ad content_type: application/pdf creator: dernst date_created: 2021-02-04T10:34:22Z date_updated: 2021-02-04T10:34:22Z file_id: '9088' file_name: 2021_NatureNeuroScience_Bozelos.pdf file_size: 683634 relation: main_file success: 1 file_date_updated: 2021-02-04T10:34:22Z has_accepted_license: '1' intvolume: ' 22' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 1-2 pmid: 1 publication: Nature Reviews Neuroscience publication_identifier: eissn: - '14710048' issn: - 1471003X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Talking science, online type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2021' ... --- _id: '9228' abstract: - lang: eng text: Legacy conferences are costly and time consuming, and exclude scientists lacking various resources or abilities. During the 2020 pandemic, we created an online conference platform, Neuromatch Conferences (NMC), aimed at developing technological and cultural changes to make conferences more democratic, scalable, and accessible. We discuss the lessons we learned. acknowledgement: We thank all of our volunteers from the NMC conferences (list of names in the appendix). We also thank the NSF for support from 1734220 to B.W., and DARPA for support to T.A. article_processing_charge: No article_type: original author: - first_name: Titipat full_name: Achakulvisut, Titipat last_name: Achakulvisut - first_name: Tulakan full_name: Ruangrong, Tulakan last_name: Ruangrong - first_name: Patrick full_name: Mineault, Patrick last_name: Mineault - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Megan A.K. full_name: Peters, Megan A.K. last_name: Peters - first_name: Panayiota full_name: Poirazi, Panayiota last_name: Poirazi - first_name: Christopher full_name: Rozell, Christopher last_name: Rozell - first_name: Brad full_name: Wyble, Brad last_name: Wyble - first_name: Dan F.M. full_name: Goodman, Dan F.M. last_name: Goodman - first_name: Konrad Paul full_name: Kording, Konrad Paul last_name: Kording citation: ama: 'Achakulvisut T, Ruangrong T, Mineault P, et al. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. 2021;25(4):265-268. doi:10.1016/j.tics.2021.01.007' apa: 'Achakulvisut, T., Ruangrong, T., Mineault, P., Vogels, T. P., Peters, M. A. K., Poirazi, P., … Kording, K. P. (2021). Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. Elsevier. https://doi.org/10.1016/j.tics.2021.01.007' chicago: 'Achakulvisut, Titipat, Tulakan Ruangrong, Patrick Mineault, Tim P Vogels, Megan A.K. Peters, Panayiota Poirazi, Christopher Rozell, Brad Wyble, Dan F.M. Goodman, and Konrad Paul Kording. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” Trends in Cognitive Sciences. Elsevier, 2021. https://doi.org/10.1016/j.tics.2021.01.007.' ieee: 'T. Achakulvisut et al., “Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences,” Trends in Cognitive Sciences, vol. 25, no. 4. Elsevier, pp. 265–268, 2021.' ista: 'Achakulvisut T, Ruangrong T, Mineault P, Vogels TP, Peters MAK, Poirazi P, Rozell C, Wyble B, Goodman DFM, Kording KP. 2021. Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences. Trends in Cognitive Sciences. 25(4), 265–268.' mla: 'Achakulvisut, Titipat, et al. “Towards Democratizing and Automating Online Conferences: Lessons from the Neuromatch Conferences.” Trends in Cognitive Sciences, vol. 25, no. 4, Elsevier, 2021, pp. 265–68, doi:10.1016/j.tics.2021.01.007.' short: T. Achakulvisut, T. Ruangrong, P. Mineault, T.P. Vogels, M.A.K. Peters, P. Poirazi, C. Rozell, B. Wyble, D.F.M. Goodman, K.P. Kording, Trends in Cognitive Sciences 25 (2021) 265–268. date_created: 2021-03-07T23:01:25Z date_published: 2021-04-01T00:00:00Z date_updated: 2023-08-07T13:59:07Z day: '01' ddc: - '570' department: - _id: TiVo doi: 10.1016/j.tics.2021.01.007 external_id: isi: - '000627418000001' pmid: - '33608214' file: - access_level: open_access checksum: 87e39ea7bd266b976e8631b66979214d content_type: application/pdf creator: dernst date_created: 2022-05-27T07:31:24Z date_updated: 2022-05-27T07:31:24Z file_id: '11415' file_name: 2021_TrendsCognitiveSciences_Achakulvisut.pdf file_size: 380720 relation: main_file success: 1 file_date_updated: 2022-05-27T07:31:24Z has_accepted_license: '1' intvolume: ' 25' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 265-268 pmid: 1 publication: Trends in Cognitive Sciences publication_identifier: eissn: - 1879-307X issn: - 1364-6613 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Towards democratizing and automating online conferences: Lessons from the Neuromatch Conferences' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 25 year: '2021' ...