[{"year":"2018","page":"131 - 138","date_updated":"2023-09-13T09:01:56Z","publication":"Current Opinion in Neurobiology","date_created":"2018-12-11T11:47:06Z","scopus_import":"1","date_published":"2018-02-01T00:00:00Z","external_id":{"isi":["000427101600018"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7268","department":[{"_id":"GaNo"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"Elsevier","intvolume":"        48","doi":"10.1016/j.conb.2017.12.005","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."}],"issue":"2","_id":"546","title":"Neural stem cells in neuropsychiatric disorders","author":[{"last_name":"Sacco","full_name":"Sacco, Roberto","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Emanuele","full_name":"Cacci, Emanuele","last_name":"Cacci"},{"orcid":"0000-0002-7673-7178","last_name":"Novarino","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publication_status":"published","oa_version":"None","month":"02","citation":{"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>","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.","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>","ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","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>.","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>."},"day":"01","article_processing_charge":"No","volume":48},{"_id":"55","author":[{"orcid":"0000-0003-1122-3982","last_name":"Pull","full_name":"Pull, Christopher","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Metzler","full_name":"Metzler, Sina","first_name":"Sina","id":"48204546-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9547-2494"},{"id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","full_name":"Naderlinger, Elisabeth","last_name":"Naderlinger"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"title":"Protection against the lethal side effects of social immunity in ants","doi":"10.1016/j.cub.2018.08.063","issue":"19","abstract":[{"text":"Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.","lang":"eng"}],"publication_status":"published","status":"public","month":"10","day":"08","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>","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.","short":"C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140.","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.","mla":"Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:<a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">10.1016/j.cub.2018.08.063</a>.","chicago":"Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” <i>Current Biology</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.cub.2018.08.063\">https://doi.org/10.1016/j.cub.2018.08.063</a>."},"oa_version":"Published Version","article_processing_charge":"No","volume":28,"oa":1,"year":"2018","date_updated":"2023-09-15T12:06:46Z","publication":"Current Biology","article_type":"original","page":"R1139 - R1140","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7999","department":[{"_id":"SyCr"}],"scopus_import":"1","date_created":"2018-12-11T11:44:23Z","external_id":{"isi":["000446693400008"]},"date_published":"2018-10-08T00:00:00Z","intvolume":"        28","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2018.08.063","open_access":"1"}],"publisher":"Cell Press","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","isi":1},{"date_published":"2018-05-01T00:00:00Z","external_id":{"arxiv":["1511.05953"]},"scopus_import":1,"date_created":"2018-12-11T11:47:09Z","department":[{"_id":"RoSe"}],"publist_id":"7260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       360","main_file_link":[{"url":"https://arxiv.org/abs/1511.05953","open_access":"1"}],"publisher":"Springer","year":"2018","oa":1,"page":"347-403","publication":"Communications in Mathematical Physics","date_updated":"2021-01-12T08:02:35Z","oa_version":"Submitted Version","day":"01","citation":{"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>.","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>.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” <i>Communications in Mathematical Physics</i>, vol. 360, no. 1. Springer, pp. 347–403, 2018.","apa":"Napiórkowski, M. M., Reuvers, R., &#38; Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-017-3064-x\">https://doi.org/10.1007/s00220-017-3064-x</a>","ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. <i>Communications in Mathematical Physics</i>. 2018;360(1):347-403. doi:<a href=\"https://doi.org/10.1007/s00220-017-3064-x\">10.1007/s00220-017-3064-x</a>","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","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."