[{"type":"journal_article","oa":1,"external_id":{"isi":["000443383300024"]},"day":"16","publisher":"Public Library of Science","publication_status":"published","year":"2018","department":[{"_id":"CaGu"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","license":"https://creativecommons.org/licenses/by/4.0/","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","article_processing_charge":"Yes","doi":"10.1371/journal.pbio.2005971","scopus_import":"1","oa_version":"Published Version","_id":"82","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-11T11:44:32Z","isi":1,"quality_controlled":"1","issue":"8","publication":"PLoS Biology","author":[{"last_name":"Chaudhry","first_name":"Waqas","full_name":"Chaudhry, Waqas"},{"full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","last_name":"Pleska","first_name":"Maros"},{"last_name":"Shah","first_name":"Nilang","full_name":"Shah, Nilang"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"full_name":"Mccall, Ingrid","last_name":"Mccall","first_name":"Ingrid"},{"last_name":"Meyer","first_name":"Justin","full_name":"Meyer, Justin"},{"full_name":"Gupta, Animesh","first_name":"Animesh","last_name":"Gupta"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"last_name":"Levin","first_name":"Bruce","full_name":"Levin, Bruce"}],"status":"public","file":[{"checksum":"527076f78265cd4ea192cd1569851587","relation":"main_file","access_level":"open_access","date_created":"2018-12-17T12:55:31Z","date_updated":"2020-07-14T12:48:10Z","creator":"dernst","content_type":"application/pdf","file_size":4007095,"file_id":"5706","file_name":"2018_Plos_Chaudhry.pdf"}],"ddc":["570"],"article_number":"2005971","volume":16,"month":"08","has_accepted_license":"1","citation":{"ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. 2018;16(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ieee":"W. Chaudhry <i>et al.</i>, “Leaky resistance and the conditions for the existence of lytic bacteriophage,” <i>PLoS Biology</i>, vol. 16, no. 8. Public Library of Science, 2018.","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971."},"abstract":[{"text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term &quot;leaky resistance.&quot; We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”.","lang":"eng"}],"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"},"related_material":{"record":[{"relation":"research_data","status":"public","id":"9810"}]},"date_published":"2018-08-16T00:00:00Z","publist_id":"7972","date_updated":"2023-09-13T08:45:41Z","intvolume":"        16"},{"day":"13","oa":1,"publication":"bioRxiv","type":"preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"department":[{"_id":"SiHi"}],"status":"public","author":[{"first_name":"Alfredo","last_name":"Llorca","full_name":"Llorca, Alfredo"},{"last_name":"Ciceri","first_name":"Gabriele","full_name":"Ciceri, Gabriele"},{"id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","full_name":"Beattie, Robert J","first_name":"Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie"},{"first_name":"Fong K.","last_name":"Wong","full_name":"Wong, Fong K."},{"full_name":"Diana, Giovanni","last_name":"Diana","first_name":"Giovanni"},{"first_name":"Eleni","last_name":"Serafeimidou","full_name":"Serafeimidou, Eleni"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen"},{"first_name":"Sebastian J.","last_name":"Arnold","full_name":"Arnold, Sebastian J."},{"first_name":"Martin","last_name":"Meyer","full_name":"Meyer, Martin"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"full_name":"Marín, Oscar","first_name":"Oscar","last_name":"Marín"}],"year":"2018","publication_status":"submitted","publisher":"Cold Spring Harbor Laboratory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","ec_funded":1,"article_processing_charge":"No","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","_id":"8547","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"citation":{"ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, <a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>","ieee":"A. Llorca <i>et al.</i>, “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>."},"oa_version":"Preprint","doi":"10.1101/494088","date_published":"2018-12-13T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2024-10-22T10:46:39Z","date_created":"2020-09-21T12:01:50Z","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"grant_number":"M02416","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","_id":"264E56E2-B435-11E9-9278-68D0E5697425"}]},{"alternative_title":["LNCS"],"publication":"Principles of Modeling","status":"public","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}],"page":"143 - 161","editor":[{"first_name":"Marten","last_name":"Lohstroh","full_name":"Lohstroh, Marten"},{"first_name":"Patricia","last_name":"Derler","full_name":"Derler, Patricia"},{"last_name":"Sirjani","first_name":"Marjan","full_name":"Sirjani, Marjan"}],"file":[{"content_type":"application/pdf","file_size":516307,"file_id":"7053","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","checksum":"9995c6ce6957333baf616fc4f20be597","relation":"main_file","access_level":"open_access","date_created":"2019-11-19T08:22:18Z","date_updated":"2020-07-14T12:48:14Z","creator":"dernst"}],"volume":10760,"ec_funded":1,"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","ddc":["000"],"month":"07","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms."