[{"year":"2018","oa":1,"page":"186 - 191","date_updated":"2023-09-19T10:16:35Z","publication":"PNAS","date_created":"2018-12-11T11:47:04Z","scopus_import":"1","date_published":"2018-01-02T00:00:00Z","external_id":{"isi":["000419128700049"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7273","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"publisher":"National Academy of Sciences","intvolume":"       115","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/152660 "}],"doi":"10.1073/pnas.1711114115","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"}],"issue":"1","_id":"543","title":"Toward a unified theory of efficient, predictive, and sparse coding","author":[{"orcid":"0000-0001-7782-4436","last_name":"Chalk","full_name":"Chalk, Matthew J","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publication_status":"published","status":"public","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","month":"01","citation":{"ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. <i>PNAS</i>. 2018;115(1):186-191. doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191.","short":"M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” <i>PNAS</i>, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>PNAS</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>.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>."},"day":"02","article_processing_charge":"No","volume":115},{"date_updated":"2024-03-25T23:30:15Z","publication":"G3: Genes, Genomes, Genetics","page":"845 - 857","related_material":{"record":[{"id":"6530","relation":"research_paper"},{"relation":"research_paper","id":"6543"},{"relation":"dissertation_contains","status":"public","id":"11193"},{"id":"6546","relation":"dissertation_contains","status":"public"}]},"oa":1,"year":"2018","publisher":"Genetics Society of America","intvolume":"         8","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7271","department":[{"_id":"DaSi"}],"date_created":"2018-12-11T11:47:05Z","scopus_import":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"external_id":{"isi":["000426693300011"]},"date_published":"2018-03-01T00:00:00Z","project":[{"grant_number":"P29638","_id":"253B6E48-B435-11E9-9278-68D0E5697425","name":"Drosophila TNFa´s Funktion in Immunzellen","call_identifier":"FWF"},{"_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","call_identifier":"FWF","name":"The role of Drosophila TNF alpha in immune cell invasion"},{"grant_number":"LSC16-021 ","_id":"2637E9C0-B435-11E9-9278-68D0E5697425","name":"Investigating the role of the novel major superfamily facilitator transporter family member MFSD1 in metastasis"},{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":" A. Ratheesh also by Marie Curie IIF GA-2012-32950BB:DICJI, Marko Roblek by the provincial government of Lower Austria, K. Valoskova and S. Wachner by DOC Fellowships from the Austrian Academy of Sciences, ","_id":"544","title":"Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues","author":[{"first_name":"Attila","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","last_name":"György","full_name":"György, Attila","orcid":"0000-0002-1819-198X"},{"last_name":"Roblek","full_name":"Roblek, Marko","first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9588-1389"},{"orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna","last_name":"Ratheesh","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","first_name":"Aparna"},{"last_name":"Valosková","full_name":"Valosková, Katarina","first_name":"Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87"},{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","full_name":"Belyaeva, Vera","last_name":"Belyaeva"},{"first_name":"Stephanie","id":"2A95E7B0-F248-11E8-B48F-1D18A9856A87","last_name":"Wachner","full_name":"Wachner, Stephanie"},{"first_name":"Yutaka","last_name":"Matsubayashi","full_name":"Matsubayashi, Yutaka"},{"first_name":"Besaiz","last_name":"Sanchez Sanchez","full_name":"Sanchez Sanchez, Besaiz"},{"first_name":"Brian","full_name":"Stramer, Brian","last_name":"Stramer"},{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"}],"doi":"10.1534/g3.117.300452","abstract":[{"text":"Drosophila melanogaster plasmatocytes, the phagocytic cells among hemocytes, are essential for immune responses, but also play key roles from early development to death through their interactions with other cell types. They regulate homeostasis and signaling during development, stem cell proliferation, metabolism, cancer, wound responses and aging, displaying intriguing molecular and functional conservation with vertebrate macrophages. Given the relative ease of genetics in Drosophila compared to vertebrates, tools permitting visualization and genetic manipulation of plasmatocytes and surrounding tissues independently at all stages would greatly aid in fully understanding these processes, but are lacking. Here we describe a comprehensive set of transgenic lines that allow this. These include extremely brightly fluorescing mCherry-based lines that allow GAL4-independent