[{"intvolume":"        11","publication_status":"published","keyword":["Design","Synthesis and processing","Mechanical engineering","Polymers"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"13","date_created":"2020-01-13T16:54:26Z","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","external_id":{"isi":["000511916800015"],"pmid":["31932589"]},"ddc":["000"],"isi":1,"_id":"7262","article_processing_charge":"No","oa":1,"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:55Z","content_type":"application/pdf","file_id":"7336","relation":"main_file","creator":"rguseino","file_name":"2020_NatureComm_Guseinov.pdf","checksum":"7db23fef2f4cda712f17f1004116ddff","file_size":1315270,"date_created":"2020-01-15T14:35:34Z"}],"department":[{"_id":"BeBi"}],"publisher":"Springer Nature","status":"public","publication":"Nature Communications","date_updated":"2026-04-08T07:25:22Z","type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"title":"Programming temporal morphing of self-actuated shells","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/geometry-meets-time/"}],"record":[{"id":"7154","relation":"research_data","status":"public"},{"status":"public","relation":"dissertation_contains","id":"8366"}]},"year":"2020","oa_version":"Published Version","author":[{"last_name":"Guseinov","first_name":"Ruslan","orcid":"0000-0001-9819-5077","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","full_name":"Guseinov, Ruslan"},{"last_name":"McMahan","first_name":"Connor","full_name":"McMahan, Connor"},{"full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","last_name":"Perez Rodriguez"},{"full_name":"Daraio, Chiara","last_name":"Daraio","first_name":"Chiara"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","last_name":"Bickel","orcid":"0000-0001-6511-9385","first_name":"Bernd"}],"citation":{"short":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, B. Bickel, Nature Communications 11 (2020).","ieee":"R. Guseinov, C. McMahan, J. Perez Rodriguez, C. Daraio, and B. Bickel, “Programming temporal morphing of self-actuated shells,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","mla":"Guseinov, Ruslan, et al. “Programming Temporal Morphing of Self-Actuated Shells.” <i>Nature Communications</i>, vol. 11, 237, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-019-14015-2\">10.1038/s41467-019-14015-2</a>.","chicago":"Guseinov, Ruslan, Connor McMahan, Jesus Perez Rodriguez, Chiara Daraio, and Bernd Bickel. “Programming Temporal Morphing of Self-Actuated Shells.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-019-14015-2\">https://doi.org/10.1038/s41467-019-14015-2</a>.","ista":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. 2020. Programming temporal morphing of self-actuated shells. Nature Communications. 11, 237.","ama":"Guseinov R, McMahan C, Perez Rodriguez J, Daraio C, Bickel B. Programming temporal morphing of self-actuated shells. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-019-14015-2\">10.1038/s41467-019-14015-2</a>","apa":"Guseinov, R., McMahan, C., Perez Rodriguez, J., Daraio, C., &#38; Bickel, B. (2020). Programming temporal morphing of self-actuated shells. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-14015-2\">https://doi.org/10.1038/s41467-019-14015-2</a>"},"article_number":"237","abstract":[{"text":"Advances in shape-morphing materials, such as hydrogels, shape-memory polymers and light-responsive polymers have enabled prescribing self-directed deformations of initially flat geometries. However, most proposed solutions evolve towards a target geometry without considering time-dependent actuation paths. To achieve more complex geometries and avoid self-collisions, it is critical to encode a spatial and temporal shape evolution within the initially flat shell. Recent realizations of time-dependent morphing are limited to the actuation of few, discrete hinges and cannot form doubly curved surfaces. Here, we demonstrate a method for encoding temporal shape evolution in architected shells that assume complex shapes and doubly curved geometries. The shells are non-periodic tessellations of pre-stressed contractile unit cells that soften in water at rates prescribed locally by mesostructure geometry. The ensuing midplane contraction is coupled to the formation of encoded curvatures. We propose an inverse design tool based on a data-driven model for unit cells’ temporal responses.","lang":"eng"}],"scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.1038/s41467-019-14015-2","month":"01","ec_funded":1,"date_published":"2020-01-13T00:00:00Z","volume":11,"corr_author":"1","has_accepted_license":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"}],"file_date_updated":"2020-07-14T12:47:55Z","language":[{"iso":"eng"}],"article_type":"original"},{"scopus_import":"1","quality_controlled":"1","ddc":["000"],"month":"01","_id":"7272","article_processing_charge":"No","oa":1,"date_published":"2020-01-01T00:00:00Z","department":[{"_id":"DaAl"}],"page":"295-306","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"publisher":"USENIX Association","status":"public","language":[{"iso":"eng"}],"publication":"Proceedings of the 2018 USENIX Annual Technical Conference","date_updated":"2025-04-15T07:40:57Z","type":"conference","publication_identifier":{"isbn":["9781939133021"]},"title":"Getting to the root of concurrent binary search tree performance","year":"2020","publication_status":"published","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"end_date":"2018-07-13","location":"Boston, MA, United States","start_date":"2018-07-11","name":"USENIX: Annual Technical Conference"},"main_file_link":[{"url":"https://www.usenix.org/system/files/conference/atc18/atc18-arbel-raviv.pdf","open_access":"1"}],"author":[{"last_name":"Arbel-Raviv","first_name":"Maya","full_name":"Arbel-Raviv, Maya"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A","last_name":"Brown","first_name":"Trevor A"},{"full_name":"Morrison, Adam","last_name":"Morrison","first_name":"Adam"}],"day":"01","date_created":"2020-01-14T07:27:08Z","citation":{"apa":"Arbel-Raviv, M., Brown, T. A., &#38; Morrison, A. (2020). Getting to the root of concurrent binary search tree