},"month":"05","volume":360,"arxiv":1,"issue":"1","abstract":[{"text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.).","lang":"eng"}],"doi":"10.1007/s00220-017-3064-x","author":[{"first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"first_name":"Robin","last_name":"Reuvers","full_name":"Reuvers, Robin"},{"first_name":"Jan","last_name":"Solovej","full_name":"Solovej, Jan"}],"title":"The Bogoliubov free energy functional II: The dilute Limit","_id":"554","status":"public","publication_status":"published","publication_identifier":{"issn":["00103616"]},"project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}]},{"publication":"Current Opinion in Structural Biology","date_updated":"2023-09-11T14:07:03Z","page":"65 - 74","article_type":"original","oa":1,"year":"2018","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/125524/"}],"intvolume":"        50","isi":1,"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","department":[{"_id":"MaLo"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7259","external_id":{"isi":["000443661300011"]},"date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:47:09Z","scopus_import":"1","publication_status":"published","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","status":"public","title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","author":[{"first_name":"Ralf","full_name":"Richter, Ralf","last_name":"Richter"},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia","full_name":"Baranova, Natalia","last_name":"Baranova","orcid":"0000-0002-3086-9124"},{"first_name":"Anthony","full_name":"Day, Anthony","last_name":"Day"},{"full_name":"Kwok, Jessica","last_name":"Kwok","first_name":"Jessica"}],"_id":"555","abstract":[{"text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.","lang":"eng"}],"doi":"10.1016/j.sbi.2017.12.002","volume":50,"article_processing_charge":"No","citation":{"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>.","chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>.","apa":"Richter, R., Baranova, N. S., Day, A., &#38; Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” <i>Current Opinion in Structural Biology</i>, vol. 50. Elsevier, pp. 65–74, 2018.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. 2018;50:65-74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","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."},"day":"01","month":"06","oa_version":"Submitted Version"},{"doi":"10.1007/s00023-018-0723-1","abstract":[{"lang":"eng","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."}],"issue":"12","_id":"556","title":"The free boundary Schur process and applications I","author":[{"first_name":"Dan","full_name":"Betea, Dan","last_name":"Betea"},{"first_name":"Jeremie","full_name":"Bouttier, Jeremie","last_name":"Bouttier"},{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Nejjar, Peter","last_name":"Nejjar"},{"last_name":"Vuletic","full_name":"Vuletic, Mirjana","first_name":"Mirjana"}],"ec_funded":1,"publication_status":"published","status":"public","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"},{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"}],"publication_identifier":{"issn":["1424-0637"]},"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:03Z","ddc":["500"],"month":"11","citation":{"mla":"Betea, Dan, et al. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>, vol. 19, no. 12, Springer Nature, 2018, pp. 3663–742, doi:<a href=\"https://doi.org/10.1007/s00023-018-0723-1\">10.1007/s00023-018-0723-1</a>.","chicago":"Betea, Dan, Jeremie Bouttier, Peter Nejjar, and Mirjana Vuletic. “The Free Boundary Schur Process and Applications I.” <i>Annales Henri Poincare</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00023-018-0723-1\">https://doi.org/10.1007/s00023-018-0723-1</a>.","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.","short":"D. Betea, J. Bouttier, P. Nejjar, M. Vuletic, Annales Henri Poincare 19 (2018) 3663–3742.","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.","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>"},"day":"13","article_processing_charge":"Yes (via OA deal)","volume":19,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"5866","date_created":"2019-01-21T15:18:55Z","date_updated":"2020-07-14T12:47:03Z","access_level":"open_access","checksum":"0c38abe73569b7166b7487ad5d23cc68","content_type":"application/pdf","file_name":"2018_Annales_Betea.pdf","creator":"dernst","relation":"main_file","file_size":3084674}],"arxiv":1,"year":"2018","oa":1,"page":"3663-3742","article_type":"original","date_updated":"2024-02-20T10:48:17Z","publication":"Annales Henri Poincare","date_created":"2018-12-11T11:47:09Z","scopus_import":"1","date_published":"2018-11-13T00:00:00Z","external_id":{"arxiv":["1704.05809"]},"publist_id":"7258","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Springer Nature","intvolume":"        19"},{"citation":{"mla":"Bergmiller, Tobias, and Nela Nikolic. <i>Time-Lapse Microscopy Data</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>.","chicago":"Bergmiller, Tobias, and Nela Nikolic. “Time-Lapse Microscopy Data.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>.","ista":"Bergmiller T, Nikolic N. 2018. Time-lapse microscopy data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>.","ama":"Bergmiller T, Nikolic N. Time-lapse microscopy data. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:74\">10.15479/AT:ISTA:74</a>","short":"T. Bergmiller, N. Nikolic, (2018).","ieee":"T. Bergmiller and N. Nikolic, “Time-lapse microscopy data.” Institute of Science and Technology Austria, 2018.","apa":"Bergmiller, T., &#38; Nikolic, N. (2018). Time-lapse microscopy data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:74\">https://doi.org/10.15479/AT:ISTA:74</a>"},"department":[{"_id":"CaGu"}],"day":"07","ddc":["579"],"publist_id":"7385","file_date_updated":"2020-07-14T12:47:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2018-02-07T00:00:00Z","oa_version":"Published Version","date_created":"2018-12-12T12:31:35Z","publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"file":[{"access_level":"open_access","content_type":"application/zip","checksum":"61ebb92213cfffeba3ddbaff984b81af","date_updated":"2020-07-14T12:47:04Z","file_name":"IST-2018-74-v1+2_15-11-05.zip","file_size":3558703796,"relation":"main_file","creator":"system","file_id":"5637","date_created":"2018-12-12T13:04:39Z"},{"file_id":"5638","date_created":"2018-12-12T13:04:55Z","file_name":"IST-2018-74-v1+3_15-07-31.zip","relation":"main_file","creator":"system","file_size":1830422606,"date_updated":"2020-07-14T12:47:04Z","access_level":"open_access","content_type":"application/zip","checksum":"bf26649af310ef6892d68576515cde6d"},{"date_updated":"2020-07-14T12:47:04Z","checksum":"8e46eedce06f22acb2be1a9b9d3f56bd","content_type":"application/zip","access_level":"open_access","creator":"system","relation":"main_file","file_size":2140849248,"file_name":"IST-2018-74-v1+4_Images_for_analysis.zip","date_created":"2018-12-12T13:05:11Z","file_id":"5639"}],"has_accepted_license":"1","article_processing_charge":"No","type":"research_data","datarep_id":"74","oa":1,"title":"Time-lapse microscopy data","author":[{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090"}],"_id":"5569","abstract":[{"text":"Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)\r\n“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;\r\nmicroscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic.","lang":"eng"}],"year":"2018","doi":"10.15479/AT:ISTA:74","keyword":["microscopy","microfluidics"],"date_updated":"2024-02-21T13:44:45Z","related_material":{"record":[{"id":"438","status":"public","relation":"research_paper"}]},"status":"public"},{"file":[{"file_id":"5600","date_created":"2018-12-12T13:02:34Z","file_name":"IST-2018-82-v1+1_GraphFlowMatchingProblems.zip","relation":"main_file","file_size":1737958,"creator":"system","access_level":"open_access","checksum":"53c17082848e12f3c2e1b4185b578208","content_type":"application/zip","date_updated":"2020-07-14T12:47:05Z"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"publisher":"Institute of Science and Technology Austria","contributor":[{"contributor_type":"researcher","last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","type":"research_data","article_processing_charge":"No","department":[{"_id":"VlKo"}],"day":"04","citation":{"ieee":"H. 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Institute of Science and Technology Austria, 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>.","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>","short":"T. Ellis, (2018).","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>","ieee":"T. 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The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.\r\n(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs  were displayed, and which stimulus segments are exact repeats or unique ball trajectories.\r\n(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions (\"sites\") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. 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Nonlinear decoding of a complex movie from the mammalian retina. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>","short":"S. Deny, O. Marre, V. Botella-Soler, G.S. Martius, G. Tkačik, (2018).","ista":"Deny S, Marre O, Botella-Soler V, Martius GS, Tkačik G. 2018. Nonlinear decoding of a complex movie from the mammalian retina, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:98\">10.15479/AT:ISTA:98</a>.","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>","chicago":"Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gašper Tkačik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:98\">https://doi.org/10.15479/AT:ISTA:98</a>.","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>."},"day":"29","department":[{"_id":"ChLa"},{"_id":"GaTk"}]},{"title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","datarep_id":"108","oa":1,"author":[{"full_name":"Igler, Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"},{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","last_name":"Guet"}],"_id":"5585","abstract":[{"text":"Mean repression values and standard error of the mean are given for all operator mutant libraries.","lang":"eng"}],"year":"2018","doi":"10.15479/AT:ISTA:108","date_updated":"2024-03-25T23:30:27Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"related_material":{"record":[{"status":"public","relation":"research_paper","id":"67"},{"id":"6371","status":"public","relation":"research_paper"}]},"status":"public","ec_funded":1,"citation":{"apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>.","mla":"Igler, Claudia, et al. <i>Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>."