visualization of plasmatocyte nuclei, cytoplasm or actin cytoskeleton from embryonic Stage 8 through adulthood in both live and fixed samples even as heterozygotes, greatly facilitating screening. These lines allow live visualization and tracking of embryonic plasmatocytes, as well as larval plasmatocytes residing at the body wall or flowing with the surrounding hemolymph. With confocal imaging, interactions of plasmatocytes and inner tissues can be seen in live or fixed embryos, larvae and adults. They permit efficient GAL4-independent FACS analysis/sorting of plasmatocytes throughout life. To facilitate genetic analysis of reciprocal signaling, we have also made a plasmatocyte-expressing QF2 line that in combination with extant GAL4 drivers allows independent genetic manipulation of both plasmatocytes and surrounding tissues, and a GAL80 line that blocks GAL4 drivers from affecting plasmatocytes, both of which function from the early embryo to the adult.","lang":"eng"}],"issue":"3","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"creator":"system","file_size":2251222,"relation":"main_file","file_name":"IST-2018-990-v1+1_2018_Gyoergy_Tools_allowing.pdf","date_updated":"2020-07-14T12:46:56Z","content_type":"application/pdf","checksum":"7d9d28b915159078a4ca7add568010e8","access_level":"open_access","date_created":"2018-12-12T10:11:48Z","file_id":"4905"}],"article_processing_charge":"No","volume":8,"has_accepted_license":"1","month":"03","ddc":["570"],"file_date_updated":"2020-07-14T12:46:56Z","citation":{"ieee":"A. György <i>et al.</i>, “Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues,” <i>G3: Genes, Genomes, Genetics</i>, vol. 8, no. 3. Genetics Society of America, pp. 845–857, 2018.","apa":"György, A., Roblek, M., Ratheesh, A., Valosková, K., Belyaeva, V., Wachner, S., … Siekhaus, D. E. (2018). Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/g3.117.300452\">https://doi.org/10.1534/g3.117.300452</a>","short":"A. György, M. Roblek, A. Ratheesh, K. Valosková, V. Belyaeva, S. Wachner, Y. Matsubayashi, B. Sanchez Sanchez, B. Stramer, D.E. Siekhaus, G3: Genes, Genomes, Genetics 8 (2018) 845–857.","ista":"György A, Roblek M, Ratheesh A, Valosková K, Belyaeva V, Wachner S, Matsubayashi Y, Sanchez Sanchez B, Stramer B, Siekhaus DE. 2018. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. G3: Genes, Genomes, Genetics. 8(3), 845–857.","ama":"György A, Roblek M, Ratheesh A, et al. Tools allowing independent visualization and genetic manipulation of Drosophila melanogaster macrophages and surrounding tissues. <i>G3: Genes, Genomes, Genetics</i>. 2018;8(3):845-857. doi:<a href=\"https://doi.org/10.1534/g3.117.300452\">10.1534/g3.117.300452</a>","mla":"György, Attila, et al. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” <i>G3: Genes, Genomes, Genetics</i>, vol. 8, no. 3, Genetics Society of America, 2018, pp. 845–57, doi:<a href=\"https://doi.org/10.1534/g3.117.300452\">10.1534/g3.117.300452</a>.","chicago":"György, Attila, Marko Roblek, Aparna Ratheesh, Katarina Valosková, Vera Belyaeva, Stephanie Wachner, Yutaka Matsubayashi, Besaiz Sanchez Sanchez, Brian Stramer, and Daria E Siekhaus. “Tools Allowing Independent Visualization and Genetic Manipulation of Drosophila Melanogaster Macrophages and Surrounding Tissues.” <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/g3.117.300452\">https://doi.org/10.1534/g3.117.300452</a>."},"pubrep_id":"990","day":"01","oa_version":"Published Version"},{"article_processing_charge":"No","volume":48,"day":"01","citation":{"ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” <i>Current Opinion in Neurobiology</i>, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","apa":"Sacco, R., Cacci, E., &#38; Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">https://doi.org/10.1016/j.conb.2017.12.005</a>","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","ama":"Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. <i>Current Opinion in Neurobiology</i>. 2018;48(2):131-138. doi:<a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">10.1016/j.conb.2017.12.005</a>","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” <i>Current Opinion in Neurobiology</i>, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:<a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">10.1016/j.conb.2017.12.005</a>.","chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.conb.2017.12.005\">https://doi.org/10.1016/j.conb.2017.12.005</a>."},"month":"02","oa_version":"None","status":"public","publication_status":"published","author":[{"full_name":"Sacco, Roberto","last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto"},{"first_name":"Emanuele","last_name":"Cacci","full_name":"Cacci, Emanuele"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"title":"Neural stem cells in neuropsychiatric disorders","_id":"546","issue":"2","abstract":[{"lang":"eng","text":"The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies."}],"doi":"10.1016/j.conb.2017.12.005","intvolume":"        48","publisher":"Elsevier","isi":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"GaNo"}],"publist_id":"7268","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-02-01T00:00:00Z","external_id":{"isi":["000427101600018"]},"scopus_import":"1","date_created":"2018-12-11T11:47:06Z","publication":"Current Opinion in Neurobiology","date_updated":"2023-09-13T09:01:56Z","page":"131 - 138","year":"2018"},{"oa":1,"year":"2018","publication":"Current Biology","date_updated":"2023-09-15T12:06:46Z","article_type":"original","page":"R1139 - R1140","department":[{"_id":"SyCr"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7999","external_id":{"isi":["000446693400008"]},"date_published":"2018-10-08T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:44:23Z","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2018.08.063","open_access":"1"}],"intvolume":"        28","publisher":"Cell Press","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-1122-3982","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","full_name":"Pull, Christopher","last_name":"Pull"},{"full_name":"Metzler, Sina","last_name":"Metzler","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","orcid":"0000-0002-9547-2494"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"title":"Protection against the lethal side effects of social immunity in ants","_id":"55","issue":"19","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"}],"doi":"10.1016/j.cub.2018.08.063","status":"public","publication_status":"published","day":"08","citation":{"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>","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.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","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>","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>.","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>."},"month":"10","oa_version":"Published Version","article_processing_charge":"No","volume":28},{"month":"05","day":"01","citation":{"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>.","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>.","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.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","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>","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.","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>"},"oa_version":"Submitted Version","arxiv":1,"volume":360,"_id":"554","author":[{"first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"last_name":"Reuvers","full_name":"Reuvers, Robin","first_name":"Robin"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"title":"The Bogoliubov free energy functional II: The dilute Limit","doi":"10.1007/s00220-017-3064-x","issue":"1","abstract":[{"lang":"eng","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.)."}],"project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"publication_identifier":{"issn":["00103616"]},"publication_status":"published","status":"public","publist_id":"7260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"scopus_import":1,"date_created":"2018-12-11T11:47:09Z","external_id":{"arxiv":["1511.05953"]},"date_published":"2018-05-01T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/1511.05953","open_access":"1"}],"intvolume":"       360","publisher":"Springer","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2018","date_updated":"2021-01-12T08:02:35Z","publication":"Communications in Mathematical Physics","page":"347-403"},{"doi":"10.1016/j.sbi.2017.12.002","abstract":[{"lang":"eng","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."}],"_id":"555","title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","author":[{"last_name":"Richter","full_name":"Richter, Ralf","first_name":"Ralf"},{"first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","last_name":"Baranova","full_name":"Baranova, Natalia","orcid":"0000-0002-3086-9124"},{"last_name":"Day","full_name":"Day, Anthony","first_name":"Anthony"},{"full_name":"Kwok, Jessica","last_name":"Kwok","first_name":"Jessica"}],"publication_status":"published","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","status":"public","oa_version":"Submitted Version","month":"06","citation":{"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.","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>","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","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>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/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.","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>.","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>."