[{"page":"3 - 19","_id":"54","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","quality_controlled":"1","date_updated":"2026-06-18T18:52:56Z","status":"public","publist_id":"8000","main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014","open_access":"1"}],"OA_type":"free access","isi":1,"publication_status":"published","volume":47,"month":"10","type":"journal_article","department":[{"_id":"CaHe"}],"scopus_import":"1","publication":"Developmental Cell","language":[{"iso":"eng"}],"ddc":["570"],"citation":{"ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","ieee":"D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” <i>Developmental Cell</i>, vol. 47, no. 1. Cell Press, pp. 3–19, 2018.","chicago":"Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">https://doi.org/10.1016/j.devcel.2018.09.014</a>.","apa":"Nunes Pinheiro, D. C., &#38; Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">https://doi.org/10.1016/j.devcel.2018.09.014</a>","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.","ama":"Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. <i>Developmental Cell</i>. 2018;47(1):3-19. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">10.1016/j.devcel.2018.09.014</a>","mla":"Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” <i>Developmental Cell</i>, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">10.1016/j.devcel.2018.09.014</a>."},"article_processing_charge":"No","publisher":"Cell Press","title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","year":"2018","date_created":"2018-12-11T11:44:23Z","intvolume":"        47","external_id":{"isi":["000446579900002"]},"article_type":"review","acknowledgement":"Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants.","issue":"1","doi":"10.1016/j.devcel.2018.09.014","abstract":[{"lang":"eng","text":"During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics."}],"day":"08","date_published":"2018-10-08T00:00:00Z","author":[{"orcid":"0000-0003-4333-7503","full_name":"Nunes Pinheiro, Diana C","first_name":"Diana C","last_name":"Nunes Pinheiro","id":"2E839F16-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bellaïche","first_name":"Yohanns","full_name":"Bellaïche, Yohanns"}],"oa":1},{"external_id":{"isi":["000419128700049"]},"year":"2018","date_created":"2018-12-11T11:47:04Z","intvolume":"       115","title":"Toward a unified theory of efficient, predictive, and sparse coding","article_processing_charge":"No","publisher":"National Academy of Sciences","citation":{"mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>.","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(1):186-191. doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>","short":"M.J. Chalk, O. Marre, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 186–191.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. Proceedings of the National Academy of Sciences of the United States of America. 115(1), 186–191."},"author":[{"first_name":"Matthew J","full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","last_name":"Chalk"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455"}],"oa":1,"date_published":"2018-01-02T00:00:00Z","day":"02","abstract":[{"text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits.","lang":"eng"}],"doi":"10.1073/pnas.1711114115","issue":"1","isi":1,"month":"01","volume":115,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"status":"public","publist_id":"7273","date_updated":"2025-05-14T10:55:59Z","quality_controlled":"1","oa_version":"Submitted Version","_id":"543","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"186 - 191","language":[{"iso":"eng"}],"project":[{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","corr_author":"1","scopus_import":"1","department":[{"_id":"GaTk"}],"type":"journal_article"},{"has_accepted_license":"1","status":"public","date_updated":"2025-04-15T08:11:42Z","title":"Cost analysis of nondeterministic probabilistic programs","publication_status":"published","month":"11","publication_identifier":{"issn":["2664-1690"]},"date_created":"2018-12-12T11:39:26Z","year":"2018","file_date_updated":"2020-07-14T12:47:00Z","ddc":["000"],"_id":"5457","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"27","oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","status":"public","id":"6175"}]},"publisher":"IST Austria","file":[{"date_created":"2018-12-12T11:53:32Z","file_size":4202966,"date_updated":"2020-07-14T12:47:00Z","creator":"system","file_name":"IST-2018-1066-v1+1_techreport.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ba3adafd36fe200385ccda583063b9eb","file_id":"5493"},{"file_size":322,"date_updated":"2020-07-14T12:47:00Z","content_type":"text/plain","creator":"dernst","file_name":"authors-names.txt","date_created":"2019-05-10T13:22:12Z","file_id":"6402","access_level":"closed","checksum":"6cf3a19164bb8e5048a9c8c84dfd9fa3","relation":"main_file"}],"citation":{"apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, &#38; Anonymous, 6. (2018). <i>Cost analysis of nondeterministic probabilistic programs</i>. IST Austria.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria, 2018.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous, <i>Cost analysis of nondeterministic probabilistic programs</i>. IST Austria, 2018.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria, 27p.