performance. In <i>Proceedings of the 2018 USENIX Annual Technical Conference</i> (pp. 295–306). Boston, MA, United States: USENIX Association.","ama":"Arbel-Raviv M, Brown TA, Morrison A. Getting to the root of concurrent binary search tree performance. In: <i>Proceedings of the 2018 USENIX Annual Technical Conference</i>. USENIX Association; 2020:295-306.","chicago":"Arbel-Raviv, Maya, Trevor A Brown, and Adam Morrison. “Getting to the Root of Concurrent Binary Search Tree Performance.” In <i>Proceedings of the 2018 USENIX Annual Technical Conference</i>, 295–306. USENIX Association, 2020.","ista":"Arbel-Raviv M, Brown TA, Morrison A. 2020. Getting to the root of concurrent binary search tree performance. Proceedings of the 2018 USENIX Annual Technical Conference. USENIX: Annual Technical Conference, 295–306.","mla":"Arbel-Raviv, Maya, et al. “Getting to the Root of Concurrent Binary Search Tree Performance.” <i>Proceedings of the 2018 USENIX Annual Technical Conference</i>, USENIX Association, 2020, pp. 295–306.","ieee":"M. Arbel-Raviv, T. A. Brown, and A. Morrison, “Getting to the root of concurrent binary search tree performance,” in <i>Proceedings of the 2018 USENIX Annual Technical Conference</i>, Boston, MA, United States, 2020, pp. 295–306.","short":"M. Arbel-Raviv, T.A. Brown, A. Morrison, in:, Proceedings of the 2018 USENIX Annual Technical Conference, USENIX Association, 2020, pp. 295–306."},"abstract":[{"text":"Many systems rely on optimistic concurrent search trees for multi-core scalability. In principle, optimistic trees have a simple performance story: searches are read-only and so run in parallel, with writes to shared memory occurring only when modifying the data structure. However, this paper shows that in practice, obtaining the full performance benefits of optimistic search trees is not so simple.\r\n\r\nWe focus on optimistic binary search trees (BSTs) and perform a detailed performance analysis of 10 state-of-the-art BSTs on large scale x86-64 hardware, using both microbenchmarks and an in-memory database system. We find and explain significant unexpected performance differences between BSTs with similar tree structure and search implementations, which we trace to subtle performance-degrading interactions of BSTs with systems software and hardware subsystems. We further derive a prescriptive approach to avoid this performance degradation, as well as algorithmic insights on optimistic BST design. Our work underlines the gap between the theory and practice of multi-core performance, and calls for further research to help bridge this gap.","lang":"eng"}]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","pmid":1,"day":"02","date_created":"2020-01-19T23:00:38Z","issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        40","publication_status":"published","oa":1,"file":[{"checksum":"92f5e8a47f454fc131fb94cd7f106e60","date_created":"2020-01-20T14:44:10Z","file_size":4460781,"file_name":"2020_JourNeuroscience_Piriya.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:56Z","access_level":"open_access","relation":"main_file","file_id":"7345","creator":"dernst"}],"publisher":"Society for Neuroscience","page":"131-142","department":[{"_id":"RySh"}],"publication":"Journal of neuroscience","status":"public","ddc":["570"],"quality_controlled":"1","external_id":{"pmid":["31767677"],"isi":["000505167600013"]},"_id":"7339","article_processing_charge":"No","isi":1,"oa_version":"Published Version","author":[{"full_name":"Piriya Ananda Babu, Lashmi","last_name":"Piriya Ananda Babu","first_name":"Lashmi"},{"full_name":"Wang, Han Ying","last_name":"Wang","first_name":"Han Ying"},{"full_name":"Eguchi, Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546","first_name":"Kohgaku","last_name":"Eguchi"},{"full_name":"Guillaud, Laurent","last_name":"Guillaud","first_name":"Laurent"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"abstract":[{"lang":"eng","text":"Cytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission."}],"citation":{"apa":"Piriya Ananda Babu, L., Wang, H. Y., Eguchi, K., Guillaud, L., &#38; Takahashi, T. (2020). Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">https://doi.org/10.1523/JNEUROSCI.1571-19.2019</a>","ama":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. <i>Journal of neuroscience</i>. 2020;40(1):131-142. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">10.1523/JNEUROSCI.1571-19.2019</a>","ista":"Piriya Ananda Babu L, Wang HY, Eguchi K, Guillaud L, Takahashi T. 2020. Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission. Journal of neuroscience. 40(1), 131–142.","chicago":"Piriya Ananda Babu, Lashmi, Han Ying Wang, Kohgaku Eguchi, Laurent Guillaud, and Tomoyuki Takahashi. “Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2020. <a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">https://doi.org/10.1523/JNEUROSCI.1571-19.2019</a>.","mla":"Piriya Ananda Babu, Lashmi, et al. “Microtubule and Actin Differentially Regulate Synaptic Vesicle Cycling to Maintain High-Frequency Neurotransmission.” <i>Journal of Neuroscience</i>, vol. 40, no. 1, Society for Neuroscience, 2020, pp. 131–42, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.1571-19.2019\">10.1523/JNEUROSCI.1571-19.2019</a>.","ieee":"L. Piriya Ananda Babu, H. Y. Wang, K. Eguchi, L. Guillaud, and T. Takahashi, “Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission,” <i>Journal of neuroscience</i>, vol. 40, no. 1. Society for Neuroscience, pp. 131–142, 2020.","short":"L. Piriya Ananda Babu, H.Y. Wang, K. Eguchi, L. Guillaud, T. Takahashi, Journal of Neuroscience 40 (2020) 131–142."