[{"intvolume":"        48","publist_id":"7268","date_updated":"2024-10-09T20:58:31Z","date_published":"2018-02-01T00:00:00Z","corr_author":"1","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."}],"citation":{"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>","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>.","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.","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","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>.","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>"},"volume":48,"month":"02","page":"131 - 138","author":[{"first_name":"Roberto","last_name":"Sacco","full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cacci, Emanuele","first_name":"Emanuele","last_name":"Cacci"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia"}],"status":"public","issue":"2","publication":"Current Opinion in Neurobiology","quality_controlled":"1","date_created":"2018-12-11T11:47:06Z","isi":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.conb.2017.12.005","scopus_import":"1","oa_version":"None","_id":"546","title":"Neural stem cells in neuropsychiatric disorders","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Elsevier","publication_status":"published","year":"2018","department":[{"_id":"GaNo"}],"type":"journal_article","day":"01","external_id":{"isi":["000427101600018"]}},{"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2018.08.063","_id":"55","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T11:44:23Z","isi":1,"publication_status":"published","year":"2018","publisher":"Cell Press","department":[{"_id":"SyCr"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2018.08.063","open_access":"1"}],"type":"journal_article","day":"08","external_id":{"isi":["000446693400008"]},"oa":1,"article_processing_charge":"No","title":"Protection against the lethal side effects of social immunity in ants","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-10-08T00:00:00Z","abstract":[{"lang":"eng","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."}],"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>","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","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>.","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.","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>.","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."},"intvolume":"        28","publist_id":"7999","date_updated":"2023-09-15T12:06:46Z","status":"public","author":[{"orcid":"0000-0003-1122-3982","last_name":"Pull","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","full_name":"Pull, Christopher"},{"full_name":"Metzler, Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","last_name":"Metzler","orcid":"0000-0002-9547-2494"},{"full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","last_name":"Naderlinger"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"issue":"19","publication":"Current Biology","volume":28,"month":"10","page":"R1139 - R1140"},{"date_published":"2018-05-01T00:00:00Z","citation":{"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.","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>","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.","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>.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","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>.","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>"},"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"}],"intvolume":"       360","publist_id":"7260","date_updated":"2025-07-10T11:52:52Z","status":"public","author":[{"last_name":"Napiórkowski","first_name":"Marcin M","full_name":"Napiórkowski, Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reuvers, Robin","first_name":"Robin","last_name":"Reuvers"},{"last_name":"Solovej","first_name":"Jan","full_name":"Solovej, Jan"}],"publication":"Communications in Mathematical Physics","issue":"1","volume":360,"month":"05","page":"347-403","language":[{"iso":"eng"}],"doi":"10.1007/s00220-017-3064-x","_id":"554","scopus_import":"1","oa_version":"Submitted Version","project":[{"grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","date_created":"2018-12-11T11:47:09Z","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"main_file_link":[{"url":"https://arxiv.org/abs/1511.05953","open_access":"1"}],"type":"journal_article","day":"01","external_id":{"arxiv":["1511.05953"]},"oa":1,"article_processing_charge":"No","title":"The Bogoliubov free energy functional II: The dilute Limit","publication_identifier":{"issn":["0010-3616"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1},{"article_processing_charge":"No","title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","year":"2018","publisher":"Elsevier","main_file_link":[{"url":"http://eprints.whiterose.ac.uk/125524/","open_access":"1"}],"department":[{"_id":"MaLo"}],"type":"journal_article","day":"01","external_id":{"isi":["000443661300011"]},"oa":1,"quality_controlled":"1","date_created":"2018-12-11T11:47:09Z","isi":1,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1016/j.sbi.2017.12.002","_id":"555","oa_version":"Submitted Version","scopus_import":"1","volume":50,"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","month":"06","page":"65 - 74","status":"public","author":[{"full_name":"Richter, Ralf","first_name":"Ralf","last_name":"Richter"},{"first_name":"Natalia","last_name":"Baranova","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Day, Anthony","first_name":"Anthony","last_name":"Day"},{"first_name":"Jessica","last_name":"Kwok","full_name":"Kwok, Jessica"}],"publication":"Current Opinion in Structural Biology","intvolume":"        50","publist_id":"7259","date_updated":"2023-09-11T14:07:03Z","date_published":"2018-06-01T00:00:00Z","citation":{"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.","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","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>.","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>","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>","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>.","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."},"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."