},"day":"01","article_processing_charge":"No","volume":50,"year":"2018","oa":1,"page":"65 - 74","article_type":"original","date_updated":"2023-09-11T14:07:03Z","publication":"Current Opinion in Structural Biology","date_created":"2018-12-11T11:47:09Z","scopus_import":"1","external_id":{"isi":["000443661300011"]},"date_published":"2018-06-01T00:00:00Z","publist_id":"7259","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MaLo"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"publisher":"Elsevier","main_file_link":[{"url":"http://eprints.whiterose.ac.uk/125524/","open_access":"1"}],"intvolume":"        50"},{"date_updated":"2024-02-20T10:48:17Z","publication":"Annales Henri Poincare","article_type":"original","page":"3663-3742","oa":1,"year":"2018","intvolume":"        19","publisher":"Springer Nature","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publist_id":"7258","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"scopus_import":"1","date_created":"2018-12-11T11:47:09Z","external_id":{"arxiv":["1704.05809"]},"date_published":"2018-11-13T00:00:00Z","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"publication_identifier":{"issn":["1424-0637"]},"ec_funded":1,"status":"public","publication_status":"published","_id":"556","author":[{"first_name":"Dan","full_name":"Betea, Dan","last_name":"Betea"},{"first_name":"Jeremie","full_name":"Bouttier, Jeremie","last_name":"Bouttier"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Nejjar, Peter","last_name":"Nejjar"},{"first_name":"Mirjana","last_name":"Vuletic","full_name":"Vuletic, Mirjana"}],"title":"The free boundary Schur process and applications I","doi":"10.1007/s00023-018-0723-1","issue":"12","abstract":[{"text":"We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions.","lang":"eng"}],"file":[{"file_id":"5866","date_created":"2019-01-21T15:18:55Z","access_level":"open_access","checksum":"0c38abe73569b7166b7487ad5d23cc68","content_type":"application/pdf","date_updated":"2020-07-14T12:47:03Z","file_name":"2018_Annales_Betea.pdf","creator":"dernst","relation":"main_file","file_size":3084674}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"arxiv":1,"volume":19,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:03Z","ddc":["500"],"month":"11","day":"13","citation":{"mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>.","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00023-018-0723-1\">https://doi.org/10.1007/s00023-018-0723-1</a>.","ieee":"D. Betea, J. Bouttier, P. Nejjar, and M. Vuletic, “The free boundary Schur process and applications I,” <i>Annales Henri Poincare</i>, vol. 19, no. 12. Springer Nature, pp. 3663–3742, 2018.","apa":"Betea, D., Bouttier, J., Nejjar, P., &#38; Vuletic, M. (2018). The free boundary Schur process and applications I. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-018-0723-1\">https://doi.org/10.1007/s00023-018-0723-1</a>","ista":"Betea D, Bouttier J, Nejjar P, Vuletic M. 2018. The free boundary Schur process and applications I. Annales Henri Poincare. 19(12), 3663–3742.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","ama":"Betea D, Bouttier J, Nejjar P, Vuletic M. The free boundary Schur process and applications I. <i>Annales Henri Poincare</i>. 2018;19(12):3663-3742. doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>"},"oa_version":"Published Version"},{"keyword":["microscopy","microfluidics"],"doi":"10.15479/AT:ISTA:74","year":"2018","abstract":[{"lang":"eng","text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic."}],"_id":"5569","author":[{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","full_name":"Nikolic, Nela","last_name":"Nikolic","orcid":"0000-0001-9068-6090"}],"oa":1,"title":"Time-lapse microscopy data","datarep_id":"74","status":"public","related_material":{"record":[{"id":"438","status":"public","relation":"research_paper"}]},"date_updated":"2024-02-21T13:44:45Z","oa_version":"Published Version","date_created":"2018-12-12T12:31:35Z","date_published":"2018-02-07T00:00:00Z","ddc":["579"],"publist_id":"7385","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:04Z","month":"02","department":[{"_id":"CaGu"}],"day":"07","citation":{"chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>.","mla":"Bergmiller, Tobias, and Nela Nikolic. <i>Time-Lapse Microscopy Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>.","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>.","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>","short":"T. Bergmiller, N. Nikolic, (2018).","apa":"Bergmiller, T., &#38; Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018."},"type":"research_data","article_processing_charge":"No","has_accepted_license":"1","file":[{"file_id":"5637","date_created":"2018-12-12T13:04:39Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","creator":"system","relation":"main_file","file_size":3558703796,"date_updated":"2020-07-14T12:47:04Z","access_level":"open_access","checksum":"61ebb92213cfffeba3ddbaff984b81af","content_type":"application/zip"},{"file_id":"5638","date_created":"2018-12-12T13:04:55Z","file_name":"IST-2018-74-v1+3_15-07-31.zip","relation":"main_file","file_size":1830422606,"creator":"system","access_level":"open_access","checksum":"bf26649af310ef6892d68576515cde6d","content_type":"application/zip","date_updated":"2020-07-14T12:47:04Z"},{"file_id":"5639","date_created":"2018-12-12T13:05:11Z","file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","relation":"main_file","file_size":2140849248,"creator":"system","date_updated":"2020-07-14T12:47:04Z","access_level":"open_access","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","content_type":"application/zip"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"publisher":"Institute of Science and Technology Austria"},{"citation":{"ama":"Alhaija H, Sellent A, Kondermann D, Rother C. 