},"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"day":"20","month":"07","file_date_updated":"2020-07-14T12:47:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"date_published":"2018-07-20T00:00:00Z","oa_version":"Published Version","date_created":"2018-12-12T12:31:40Z","publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2020-07-14T12:47:07Z","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","checksum":"1435781526c77413802adee0d4583cce","access_level":"open_access","file_size":16507,"relation":"main_file","creator":"system","file_name":"IST-2018-108-v1+1_data_figures.xlsx","date_created":"2018-12-12T13:02:45Z","file_id":"5611"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"has_accepted_license":"1","article_processing_charge":"No","type":"research_data"},{"date_updated":"2024-02-21T13:45:12Z","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"status":"public","related_material":{"record":[{"id":"131","status":"public","relation":"research_paper"}]},"author":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"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)","datarep_id":"109","oa":1,"_id":"5586","year":"2018","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"}],"keyword":["schistosoma","Z-chromosome","gene expression"],"doi":"10.15479/AT:ISTA:109","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"file":[{"creator":"system","file_size":11918144,"relation":"main_file","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","checksum":"e60b484bd6f55c08eb66a189cb72c923","content_type":"application/zip","access_level":"open_access","date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T13:02:35Z","file_id":"5601"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","contributor":[{"orcid":"0000-0002-8101-2518","last_name":"Picard","first_name":"Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data","article_processing_charge":"No","day":"24","department":[{"_id":"BeVi"}],"citation":{"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>.","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>.","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>","short":"B. Vicoso, (2018).","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>.","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>","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."},"file_date_updated":"2020-07-14T12:47:08Z","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_published":"2018-07-24T00:00:00Z","date_created":"2018-12-12T12:31:40Z","oa_version":"Published Version"},{"date_published":"2018-09-21T00:00:00Z","oa_version":"Published Version","date_created":"2018-12-12T12:31:41Z","day":"21","department":[{"_id":"GaTk"}],"citation":{"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>.","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>.","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.","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>","short":"D. De Martino, G. Tkačik, (2018).","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>.","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>"},"ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:08Z","month":"09","has_accepted_license":"1","type":"research_data","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"file":[{"file_id":"5641","date_created":"2018-12-12T13:05:13Z","file_name":"IST-2018-111-v1+1_CODES.zip","relation":"main_file","creator":"system","file_size":14376,"access_level":"open_access","checksum":"97992e3e8cf8544ec985a48971708726","content_type":"application/zip","date_updated":"2020-07-14T12:47:08Z"}],"publisher":"Institute of Science and Technology Austria","year":"2018","abstract":[{"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).","lang":"eng"}],"keyword":["metabolic networks","e.coli core","maximum entropy","monte carlo markov chain sampling","ellipsoidal rounding"],"doi":"10.15479/AT:ISTA:62","author":[{"orcid":"0000-0002-5214-4706","last_name":"De Martino","full_name":"De Martino, Daniele","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"title":"Supporting materials \"STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH\"","datarep_id":"111","_id":"5587","status":"public","related_material":{"record":[{"relation":"research_paper","status":"public","id":"161"}]},"ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"date_updated":"2024-02-21T13:45:39Z"},{"date_updated":"2021-01-12T08:03:05Z","publication":"Neurotrophic Factors","page":"201 - 215","oa":1,"year":"2018","alternative_title":["Methods in Molecular Biology"],"publisher":"Springer","intvolume":"      1727","language":[{"iso":"eng"}],"type":"book_chapter","quality_controlled":"1","publist_id":"7252","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RySh"}],"date_created":"2018-12-11T11:47:11Z","scopus_import":1,"date_published":"2018-01-01T00:00:00Z","external_id":{"pmid":["29222783"]},"status":"public","publication_status":"published","_id":"562","editor":[{"last_name":"Skaper","full_name":"Skaper, Stephen D.","first_name":"Stephen D."