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria; 2018.","mla":"Anonymous, 1, et al. <i>Cost Analysis of Nondeterministic Probabilistic Programs</i>. IST Austria, 2018.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, 6 Anonymous, Cost Analysis of Nondeterministic Probabilistic Programs, IST Austria, 2018."},"day":"11","abstract":[{"lang":"eng","text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs, which aims at automated methods for analyzing the resource-usage of such programs. Previous approaches for this problem could only handle nonnegative bounded costs. However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols, both positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic probabilistic programs. Our approach can handle (a) general positive and negative costs with bounded updates in variables; and (b) nonnegative costs with general updates to variables. We show that several natural examples which could not be handled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime. Finally, we show the effectiveness of our approach by presenting experimental results on a variety of programs, motivated by real-world applications, for which we efficiently synthesize tight resource-usage bounds."}],"author":[{"first_name":"1","full_name":"Anonymous, 1","last_name":"Anonymous"},{"last_name":"Anonymous","full_name":"Anonymous, 2","first_name":"2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"},{"last_name":"Anonymous","first_name":"4","full_name":"Anonymous, 4"},{"full_name":"Anonymous, 5","first_name":"5","last_name":"Anonymous"},{"first_name":"6","full_name":"Anonymous, 6","last_name":"Anonymous"}],"language":[{"iso":"eng"}],"oa":1,"pubrep_id":"1066","date_published":"2018-11-11T00:00:00Z","type":"technical_report","scopus_import":1,"corr_author":"1","alternative_title":["IST Austria Technical Report"]},{"issue":"19","article_type":"original","doi":"10.1016/j.cub.2018.08.063","day":"08","abstract":[{"text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.","lang":"eng"}],"author":[{"orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher","first_name":"Christopher","last_name":"Pull","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","first_name":"Sina","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","last_name":"Naderlinger","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth"},{"last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","full_name":"Cremer, Sylvia"}],"oa":1,"date_published":"2018-10-08T00:00:00Z","ddc":["570"],"publisher":"Cell Press","article_processing_charge":"No","citation":{"apa":"Pull, C., Metzler, S., Naderlinger, E., &#38; Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>.","ista":"Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140.","ieee":"C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” <i>Current Biology</i>, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018.","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>.","ama":"Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. <i>Current Biology</i>. 2018;28(19):R1139-R1140. doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140."},"title":"Protection against the lethal side effects of social immunity in ants","external_id":{"isi":["000446693400008"]},"year":"2018","date_created":"2018-12-11T11:44:23Z","intvolume":"        28","department":[{"_id":"SyCr"}],"type":"journal_article","scopus_import":"1","publication":"Current Biology","language":[{"iso":"eng"}],"_id":"55","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"R1139 - R1140","oa_version":"Published Version","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2018.08.063","open_access":"1"}],"status":"public","date_updated":"2026-06-18T18:53:43Z","publist_id":"7999","isi":1,"publication_status":"published","month":"10","volume":28},{"date_published":"2018-05-01T00:00:00Z","author":[{"first_name":"Marcin M","full_name":"Napiórkowski, Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski"},{"last_name":"Reuvers","first_name":"Robin","full_name":"Reuvers, Robin"},{"last_name":"Solovej","first_name":"Jan","full_name":"Solovej, Jan"}],"arxiv":1,"oa":1,"abstract":[{"text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.).","lang":"eng"}],"day":"01","doi":"10.1007/s00220-017-3064-x","issue":"1","date_created":"2018-12-11T11:47:09Z","year":"2018","intvolume":"       360","external_id":{"arxiv":["1511.05953"]},"publication_identifier":{"issn":["0010-3616"]},"title":"The Bogoliubov free energy functional II: The dilute Limit","citation":{"apa":"Napiórkowski, M. M., Reuvers, R., &#38; Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” <i>Communications in Mathematical Physics</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1. Springer, pp. 347–403, 2018.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>.","ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. 2018;360(1):347-403. doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403."