}],"citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in <i>Principles of Modeling</i>, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” <i>Principles of Modeling</i>, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, &#38; M. Sirjani (Eds.), <i>Principles of Modeling</i> (Vol. 10760, pp. 143–161). Springer. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. <i>Principles of Modeling</i>. Vol 10760. Springer; 2018:143-161. doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In <i>Principles of Modeling</i>, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>."},"date_published":"2018-07-20T00:00:00Z","publist_id":"7968","date_updated":"2025-04-15T06:26:15Z","intvolume":"     10760","type":"book_chapter","day":"20","oa":1,"year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Computing average response time","doi":"10.1007/978-3-319-95246-8_9","_id":"86","oa_version":"Submitted Version","scopus_import":1,"file_date_updated":"2020-07-14T12:48:14Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:33Z","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1"},{"date_updated":"2024-10-21T06:02:43Z","intvolume":"         8","keyword":["Multidisciplinary"],"abstract":[{"text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting.","lang":"eng"}],"citation":{"ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. 2018;8. doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>.","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>, vol. 8, 2724, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” <i>Scientific Reports</i>, vol. 8. Springer Nature, 2018.","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &#38; Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>"},"has_accepted_license":"1","date_published":"2018-02-09T00:00:00Z","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"},"file":[{"file_id":"8619","file_name":"2018_ScientificReports_Gregor.pdf","success":1,"content_type":"application/pdf","file_size":2818077,"access_level":"open_access","date_created":"2020-10-06T16:35:16Z","date_updated":"2020-10-06T16:35:16Z","creator":"dernst","checksum":"e642080fcbde9584c63544f587c74f03","relation":"main_file"}],"month":"02","volume":8,"article_number":"2724","ddc":["570"],"publication":"Scientific Reports","status":"public","author":[{"full_name":"Gregor, Carola","last_name":"Gregor","first_name":"Carola"},{"last_name":"Sidenstein","first_name":"Sven C.","full_name":"Sidenstein, Sven C."},{"first_name":"Martin","last_name":"Andresen","full_name":"Andresen, Martin"},{"first_name":"Steffen J.","last_name":"Sahl","full_name":"Sahl, Steffen J."},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"full_name":"Hell, Stefan W.","first_name":"Stefan W.","last_name":"Hell"}],"isi":1,"date_created":"2020-10-06T16:33:37Z","quality_controlled":"1","_id":"8618","oa_version":"Published Version","scopus_import":"1","doi":"10.1038/s41598-018-19947-1","language":[{"iso":"eng"}],"file_date_updated":"2020-10-06T16:35:16Z","article_type":"original","publication_identifier":{"issn":["2045-2322"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","day":"09","pmid":1,"external_id":{"pmid":["29426833"],"isi":["000424630400037"]},"oa":1,"type":"journal_article","department":[{"_id":"JoDa"}],"publication_status":"published","year":"2018","publisher":"Springer Nature"},{"date_created":"2018-12-11T11:49:10Z","isi":1,"project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","doi":"10.1242/jcs.204198","oa_version":"Published Version","scopus_import":"1","_id":"913","file_date_updated":"2020-07-14T12:48:15Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0021-9533"]},"title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","article_processing_charge":"No","type":"journal_article","oa":1,"day":"29","external_id":{"isi":["000424842400019"]},"publisher":"Company of Biologists","publication_status":"published","year":"2018","department":[{"_id":"JiFr"}],"publist_id":"6530","date_updated":"2025-07-10T12:01:38Z","pubrep_id":"988","intvolume":"       131","corr_author":"1","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis."}],"citation":{"ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.","chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>. Company of Biologists, 2018. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>.","ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. 2018;131(2). doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>","apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., &#38; Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 131, no. 2. Company of Biologists, 2018.","mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>.","short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018)."