}]},{"department":[{"_id":"LaEr"},{"_id":"JaMa"}],"publisher":"Springer Nature","publication_status":"published","year":"2018","oa":1,"day":"13","external_id":{"arxiv":["1704.05809"],"isi":["000450487900003"]},"type":"journal_article","title":"The free boundary Schur process and applications I","article_processing_charge":"Yes (via OA deal)","license":"https://creativecommons.org/licenses/by/4.0/","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["1424-0637"]},"file_date_updated":"2020-07-14T12:47:03Z","language":[{"iso":"eng"}],"article_type":"original","oa_version":"Published Version","scopus_import":"1","_id":"556","doi":"10.1007/s00023-018-0723-1","quality_controlled":"1","project":[{"name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804"},{"grant_number":"716117","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"}],"isi":1,"date_created":"2018-12-11T11:47:09Z","author":[{"last_name":"Betea","first_name":"Dan","full_name":"Betea, Dan"},{"last_name":"Bouttier","first_name":"Jeremie","full_name":"Bouttier, Jeremie"},{"first_name":"Peter","last_name":"Nejjar","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","full_name":"Nejjar, Peter"},{"first_name":"Mirjana","last_name":"Vuletic","full_name":"Vuletic, Mirjana"}],"status":"public","publication":"Annales Henri Poincare","issue":"12","month":"11","ddc":["500"],"ec_funded":1,"volume":19,"file":[{"relation":"main_file","checksum":"0c38abe73569b7166b7487ad5d23cc68","date_updated":"2020-07-14T12:47:03Z","creator":"dernst","date_created":"2019-01-21T15:18:55Z","access_level":"open_access","file_size":3084674,"content_type":"application/pdf","file_name":"2018_Annales_Betea.pdf","file_id":"5866"}],"page":"3663-3742","date_published":"2018-11-13T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"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.","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>.","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>","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>","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.","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>.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742."},"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"}],"has_accepted_license":"1","intvolume":"        19","date_updated":"2025-09-18T07:34:29Z","publist_id":"7258"},{"month":"01","title":"Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow","ddc":["001"],"article_processing_charge":"No","license":"https://creativecommons.org/publicdomain/zero/1.0/","file":[{"relation":"main_file","checksum":"53c17082848e12f3c2e1b4185b578208","date_updated":"2020-07-14T12:47:05Z","creator":"system","date_created":"2018-12-12T13:02:34Z","access_level":"open_access","file_size":1737958,"content_type":"application/zip","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","file_id":"5600"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"82","author":[{"last_name":"Alhaija","first_name":"Hassan","full_name":"Alhaija, Hassan"},{"full_name":"Sellent, Anita","first_name":"Anita","last_name":"Sellent"},{"first_name":"Daniel","last_name":"Kondermann","full_name":"Kondermann, Daniel"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"department":[{"_id":"VlKo"}],"status":"public","publisher":"Institute of Science and Technology Austria","year":"2018","oa":1,"day":"04","type":"research_data","keyword":["graph matching","quadratic assignment problem<"],"date_updated":"2024-02-21T13:41:17Z","date_created":"2018-12-12T12:31:36Z","file_date_updated":"2020-07-14T12:47:05Z","date_published":"2018-01-04T00:00:00Z","related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-319-24947-6_23","relation":"research_paper"}]},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Graph matching problems for large displacement optical flow of RGB-D images."}],"_id":"5573","citation":{"ista":"Alhaija H, Sellent A, Kondermann D, Rother C. 2018. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:82\">10.15479/AT:ISTA:82</a>.","apa":"Alhaija, H., Sellent, A., Kondermann, D., &#38; Rother, C. (2018). Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:82\">https://doi.org/10.15479/AT:ISTA:82</a>","short":"H. Alhaija, A. Sellent, D. Kondermann, C. Rother, (2018).","ieee":"H. Alhaija, A. Sellent, D. Kondermann, and C. 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>.","ama":"Alhaija H, Sellent A, Kondermann D, Rother C. Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:82\">10.15479/AT:ISTA:82</a>"},"contributor":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda","contributor_type":"researcher"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:82"},{"date_created":"2018-12-12T12:31:39Z","date_updated":"2025-04-15T07:11:03Z","doi":"10.15479/AT:ISTA:95","has_accepted_license":"1","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"_id":"5583","citation":{"ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","short":"T. Ellis, (2018).","mla":"Ellis, Thomas. <i>Data and Python Scripts Supporting Python Package FAPS</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>.","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:95\">https://doi.org/10.15479/AT:ISTA:95</a>","ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>","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>.","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:95\">10.15479/AT:ISTA:95</a>."},"abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. 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.