[{"has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2020-09-14T00:00:00Z","ddc":["570"],"external_id":{"isi":["000579945300001"]},"status":"public","citation":{"short":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M.J. Case, Y. Fukazawa, R. Shigemoto, International Journal of Molecular Sciences 21 (2020).","ieee":"D. Kleindienst, J.-C. Montanaro-Punzengruber, P. Bhandari, M. J. Case, Y. Fukazawa, and R. Shigemoto, “Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses,” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18. MDPI, 2020.","chicago":"Kleindienst, David, Jacqueline-Claire Montanaro-Punzengruber, Pradeep Bhandari, Matthew J Case, Yugo Fukazawa, and Ryuichi Shigemoto. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>.","ista":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. 2020. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. International Journal of Molecular Sciences. 21(18), 6737.","mla":"Kleindienst, David, et al. “Deep Learning-Assisted High-Throughput Analysis of Freeze-Fracture Replica Images Applied to Glutamate Receptors and Calcium Channels at Hippocampal Synapses.” <i>International Journal of Molecular Sciences</i>, vol. 21, no. 18, 6737, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>.","apa":"Kleindienst, D., Montanaro-Punzengruber, J.-C., Bhandari, P., Case, M. J., Fukazawa, Y., &#38; Shigemoto, R. (2020). Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms21186737\">https://doi.org/10.3390/ijms21186737</a>","ama":"Kleindienst D, Montanaro-Punzengruber J-C, Bhandari P, Case MJ, Fukazawa Y, Shigemoto R. Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses. <i>International Journal of Molecular Sciences</i>. 2020;21(18). doi:<a href=\"https://doi.org/10.3390/ijms21186737\">10.3390/ijms21186737</a>"},"intvolume":"        21","related_material":{"record":[{"relation":"dissertation_contains","id":"9562","status":"public"}]},"type":"journal_article","month":"09","oa_version":"Published Version","date_updated":"2024-03-25T23:30:16Z","abstract":[{"lang":"eng","text":"The molecular anatomy of synapses defines their characteristics in transmission and plasticity. Precise measurements of the number and distribution of synaptic proteins are important for our understanding of synapse heterogeneity within and between brain regions. Freeze–fracture replica immunogold electron microscopy enables us to analyze them quantitatively on a two-dimensional membrane surface. Here, we introduce Darea software, which utilizes deep learning for analysis of replica images and demonstrate its usefulness for quick measurements of the pre- and postsynaptic areas, density and distribution of gold particles at synapses in a reproducible manner. We used Darea for comparing glutamate receptor and calcium channel distributions between hippocampal CA3-CA1 spine synapses on apical and basal dendrites, which differ in signaling pathways involved in synaptic plasticity. We found that apical synapses express a higher density of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors and a stronger increase of AMPA receptors with synaptic size, while basal synapses show a larger increase in N-methyl-D-aspartate (NMDA) receptors with size. Interestingly, AMPA and NMDA receptors are segregated within postsynaptic sites and negatively correlated in density among both apical and basal synapses. In the presynaptic sites, Cav2.1 voltage-gated calcium channels show similar densities in apical and basal synapses with distributions consistent with an exclusion zone model of calcium channel-release site topography."}],"file_date_updated":"2020-09-21T14:08:58Z","date_created":"2020-09-20T22:01:35Z","volume":21,"year":"2020","acknowledgement":"This research was funded by Austrian Academy of Sciences, DOC fellowship to D.K., European Research\r\nCouncil Advanced Grant 694539 and European Union Human Brain Project (HBP) SGA2 785907 to R.S.