},"date_updated":"2026-04-16T08:27:29Z","publication_identifier":{"issn":["0270-6474"],"eissn":["1529-2401"]},"type":"journal_article","title":"Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission","year":"2020","date_published":"2020-01-02T00:00:00Z","volume":40,"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:56Z","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","doi":"10.1523/JNEUROSCI.1571-19.2019","month":"01"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","tmp":{"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","short":"CC BY-NC (4.0)"},"pmid":1,"date_created":"2020-01-20T13:32:12Z","day":"01","acknowledged_ssus":[{"_id":"LifeSc"}],"publication_status":"published","intvolume":"        23","publisher":"Wiley","page":"565-574","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"file":[{"creator":"dernst","file_id":"8776","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-11-19T11:27:10Z","file_name":"2020_EcologyLetters_Milutinovic.pdf","file_size":561749,"date_created":"2020-11-19T11:27:10Z","checksum":"0cd8be386fa219db02845b7c3991ce04","success":1}],"oa":1,"publication":"Ecology Letters","status":"public","ddc":["570"],"external_id":{"pmid":["31950595"],"isi":["000507515900001"]},"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","_id":"7343","isi":1,"acknowledgement":"We thank Bernhardt Steinwender and Jorgen Eilenberg for the fungal strains, Xavier Espadaler, Mireia Diaz, Christiane Wanke, Lumi Viljakainen and the Social Immunity Team at IST Austria, for help with ant collection, and Wanda Gorecka and Gertraud Stift of the IST Austria Life Science Facility for technical support. We are thankful to Dieter Ebert for input at all stages of the project, Roger Mundry for statistical advice, Hinrich Schulenburg, Paul Schmid-Hempel, Yuko\r\nUlrich and Joachim Kurtz for project discussion, Bor Kavcic for advice on growth curves, Marcus Roper for advice on modelling work and comments on the manuscript, as well as Marjon de Vos, Weini Huang and the Social Immunity Team for comments on the manuscript.\r\nThis study was funded by the German Research Foundation (DFG) within the Priority Programme 1399 Host-parasite Coevolution (CR 118/3 to S.C.) and the People Programme\r\n(Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no 291734 (ISTFELLOW to B.M.). ","author":[{"first_name":"Barbara","orcid":"0000-0002-8214-4758","last_name":"Milutinovic","full_name":"Milutinovic, Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth","last_name":"Naderlinger"},{"full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"oa_version":"Published Version","abstract":[{"text":"Coinfections with multiple pathogens can result in complex within‐host dynamics affecting virulence and transmission. While multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defences of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different‐species coinfections. Here, it decreased overall pathogen sporulation success while increasing co‐sporulation on individual cadavers and maintaining a higher pathogen diversity at the community level. Mathematical modelling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast‐germinating, thus less grooming‐sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host level and population level.","lang":"eng"}],"citation":{"apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., &#38; Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/ele.13458\">https://doi.org/10.1111/ele.13458</a>","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. <i>Ecology Letters</i>. 2020;23(3):565-574. doi:<a href=\"https://doi.org/10.1111/ele.13458\">10.1111/ele.13458</a>","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens,” <i>Ecology Letters</i>, vol. 23, no. 3. Wiley, pp. 565–574, 2020.","mla":"Milutinovic, Barbara, et al. “Social Immunity Modulates Competition between Coinfecting Pathogens.” <i>Ecology Letters</i>, vol. 23, no. 3, Wiley, 2020, pp. 565–74, doi:<a href=\"https://doi.org/10.1111/ele.13458\">10.1111/ele.13458</a>.","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens. Ecology Letters. 23(3), 565–574.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” <i>Ecology Letters</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/ele.13458\">https://doi.org/10.1111/ele.13458</a>.","short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, Ecology Letters 23 (2020) 565–574."},"publication_identifier":{"issn":["1461-023X"],"eissn":["1461-0248"]},"type":"journal_article","date_updated":"2025-06-12T07:32:35Z","year":"2020","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/social-ants-shapes-disease-outcome/"}],"record":[{"relation":"research_data","status":"public","id":"13060"}]},"title":"Social immunity modulates competition between coinfecting pathogens","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Host-Parasite Coevolution","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","grant_number":"CR-118/3-1"}],"file_date_updated":"2020-11-19T11:27:10Z","has_accepted_license":"1","corr_author":"1","volume":23,"date_published":"2020-03-01T00:00:00Z","ec_funded":1,"article_type":"letter_note","language":[{"iso":"eng"}],"scopus_import":"1","month":"03","license":"https://creativecommons.org/licenses/by-nc/4.0/","doi":"10.1111/ele.13458"},{"scopus_import":"1","month":"02","doi":"10.4230/LIPIcs.OPODIS.2019.21","file_date_updated":"2020-07-14T12:47:56Z","has_accepted_license":"1","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"date_published":"2020-02-10T00:00:00Z","volume":153,"language":[{"iso":"eng"}],"arxiv":1,"type":"conference","date_updated":"2025-04-15T08:10:32Z","year":"2020","title":"The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game","author":[{"first_name":"Laura","orcid":"0000-0002-6978-7329","last_name":"Schmid","full_name":"Schmid, Laura","id":"38B437DE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}],"oa_version":"Preprint","conference":{"name":"OPODIS: International Conference on Principles of Distributed Systems","start_date":"2019-12-17","location":"Neuchâtel, Switzerland","end_date":"2019-12-19"},"abstract":[{"lang":"eng","text":"The Price of Anarchy (PoA) is a well-established game-theoretic concept to shed light on coordination issues arising in open distributed systems. Leaving agents to selfishly optimize comes with the risk of ending up in sub-optimal states (in terms of performance and/or costs), compared to a centralized system design. However, the PoA relies on strong assumptions about agents' rationality (e.g., resources and information) and interactions, whereas in many distributed systems agents interact locally with bounded resources. They do so repeatedly over time (in contrast to \"one-shot games\"), and