},"date_published":"2018-01-29T00:00:00Z","file":[{"date_updated":"2020-07-14T12:48:15Z","creator":"dernst","date_created":"2019-04-12T08:46:32Z","access_level":"open_access","relation":"main_file","checksum":"bf156c20a4f117b4b932370d54cbac8c","file_name":"2017_adamowski_PATELLINS_are.pdf","file_id":"6299","file_size":14925985,"content_type":"application/pdf"}],"article_number":"jcs.204198","ddc":["581"],"ec_funded":1,"volume":131,"month":"01","publication":"Journal of Cell Science","issue":"2","author":[{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"full_name":"Rodríguez Furlán, Cecilia","first_name":"Cecilia","last_name":"Rodríguez Furlán"},{"first_name":"Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"full_name":"Norambuena, Lorena","last_name":"Norambuena","first_name":"Lorena"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"status":"public"},{"intvolume":"         4","date_updated":"2021-12-03T07:31:05Z","date_published":"2018-06-30T00:00:00Z","citation":{"short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” <i>Opera Medica et Physiologica</i>, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:<a href=\"https://doi.org/10.20388/omp2018.00s1.001\">10.20388/omp2018.00s1.001</a>.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” <i>Opera Medica et Physiologica</i>, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod. <a href=\"https://doi.org/10.20388/omp2018.00s1.001\">https://doi.org/10.20388/omp2018.00s1.001</a>","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. <i>Opera Medica et Physiologica</i>. 2018;4(S1):11. doi:<a href=\"https://doi.org/10.20388/omp2018.00s1.001\">10.20388/omp2018.00s1.001</a>","chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” <i>Opera Medica et Physiologica</i>. Lobachevsky State University of Nizhny Novgorod, 2018. <a href=\"https://doi.org/10.20388/omp2018.00s1.001\">https://doi.org/10.20388/omp2018.00s1.001</a>.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11."},"volume":4,"month":"06","page":"11","author":[{"last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"status":"public","alternative_title":["Molecular and cellular neuroscience"],"issue":"S1","publication":"Opera Medica et Physiologica","quality_controlled":"1","date_created":"2021-03-07T23:01:25Z","article_type":"letter_note","language":[{"iso":"eng"}],"doi":"10.20388/omp2018.00s1.001","oa_version":"Published Version","scopus_import":"1","_id":"9229","title":"Diffraction-unlimited optical imaging for synaptic physiology","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"publisher":"Lobachevsky State University of Nizhny Novgorod","publication_status":"published","year":"2018","main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"department":[{"_id":"JoDa"}],"type":"journal_article","oa":1,"day":"30"},{"date_created":"2021-06-07T06:11:28Z","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","_id":"9471","doi":"10.1073/pnas.1713333115","file_date_updated":"2021-06-07T06:16:38Z","language":[{"iso":"eng"}],"article_type":"original","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"title":"FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis","article_processing_charge":"No","oa":1,"pmid":1,"external_id":{"pmid":["29712855"]},"day":"15","type":"journal_article","department":[{"_id":"DaZi"}],"publisher":"National Academy of Sciences","publication_status":"published","year":"2018","date_updated":"2021-12-14T07:53:40Z","extern":"1","intvolume":"       115","keyword":["Multidisciplinary"],"abstract":[{"text":"The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.","lang":"eng"}],"citation":{"chicago":"Frost, Jennifer M., M. Yvonne Kim, Guen Tae Park, Ping-Hung Hsieh, Miyuki Nakamura, Samuel J. H. Lin, Hyunjin Yoo, et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>.","ama":"Frost JM, Kim MY, Park GT, et al. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(20):E4720-E4729. doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>","apa":"Frost, J. M., Kim, M. Y., Park, G. T., Hsieh, P.-H., Nakamura, M., Lin, S. J. H., … Fischer, R. L. (2018). FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713333115\">https://doi.org/10.1073/pnas.1713333115</a>","ieee":"J. M. Frost <i>et al.</i>, “FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20. National Academy of Sciences, pp. E4720–E4729, 2018.","mla":"Frost, Jennifer M., et al. “FACT Complex Is Required for DNA Demethylation at Heterochromatin during Reproduction in Arabidopsis.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 20, National Academy of Sciences, 2018, pp. E4720–29, doi:<a href=\"https://doi.org/10.1073/pnas.1713333115\">10.1073/pnas.1713333115</a>.","short":"J.M. Frost, M.Y. Kim, G.T. Park, P.-H. Hsieh, M. Nakamura, S.J.H. Lin, H. Yoo, J. Choi, Y. Ikeda, T. Kinoshita, Y. Choi, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 115 (2018) E4720–E4729.","ista":"Frost JM, Kim MY, Park GT, Hsieh P-H, Nakamura M, Lin SJH, Yoo H, Choi J, Ikeda Y, Kinoshita T, Choi Y, Zilberman D, Fischer RL. 2018. FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis. Proceedings of the National Academy of Sciences. 115(20), E4720–E4729."},"has_accepted_license":"1","date_published":"2018-05-15T00:00:00Z","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)"},"related_material":{"link":[{"url":"https://doi.org/10.1101/187674 ","relation":"earlier_version"}]},"file":[{"content_type":"application/pdf","file_size":3045260,"file_id":"9472","file_name":"2018_PNAS_Frost.pdf","success":1,"checksum":"810260dc0e3cc3033e15c19ad0dc123e","relation":"main_file","date_created":"2021-06-07T06:16:38Z","access_level":"open_access","date_updated":"2021-06-07T06:16:38Z","creator":"asandaue"}],"page":"E4720-E4729","month":"05","ddc":["580"],"volume":115,"issue":"20","publication":"Proceedings of the National Academy of Sciences","author":[{"full_name":"Frost, Jennifer M.","last_name":"Frost","first_name":"Jennifer M."