\r\nWe acknowledge Elena Hollergschwandtner for technical support.","_id":"8532","publication_identifier":{"issn":["16616596"],"eissn":["14220067"]},"quality_controlled":"1","doi":"10.3390/ijms21186737","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020","_id":"25CA28EA-B435-11E9-9278-68D0E5697425"},{"name":"Mechanism of formation and maintenance of input side-dependent asymmetry in the hippocampus","_id":"25D32BC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"785907","call_identifier":"H2020","_id":"26436750-B435-11E9-9278-68D0E5697425","name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)"}],"issue":"18","language":[{"iso":"eng"}],"isi":1,"day":"14","file":[{"file_id":"8551","date_updated":"2020-09-21T14:08:58Z","checksum":"2e4f62f3cfe945b7391fc3070e5a289f","date_created":"2020-09-21T14:08:58Z","access_level":"open_access","file_name":"2020_JournMolecSciences_Kleindienst.pdf","success":1,"file_size":5748456,"content_type":"application/pdf","relation":"main_file","creator":"dernst"}],"author":[{"full_name":"Kleindienst, David","id":"42E121A4-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Kleindienst"},{"id":"3786AB44-F248-11E8-B48F-1D18A9856A87","full_name":"Montanaro-Punzengruber, Jacqueline-Claire","first_name":"Jacqueline-Claire","last_name":"Montanaro-Punzengruber"},{"first_name":"Pradeep","last_name":"Bhandari","orcid":"0000-0003-0863-4481","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","full_name":"Bhandari, Pradeep"},{"full_name":"Case, Matthew J","id":"44B7CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","last_name":"Case"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"}],"article_number":"6737","title":"Deep learning-assisted high-throughput analysis of freeze-fracture replica images applied to glutamate receptors and calcium channels at hippocampal synapses","department":[{"_id":"RySh"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"MDPI","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"No","scopus_import":"1","publication":"International Journal of Molecular Sciences"},{"isi":1,"language":[{"iso":"eng"}],"issue":"3","project":[{"name":"Human Brain Project Specific Grant Agreement 1 (HBP SGA 1)","call_identifier":"H2020","_id":"25CBA828-B435-11E9-9278-68D0E5697425","grant_number":"720270"},{"name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","_id":"26436750-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"785907"}],"doi":"10.1111/bpa.12802","quality_controlled":"1","publication_identifier":{"eissn":["17503639"],"issn":["10156305"]},"publication":"Brain Pathology","scopus_import":"1","ec_funded":1,"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"department":[{"_id":"RySh"}],"title":"Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's disease","author":[{"full_name":"Martín-Belmonte, Alejandro","first_name":"Alejandro","last_name":"Martín-Belmonte"},{"full_name":"Aguado, Carolina","first_name":"Carolina","last_name":"Aguado"},{"full_name":"Alfaro-Ruíz, Rocío","last_name":"Alfaro-Ruíz","first_name":"Rocío"},{"full_name":"Moreno-Martínez, Ana Esther","last_name":"Moreno-Martínez","first_name":"Ana Esther"},{"last_name":"De La Ossa","first_name":"Luis","full_name":"De La Ossa, Luis"},{"first_name":"José","last_name":"Martínez-Hernández","full_name":"Martínez-Hernández, José"},{"full_name":"Buisson, Alain","last_name":"Buisson","first_name":"Alain"},{"full_name":"Früh, Simon","last_name":"Früh","first_name":"Simon"},{"full_name":"Bettler, Bernhard","last_name":"Bettler","first_name":"Bernhard"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"first_name":"Rafael","last_name":"Luján","full_name":"Luján, Rafael"}],"day":"01","file":[{"date_updated":"2020-09-22T09:47:19Z","file_id":"8554","checksum":"549cc1b18f638a21d17a939ba5563fa9","date_created":"2020-09-22T09:47:19Z","access_level":"open_access","success":1,"file_name":"2020_BrainPathology_MartinBelmonte.pdf","content_type":"application/pdf","relation":"main_file","file_size":4220935,"creator":"dernst"}],"intvolume":"        30","citation":{"short":"A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, S. Früh, B. Bettler, R. Shigemoto, Y. Fukazawa, R. Luján, Brain Pathology 30 (2020) 554–575.","ieee":"A. Martín-Belmonte <i>et al.