}],"title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","author":[{"first_name":"Dimitar","full_name":"Dimitrov, Dimitar","last_name":"Dimitrov"},{"full_name":"Guillaud, Laurent","last_name":"Guillaud","first_name":"Laurent"},{"id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku","last_name":"Eguchi","orcid":"0000-0002-6170-2546"},{"last_name":"Takahashi","full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki"}],"doi":"10.1007/978-1-4939-7571-6_15","abstract":[{"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.","lang":"eng"}],"file":[{"file_id":"7046","date_created":"2019-11-19T07:47:43Z","access_level":"open_access","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","content_type":"application/pdf","date_updated":"2020-07-14T12:47:09Z","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","file_size":787407,"relation":"main_file","creator":"dernst"}],"article_processing_charge":"No","volume":1727,"has_accepted_license":"1","pmid":1,"month":"01","ddc":["570"],"file_date_updated":"2020-07-14T12:47:09Z","citation":{"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>","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","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.","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.","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>"},"day":"01","oa_version":"Submitted Version"},{"oa":1,"year":"2018","date_updated":"2023-09-11T13:42:38Z","publication":"Genetics","page":"1231-1245","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"200"}]},"publist_id":"7251","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"date_created":"2018-12-11T11:47:12Z","scopus_import":"1","date_published":"2018-03-01T00:00:00Z","external_id":{"isi":["000426219600025"]},"publisher":"Genetics Society of America","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/205484v1","open_access":"1"}],"intvolume":"       208","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"_id":"563","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","author":[{"orcid":"0000-0002-4884-9682","first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","full_name":"Ringbauer, Harald"},{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov"},{"last_name":"Field","full_name":"Field, David","first_name":"David"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"doi":"10.1534/genetics.117.300638","abstract":[{"lang":"eng","text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow."}],"issue":"3","publication_status":"published","status":"public","month":"03","citation":{"mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” <i>Genetics</i>, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:<a href=\"https://doi.org/10.1534/genetics.117.300638\">10.1534/genetics.117.300638</a>.","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300638\">https://doi.org/10.1534/genetics.117.300638</a>.","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” <i>Genetics</i>, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., &#38; Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300638\">https://doi.org/10.1534/genetics.117.300638</a>","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. <i>Genetics</i>. 2018;208(3):1231-1245. doi:<a href=\"https://doi.org/10.1534/genetics.117.300638\">10.1534/genetics.117.300638</a>"},"day":"01","oa_version":"Preprint","article_processing_charge":"No","volume":208},{"department":[{"_id":"NiBa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7250","date_published":"2018-07-01T00:00:00Z","external_id":{"isi":["000440392900014"]},"scopus_import":"1","date_created":"2018-12-11T11:47:12Z","intvolume":"       122","publisher":"Academic Press","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2018","publication":"Theoretical Population Biology","date_updated":"2025-05-28T11:42:45Z","related_material":{"record":[{"id":"9842","relation":"research_data","status":"public"}]},"article_type":"original","page":"110-127","day":"01","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>.","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>.","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.","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>","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>","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."},"ddc":["519","576"],"file_date_updated":"2020-07-14T12:47:09Z","month":"07","oa_version":"Submitted Version","file":[{"file_id":"7199","date_created":"2019-12-21T09:36:39Z","file_name":"bartonetheridge.pdf","file_size":2287682,"creator":"nbarton","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"0b96f6db47e3e91b5e7d103b847c239d","date_updated":"2020-07-14T12:47:09Z"}],"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"has_accepted_license":"1","article_processing_charge":"No","volume":122,"author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"}],"title":"Establishment in a new habitat by polygenic adaptation","_id":"564","issue":"7","abstract":[{"lang":"eng","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."