},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"full_name":"Park, Guen Tae","first_name":"Guen Tae","last_name":"Park"},{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"full_name":"Nakamura, Miyuki","first_name":"Miyuki","last_name":"Nakamura"},{"last_name":"Lin","first_name":"Samuel J. H.","full_name":"Lin, Samuel J. H."},{"full_name":"Yoo, Hyunjin","first_name":"Hyunjin","last_name":"Yoo"},{"full_name":"Choi, Jaemyung","first_name":"Jaemyung","last_name":"Choi"},{"full_name":"Ikeda, Yoko","first_name":"Yoko","last_name":"Ikeda"},{"full_name":"Kinoshita, Tetsu","last_name":"Kinoshita","first_name":"Tetsu"},{"full_name":"Choi, Yeonhee","last_name":"Choi","first_name":"Yeonhee"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."}],"status":"public"},{"date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:26:53Z","_id":"9807","citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">https://doi.org/10.6084/m9.figshare.7295339.v1</a>.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">https://doi.org/10.6084/m9.figshare.7295339.v1</a>","mla":"Higareda Almaraz, Juan, et al. <i>Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","ieee":"J. Higareda Almaraz <i>et al.</i>, “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.7295339.v1\">10.6084/m9.figshare.7295339.v1</a>."},"abstract":[{"text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).","lang":"eng"}],"oa_version":"Published Version","doi":"10.6084/m9.figshare.7295339.v1","date_published":"2018-11-03T00:00:00Z","related_material":{"record":[{"id":"20","status":"public","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"11","article_processing_charge":"No","title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","day":"03","oa":1,"type":"research_data_reference","status":"public","department":[{"_id":"SiHi"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7295339.v1","open_access":"1"}],"author":[{"first_name":"Juan","last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan"},{"full_name":"Karbiener, Michael","first_name":"Michael","last_name":"Karbiener"},{"last_name":"Giroud","first_name":"Maude","full_name":"Giroud, Maude"},{"first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"full_name":"Herzig, Stephan","first_name":"Stephan","last_name":"Herzig"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"year":"2018","publisher":"Springer Nature"},{"date_published":"2018-11-03T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"20"}]},"oa_version":"Published Version","citation":{"apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., &#38; Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">https://doi.org/10.6084/m9.figshare.7295369.v1</a>","mla":"Higareda Almaraz, Juan, et al. <i>Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>.","ieee":"J. Higareda Almaraz <i>et al.</i>, “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">https://doi.org/10.6084/m9.figshare.7295369.v1</a>.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.7295369.v1\">10.6084/m9.figshare.7295369.v1</a>."},"_id":"9808","abstract":[{"lang":"eng","text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb)."}],"doi":"10.6084/m9.figshare.7295369.v1","date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:31:57Z","author":[{"full_name":"Higareda Almaraz, Juan","last_name":"Higareda Almaraz","first_name":"Juan"},{"first_name":"Michael","last_name":"Karbiener","full_name":"Karbiener, Michael"},{"full_name":"Giroud, Maude","first_name":"Maude","last_name":"Giroud"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-7462-0048","last_name":"Pauler"},{"full_name":"Gerhalter, Teresa","last_name":"Gerhalter","first_name":"Teresa"},{"last_name":"Herzig","first_name":"Stephan","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","last_name":"Scheideler","first_name":"Marcel"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295369.v1"}],"department":[{"_id":"SiHi"}],"status":"public","publisher":"Springer Nature","year":"2018","oa":1,"day":"03","type":"research_data_reference","month":"11","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"date_created":"2021-08-06T12:43:44Z","date_updated":"2023-09-13T08:45:41Z","related_material":{"record":[{"id":"82","relation":"used_in_publication","status":"public"}]},"date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971.s008","citation":{"ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">https://doi.org/10.1371/journal.pbio.2005971.s008</a>","ieee":"W. Chaudhry <i>et al.</i>, “Numerical data used in figures.” Public Library of Science, 2018.","mla":"Chaudhry, Waqas, et al. <i>Numerical Data Used in Figures</i>. Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">https://doi.org/10.1371/journal.pbio.2005971.s008</a>.","ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971.s008\">10.1371/journal.pbio.2005971.s008</a>"},"_id":"9810","oa_version":"Published Version","article_processing_charge":"No","title":"Numerical data used in figures","month":"08","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"status":"public","author":[{"last_name":"Chaudhry","first_name":"Waqas","full_name":"Chaudhry, Waqas"},{"orcid":"0000-0001-7460-7479","last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Shah, Nilang","last_name":"Shah","first_name":"Nilang"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"full_name":"Mccall, Ingrid","last_name":"Mccall","first_name":"Ingrid"},{"last_name":"Meyer","first_name":"Justin","full_name":"Meyer, Justin"},{"first_name":"Animesh","last_name":"Gupta","full_name":"Gupta, Animesh"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"full_name":"Levin, Bruce","first_name":"Bruce","last_name":"Levin"}],"type":"research_data_reference","day":"16"},{"month":"05","article_processing_charge":"No","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.6401390.v1"}],"department":[{"_id":"FyKo"}],"author":[{"last_name":"Zapata","first_name":"Luis","full_name":"Zapata, Luis"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"},{"first_name":"Stephan","last_name":"Ossowski","full_name":"Ossowski, Stephan"},{"full_name":"Schaefer, Martin","last_name":"Schaefer","first_name":"Martin"}],"year":"2018","publisher":"Springer Nature","day":"31","oa":1,"type":"research_data_reference","date_updated":"2025-04-15T08:30:30Z","date_created":"2021-08-06T12:53:49Z","date_published":"2018-05-31T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"279"}]},"_id":"9811","citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>.","mla":"Zapata, Luis, et al. <i>Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">https://doi.org/10.6084/m9.figshare.6401390.v1</a>","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">10.6084/m9.figshare.6401390.v1</a>","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.6401390.v1\">https://doi.org/10.6084/m9.figshare.6401390.v1</a>."},"abstract":[{"text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)","lang":"eng"}],"oa_version":"Preprint","doi":"10.6084/m9.figshare.6401390.v1"},{"date_updated":"2025-04-15T08:30:30Z","date_created":"2021-08-06T12:58:25Z","oa_version":"Published Version","citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","mla":"Zapata, Luis, et al. <i>Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome</i>. Springer Nature, 2018, doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. <a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">https://doi.org/10.6084/m9.figshare.6401414.v1</a>.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:<a href=\"https://doi.org/10.6084/m9.figshare.6401414.v1\">10.6084/m9.figshare.6401414.v1</a>"},"_id":"9812","abstract":[{"text":"This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb)","lang":"eng"}],"doi":"10.6084/m9.figshare.6401414.v1","date_published":"2018-05-31T00:00:00Z","related_material":{"record":[{"id":"279","relation":"used_in_publication","status":"public"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"05","title":"Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","article_processing_charge":"No","oa":1,"day":"31","type":"research_data_reference","author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"full_name":"Serrano, Luis","first_name":"Luis","last_name":"Serrano"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ossowski, Stephan","first_name":"Stephan","last_name":"Ossowski"},{"last_name":"Schaefer","first_name":"Martin","full_name":"Schaefer, Martin"}],"status":"public","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401414.v1","open_access":"1"}],"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","year":"2018"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","title":"Supplemental material for Bodova et al., 2018","month":"04","type":"research_data_reference","day":"30","oa":1,"year":"2018","publisher":"Genetics Society of America","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"status":"public","author":[{"orcid":"0000-0002-7214-0171","last_name":"Bod'ová","first_name":"Katarína","full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","orcid":"0000-0001-6118-0541","first_name":"Melinda"}],"date_created":"2021-08-06T13:04:32Z","date_updated":"2025-04-15T07:17:08Z","doi":"10.25386/genetics.6148304.v1","_id":"9813","citation":{"apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., &#38; Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","mla":"Bodova, Katarina, et al. <i>Supplemental Material for Bodova et Al., 2018</i>. Genetics Society of America, 2018, doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">https://doi.org/10.25386/genetics.6148304.v1</a>.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:<a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, <a href=\"https://doi.org/10.25386/genetics.6148304.v1\">10.25386/genetics.6148304.v1</a>."},"abstract":[{"lang":"eng","text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables."}],"oa_version":"Published Version","related_material":{"record":[{"id":"316","status":"public","relation":"used_in_publication"}]},"date_published":"2018-04-30T00:00:00Z"},{"intvolume":"        98","publist_id":"8008","date_updated":"2023-09-11T12:55:03Z","date_published":"2018-10-15T00:00:00Z","citation":{"ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. <i>Physical Review B</i>. 2018;98(16). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">10.1103/PhysRevB.98.161122</a>","chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">https://doi.org/10.1103/PhysRevB.98.161122</a>.","mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” <i>Physical Review B</i>, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">10.1103/PhysRevB.98.161122</a>.","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018).","ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” <i>Physical Review B</i>, vol. 98, no. 16. American Physical Society, 2018.","apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., &#38; Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.161122\">https://doi.org/10.1103/PhysRevB.98.161122</a>"},"abstract":[{"text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase.","lang":"eng"}],"acknowledgement":"F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","volume":98,"article_number":"161122","month":"10","status":"public","author":[{"full_name":"Hetterich, Daniel","last_name":"Hetterich","first_name":"Daniel"},{"full_name":"Yao, Norman","last_name":"Yao","first_name":"Norman"},{"first_name":"Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","full_name":"Serbyn, Maksym"},{"first_name":"Frank","last_name":"Pollmann","full_name":"Pollmann, Frank"},{"full_name":"Trauzettel, Björn","last_name":"Trauzettel","first_name":"Björn"}],"publication":"Physical Review B","issue":"16","quality_controlled":"1","date_created":"2018-12-11T11:44:20Z","isi":1,"article_type":"original","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.98.161122","_id":"46","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","title":"Detection and characterization of many-body localization in central spin models","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","arxiv":1,"publication_status":"published","year":"2018","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"main_file_link":[{"url":"https://arxiv.org/abs/1806.08316","open_access":"1"}],"type":"journal_article","day":"15","external_id":{"isi":["000448596500002"],"arxiv":["1806.08316"]},"oa":1},{"date_updated":"2023-09-13T09:03:18Z","publist_id":"7359","intvolume":"        41","citation":{"ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","ieee":"L. Fan <i>et al.</i>, “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” <i>Plant, Cell and Environment</i>, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” <i>Plant, Cell and Environment</i>, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:<a href=\"https://doi.org/10.1111/pce.13153\">10.1111/pce.13153</a>.","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. <i>Plant, Cell and Environment</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/pce.13153\">https://doi.org/10.1111/pce.13153</a>","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. <i>Plant, Cell and Environment</i>. 2018;41:850-864. doi:<a href=\"https://doi.org/10.1111/pce.13153\">10.1111/pce.13153</a>","chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” <i>Plant, Cell and Environment</i>. Wiley-Blackwell, 2018. <a href=\"https://doi.org/10.1111/pce.13153\">https://doi.org/10.1111/pce.13153</a>."},"abstract":[{"lang":"eng","text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. "}],"has_accepted_license":"1","date_published":"2018-05-01T00:00:00Z","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"},"file":[{"checksum":"6a20f843565f962cb20281cdf5e40914","relation":"main_file","date_created":"2019-11-18T16:22:22Z","access_level":"open_access","creator":"dernst","date_updated":"2020-07-14T12:46:32Z","content_type":"application/pdf","file_size":1937976,"file_id":"7042","file_name":"2018_PlantCellEnv_Fan.pdf"}],"page":"850 - 864","month":"05","ddc":["580"],"acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","volume":41,"publication":"Plant, Cell and Environment","author":[{"full_name":"Fan, Ligang","first_name":"Ligang","last_name":"Fan"},{"full_name":"Zhao, Lei","last_name":"Zhao","first_name":"Lei"},{"full_name":"Hu, Wei","first_name":"Wei","last_name":"Hu"},{"full_name":"Li, Weina","last_name":"Li","first_name":"Weina"},{"full_name":"Novák, Ondřej","first_name":"Ondřej","last_name":"Novák"},{"last_name":"Strnad","first_name":"Miroslav","full_name":"Strnad, Miroslav"},{"full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","orcid":"0000-0002-1998-6741","last_name":"Simon"},{"first_name":"Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"last_name":"Shen","first_name":"Jinbo","full_name":"Shen, Jinbo"},{"full_name":"Jiang, Liwen","first_name":"Liwen","last_name":"Jiang"},{"full_name":"Qiu, Quan","first_name":"Quan","last_name":"Qiu"}],"status":"public","isi":1,"date_created":"2018-12-11T11:46:36Z","quality_controlled":"1","scopus_import":"1","oa_version":"Submitted Version","_id":"462","doi":"10.1111/pce.13153","file_date_updated":"2020-07-14T12:46:32Z","language":[{"iso":"eng"}],"article_type":"original","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","article_processing_charge":"No","oa":1,"day":"01","pmid":1,"external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"type":"journal_article","department":[{"_id":"JiFr"}],"publisher":"Wiley-Blackwell","year":"2018","publication_status":"published"},{"acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/j.jbiotec.2018.01.008","oa_version":"None","scopus_import":"1","_id":"503","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:50Z","isi":1,"quality_controlled":"1","type":"journal_article","external_id":{"isi":["000425715100006"]},"day":"20","publisher":"Elsevier","year":"2018","publication_status":"published","department":[{"_id":"CaGu"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","article_processing_charge":"No","corr_author":"1","abstract":[{"lang":"eng","text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry."}],"citation":{"chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>.","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. 2018;268:40-52. doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>","apa":"Tomasek, K., Bergmiller, T., &#38; Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. <i>Journal of Biotechnology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">https://doi.org/10.1016/j.jbiotec.2018.01.008</a>","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” <i>Journal of Biotechnology</i>, vol. 268, Elsevier, 2018, pp. 40–52, doi:<a href=\"https://doi.org/10.1016/j.jbiotec.2018.01.008\">10.1016/j.jbiotec.2018.01.008</a>.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” <i>Journal of Biotechnology</i>, vol. 268. Elsevier, pp. 40–52, 2018.","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52."},"date_published":"2018-02-20T00:00:00Z","publist_id":"7317","date_updated":"2024-10-09T20:58:29Z","intvolume":"       268","publication":"Journal of Biotechnology","author":[{"full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","orcid":"0000-0003-3768-877X","first_name":"Kathrin"},{"first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"}],"status":"public","page":"40 - 52","volume":268,"acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","month":"02"},{"scopus_import":"1","oa_version":"Submitted Version","_id":"519","doi":"10.1016/j.jmmm.2017.12.073","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:37Z","article_type":"original","isi":1,"date_created":"2018-12-11T11:46:56Z","quality_controlled":"1","oa":1,"external_id":{"isi":["000425547700061"]},"day":"15","type":"journal_article","department":[{"_id":"BjHo"}],"publisher":"Elsevier","publication_status":"published","year":"2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","article_processing_charge":"No","abstract":[{"lang":"eng","text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. "}],"citation":{"ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” <i>Journal of Magnetism and Magnetic Materials</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">https://doi.org/10.1016/j.jmmm.2017.12.073</a>.","ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. <i>Journal of Magnetism and Magnetic Materials</i>. 2018;452:427-441. doi:<a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">10.1016/j.jmmm.2017.12.073</a>","apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. <i>Journal of Magnetism and Magnetic Materials</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">https://doi.org/10.1016/j.jmmm.2017.12.073</a>","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” <i>Journal of Magnetism and Magnetic Materials</i>, vol. 452. Elsevier, pp. 427–441, 2018.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” <i>Journal of Magnetism and Magnetic Materials</i>, vol. 452, Elsevier, 2018, pp. 427–41, doi:<a href=\"https://doi.org/10.1016/j.jmmm.2017.12.073\">10.1016/j.jmmm.2017.12.073</a>.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441."},"corr_author":"1","has_accepted_license":"1","date_published":"2018-04-15T00:00:00Z","date_updated":"2024-10-09T20:58:32Z","publist_id":"7297","intvolume":"       452","publication":"Journal of Magnetism and Magnetic Materials","author":[{"full_name":"Altmeyer, Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","last_name":"Altmeyer","first_name":"Sebastian"}],"status":"public","file":[{"file_id":"7838","file_name":"2018_Magnetism_Altmeyer.pdf","content_type":"application/pdf","file_size":17309535,"access_level":"open_access","date_created":"2020-05-14T14:41:17Z","creator":"dernst","date_updated":"2020-07-14T12:46:37Z","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","relation":"main_file"}],"page":"427 - 441","month":"04","ddc":["530"],"acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","volume":452},{"date_published":"2018-03-01T00:00:00Z","citation":{"ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. <i>Computational Geometry: Theory and Applications</i>. 2018;68:119-133. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">10.1016/j.comgeo.2017.06.014</a>","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">https://doi.org/10.1016/j.comgeo.2017.06.014</a>.","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” <i>Computational Geometry: Theory and Applications</i>, vol. 68. Elsevier, pp. 119–133, 2018.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” <i>Computational Geometry: Theory and Applications</i>, vol. 68, Elsevier, 2018, pp. 119–33, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">10.1016/j.comgeo.2017.06.014</a>.","apa":"Edelsbrunner, H., &#38; Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2017.06.014\">https://doi.org/10.1016/j.comgeo.2017.06.014</a>"},"abstract":[{"lang":"eng","text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software."