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Rother, “Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018.","mla":"Alhaija, Hassan, et al. <i>Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:82\">10.15479/AT:ISTA:82</a>.","chicago":"Alhaija, Hassan, Anita Sellent, Daniel Kondermann, and Carsten Rother. “Graph Matching Problems for GraphFlow – 6D Large Displacement Scene Flow.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:82\">https://doi.org/10.15479/AT:ISTA:82</a>."},"department":[{"_id":"VlKo"}],"day":"04","ddc":["001"],"file_date_updated":"2020-07-14T12:47:05Z","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-01-04T00:00:00Z","date_created":"2018-12-12T12:31:36Z","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2018-12-12T13:02:34Z","file_id":"5600","content_type":"application/zip","checksum":"53c17082848e12f3c2e1b4185b578208","access_level":"open_access","date_updated":"2020-07-14T12:47:05Z","relation":"main_file","file_size":1737958,"creator":"system","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"contributor":[{"last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","contributor_type":"researcher"}],"has_accepted_license":"1","article_processing_charge":"No","type":"research_data","title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","oa":1,"datarep_id":"82","author":[{"full_name":"Alhaija, Hassan","last_name":"Alhaija","first_name":"Hassan"},{"first_name":"Anita","full_name":"Sellent, Anita","last_name":"Sellent"},{"full_name":"Kondermann, Daniel","last_name":"Kondermann","first_name":"Daniel"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"}],"_id":"5573","abstract":[{"lang":"eng","text":"Graph matching problems for large displacement optical flow of RGB-D images."}],"year":"2018","doi":"10.15479/AT:ISTA:82","keyword":["graph matching","quadratic assignment problem<"],"date_updated":"2024-02-21T13:41:17Z","related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-319-24947-6_23","relation":"research_paper"}]},"status":"public"},{"article_processing_charge":"No","type":"research_data","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","file":[{"relation":"main_file","file_size":12283857,"creator":"system","file_name":"IST-2018-86-v1+1_Data_Check_IOP_Scopus_vs._Publisher.zip","date_updated":"2020-07-14T12:47:05Z","checksum":"c7a61147bd15cb4ae45878d270628c06","content_type":"application/zip","access_level":"open_access","date_created":"2018-12-12T13:05:14Z","file_id":"5642"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"date_created":"2018-12-12T12:31:37Z","oa_version":"Submitted Version","date_published":"2018-01-16T00:00:00Z","ddc":["020"],"file_date_updated":"2020-07-14T12:47:05Z","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Villányi, M. (2018). Data Check IOP Scopus vs. Publisher. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:86\">https://doi.org/10.15479/AT:ISTA:86</a>","ieee":"M. Villányi, “Data Check IOP Scopus vs. Publisher.” Institute of Science and Technology Austria, 2018.","ista":"Villányi M. 2018. Data Check IOP Scopus vs. Publisher, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:86\">10.15479/AT:ISTA:86</a>.","ama":"Villányi M. Data Check IOP Scopus vs. Publisher. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:86\">10.15479/AT:ISTA:86</a>","short":"M. Villányi, (2018).","chicago":"Villányi, Márton. “Data Check IOP Scopus vs. Publisher.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:86\">https://doi.org/10.15479/AT:ISTA:86</a>.","mla":"Villányi, Márton. <i>Data Check IOP Scopus vs. Publisher</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:86\">10.15479/AT:ISTA:86</a>."},"day":"16","department":[{"_id":"E-Lib"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"278"}]},"status":"public","date_updated":"2024-02-21T13:42:21Z","doi":"10.15479/AT:ISTA:86","keyword":["Publication analysis","Bibliography","Open Access"],"abstract":[{"text":"Comparison of Scopus' and publisher's data on Austrian publication output at IOP. ","lang":"ger"}],"year":"2018","_id":"5574","datarep_id":"86","oa":1,"title":"Data Check IOP Scopus vs. Publisher","author":[{"first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","last_name":"Villányi","full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426"}]},{"date_updated":"2024-02-21T13:43:25Z","related_material":{"record":[{"id":"278","status":"public","relation":"part_of_dissertation"}]},"status":"public","_id":"5575","datarep_id":"87","title":"Data Check RSC Scopus vs. FWF","oa":1,"author":[{"orcid":"0000-0001-8126-0426","full_name":"Villányi, Márton","last_name":"Villányi","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","first_name":"Márton"}],"doi":"10.15479/AT:ISTA:87","keyword":["Publication analysis","Bibliography","Open Access"],"abstract":[{"lang":"ger","text":"Comparison of Scopus' and FWF's data on Austrian publication output at RSC. 