their strategies may evolve. Using a more realistic evolutionary game model, this paper introduces a realized evolutionary Price of Anarchy (ePoA). The ePoA allows an exploration of equilibrium selection in dynamic distributed systems with multiple equilibria, based on local interactions of simple memoryless agents. Considering a fundamental game related to virus propagation on networks, we present analytical bounds on the ePoA in basic network topologies and for different strategy update dynamics. In particular, deriving stationary distributions of the stochastic evolutionary process, we find that the Nash equilibria are not always the most abundant states, and that different processes can feature significant off-equilibrium behavior, leading to a significantly higher ePoA compared to the PoA studied traditionally in the literature. "}],"article_number":"21","citation":{"ieee":"L. Schmid, K. Chatterjee, and S. Schmid, “The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game,” in <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, Neuchâtel, Switzerland, 2020, vol. 153.","mla":"Schmid, Laura, et al. “The Evolutionary Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, vol. 153, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">10.4230/LIPIcs.OPODIS.2019.21</a>.","ista":"Schmid L, Chatterjee K, Schmid S. 2020. The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. Proceedings of the 23rd International Conference on Principles of Distributed Systems. OPODIS: International Conference on Principles of Distributed Systems, LIPIcs, vol. 153, 21.","chicago":"Schmid, Laura, Krishnendu Chatterjee, and Stefan Schmid. “The Evolutionary Price of Anarchy: Locally Bounded Agents in a Dynamic Virus Game.” In <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>, Vol. 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.21</a>.","short":"L. Schmid, K. Chatterjee, S. Schmid, in:, Proceedings of the 23rd International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","apa":"Schmid, L., Chatterjee, K., &#38; Schmid, S. (2020). The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. In <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i> (Vol. 153). Neuchâtel, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.21</a>","ama":"Schmid L, Chatterjee K, Schmid S. The evolutionary price of anarchy: Locally bounded agents in a dynamic virus game. In: <i>Proceedings of the 23rd International Conference on Principles of Distributed Systems</i>. Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.21\">10.4230/LIPIcs.OPODIS.2019.21</a>"},"ddc":["000"],"quality_controlled":"1","external_id":{"arxiv":["1906.00110"]},"article_processing_charge":"No","_id":"7346","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:56Z","creator":"dernst","file_id":"7608","relation":"main_file","file_name":"2019_LIPIcS_Schmid.pdf","file_size":630752,"date_created":"2020-03-23T09:14:06Z","checksum":"9a91916ac2c21ab42458fcda39ef0b8d"}],"oa":1,"publication":"Proceedings of the 23rd International Conference on Principles of Distributed Systems","alternative_title":["LIPIcs"],"status":"public","publication_status":"published","intvolume":"       153","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2020-01-21T16:00:26Z","day":"10"},{"publication_status":"published","intvolume":"       152","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"15","date_created":"2020-01-21T11:22:21Z","external_id":{"arxiv":["1910.06097"]},"quality_controlled":"1","ddc":["000"],"article_processing_charge":"No","_id":"7348","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"file":[{"file_size":617206,"date_created":"2020-01-21T11:21:04Z","checksum":"b9a691d658d075c6369d3304d17fb818","file_name":"main.pdf","date_updated":"2020-07-14T12:47:56Z","content_type":"application/pdf","access_level":"open_access","creator":"bkragl","file_id":"7349","relation":"main_file"}],"alternative_title":["LIPIcs"],"status":"public","publication":"28th EACSL Annual Conference on Computer Science Logic","type":"conference","arxiv":1,"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771320"]},"date_updated":"2025-04-15T06:26:07Z","year":"2020","title":"Monitoring event frequencies","author":[{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl","full_name":"Kragl, Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"}],"conference":{"start_date":"2020-01-13","location":"Barcelona, Spain","end_date":"2020-01-16","name":"CSL: Computer Science Logic"},"oa_version":"Published Version","citation":{"short":"T. Ferrere, T.A. Henzinger, B. Kragl, in:, 28th EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020.","ista":"Ferrere T, Henzinger TA, Kragl B. 2020. Monitoring event frequencies. 28th EACSL Annual Conference on Computer Science Logic. CSL: Computer Science Logic, LIPIcs, vol. 152, 20.","chicago":"Ferrere, Thomas, Thomas A Henzinger, and Bernhard Kragl. “Monitoring Event Frequencies.” In <i>28th EACSL Annual Conference on Computer Science Logic</i>, Vol. 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">https://doi.org/10.4230/LIPIcs.CSL.2020.20</a>.","ieee":"T. Ferrere, T. A. Henzinger, and B. Kragl, “Monitoring event frequencies,” in <i>28th EACSL Annual Conference on Computer Science Logic</i>, Barcelona, Spain, 2020, vol. 152.","mla":"Ferrere, Thomas, et al. “Monitoring Event Frequencies.” <i>28th EACSL Annual Conference on Computer Science Logic</i>, vol. 152, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">10.4230/LIPIcs.CSL.2020.20</a>.","ama":"Ferrere T, Henzinger TA, Kragl B. Monitoring event frequencies. In: <i>28th EACSL Annual Conference on Computer Science Logic</i>. Vol 152. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">10.4230/LIPIcs.CSL.2020.20</a>","apa":"Ferrere, T., Henzinger, T. A., &#38; Kragl, B. (2020). Monitoring event frequencies. In <i>28th EACSL Annual Conference on Computer Science Logic</i> (Vol. 152). Barcelona, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2020.20\">https://doi.org/10.4230/LIPIcs.CSL.2020.20</a>"},"article_number":"20","abstract":[{"lang":"eng","text":"The monitoring of event frequencies can be used to recognize behavioral anomalies, to identify trends, and to deduce or discard hypotheses about the underlying system. For example, the performance of a web server may be monitored based on the ratio of the total count of requests from the least and most active clients. Exact frequency monitoring, however, can be prohibitively expensive; in the above example it would require as many counters as there are clients. In this paper, we propose the efficient probabilistic monitoring of common frequency properties, including the mode (i.e., the most common event) and the median of an event sequence. We define a logic to express composite frequency properties as a combination of atomic frequency properties. Our main contribution is an algorithm that, under suitable probabilistic assumptions, can be used to monitor these important frequency properties with four counters, independent of the number of different events. Our algorithm samples longer and longer subwords of an infinite event sequence. We prove the almost-sure convergence of our algorithm by generalizing ergodic theory from increasing-length prefixes to increasing-length subwords of an infinite sequence. A similar algorithm could be used to learn a connected Markov chain of a given structure from observing its outputs, to arbitrary precision, for a given confidence. "}],"scopus_import":1,"doi":"10.4230/LIPIcs.CSL.2020.20","month":"01","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:56Z","project":[{"name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"volume":152,"date_published":"2020-01-15T00:00:00Z","language":[{"iso":"eng"}]},{"article_processing_charge":"No","_id":"7350","isi":1,"ddc":["580"],"external_id":{"pmid":["32038671"],"isi":["000511376000001"]},"quality_controlled":"1","publication":"Frontiers in Plant Science","status":"public","oa":1,"file":[{"creator":"dernst","file_id":"7366","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:56Z","file_name":"2020_FrontiersPlantScience_Nibau.pdf","date_created":"2020-01-27T09:07:02Z","file_size":1951438,"checksum":"d1f92e60a713fbd15097ce895e5c7ccb"}],"publisher":"Frontiers Media","department":[{"_id":"EvBe"}],"intvolume":"        10","publication_status":"published","pmid":1,"date_created":"2020-01-22T15:23:57Z","day":"22","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","doi":"10.3389/fpls.2019.01680","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","volume":10,"date_published":"2020-01-22T00:00:00Z","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:56Z","corr_author":"1","title":"Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2","year":"2020","date_updated":"2025-06-12T07:33:02Z","publication_identifier":{"issn":["1664-462X"]},"type":"journal_article","abstract":[{"text":"The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition.","lang":"eng"}],"citation":{"apa":"Nibau, C., Gallemi, M., Dadarou, D., Doonan, J. H., &#38; Cavallari, N. (2020). Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2019.01680\">https://doi.org/10.3389/fpls.2019.01680</a>","ama":"Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N. Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. <i>Frontiers in Plant Science</i>. 2020;10. doi:<a href=\"https://doi.org/10.3389/fpls.2019.01680\">10.3389/fpls.2019.01680</a>","mla":"Nibau, Candida, et al. “Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2.” <i>Frontiers in Plant Science</i>, vol. 10, 1680, Frontiers Media, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2019.01680\">10.3389/fpls.2019.01680</a>.","ieee":"C. Nibau, M. Gallemi, D. Dadarou, J. H. Doonan, and N. Cavallari, “Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2,” <i>Frontiers in Plant Science</i>, vol. 10. Frontiers Media, 2020.","ista":"Nibau C, Gallemi M, Dadarou D, Doonan JH, Cavallari N. 2020. Thermo-sensitive alternative splicing of FLOWERING LOCUS M is modulated by cyclin-dependent kinase G2. Frontiers in Plant Science. 10, 1680.","chicago":"Nibau, Candida, Marçal Gallemi, Despoina Dadarou, John H. Doonan, and Nicola Cavallari. “Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2020. <a href=\"https://doi.org/10.3389/fpls.2019.01680\">https://doi.org/10.3389/fpls.2019.01680</a>.","short":"C. Nibau, M. Gallemi, D. Dadarou, J.H. Doonan, N. Cavallari, Frontiers in Plant Science 10 (2020)."},"article_number":"1680","oa_version":"Published Version","author":[{"last_name":"Nibau","first_name":"Candida","full_name":"Nibau, Candida"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal","last_name":"Gallemi","first_name":"Marçal","orcid":"0000-0003-4675-6893"},{"first_name":"Despoina","last_name":"Dadarou","full_name":"Dadarou, Despoina"},{"last_name":"Doonan","first_name":"John H.","full_name":"Doonan, John H."},{"full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicola","last_name":"Cavallari"}]},{"oa":1,"file":[{"relation":"main_file","file_id":"7365","creator":"dernst","date_updated":"2020-07-14T12:47:56Z","content_type":"application/pdf","access_level":"open_access","checksum":"2af1a1a3cc33557b345145276f221668","file_size":679707,"date_created":"2020-01-27T07:32:46Z","file_name":"2020_SoftwareX_Lopez.pdf"}],"publisher":"Elsevier","department":[{"_id":"BjHo"}],"publication":"SoftwareX","status":"public","ddc":["000"],"quality_controlled":"1","external_id":{"isi":["000552271200011"],"arxiv":["1908.00587"]},"article_processing_charge":"No","_id":"7364","isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"17","date_created":"2020-01-26T23:00:35Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"intvolume":"        11","publication_status":"published","date_published":"2020-01-17T00:00:00Z","volume":11,"file_date_updated":"2020-07-14T12:47:56Z","has_accepted_license":"1","corr_author":"1","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"01","doi":"10.1016/j.softx.2019.100395","oa_version":"Published Version","author":[{"full_name":"Lopez Alonso, Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","first_name":"Jose M","orcid":"0000-0002-0384-2022","last_name":"Lopez