}],"doi":"10.1016/j.tpb.2017.11.007","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"publication_status":"published","status":"public","ec_funded":1},{"issue":"1","abstract":[{"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. ","lang":"eng"}],"doi":"10.1534/genetics.117.300426","author":[{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"The spread of an inversion with migration and selection","_id":"565","status":"public","publication_status":"published","oa_version":"Published Version","day":"01","citation":{"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>","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” <i>Genetics</i>, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","apa":"Charlesworth, B., &#38; Barton, N. H. (2018). The spread of an inversion with migration and selection. <i>Genetics</i>. Genetics . <a href=\"https://doi.org/10.1534/genetics.117.300426\">https://doi.org/10.1534/genetics.117.300426</a>","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” <i>Genetics</i>. Genetics , 2018. <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 , 2018, pp. 377–82, doi:<a href=\"https://doi.org/10.1534/genetics.117.300426\">10.1534/genetics.117.300426</a>."},"pmid":1,"month":"01","volume":208,"article_processing_charge":"No","year":"2018","oa":1,"article_type":"original","page":"377 - 382","publication":"Genetics","date_updated":"2023-09-19T10:12:31Z","external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"date_published":"2018-01-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:47:12Z","department":[{"_id":"NiBa"}],"publist_id":"7249","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/","open_access":"1"}],"intvolume":"       208","publisher":"Genetics "},{"language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","isi":1,"publisher":"Institute of Mathematical Statistics","intvolume":"        28","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.07776 "}],"date_created":"2018-12-11T11:47:13Z","scopus_import":"1","date_published":"2018-03-03T00:00:00Z","external_id":{"isi":["000431721800005"],"arxiv":["1612.07776 "]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"LaEr"}],"page":"148-203","article_type":"original","related_material":{"record":[{"id":"149","status":"public","relation":"dissertation_contains"}]},"date_updated":"2023-09-13T08:47:52Z","publication":"Annals Applied Probability ","year":"2018","oa":1,"article_processing_charge":"No","volume":28,"arxiv":1,"oa_version":"Preprint","month":"03","citation":{"apa":"Alt, J., Erdös, L., &#38; Krüger, T. H. (2018). Local inhomogeneous circular law. <i>Annals Applied Probability </i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/17-AAP1302\">https://doi.org/10.1214/17-AAP1302</a>","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” <i>Annals Applied Probability </i>, vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018.","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203.","ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. <i>Annals Applied Probability </i>. 2018;28(1):148-203. doi:<a href=\"https://doi.org/10.1214/17-AAP1302\">10.1214/17-AAP1302</a>","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability  28 (2018) 148–203.","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” <i>Annals Applied Probability </i>. Institute of Mathematical Statistics, 2018. <a href=\"https://doi.org/10.1214/17-AAP1302\">https://doi.org/10.1214/17-AAP1302</a>.","mla":"Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” <i>Annals Applied Probability </i>, vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:<a href=\"https://doi.org/10.1214/17-AAP1302\">10.1214/17-AAP1302</a>."},"day":"03","ec_funded":1,"publication_status":"published","status":"public","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems"}],"doi":"10.1214/17-AAP1302","abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n"}],"issue":"1","_id":"566","title":"Local inhomogeneous circular law","author":[{"full_name":"Alt, Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes"},{"orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László"},{"orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","full_name":"Krüger, Torben H","last_name":"Krüger"}]},{"page":"2959-2961","date_updated":"2023-09-11T14:12:06Z","publication":"Journal of Experimental Medicine","year":"2018","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"intvolume":"       215","publisher":"Rockefeller University Press","scopus_import":"1","date_created":"2018-12-16T22:59:18Z","external_id":{"isi":["000451920600002"]},"date_published":"2018-11-20T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"MiSi"}],"publication_status":"published","status":"public","publication_identifier":{"issn":["00221007"]},"doi":"10.1084/jem.20181934","issue":"12","abstract":[{"lang":"eng","text":"The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocyte-packed environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific micro-anatomical route via lymph node conduits."