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"research_paper","id":"286"}]},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"date_published":"2018-02-12T00:00:00Z","file_date_updated":"2020-07-14T12:47:07Z","datarep_id":"95","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_size":122048,"content_type":"text/csv","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","file_id":"5606","relation":"main_file","checksum":"fc6aab51439f2622ba6df8632e66fd4f","creator":"system","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:41Z","access_level":"open_access"},{"file_id":"5607","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","content_type":"text/csv","file_size":235980,"date_created":"2018-12-12T13:02:42Z","access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:47:07Z","checksum":"92347586ae4f8a6eb7c04354797bf314","relation":"main_file"},{"file_size":311712,"content_type":"text/csv","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv","file_id":"5608","relation":"main_file","checksum":"3300813645a54e6c5c39f41917228354","creator":"system","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:43Z","access_level":"open_access"},{"relation":"main_file","checksum":"e739fc473567fd8f39438b445fc46147","date_updated":"2020-07-14T12:47:07Z","creator":"system","date_created":"2018-12-12T13:02:44Z","access_level":"open_access","file_size":342090,"content_type":"application/zip","file_name":"IST-2018-95-v1+4_faps_scripts.zip","file_id":"5609"}],"article_processing_charge":"No","title":"Data and Python scripts supporting Python package FAPS","month":"02","type":"research_data","day":"12","oa":1,"year":"2018","publisher":"Institute of Science and Technology Austria","status":"public","department":[{"_id":"NiBa"}],"author":[{"full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","orcid":"0000-0002-8511-0254","first_name":"Thomas"}]},{"abstract":[{"lang":"eng","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. "}],"_id":"5584","citation":{"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>.","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","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.","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>","ama":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 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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>."},"oa_version":"Published Version","has_accepted_license":"1","doi":"10.15479/AT:ISTA:98","date_published":"2018-03-29T00:00:00Z","file_date_updated":"2020-07-14T12:47:07Z","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"292"}]},"date_updated":"2025-04-15T08:18:24Z","date_created":"2018-12-12T12:31:39Z","project":[{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 25651-N26"}],"keyword":["retina","decoding","regression","neural networks","complex stimulus"],"day":"29","oa":1,"type":"research_data","status":"public","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"author":[{"first_name":"Stephane","last_name":"Deny","full_name":"Deny, Stephane"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Botella-Soler, Vicente","first_name":"Vicente","last_name":"Botella-Soler"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"year":"2018","publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2018-12-12T13:02:24Z","access_level":"open_access","date_updated":"2020-07-14T12:47:07Z","creator":"system","checksum":"6808748837b9afbbbabc2a356ca2b88a","relation":"main_file","file_id":"5590","file_name":"IST-2018-98-v1+1_BBalls_area2_tile2_20x20.mat","content_type":"application/octet-stream","file_size":1142543971},{"content_type":"application/pdf","file_size":702336,"file_id":"5591","file_name":"IST-2018-98-v1+2_ExperimentStructure.pdf","checksum":"d6d6cd07743038fe3a12352983fcf9dd","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T13:02:25Z","date_updated":"2020-07-14T12:47:07Z","creator":"system"},{"date_updated":"2020-07-14T12:47:07Z","creator":"system","access_level":"open_access","date_created":"2018-12-12T13:02:26Z","relation":"main_file","checksum":"0c9cfb4dab35bb3dc25a04395600b1c8","file_name":"IST-2018-98-v1+3_GoodLocations_area2_20x20.mat","file_id":"5592","file_size":432,"content_type":"application/octet-stream"},{"checksum":"2a83b011012e21e934b4596285b1a183","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T13:02:26Z","date_updated":"2020-07-14T12:47:07Z","creator":"system","content_type":"text/plain","file_size":986,"file_id":"5593","file_name":"IST-2018-98-v1+4_README.txt"}],"datarep_id":"98","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","article_processing_charge":"No","ddc":["570"],"title":"Nonlinear decoding of a complex movie from the mammalian retina"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"109","file":[{"date_created":"2018-12-12T13:02:35Z","access_level":"open_access","date_updated":"2020-07-14T12:47:08Z","creator":"system","checksum":"e60b484bd6f55c08eb66a189cb72c923","relation":"main_file","file_id":"5601","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","content_type":"application/zip","file_size":11918144}],"ddc":["570"],"title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","article_processing_charge":"No","month":"07","type":"research_data","oa":1,"day":"24","publisher":"Institute of Science and Technology Austria","year":"2018","author":[{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"status":"public","department":[{"_id":"BeVi"}],"date_created":"2018-12-12T12:31:40Z","date_updated":"2025-04-15T08:18:37Z","keyword":["schistosoma","Z-chromosome","gene expression"],"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28842-B22"}],"contributor":[{"orcid":"0000-0002-8101-2518","last_name":"Picard","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:109","oa_version":"Published Version","citation":{"ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","short":"B. Vicoso, (2018).","mla":"Vicoso, Beatriz. <i>Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018)</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>."},"_id":"5586","abstract":[{"text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018).","lang":"eng"}],"related_material":{"record":[{"relation":"research_paper","status":"public","id":"131"}]},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"file_date_updated":"2020-07-14T12:47:08Z","date_published":"2018-07-24T00:00:00Z"},{"date_updated":"2025-04-15T06:50:08Z","date_created":"2018-12-12T12:31:41Z","keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27"}],"oa_version":"Published Version","citation":{"ista":"De Martino D, Tkačik G. 2018. Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>.","apa":"De Martino, D., &#38; Tkačik, G. (2018). Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:62\">https://doi.org/10.15479/AT:ISTA:62</a>","ieee":"D. De Martino and G. Tkačik, “Supporting materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018.","mla":"De Martino, Daniele, and Gašper Tkačik. <i>Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>.","short":"D. De Martino, G. Tkačik, (2018).","chicago":"De Martino, Daniele, and Gašper Tkačik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:62\">https://doi.org/10.15479/AT:ISTA:62</a>.","ama":"De Martino D, Tkačik G. Supporting materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:62\">10.15479/AT:ISTA:62</a>"},"_id":"5587","abstract":[{"lang":"eng","text":"Supporting material to the article \r\nSTATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\r\n\r\nboundscoli.dat\r\nFlux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium. \r\n\r\npolcoli.dat\r\nMatrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium, \r\nobtained from the soichiometric matrix by standard linear algebra  (reduced row echelon form).\r\n\r\nellis.dat\r\nApproximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\npoint0.dat\r\nCenter of the approximate Lowner-John ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium\r\nobtained with the Lovasz method.\r\n\r\nlovasz.cpp  \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), and it gives in output an approximate Lowner-John ellipsoid rounding the polytope\r\nwith the Lovasz method \r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015).\r\n\r\nsampleHRnew.cpp  \r\nThis c++ code file receives in input the polytope of the feasible steady states of a metabolic network, \r\n(matrix and bounds), the ellipsoid rounding the polytope, a point inside and  \r\nit gives in output a max entropy sampling at fixed average growth rate \r\nof the steady states by performing an Hit-and-Run Monte Carlo Markov chain.\r\nNB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260. \r\nFor further details we refer to  PLoS ONE 10.4 e0122670 (2015)."}],"doi":"10.15479/AT:ISTA:62","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:08Z","date_published":"2018-09-21T00:00:00Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"161"}]},"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"file":[{"relation":"main_file","checksum":"97992e3e8cf8544ec985a48971708726","date_updated":"2020-07-14T12:47:08Z","creator":"system","date_created":"2018-12-12T13:05:13Z","access_level":"open_access","file_size":14376,"content_type":"application/zip","file_name":"IST-2018-111-v1+1_CODES.zip","file_id":"5641"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"111","month":"09","title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","ddc":["530"],"article_processing_charge":"No","ec_funded":1,"oa":1,"day":"21","type":"research_data","author":[{"full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GaTk"}],"status":"public","publisher":"Institute of Science and Technology Austria","year":"2018"},{"quality_controlled":"1","date_created":"2018-12-11T11:47:11Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:09Z","doi":"10.1007/978-1-4939-7571-6_15","_id":"562","oa_version":"Submitted Version","scopus_import":1,"article_processing_charge":"No","title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2018","publisher":"Springer","department":[{"_id":"RySh"}],"type":"book_chapter","pmid":1,"external_id":{"pmid":["29222783"]},"day":"01","oa":1,"intvolume":"      1727","publist_id":"7252","date_updated":"2021-01-12T08:03:05Z","date_published":"2018-01-01T00:00:00Z","has_accepted_license":"1","citation":{"ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., &#38; Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), <i>Neurotrophic Factors</i> (Vol. 1727, pp. 201–215). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">https://doi.org/10.1007/978-1-4939-7571-6_15</a>","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in <i>Neurotrophic Factors</i>, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” <i>Neurotrophic Factors</i>, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:<a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">10.1007/978-1-4939-7571-6_15</a>.","chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In <i>Neurotrophic Factors</i>, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. <a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">https://doi.org/10.1007/978-1-4939-7571-6_15</a>.","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. <i>Neurotrophic Factors</i>. Vol 1727. Springer; 2018:201-215. doi:<a href=\"https://doi.org/10.1007/978-1-4939-7571-6_15\">10.1007/978-1-4939-7571-6_15</a>"},"abstract":[{"lang":"eng","text":"Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals."}],"volume":1727,"ddc":["570"],"month":"01","page":"201 - 215","editor":[{"full_name":"Skaper, Stephen D.","first_name":"Stephen D.","last_name":"Skaper"}],"file":[{"file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","file_id":"7046","file_size":787407,"content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:47:09Z","access_level":"open_access","date_created":"2019-11-19T07:47:43Z","relation":"main_file","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd"}],"status":"public","author":[{"last_name":"Dimitrov","first_name":"Dimitar","full_name":"Dimitrov, Dimitar"},{"last_name":"Guillaud","first_name":"Laurent","full_name":"Guillaud, Laurent"},{"first_name":"Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku"},{"first_name":"Tomoyuki","last_name":"Takahashi","full_name":"Takahashi, Tomoyuki"}],"alternative_title":["Methods in Molecular Biology"],"publication":"Neurotrophic Factors"},{"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:09Z","article_type":"original","oa_version":"Submitted Version","scopus_import":"1","_id":"564","doi":"10.1016/j.tpb.2017.11.007","quality_controlled":"1","project":[{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"isi":1,"date_created":"2018-12-11T11:47:12Z","department":[{"_id":"NiBa"}],"publisher":"Academic Press","publication_status":"published","year":"2018","oa":1,"external_id":{"isi":["000440392900014"]},"day":"01","type":"journal_article","title":"Establishment in a new habitat by polygenic adaptation","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-07-01T00:00:00Z","related_material":{"record":[{"id":"9842","relation":"research_data","status":"public"}]},"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"abstract":[{"text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population.","lang":"eng"}],"citation":{"chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>. Academic Press, 2018. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. 