Alonso"},{"full_name":"Feldmann, Daniel","last_name":"Feldmann","first_name":"Daniel"},{"full_name":"Rampp, Markus","last_name":"Rampp","first_name":"Markus"},{"full_name":"Vela-Martín, Alberto","first_name":"Alberto","last_name":"Vela-Martín"},{"id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","full_name":"Shi, Liang","last_name":"Shi","first_name":"Liang"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"}],"abstract":[{"text":"We present nsCouette, a highly scalable software tool to solve the Navier–Stokes equations for incompressible fluid flow between differentially heated and independently rotating, concentric cylinders. It is based on a pseudospectral spatial discretization and dynamic time-stepping. It is implemented in modern Fortran with a hybrid MPI-OpenMP parallelization scheme and thus designed to compute turbulent flows at high Reynolds and Rayleigh numbers. An additional GPU implementation (C-CUDA) for intermediate problem sizes and a version for pipe flow (nsPipe) are also provided.","lang":"eng"}],"citation":{"apa":"Lopez Alonso, J. M., Feldmann, D., Rampp, M., Vela-Martín, A., Shi, L., &#38; Avila, M. (2020). nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. <i>SoftwareX</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.softx.2019.100395\">https://doi.org/10.1016/j.softx.2019.100395</a>","ama":"Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. <i>SoftwareX</i>. 2020;11. doi:<a href=\"https://doi.org/10.1016/j.softx.2019.100395\">10.1016/j.softx.2019.100395</a>","mla":"Lopez Alonso, Jose M., et al. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” <i>SoftwareX</i>, vol. 11, 100395, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.softx.2019.100395\">10.1016/j.softx.2019.100395</a>.","ieee":"J. M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, and M. Avila, “nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow,” <i>SoftwareX</i>, vol. 11. Elsevier, 2020.","chicago":"Lopez Alonso, Jose M, Daniel Feldmann, Markus Rampp, Alberto Vela-Martín, Liang Shi, and Marc Avila. “NsCouette – A High-Performance Code for Direct Numerical Simulations of Turbulent Taylor–Couette Flow.” <i>SoftwareX</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.softx.2019.100395\">https://doi.org/10.1016/j.softx.2019.100395</a>.","ista":"Lopez Alonso JM, Feldmann D, Rampp M, Vela-Martín A, Shi L, Avila M. 2020. nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow. SoftwareX. 11, 100395.","short":"J.M. Lopez Alonso, D. Feldmann, M. Rampp, A. Vela-Martín, L. Shi, M. Avila, SoftwareX 11 (2020)."},"article_number":"100395","date_updated":"2026-04-02T14:16:50Z","publication_identifier":{"eissn":["2352-7110"]},"arxiv":1,"type":"journal_article","title":"nsCouette – A high-performance code for direct numerical simulations of turbulent Taylor–Couette flow","year":"2020"},{"citation":{"ama":"Cubero RJ, Marsili M, Roudi Y. Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. 2020;48:85-102. doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>","apa":"Cubero, R. J., Marsili, M., &#38; Roudi, Y. (2020). Multiscale relevance and informative encoding in neuronal spike trains. <i>Journal of Computational Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>","short":"R.J. Cubero, M. Marsili, Y. Roudi, Journal of Computational Neuroscience 48 (2020) 85–102.","chicago":"Cubero, Ryan J, Matteo Marsili, and Yasser Roudi. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10827-020-00740-x\">https://doi.org/10.1007/s10827-020-00740-x</a>.","ista":"Cubero RJ, Marsili M, Roudi Y. 2020. Multiscale relevance and informative encoding in neuronal spike trains. Journal of Computational Neuroscience. 48, 85–102.","mla":"Cubero, Ryan J., et al. “Multiscale Relevance and Informative Encoding in Neuronal Spike Trains.” <i>Journal of Computational Neuroscience</i>, vol. 48, Springer Nature, 2020, pp. 85–102, doi:<a href=\"https://doi.org/10.1007/s10827-020-00740-x\">10.1007/s10827-020-00740-x</a>.","ieee":"R. J. Cubero, M. Marsili, and Y. Roudi, “Multiscale relevance and informative encoding in neuronal spike trains,” <i>Journal of Computational Neuroscience</i>, vol. 48. Springer Nature, pp. 85–102, 2020."},"abstract":[{"lang":"eng","text":"Neuronal responses to complex stimuli and tasks can encompass a wide range of time scales. Understanding these responses requires measures that characterize how the information on these response patterns are represented across multiple temporal resolutions. In this paper we propose a metric – which we call multiscale relevance (MSR) – to capture the dynamical variability of the activity of single neurons across different time scales. The MSR is a non-parametric, fully featureless indicator in that it uses only the time stamps of the firing activity without resorting to any a priori covariate or invoking any specific structure in the tuning curve for neural activity. When applied to neural data from the mEC and from the ADn and PoS regions of freely-behaving rodents, we found that neurons having low MSR tend to have low mutual information and low firing sparsity across the correlates that are believed to be encoded by the region of the brain where the recordings were made. In addition, neurons with high MSR contain significant information on spatial navigation and allow to decode spatial position or head direction as efficiently as those neurons whose firing activity has high mutual information with the covariate to be decoded and significantly better than the set of neurons with high local variations in their interspike intervals. Given these results, we propose that the MSR can be used as a measure to rank and select neurons for their information content without the need to appeal to any a priori covariate."