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Villányi, “Taylor&#38;Francis Austrian Publications 2013-2017.” Institute of Science and Technology Austria, 2018."},"day":"16","department":[{"_id":"E-Lib"}],"date_created":"2018-12-12T12:31:39Z","oa_version":"Submitted Version","date_published":"2018-01-16T00:00:00Z"},{"contributor":[{"first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","type":"research_data","article_processing_charge":"No","file":[{"file_id":"5606","date_created":"2018-12-12T13:02:41Z","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","file_size":122048,"creator":"system","relation":"main_file","access_level":"open_access","content_type":"text/csv","checksum":"fc6aab51439f2622ba6df8632e66fd4f","date_updated":"2020-07-14T12:47:07Z"},{"file_id":"5607","date_created":"2018-12-12T13:02:42Z","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","creator":"system","relation":"main_file","file_size":235980,"date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","checksum":"92347586ae4f8a6eb7c04354797bf314","content_type":"text/csv"},{"file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","relation":"main_file","creator":"system","file_size":311712,"access_level":"open_access","checksum":"3300813645a54e6c5c39f41917228354","content_type":"text/csv","date_updated":"2020-07-14T12:47:07Z","file_id":"5608","date_created":"2018-12-12T13:02:43Z"},{"file_size":342090,"relation":"main_file","creator":"system","file_name":"IST-2018-95-v1+4_faps_scripts.zip","date_updated":"2020-07-14T12:47:07Z","checksum":"e739fc473567fd8f39438b445fc46147","content_type":"application/zip","access_level":"open_access","date_created":"2018-12-12T13:02:44Z","file_id":"5609"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"publisher":"Institute of Science and Technology Austria","date_published":"2018-02-12T00:00:00Z","date_created":"2018-12-12T12:31:39Z","oa_version":"Published Version","department":[{"_id":"NiBa"}],"day":"12","citation":{"chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>.","mla":"Ellis, Thomas. <i>Data and Python Scripts Supporting Python Package FAPS</i>. 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Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone."}],"doi":"10.15479/AT:ISTA:95","author":[{"full_name":"Ellis, Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-8511-0254"}],"oa":1,"title":"Data and Python scripts supporting Python package FAPS","datarep_id":"95","_id":"5583"},{"date_published":"2018-03-29T00:00:00Z","date_created":"2018-12-12T12:31:39Z","oa_version":"Published Version","day":"29","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"citation":{"mla":"Deny, Stephane, et al. <i>Nonlinear Decoding of a Complex Movie from the Mammalian Retina</i>. 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Tkačik, (2018)."},"month":"03","file_date_updated":"2020-07-14T12:47:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"has_accepted_license":"1","type":"research_data","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"file":[{"date_updated":"2020-07-14T12:47:07Z","content_type":"application/octet-stream","checksum":"6808748837b9afbbbabc2a356ca2b88a","access_level":"open_access","relation":"main_file","file_size":1142543971,"creator":"system","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","date_created":"2018-12-12T13:02:24Z","file_id":"5590"},{"content_type":"application/pdf","checksum":"d6d6cd07743038fe3a12352983fcf9dd","access_level":"open_access","date_updated":"2020-07-14T12:47:07Z","file_size":702336,"relation":"main_file","creator":"system","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","date_created":"2018-12-12T13:02:25Z","file_id":"5591"},{"file_id":"5592","date_created":"2018-12-12T13:02:26Z","date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","content_type":"application/octet-stream","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","relation":"main_file","creator":"system","file_size":432},{"creator":"system","relation":"main_file","file_size":986,"file_name":"IST-2018-98-v1+4_README.txt","date_updated":"2020-07-14T12:47:07Z","checksum":"2a83b011012e21e934b4596285b1a183","content_type":"text/plain","access_level":"open_access","date_created":"2018-12-12T13:02:26Z","file_id":"5593"}],"publisher":"Institute of Science and Technology Austria","year":"2018","abstract":[{"text":"This package contains data for the publication \"Nonlinear decoding of a complex movie from the mammalian retina\" by Deny S. et al, PLOS Comput Biol (2018). \r\n\r\nThe data consists of\r\n(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. 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. 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