2018;122(7):110-127. doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>","apa":"Barton, N. H., &#38; Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. <i>Theoretical Population Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">https://doi.org/10.1016/j.tpb.2017.11.007</a>","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” <i>Theoretical Population Biology</i>, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” <i>Theoretical Population Biology</i>, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:<a href=\"https://doi.org/10.1016/j.tpb.2017.11.007\">10.1016/j.tpb.2017.11.007</a>.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127."},"has_accepted_license":"1","intvolume":"       122","date_updated":"2025-04-15T07:11:04Z","publist_id":"7250","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"status":"public","publication":"Theoretical Population Biology","issue":"7","month":"07","ddc":["519","576"],"volume":122,"ec_funded":1,"file":[{"checksum":"0b96f6db47e3e91b5e7d103b847c239d","relation":"main_file","date_created":"2019-12-21T09:36:39Z","access_level":"open_access","date_updated":"2020-07-14T12:47:09Z","creator":"nbarton","content_type":"application/pdf","file_size":2287682,"file_id":"7199","file_name":"bartonetheridge.pdf"}],"page":"110-127"},{"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300426","scopus_import":"1","oa_version":"Published Version","_id":"565","quality_controlled":"1","date_created":"2018-12-11T11:47:12Z","isi":1,"publisher":"Genetics Society of America","year":"2018","publication_status":"published","department":[{"_id":"NiBa"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}],"type":"journal_article","oa":1,"day":"01","external_id":{"isi":["000419356300025"],"pmid":["29158424"]},"pmid":1,"title":"The spread of an inversion with migration and selection","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-01-01T00:00:00Z","abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"citation":{"ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","apa":"Charlesworth, B., &#38; Barton, N. H. (2018). The spread of an inversion with migration and selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 2018, pp. 377–82, doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>.","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 377–382, 2018.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>.","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. <i>Genetics</i>. 2018;208(1):377-382. doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>"},"intvolume":"       208","publist_id":"7249","date_updated":"2025-06-03T11:31:54Z","author":[{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"status":"public","publication":"Genetics","issue":"1","volume":208,"month":"01","page":"377 - 382"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2055-0278"]},"title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","article_processing_charge":"No","oa":1,"day":"03","external_id":{"isi":["000454576600017"],"pmid":["30518833"]},"pmid":1,"type":"journal_article","department":[{"_id":"JiFr"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833"}],"publisher":"Nature Research","year":"2018","publication_status":"published","isi":1,"date_created":"2018-12-16T22:59:18Z","quality_controlled":"1","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","grant_number":"742985"}],"scopus_import":"1","oa_version":"Submitted Version","_id":"5673","doi":"10.1038/s41477-018-0318-3","language":[{"iso":"eng"}],"page":"1082-1088","month":"12","ec_funded":1,"volume":4,"issue":"12","publication":"Nature Plants","author":[{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783","last_name":"Glanc","first_name":"Matous"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","last_name":"Fendrych","orcid":"0000-0002-9767-8699"},{"first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"status":"public","date_updated":"2025-04-14T07:45:02Z","intvolume":"         4","citation":{"ista":"Glanc M, Fendrych M, Friml J. 2018. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. Nature Plants. 4(12), 1082–1088.","ama":"Glanc M, Fendrych M, Friml J. Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. <i>Nature Plants</i>. 2018;4(12):1082-1088. doi:<a href=\"https://doi.org/10.1038/s41477-018-0318-3\">10.1038/s41477-018-0318-3</a>","chicago":"Glanc, Matous, Matyas Fendrych, and Jiří Friml. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” <i>Nature Plants</i>. Nature Research, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0318-3\">https://doi.org/10.1038/s41477-018-0318-3</a>.","short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 1082–1088.","ieee":"M. Glanc, M. Fendrych, and J. Friml, “Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division,” <i>Nature Plants</i>, vol. 4, no. 12. Nature Research, pp. 1082–1088, 2018.","mla":"Glanc, Matous, et al. “Mechanistic Framework for Cell-Intrinsic Re-Establishment of PIN2 Polarity after Cell Division.” <i>Nature Plants</i>, vol. 4, no. 12, Nature Research, 2018, pp. 1082–88, doi:<a href=\"https://doi.org/10.1038/s41477-018-0318-3\">10.1038/s41477-018-0318-3</a>.","apa":"Glanc, M., Fendrych, M., &#38; Friml, J. (2018). Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division. <i>Nature Plants</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41477-018-0318-3\">https://doi.org/10.1038/s41477-018-0318-3</a>"},"abstract":[{"text":"Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into post-cytokinetic re-establishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cell-intrinsic manner and that re-establishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basal-to-apical transcytosis. Furthermore, we identify a PINOID-related kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of post-cytokinetic PIN2 polarity re-establishment.","lang":"eng"}],"date_published":"2018-12-03T00:00:00Z"},{"department":[{"_id":"CaHe"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162"}],"publisher":"Rockefeller University Press","year":"2018","publication_status":"published","oa":1,"day":"01","external_id":{"isi":["000451960800018"],"pmid":["30228162 "]},"pmid":1,"type":"journal_article","title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0021-9525"]},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","_id":"5676","doi":"10.1083/jcb.201804048","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"isi":1,"date_created":"2018-12-16T22:59:19Z","author":[{"first_name":"Lara","last_name":"Carvalho","full_name":"Carvalho, Lara"},{"full_name":"Patricio, Pedro","last_name":"Patricio","first_name":"Pedro"},{"last_name":"Ponte","first_name":"Susana","full_name":"Ponte, Susana"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"},{"full_name":"Almeida, Luis","first_name":"Luis","last_name":"Almeida"},{"first_name":"André S.","last_name":"Nunes","full_name":"Nunes, André S."