}],"oa_version":"Published Version","author":[{"full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","orcid":"0000-0003-0002-1867","first_name":"Ryan J","last_name":"Cubero"},{"first_name":"Matteo","last_name":"Marsili","full_name":"Marsili, Matteo"},{"full_name":"Roudi, Yasser","first_name":"Yasser","last_name":"Roudi"}],"title":"Multiscale relevance and informative encoding in neuronal spike trains","year":"2020","date_updated":"2025-04-14T07:44:02Z","type":"journal_article","publication_identifier":{"issn":["0929-5313"],"eissn":["1573-6873"]},"language":[{"iso":"eng"}],"article_type":"original","ec_funded":1,"volume":48,"date_published":"2020-02-01T00:00:00Z","corr_author":"1","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:56Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.1007/s10827-020-00740-x","month":"02","scopus_import":"1","date_created":"2020-01-28T10:34:00Z","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        48","publication_status":"published","keyword":["Time series analysis","Multiple time scale analysis","Spike train data","Information theory","Bayesian decoding"],"status":"public","publication":"Journal of Computational Neuroscience","oa":1,"file":[{"file_name":"10827_2020_740_MOESM1_ESM.pdf","file_size":1941355,"date_created":"2020-01-28T09:31:09Z","checksum":"036e9451d6cd0c190ad25791bf82393b","creator":"rcubero","relation":"supplementary_material","file_id":"7380","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:56Z"},{"file_id":"7381","relation":"main_file","creator":"rcubero","date_updated":"2020-07-14T12:47:56Z","content_type":"application/pdf","access_level":"open_access","checksum":"4dd8b1fd4b54486f79d82ac7b2a412b2","date_created":"2020-01-28T09:31:09Z","file_size":3257880,"file_name":"Cubero2020_Article_MultiscaleRelevanceAndInformat.pdf"}],"page":"85-102","department":[{"_id":"SaSi"}],"publisher":"Springer Nature","acknowledgement":"This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation). RJC is currently receiving funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","isi":1,"_id":"7369","article_processing_charge":"Yes (via OA deal)","quality_controlled":"1","external_id":{"isi":["000515321800006"]},"ddc":["004","519","570"]},{"day":"28","date_created":"2020-01-28T10:41:49Z","contributor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","contributor_type":"project_leader","orcid":"0000-0001-6220-2052","first_name":"Calin C"}],"abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"citation":{"ama":"Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>","apa":"Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>","short":"R. Grah, (2020).","ieee":"R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.","mla":"Grah, Rok. <i>Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","ista":"Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">10.15479/AT:ISTA:7383</a>.","chicago":"Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7383\">https://doi.org/10.15479/AT:ISTA:7383</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","author":[{"last_name":"Grah","orcid":"0000-0003-2539-3560","first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7652"}]},"title":"Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation","keyword":["Matlab scripts","analysis of microfluidics","mathematical model"],"year":"2020","date_updated":"2025-06-12T07:34:12Z","type":"research_data","status":"public","date_published":"2020-01-28T00:00:00Z","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:57Z","content_type":"application/zip","file_id":"7384","relation":"main_file","creator":"rgrah","file_name":"Scripts.zip","checksum":"9d292cf5207b3829225f44c044cdb3fd","file_size":73363365,"date_created":"2020-01-28T10:39:40Z"},{"creator":"rgrah","file_id":"7385","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:47:57Z","content_type":"text/plain","file_name":"READ_ME_MAIN.txt","date_created":"2020-01-28T10:39:30Z","file_size":962,"checksum":"4076ceab32ef588cc233802bab24c1ab"}],"oa":1,"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:57Z","corr_author":"1","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"_id":"7383","article_processing_charge":"No","doi":"10.15479/AT:ISTA:7383","month":"01"},{"isi":1,"_id":"7389","article_processing_charge":"No","external_id":{"arxiv":["2002.00859"],"isi":["000551418100018"]},"quality_controlled":"1","ddc":["515"],"status":"public","publication":"Transactions of the American Mathematical Society","oa":1,"page":"5855-5883","department":[{"_id":"LaEr"}],"publisher":"American Mathematical Society","intvolume":"       373","publication_status":"published","keyword":["Wasserstein space","isometric embeddings","isometric rigidity","exotic isometry flow"],"date_created":"2020-01-29T10:20:46Z","day":"01","issue":"8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.00859"}],"doi":"10.1090/tran/8113","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original","ec_funded":1,"date_published":"2020-08-01T00:00:00Z","volume":373,"project":[{"call_identifier":"H2020","name":"Geometric study of Wasserstein spaces and free probability","grant_number":"846294","_id":"26A455A6-B435-11E9-9278-68D0E5697425"}],"title":"Isometric study of Wasserstein spaces - the real line","year":"2020","date_updated":"2025-07-10T11:54:32Z","type":"journal_article","arxiv":1,"publication_identifier":{"eissn":["1088-6850"],"issn":["0002-9947"]},"citation":{"ama":"Geher GP, Titkos T, Virosztek D. Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. 2020;373(8):5855-5883. doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>","apa":"Geher, G. P., Titkos, T., &#38; Virosztek, D. (2020). Isometric study of Wasserstein spaces - the real line. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>","short":"G.P. Geher, T. Titkos, D. Virosztek, Transactions of the American Mathematical Society 373 (2020) 5855–5883.","mla":"Geher, Gyorgy Pal, et al. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8, American Mathematical Society, 2020, pp. 5855–83, doi:<a href=\"https://doi.org/10.1090/tran/8113\">10.1090/tran/8113</a>.","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Isometric study of Wasserstein spaces - the real line,” <i>Transactions of the American Mathematical Society</i>, vol. 373, no. 8. American Mathematical Society, pp. 5855–5883, 2020.","ista":"Geher GP, Titkos T, Virosztek D. 2020. Isometric study of Wasserstein spaces - the real line. Transactions of the American Mathematical Society. 373(8), 5855–5883.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Isometric Study of Wasserstein Spaces - the Real Line.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2020. <a href=\"https://doi.org/10.1090/tran/8113\">https://doi.org/10.1090/tran/8113</a>."