},"article_processing_charge":"No","publisher":"Springer","language":[{"iso":"eng"}],"publication":"Communications in Mathematical Physics","project":[{"call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"scopus_import":"1","type":"journal_article","department":[{"_id":"RoSe"}],"volume":360,"month":"05","publication_status":"published","publist_id":"7260","status":"public","date_updated":"2025-07-10T11:52:52Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05953"}],"quality_controlled":"1","oa_version":"Submitted Version","_id":"554","page":"347-403","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"publication":"Current Opinion in Structural Biology","scopus_import":"1","type":"journal_article","department":[{"_id":"MaLo"}],"isi":1,"publication_status":"published","month":"06","volume":50,"publist_id":"7259","date_updated":"2023-09-11T14:07:03Z","status":"public","main_file_link":[{"url":"http://eprints.whiterose.ac.uk/125524/","open_access":"1"}],"quality_controlled":"1","_id":"555","oa_version":"Submitted Version","page":"65 - 74","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-06-01T00:00:00Z","author":[{"full_name":"Richter, Ralf","first_name":"Ralf","last_name":"Richter"},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","full_name":"Baranova, Natalia","first_name":"Natalia","orcid":"0000-0002-3086-9124"},{"last_name":"Day","full_name":"Day, Anthony","first_name":"Anthony"},{"last_name":"Kwok","full_name":"Kwok, Jessica","first_name":"Jessica"}],"oa":1,"abstract":[{"text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.","lang":"eng"}],"day":"01","doi":"10.1016/j.sbi.2017.12.002","article_type":"original","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","year":"2018","date_created":"2018-12-11T11:47:09Z","intvolume":"        50","external_id":{"isi":["000443661300011"]},"title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","citation":{"short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. 2018;50:65-74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>","mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>, vol. 50, Elsevier, 2018, pp. 65–74, doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>.","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” <i>Current Opinion in Structural Biology</i>, vol. 50. Elsevier, pp. 65–74, 2018.","ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74.","chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>.","apa":"Richter, R., Baranova, N. S., Day, A., &#38; Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. 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The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs  were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. ","lang":"eng"}],"project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","call_identifier":"FWF"}],"day":"29","date_published":"2018-03-29T00:00:00Z","author":[{"last_name":"Deny","first_name":"Stephane","full_name":"Deny, Stephane"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"last_name":"Botella-Soler","first_name":"Vicente","full_name":"Botella-Soler, Vicente"},{"first_name":"Georg S","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"}],"oa":1,"datarep_id":"98","type":"research_data","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"doi":"10.15479/AT:ISTA:98","date_updated":"2025-04-15T08:18:24Z","status":"public","title":"Nonlinear decoding of a complex movie from the mammalian retina","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"has_accepted_license":"1","date_created":"2018-12-12T12:31:39Z","year":"2018","month":"03","oa_version":"Published Version","_id":"5584","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"file_date_updated":"2020-07-14T12:47:07Z","citation":{"ieee":"S. Deny, O. Marre, V. Botella-Soler, G. S. Martius, and G. Tkačik, “Nonlinear decoding of a complex movie from the mammalian retina.” Institute of Science and Technology Austria, 2018.","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>.","apa":"Deny, S., Marre, O., Botella-Soler, V., Martius, G. S., &#38; Tkačik, G. (2018). Nonlinear decoding of a complex movie from the mammalian retina. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","mla":"Deny, Stephane, et al. <i>Nonlinear Decoding of a Complex Movie from the Mammalian Retina</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>.","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>"},"related_material":{"record":[{"id":"292","status":"public","relation":"used_in_publication"}]},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"file_size":1142543971,"date_updated":"2020-07-14T12:47:07Z","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","creator":"system","content_type":"application/octet-stream","date_created":"2018-12-12T13:02:24Z","file_id":"5590","relation":"main_file","access_level":"open_access","checksum":"6808748837b9afbbbabc2a356ca2b88a"},{"relation":"main_file","access_level":"open_access","checksum":"d6d6cd07743038fe3a12352983fcf9dd","file_id":"5591","date_created":"2018-12-12T13:02:25Z","creator":"system","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:07Z","file_size":702336},{"date_created":"2018-12-12T13:02:26Z","date_updated":"2020-07-14T12:47:07Z","file_size":432,"creator":"system","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","content_type":"application/octet-stream","relation":"main_file","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","access_level":"open_access","file_id":"5592"},{"file_id":"5593","access_level":"open_access","checksum":"2a83b011012e21e934b4596285b1a183","relation":"main_file","content_type":"text/plain","creator":"system","file_name":"IST-2018-98-v1+4_README.txt","file_size":986,"date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:26Z"}]}]