},{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"last_name":"Jacinto","first_name":"Antonio","full_name":"Jacinto, Antonio"}],"status":"public","publication":"Journal of Cell Biology","issue":"12","month":"12","ec_funded":1,"volume":217,"page":"4267-4283","date_published":"2018-12-01T00:00:00Z","citation":{"ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. <i>Journal of Cell Biology</i>. 2018;217(12):4267-4283. doi:<a href=\"https://doi.org/10.1083/jcb.201804048\">10.1083/jcb.201804048</a>","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201804048\">https://doi.org/10.1083/jcb.201804048</a>.","mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” <i>Journal of Cell Biology</i>, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:<a href=\"https://doi.org/10.1083/jcb.201804048\">10.1083/jcb.201804048</a>.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","ieee":"L. Carvalho <i>et al.</i>, “Occluding junctions as novel regulators of tissue mechanics during wound repair,” <i>Journal of Cell Biology</i>, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018.","apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201804048\">https://doi.org/10.1083/jcb.201804048</a>","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283."},"abstract":[{"text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge.","lang":"eng"}],"intvolume":"       217","date_updated":"2025-07-10T11:52:53Z"},{"date_created":"2018-12-16T22:59:19Z","quality_controlled":"1","doi":"10.1561/1000000053","oa_version":"Submitted Version","scopus_import":"1","_id":"5677","article_type":"original","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1551-3939"]},"title":"Contracts for system design","article_processing_charge":"No","type":"journal_article","oa":1,"day":"01","publisher":"Now Publishers","publication_status":"published","year":"2018","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-00757488/"}],"department":[{"_id":"ToHe"}],"date_updated":"2023-10-17T11:53:09Z","intvolume":"        12","abstract":[{"text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector.","lang":"eng"}],"citation":{"ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400.","ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. <i>Foundations and Trends in Electronic Design Automation</i>. 2018;12(2-3):124-400. doi:<a href=\"https://doi.org/10.1561/1000000053\">10.1561/1000000053</a>","chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” <i>Foundations and Trends in Electronic Design Automation</i>. Now Publishers, 2018. <a href=\"https://doi.org/10.1561/1000000053\">https://doi.org/10.1561/1000000053</a>.","mla":"Benveniste, Albert, et al. “Contracts for System Design.” <i>Foundations and Trends in Electronic Design Automation</i>, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:<a href=\"https://doi.org/10.1561/1000000053\">10.1561/1000000053</a>.","ieee":"A. Benveniste <i>et al.</i>, “Contracts for system design,” <i>Foundations and Trends in Electronic Design Automation</i>, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400.","apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. <i>Foundations and Trends in Electronic Design Automation</i>. Now Publishers. <a href=\"https://doi.org/10.1561/1000000053\">https://doi.org/10.1561/1000000053</a>"},"date_published":"2018-05-01T00:00:00Z","page":"124-400","volume":12,"month":"05","issue":"2-3","publication":"Foundations and Trends in Electronic Design Automation","author":[{"full_name":"Benveniste, Albert","last_name":"Benveniste","first_name":"Albert"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"last_name":"Caillaud","first_name":"Benoît","full_name":"Caillaud, Benoît"},{"first_name":"Roberto","last_name":"Passerone","full_name":"Passerone, Roberto"},{"full_name":"Raclet, Jean Baptiste","last_name":"Raclet","first_name":"Jean Baptiste"},{"first_name":"Philipp","last_name":"Reinkemeier","full_name":"Reinkemeier, Philipp"},{"full_name":"Sangiovanni-Vincentelli, Alberto","last_name":"Sangiovanni-Vincentelli","first_name":"Alberto"},{"last_name":"Damm","first_name":"Werner","full_name":"Damm, Werner"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kim G.","last_name":"Larsen","full_name":"Larsen, Kim G."}],"status":"public"},{"date_updated":"2025-04-15T08:18:38Z","date_created":"2018-12-19T14:22:35Z","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"_id":"5757","abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}],"citation":{"ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>","short":"C. Fraisse, (2018).","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>"},"oa_version":"Published Version","has_accepted_license":"1","doi":"10.15479/at:ista:/5757","contributor":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2018-12-19T00:00:00Z","file_date_updated":"2020-07-14T12:47:11Z","related_material":{"record":[{"status":"public","relation":"research_paper","id":"6089"}]},"file":[{"relation":"main_file","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:52Z","access_level":"open_access","file_size":369837892,"content_type":"application/zip","file_name":"FileS1.zip","file_id":"5758"},{"file_name":"FileS2.zip","file_id":"5759","file_size":84856909,"content_type":"application/zip","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","relation":"main_file","checksum":"3592e467b4d8206650860b612d6e12f3"},{"relation":"main_file","checksum":"c37ac5d5437c457338afc128c1240655","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","access_level":"open_access","file_size":881133,"content_type":"text/plain","file_name":"FileS3.txt","file_id":"5760"},{"file_size":883742,"content_type":"text/plain","file_name":"FileS4.txt","file_id":"5761","relation":"main_file","checksum":"943dfd14da61817441e33e3e3cb8cdb9","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","date_created":"2018-12-19T14:19:49Z","access_level":"open_access"},{"file_id":"5762","file