[{"title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung","publist_id":"6843","author":[{"full_name":"Andrae, Magdalena","last_name":"Andrae","first_name":"Magdalena"},{"last_name":"Villányi","full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898","apa":"Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1898."},"date_created":"2018-12-11T11:48:36Z","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1898","page":"274 - 280","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","day":"01","year":"2017","has_accepted_license":"1","popular_science":"1","oa":1,"publisher":"VÖB","file_date_updated":"2020-07-14T12:48:09Z","department":[{"_id":"E-Lib"}],"ddc":["020"],"date_updated":"2021-01-12T08:16:45Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"807","license":"https://creativecommons.org/licenses/by/4.0/","issue":"2","volume":70,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-01-18T13:39:26Z","file_name":"2017_VOEB_Andrae.pdf","date_updated":"2020-07-14T12:48:09Z","file_size":125065,"creator":"dernst","checksum":"558c18bcf5580d87dd371ec626d52075","file_id":"5851","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["10222588"]},"intvolume":" 70","month":"08","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.","lang":"eng"}]},{"oa":1,"publisher":"VÖB","date_created":"2018-12-11T11:48:42Z","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1678","page":"200 - 207","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","day":"01","year":"2017","has_accepted_license":"1","title":"Metadata for research data in practice","publist_id":"6823","author":[{"id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Petritsch","full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 70 (2017) 200–207.","ama":"Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207. doi:10.31263/voebm.v70i2.1678","apa":"Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1678","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1678."},"intvolume":" 70","month":"08","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.","lang":"eng"}],"issue":"2","volume":70,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-01-18T13:32:17Z","file_name":"2017_VOEB_Petritsch.pdf","date_updated":"2020-07-14T12:48:11Z","file_size":7843975,"creator":"dernst","file_id":"5850","checksum":"7c4544d07efa2c2add8612b489abb4e2","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["10222588"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"825","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:48:11Z","ddc":["020"],"date_updated":"2021-01-12T08:17:44Z"},{"article_number":"e30674","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674.","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674."},"title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","external_id":{"pmid":["29140247"]},"article_processing_charge":"No","author":[{"last_name":"Lyons","full_name":"Lyons, David B","first_name":"David B"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","publication":"eLife","day":"15","year":"2017","has_accepted_license":"1","date_created":"2021-06-02T14:28:58Z","date_published":"2017-11-15T00:00:00Z","doi":"10.7554/elife.30674","_id":"9445","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["570"],"extern":"1","date_updated":"2021-12-14T07:54:36Z","file_date_updated":"2021-06-02T14:33:36Z","department":[{"_id":"DaZi"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"intvolume":" 6","month":"11","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":1603102,"date_updated":"2021-06-02T14:33:36Z","creator":"cziletti","file_name":"2017_eLife_Lyons.pdf","date_created":"2021-06-02T14:33:36Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"4cfcdd67511ae4aed3d993550e46e146","file_id":"9446"}],"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"volume":6},{"citation":{"mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ben","full_name":"Clifton, Ben","last_name":"Clifton"},{"first_name":"Jason","full_name":"Whitfield, Jason","last_name":"Whitfield"},{"first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero"},{"first_name":"Michel","full_name":"Herde, Michel","last_name":"Herde"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L"},{"last_name":"Jackson","full_name":"Jackson, Colin","first_name":"Colin"}],"publist_id":"6451","editor":[{"last_name":"Stein","full_name":"Stein, Viktor","first_name":"Viktor"}],"title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","project":[{"grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"year":"2017","publication":"Synthetic Protein Switches","day":"15","page":"71 - 87","date_created":"2018-12-11T11:49:24Z","doi":"10.1007/978-1-4939-6940-1_5","date_published":"2017-03-15T00:00:00Z","publisher":"Springer","quality_controlled":"1","date_updated":"2021-01-12T08:22:13Z","department":[{"_id":"HaJa"}],"_id":"957","series_title":"Synthetic Protein Switches","type":"book_chapter","status":"public","publication_status":"published","publication_identifier":{"issn":["10643745"]},"language":[{"iso":"eng"}],"volume":1596,"abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"oa_version":"None","scopus_import":1,"alternative_title":["Methods in Molecular Biology"],"intvolume":" 1596","month":"03"},{"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"article_number":"37","title":"Timed network games with clocks","publist_id":"6438","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni"},{"last_name":"Guha","full_name":"Guha, Shibashis","first_name":"Shibashis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37."},"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2018-12-11T11:49:26Z","doi":"10.4230/LIPIcs.MFCS.2017.37","date_published":"2017-06-01T00:00:00Z","day":"01","year":"2017","has_accepted_license":"1","pubrep_id":"829","status":"public","conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","start_date":"2017-08-21","end_date":"2017-08-25","location":"Aalborg, Denmark"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"963","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:48:18Z","ddc":["004"],"date_updated":"2023-02-23T12:35:50Z","intvolume":" 83","month":"06","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ","lang":"eng"}],"related_material":{"record":[{"id":"6005","status":"public","relation":"later_version"}]},"volume":83,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f55eaf7f3c36ea07801112acfedd17d5","file_id":"5059","creator":"system","date_updated":"2020-07-14T12:48:18Z","file_size":369730,"date_created":"2018-12-12T10:14:10Z","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf"}],"publication_status":"published","publication_identifier":{"issn":["18688969"]}},{"title":"Data from: Error-robust modes of the retinal population code","department":[{"_id":"GaTk"}],"author":[{"last_name":"Prentice","full_name":"Prentice, Jason","first_name":"Jason"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Mark","last_name":"Ioffe","full_name":"Ioffe, Mark"},{"first_name":"Adrianna","full_name":"Loback, Adrianna","last_name":"Loback"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-21T16:34:41Z","citation":{"mla":"Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc."},"status":"public","type":"research_data_reference","_id":"9709","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1197"}]},"doi":"10.5061/dryad.1f1rc","date_published":"2017-10-18T00:00:00Z","date_created":"2021-07-23T11:34:34Z","day":"18","year":"2017","month":"10","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}],"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}]},{"publication_status":"published","publication_identifier":{"issn":["15537390"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:14:35Z","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","creator":"system","date_updated":"2020-07-14T12:46:46Z","file_size":1308475,"checksum":"22426d9382f21554bad5fa5967afcfd0","file_id":"5088","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":13,"issue":"12","related_material":{"record":[{"relation":"research_data","status":"public","id":"9844"},{"id":"9845","status":"public","relation":"research_data"},{"relation":"research_data","id":"9846","status":"public"}]},"abstract":[{"lang":"eng","text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 13","month":"12","date_updated":"2023-02-23T14:10:34Z","ddc":["576","579"],"department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:46:46Z","_id":"541","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"959","status":"public","year":"2017","has_accepted_license":"1","publication":"PLoS Genetics","day":"18","date_created":"2018-12-11T11:47:04Z","doi":"10.1371/journal.pgen.1007122","date_published":"2017-12-18T00:00:00Z","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","citation":{"chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. 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