</i>, “Reduction in the neuronal surface of post and presynaptic GABA&#62;B&#60; receptors in the hippocampus in a mouse model of Alzheimer’s disease,” <i>Brain Pathology</i>, vol. 30, no. 3. Wiley, pp. 554–575, 2020.","chicago":"Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA&#62;B&#60; Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” <i>Brain Pathology</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/bpa.12802\">https://doi.org/10.1111/bpa.12802</a>.","mla":"Martín-Belmonte, Alejandro, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA&#62;B&#60; Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” <i>Brain Pathology</i>, vol. 30, no. 3, Wiley, 2020, pp. 554–75, doi:<a href=\"https://doi.org/10.1111/bpa.12802\">10.1111/bpa.12802</a>.","ista":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Früh S, Bettler B, Shigemoto R, Fukazawa Y, Luján R. 2020. Reduction in the neuronal surface of post and presynaptic GABA&#62;B&#60; receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 30(3), 554–575.","apa":"Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Reduction in the neuronal surface of post and presynaptic GABA&#62;B&#60; receptors in the hippocampus in a mouse model of Alzheimer’s disease. <i>Brain Pathology</i>. Wiley. <a href=\"https://doi.org/10.1111/bpa.12802\">https://doi.org/10.1111/bpa.12802</a>","ama":"Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Reduction in the neuronal surface of post and presynaptic GABA&#62;B&#60; receptors in the hippocampus in a mouse model of Alzheimer’s disease. <i>Brain Pathology</i>. 2020;30(3):554-575. doi:<a href=\"https://doi.org/10.1111/bpa.12802\">10.1111/bpa.12802</a>"},"status":"public","external_id":{"pmid":["31729777"],"isi":["000502270900001"]},"date_published":"2020-05-01T00:00:00Z","ddc":["570"],"publication_status":"published","oa":1,"has_accepted_license":"1","_id":"7207","year":"2020","volume":30,"date_created":"2019-12-22T23:00:43Z","file_date_updated":"2020-09-22T09:47:19Z","page":"554-575","abstract":[{"text":"The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD.","lang":"eng"}],"date_updated":"2023-09-06T14:48:01Z","month":"05","type":"journal_article","oa_version":"Published Version"},{"volume":98,"date_created":"2018-12-11T11:44:15Z","date_updated":"2023-09-18T09:18:44Z","abstract":[{"lang":"eng","text":"Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus."}],"oa_version":"Preprint","month":"10","type":"journal_article","_id":"31","acknowledgement":"This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013).","year":"2018","date_published":"2018-10-17T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/243816v2.full"}],"oa":1,"publication_status":"published","intvolume":"        98","citation":{"ama":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. <i>Physical Review E</i>. 2018;98(4). doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.042410\">10.1103/PhysRevE.98.042410</a>","mla":"Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” <i>Physical Review E</i>, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevE.98.042410\">10.1103/PhysRevE.98.042410</a>.","ista":"Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410.","apa":"Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., &#38; Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.98.042410\">https://doi.org/10.1103/PhysRevE.98.042410</a>","ieee":"U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” <i>Physical Review E</i>, vol. 98, no. 4. American Physical Society, 2018.","chicago":"Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” <i>Physical Review E</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevE.98.042410\">https://doi.org/10.1103/PhysRevE.98.042410</a>.","short":"U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018)."},"status":"public","external_id":{"isi":["000447486100004"]},"title":"Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons","article_number":"042410","publist_id":"8024","author":[{"full_name":"Ferrari, Ulisse","first_name":"Ulisse","last_name":"Ferrari"},{"full_name":"Deny, Stephane","last_name":"Deny","first_name":"Stephane"},{"first_name":"Matthew J","last_name":"Chalk","full_name":"Chalk, Matthew J"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"}],"day":"17","publication":"Physical Review E","scopus_import":"1","ec_funded":1,"article_processing_charge":"No","article_type":"original","publisher":"American Physical Society","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"GaTk"}],"doi":"10.1103/PhysRevE.98.042410","quality_controlled":"1","publication_identifier":{"issn":["24700045"]},"isi":1,"language":[{"iso":"eng"}],"issue":"4","project":[{"name":"Human Brain Project Specific Grant Agreement 2 (HBP SGA 2)","_id":"26436750-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"785907"}]}]