_name":"FileS5.txt","content_type":"text/plain","file_size":2495437,"date_created":"2018-12-19T14:19:49Z","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","relation":"main_file"},{"file_size":15913457,"content_type":"text/plain","file_name":"FileS6.txt","file_id":"5763","relation":"main_file","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","date_created":"2018-12-19T14:19:50Z"},{"relation":"main_file","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","access_level":"open_access","file_size":2584120,"content_type":"text/plain","file_name":"FileS7.txt","file_id":"5764"},{"content_type":"text/plain","file_size":2446059,"file_id":"5765","file_name":"FileS8.txt","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","relation":"main_file","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","creator":"cfraisse","date_updated":"2020-07-14T12:47:11Z"},{"file_name":"FileS9.txt","file_id":"5766","file_size":100737,"content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","date_created":"2018-12-19T14:19:50Z","access_level":"open_access","relation":"main_file","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","article_processing_charge":"No","ec_funded":1,"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","ddc":["576"],"day":"19","oa":1,"type":"research_data","status":"public","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"}],"year":"2018","publisher":"Institute of Science and Technology Austria"},{"type":"journal_article","oa":1,"external_id":{"isi":["000452994400048"]},"day":"14","publisher":"American Association for the Advancement of Science","year":"2018","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aao0980"}],"department":[{"_id":"MaSe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"title":"Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor","article_processing_charge":"No","doi":"10.1126/science.aao0980","scopus_import":"1","oa_version":"Published Version","_id":"5767","article_type":"original","language":[{"iso":"eng"}],"date_created":"2018-12-19T14:53:50Z","isi":1,"quality_controlled":"1","issue":"6420","publication":"Science","author":[{"full_name":"Gotlieb, Kenneth","first_name":"Kenneth","last_name":"Gotlieb"},{"full_name":"Lin, Chiu-Yun","last_name":"Lin","first_name":"Chiu-Yun"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn"},{"last_name":"Zhang","first_name":"Wentao","full_name":"Zhang, Wentao"},{"full_name":"Smallwood, Christopher L.","first_name":"Christopher L.","last_name":"Smallwood"},{"last_name":"Jozwiak","first_name":"Christopher","full_name":"Jozwiak, Christopher"},{"full_name":"Eisaki, Hiroshi","last_name":"Eisaki","first_name":"Hiroshi"},{"full_name":"Hussain, Zahid","last_name":"Hussain","first_name":"Zahid"},{"full_name":"Vishwanath, Ashvin","last_name":"Vishwanath","first_name":"Ashvin"},{"full_name":"Lanzara, Alessandra","first_name":"Alessandra","last_name":"Lanzara"}],"status":"public","page":"1271-1275","acknowledgement":" M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307","volume":362,"month":"12","abstract":[{"text":"Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. ","lang":"eng"}],"citation":{"ista":"Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275.","mla":"Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” <i>Science</i>, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:<a href=\"https://doi.org/10.1126/science.aao0980\">10.1126/science.aao0980</a>.","ieee":"K. Gotlieb <i>et al.</i>, “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” <i>Science</i>, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018.","short":"K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275.","apa":"Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aao0980\">https://doi.org/10.1126/science.aao0980</a>","ama":"Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. <i>Science</i>. 2018;362(6420):1271-1275. doi:<a href=\"https://doi.org/10.1126/science.aao0980\">10.1126/science.aao0980</a>","chicago":"Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” <i>Science</i>. American Association for the Advancement of Science, 2018. <a href=\"https://doi.org/10.1126/science.aao0980\">https://doi.org/10.1126/science.aao0980</a>."},"date_published":"2018-12-14T00:00:00Z","date_updated":"2023-09-18T08:11:56Z","intvolume":"       362"},{"publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"50","status":"public","author":[{"full_name":"Qu, Kun","first_name":"Kun","last_name":"Qu"},{"full_name":"Glass, Bärbel","first_name":"Bärbel","last_name":"Glass"},{"full_name":"Doležal, Michal","last_name":"Doležal","first_name":"Michal"},{"full_name":"Schur, Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian"},{"full_name":"Murciano, Brice","last_name":"Murciano","first_name":"Brice"},{"first_name":"Alan","last_name":"Rein","full_name":"Rein, Alan"},{"full_name":"Rumlová, Michaela","first_name":"Michaela","last_name":"Rumlová"},{"first_name":"Tomáš","last_name":"Ruml","full_name":"Ruml, Tomáš"},{"first_name":"Hans-Georg","last_name":"Kräusslich","full_name":"Kräusslich, Hans-Georg"},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."}],"page":"E11751-E11760","volume":115,"month":"12","citation":{"chicago":"Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” <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.1811580115\">https://doi.org/10.1073/pnas.1811580115</a>.","ama":"Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(50):E11751-E11760. doi:<a href=\"https://doi.org/10.1073/pnas.1811580115\">10.1073/pnas.1811580115</a>","apa":"Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. <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.1811580115\">https://doi.org/10.1073/pnas.1811580115</a>","short":"K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E11751–E11760.","ieee":"K. Qu <i>et al.</i>, “Structure and architecture of immature and mature murine leukemia virus capsids,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50. National Academy of Sciences, pp. E11751–E11760, 2018.","mla":"Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50, National Academy of Sciences, 2018, pp. E11751–60, doi:<a href=\"https://doi.org/10.1073/pnas.1811580115\">10.1073/pnas.1811580115</a>.","ista":"Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences of the United States of America. 115(50), E11751–E11760."