}],"corr_author":"1","has_accepted_license":"1","intvolume":"        68","date_updated":"2025-04-15T08:37:54Z","publist_id":"7289","status":"public","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel"}],"publication":"Computational Geometry: Theory and Applications","month":"03","ec_funded":1,"volume":68,"ddc":["000"],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:38Z","date_created":"2019-02-12T06:47:52Z","access_level":"open_access","relation":"main_file","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","file_name":"2018_Edelsbrunner.pdf","file_id":"5953","file_size":708357,"content_type":"application/pdf"}],"page":"119 - 133","file_date_updated":"2020-07-14T12:46:38Z","language":[{"iso":"eng"}],"_id":"530","oa_version":"Preprint","scopus_import":"1","doi":"10.1016/j.comgeo.2017.06.014","quality_controlled":"1","project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7"}],"isi":1,"date_created":"2018-12-11T11:46:59Z","department":[{"_id":"HeEd"}],"year":"2018","publication_status":"published","publisher":"Elsevier","external_id":{"isi":["000415778300010"]},"day":"01","oa":1,"type":"journal_article","article_processing_charge":"No","title":"Multiple covers with balls I: Inclusion–exclusion","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"OA_type":"free access","year":"2018","publication_status":"published","publisher":"Cell Press","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"department":[{"_id":"CaHe"}],"type":"journal_article","day":"08","external_id":{"isi":["000446579900002"]},"oa":1,"article_processing_charge":"No","title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"review","language":[{"iso":"eng"}],"doi":"10.1016/j.devcel.2018.09.014","_id":"54","oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T11:44:23Z","isi":1,"status":"public","author":[{"full_name":"Nunes Pinheiro, Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","first_name":"Diana C","last_name":"Nunes Pinheiro","orcid":"0000-0003-4333-7503"},{"last_name":"Bellaïche","first_name":"Yohanns","full_name":"Bellaïche, Yohanns"}],"issue":"1","publication":"Developmental Cell","volume":47,"acknowledgement":"Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants.","month":"10","page":"3 - 19","date_published":"2018-10-08T00:00:00Z","abstract":[{"text":"During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics.","lang":"eng"}],"citation":{"ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","ieee":"D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” <i>Developmental Cell</i>, vol. 47, no. 1. Cell Press, pp. 3–19, 2018.","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19.","mla":"Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” <i>Developmental Cell</i>, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">10.1016/j.devcel.2018.09.014</a>.","apa":"Nunes Pinheiro, D. C., &#38; Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">https://doi.org/10.1016/j.devcel.2018.09.014</a>","ama":"Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. <i>Developmental Cell</i>. 2018;47(1):3-19. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">10.1016/j.devcel.2018.09.014</a>","chicago":"Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.09.014\">https://doi.org/10.1016/j.devcel.2018.09.014</a>."},"intvolume":"        47","publist_id":"8000","date_updated":"2025-07-03T11:46:39Z"},{"doi":"10.1073/pnas.1711114115","oa_version":"Submitted Version","scopus_import":"1","_id":"543","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:47:04Z","isi":1,"project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","grant_number":"P 25651-N26"}],"quality_controlled":"1","type":"journal_article","oa":1,"external_id":{"isi":["000419128700049"]},"day":"02","publisher":"National Academy of Sciences","year":"2018","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1101/152660 ","open_access":"1"}],"department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Toward a unified theory of efficient, predictive, and sparse coding","article_processing_charge":"No","corr_author":"1","citation":{"chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>.","ama":"Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(1):186-191. doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1711114115\">https://doi.org/10.1073/pnas.1711114115</a>","short":"M.J. Chalk, O. Marre, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 186–191.","mla":"Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:<a href=\"https://doi.org/10.1073/pnas.1711114115\">10.1073/pnas.1711114115</a>.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018.","ista":"Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. Proceedings of the National Academy of Sciences of the United States of America. 115(1), 186–191."},"abstract":[{"text":"A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits.","lang":"eng"}],"date_published":"2018-01-02T00:00:00Z","publist_id":"7273","date_updated":"2025-05-14T10:55:59Z","intvolume":"       115","issue":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","author":[{"id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","full_name":"Chalk, Matthew J","first_name":"Matthew J","last_name":"Chalk","orcid":"0000-0001-7782-4436"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"status":"public","page":"186 - 191","volume":115,"month":"01"}]