}],"_id":"5672","author":[{"id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Reversat, Anne","last_name":"Reversat","orcid":"0000-0003-0666-8928"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K"}],"title":"IgM's exit route","volume":215,"article_processing_charge":"No","has_accepted_license":"1","file":[{"file_name":"2018_JournalExperMed_Reversat.pdf","relation":"main_file","creator":"dernst","file_size":1216437,"date_updated":"2020-07-14T12:47:09Z","access_level":"open_access","checksum":"687beea1d64c213f4cb9e3c29ec11a14","content_type":"application/pdf","file_id":"5931","date_created":"2019-02-06T08:49:52Z"}],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","month":"11","file_date_updated":"2020-07-14T12:47:09Z","ddc":["570"],"day":"20","citation":{"mla":"Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” <i>Journal of Experimental Medicine</i>, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61, doi:<a href=\"https://doi.org/10.1084/jem.20181934\">10.1084/jem.20181934</a>.","chicago":"Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” <i>Journal of Experimental Medicine</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1084/jem.20181934\">https://doi.org/10.1084/jem.20181934</a>.","ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961.","ama":"Reversat A, Sixt MK. IgM’s exit route. <i>Journal of Experimental Medicine</i>. 2018;215(12):2959-2961. doi:<a href=\"https://doi.org/10.1084/jem.20181934\">10.1084/jem.20181934</a>","short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.","ieee":"A. Reversat and M. K. Sixt, “IgM’s exit route,” <i>Journal of Experimental Medicine</i>, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.","apa":"Reversat, A., &#38; Sixt, M. K. (2018). IgM’s exit route. <i>Journal of Experimental Medicine</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1084/jem.20181934\">https://doi.org/10.1084/jem.20181934</a>"}},{"oa_version":"Submitted Version","pmid":1,"month":"12","citation":{"short":"M. Glanc, M. Fendrych, J. Friml, Nature Plants 4 (2018) 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>","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.","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.","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>","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>.","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>."},"day":"03","volume":4,"article_processing_charge":"No","doi":"10.1038/s41477-018-0318-3","abstract":[{"lang":"eng","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."}],"issue":"12","_id":"5673","title":"Mechanistic framework for cell-intrinsic re-establishment of PIN2 polarity after cell division","author":[{"last_name":"Glanc","full_name":"Glanc, Matous","first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"status":"public","publication_status":"published","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"publication_identifier":{"issn":["2055-0278"]},"date_created":"2018-12-16T22:59:18Z","scopus_import":"1","external_id":{"isi":["000454576600017"],"pmid":["30518833"]},"date_published":"2018-12-03T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"publisher":"Nature Research","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30518833"}],"intvolume":"         4","year":"2018","oa":1,"page":"1082-1088","date_updated":"2023-10-17T12:19:28Z","publication":"Nature Plants"},{"publication_status":"published","status":"public","ec_funded":1,"publication_identifier":{"issn":["00219525"]},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"issue":"12","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"}],"doi":"10.1083/jcb.201804048","author":[{"first_name":"Lara","full_name":"Carvalho, Lara","last_name":"Carvalho"},{"first_name":"Pedro","full_name":"Patricio, Pedro","last_name":"Patricio"},{"full_name":"Ponte, Susana","last_name":"Ponte","first_name":"Susana"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Luis","full_name":"Almeida, Luis","last_name":"Almeida"},{"first_name":"André S.","full_name":"Nunes, André S.","last_name":"Nunes"},{"last_name":"Araújo","full_name":"Araújo, Nuno A.M.","first_name":"Nuno A.M."},{"last_name":"Jacinto","full_name":"Jacinto, Antonio","first_name":"Antonio"}],"title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","_id":"5676","volume":217,"article_processing_charge":"No","oa_version":"Submitted Version","day":"01","citation":{"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>","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>","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.","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.","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>.","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>."},"pmid":1,"month":"12","page":"4267-4283","publication":"Journal of Cell Biology","date_updated":"2023-09-13T09:11:17Z","year":"2018","oa":1,"isi":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"       217","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162","open_access":"1"}],"publisher":"Rockefeller University Press","external_id":{"isi":["000451960800018"],"pmid":["30228162 "]},"date_published":"2018-12-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-16T22:59:19Z","department":[{"_id":"CaHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"}]