},"abstract":[{"lang":"eng","text":"Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry."}],"date_published":"2018-12-11T00:00:00Z","date_updated":"2025-06-03T11:56:09Z","intvolume":"       115","type":"journal_article","external_id":{"pmid":["30478053"],"isi":["000452866000022"]},"day":"11","pmid":1,"oa":1,"publication_status":"published","year":"2018","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30478053"}],"department":[{"_id":"FlSc"}],"publication_identifier":{"issn":["0027-8424"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","title":"Structure and architecture of immature and mature murine leukemia virus capsids","doi":"10.1073/pnas.1811580115","_id":"5770","oa_version":"Submitted Version","scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2018-12-20T21:09:37Z","isi":1,"quality_controlled":"1"},{"status":"public","author":[{"first_name":"Alexey A.","last_name":"Kotlobay","full_name":"Kotlobay, Alexey A."},{"id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","full_name":"Sarkisyan, Karen","first_name":"Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan"},{"first_name":"Yuliana A.","last_name":"Mokrushina","full_name":"Mokrushina, Yuliana A."},{"full_name":"Marcet-Houben, Marina","first_name":"Marina","last_name":"Marcet-Houben"},{"full_name":"Serebrovskaya, Ekaterina O.","first_name":"Ekaterina O.","last_name":"Serebrovskaya"},{"full_name":"Markina, Nadezhda M.","last_name":"Markina","first_name":"Nadezhda M."},{"full_name":"Gonzalez Somermeyer, Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","first_name":"Louisa"},{"full_name":"Gorokhovatsky, Andrey Y.","first_name":"Andrey Y.","last_name":"Gorokhovatsky"},{"full_name":"Vvedensky, Andrey","first_name":"Andrey","last_name":"Vvedensky"},{"last_name":"Purtov","first_name":"Konstantin V.","full_name":"Purtov, Konstantin V."},{"full_name":"Petushkov, Valentin N.","first_name":"Valentin N.","last_name":"Petushkov"},{"last_name":"Rodionova","first_name":"Natalja S.","full_name":"Rodionova, Natalja S."},{"full_name":"Chepurnyh, Tatiana V.","first_name":"Tatiana V.","last_name":"Chepurnyh"},{"full_name":"Fakhranurova, Liliia","last_name":"Fakhranurova","first_name":"Liliia"},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"first_name":"Rustam","last_name":"Ziganshin","full_name":"Ziganshin, Rustam"},{"full_name":"Tsarkova, Aleksandra S.","last_name":"Tsarkova","first_name":"Aleksandra S."},{"last_name":"Kaskova","first_name":"Zinaida M.","full_name":"Kaskova, Zinaida M."},{"last_name":"Shender","first_name":"Victoria","full_name":"Shender, Victoria"},{"last_name":"Abakumov","first_name":"Maxim","full_name":"Abakumov, Maxim"},{"first_name":"Tatiana O.","last_name":"Abakumova","full_name":"Abakumova, Tatiana O."},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"full_name":"Eroshkin, Fedor M.","first_name":"Fedor M.","last_name":"Eroshkin"},{"last_name":"Zaraisky","first_name":"Andrey G.","full_name":"Zaraisky, Andrey G."},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"last_name":"Dolgov","first_name":"Sergey V.","full_name":"Dolgov, Sergey V."},{"first_name":"Tatiana Y.","last_name":"Mitiouchkina","full_name":"Mitiouchkina, Tatiana Y."},{"full_name":"Kopantzev, Eugene P.","first_name":"Eugene P.","last_name":"Kopantzev"},{"last_name":"Waldenmaier","first_name":"Hans E.","full_name":"Waldenmaier, Hans E."},{"first_name":"Anderson G.","last_name":"Oliveira","full_name":"Oliveira, Anderson G."},{"first_name":"Yuichi","last_name":"Oba","full_name":"Oba, Yuichi"},{"last_name":"Barsova","first_name":"Ekaterina","full_name":"Barsova, Ekaterina"},{"full_name":"Bogdanova, Ekaterina A.","first_name":"Ekaterina A.","last_name":"Bogdanova"},{"full_name":"Gabaldón, Toni","last_name":"Gabaldón","first_name":"Toni"},{"full_name":"Stevani, Cassius V.","first_name":"Cassius V.","last_name":"Stevani"},{"last_name":"Lukyanov","first_name":"Sergey","full_name":"Lukyanov, Sergey"},{"full_name":"Smirnov, Ivan V.","last_name":"Smirnov","first_name":"Ivan V."},{"last_name":"Gitelson","first_name":"Josef I.","full_name":"Gitelson, Josef I."},{"first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."}],"issue":"50","publication":"Proceedings of the National Academy of Sciences of the United States of America","volume":115,"ddc":["580"],"month":"12","page":"12728-12732","file":[{"file_id":"5926","file_name":"2018_PNAS_Kotlobay.pdf","content_type":"application/pdf","file_size":1271988,"date_created":"2019-02-05T15:21:40Z","access_level":"open_access","date_updated":"2020-07-14T12:47:11Z","creator":"dernst","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","relation":"main_file"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"date_published":"2018-12-11T00:00:00Z","has_accepted_license":"1","abstract":[{"text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering.","lang":"eng"}],"citation":{"short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:<a href=\"https://doi.org/10.1073/pnas.1803615115\">10.1073/pnas.1803615115</a>.","ieee":"A. A. Kotlobay <i>et al.</i>, “Genetically encodable bioluminescent system from fungi,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018.","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. <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.1803615115\">https://doi.org/10.1073/pnas.1803615115</a>","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(50):12728-12732. doi:<a href=\"https://doi.org/10.1073/pnas.1803615115\">10.1073/pnas.1803615115</a>","chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” <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.1803615115\">https://doi.org/10.1073/pnas.1803615115</a>.","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732."},"intvolume":"       115","date_updated":"2025-07-10T11:52:58Z","publication_status":"published","year":"2018","publisher":"National Academy of Sciences","department":[{"_id":"FyKo"}],"type":"journal_article","external_id":{"isi":["000452866000068"]},"day":"11","oa":1,"article_processing_charge":"No","title":"Genetically encodable bioluminescent system from fungi","publication_identifier":{"issn":["0027-8424"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:11Z","doi":"10.1073/pnas.1803615115","_id":"5780","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","date_created":"2018-12-23T22:59:18Z","isi":1}]