},"abstract":[{"text":"Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space\r\nW_p(R) for all p \\in [1,\\infty) \\setminus {2}. We show that W_2(R) is also exceptional regarding the\r\nparameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying\r\nspace, we prove that the exceptionality of p = 2 disappears if we replace R by the compact\r\ninterval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if\r\np is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))\r\ncannot be embedded into Isom(W_1(R)).","lang":"eng"}],"oa_version":"Preprint","author":[{"first_name":"Gyorgy Pal","last_name":"Geher","full_name":"Geher, Gyorgy Pal"},{"last_name":"Titkos","first_name":"Tamas","full_name":"Titkos, Tamas"},{"last_name":"Virosztek","first_name":"Daniel","orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","full_name":"Virosztek, Daniel"}]},{"abstract":[{"lang":"eng","text":"We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean  space,  motivated  by  the  famous  theorem  of  Gromov  about  the  waist  of  radially symmetric Gaussian measures.  In particular, it turns our possible to extend Gromov’s original result  to  the  case  of  not  necessarily  radially  symmetric  Gaussian  measure.   We  also  provide examples of measures having no t-neighborhood waist property, including a rather wide class\r\nof compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2.\r\nWe  use  a  simpler  form  of  Gromov’s  pancake  argument  to  produce  some  estimates  of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for reader’s convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian\r\nmeasures."}],"citation":{"apa":"Akopyan, A., &#38; Karasev, R. (2020). Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In B. Klartag &#38; E. Milman (Eds.), <i>Geometric Aspects of Functional Analysis</i> (Vol. 2256, pp. 1–27). Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>","ama":"Akopyan A, Karasev R. Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Klartag B, Milman E, eds. <i>Geometric Aspects of Functional Analysis</i>. Vol 2256. LNM. Springer Nature; 2020:1-27. doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>","mla":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, vol. 2256, Springer Nature, 2020, pp. 1–27, doi:<a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">10.1007/978-3-030-36020-7_1</a>.","ieee":"A. Akopyan and R. Karasev, “Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures,” in <i>Geometric Aspects of Functional Analysis</i>, vol. 2256, B. Klartag and E. Milman, Eds. Springer Nature, 2020, pp. 1–27.","ista":"Akopyan A, Karasev R. 2020.Gromov’s waist of non-radial Gaussian measures and radial non-Gaussian measures. In: Geometric Aspects of Functional Analysis. vol. 2256, 1–27.","chicago":"Akopyan, Arseniy, and Roman Karasev. “Gromov’s Waist of Non-Radial Gaussian Measures and Radial Non-Gaussian Measures.” In <i>Geometric Aspects of Functional Analysis</i>, edited by Bo’az Klartag and Emanuel Milman, 2256:1–27. LNM. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-36020-7_1\">https://doi.org/10.1007/978-3-030-36020-7_1</a>.","short":"A. Akopyan, R. Karasev, in:, B. Klartag, E. Milman (Eds.), Geometric Aspects of Functional Analysis, Springer Nature, 2020, pp. 1–27."},"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy","last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"}],"editor":[{"full_name":"Klartag, Bo'az","first_name":"Bo'az","last_name":"Klartag"},{"full_name":"Milman, Emanuel","last_name":"Milman","first_name":"Emanuel"}],"oa_version":"Preprint","year":"2020","title":"Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures","publication_identifier":{"eisbn":["9783030360207"],"eissn":["1617-9692"],"isbn":["9783030360191"],"issn":["0075-8434"]},"type":"book_chapter","arxiv":1,"date_updated":"2025-07-10T11:54:33Z","language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"volume":2256,"date_published":"2020-06-21T00:00:00Z","ec_funded":1,"doi":"10.1007/978-3-030-36020-7_1","month":"06","scopus_import":"1","date_created":"2018-12-11T11:44:29Z","day":"21","main_file_link":[{"url":"https://arxiv.org/abs/1808.07350","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","intvolume":"      2256","publication":"Geometric Aspects of Functional Analysis","status":"public","series_title":"LNM","publisher":"Springer Nature","department":[{"_id":"HeEd"},{"_id":"JaMa"}],"page":"1-27","oa":1,"_id":"74","article_processing_charge":"No","isi":1,"quality_controlled":"1","external_id":{"isi":["000557689300003"],"arxiv":["1808.07350"]}},{"date_published":"2020-01-01T00:00:00Z","volume":136,"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","doi":"10.1016/bs.ctdb.2019.07.001","author":[{"first_name":"Ashley E.E.","last_name":"Bruce","full_name":"Bruce, Ashley E.E."},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"editor":[{"full_name":"Solnica-Krezel, Lilianna ","last_name":"Solnica-Krezel","first_name":"Lilianna "}],"oa_version":"None","abstract":[{"text":"Epiboly is a conserved gastrulation movement describing the thinning and spreading of a sheet or multi-layer of cells. The zebrafish embryo has emerged as a vital model system to address the cellular and molecular mechanisms that drive epiboly. In the zebrafish embryo, the blastoderm, consisting of a simple squamous epithelium (the enveloping layer) and an underlying mass of deep cells, as well as a yolk nuclear syncytium (the yolk syncytial layer) undergo epiboly to internalize the yolk cell during gastrulation. The major events during zebrafish epiboly are: expansion of the enveloping layer and the internal yolk syncytial layer, reduction and removal of the yolk membrane ahead of the advancing blastoderm margin and deep cell rearrangements between the enveloping layer and yolk syncytial layer to thin the blastoderm. Here, work addressing the cellular and molecular mechanisms as well as the sources of the mechanical forces that underlie these events is reviewed. The contribution of recent findings to the current model of epiboly as well as open questions and future prospects are also discussed.","lang":"eng"}],"citation":{"ama":"Bruce AEE, Heisenberg C-PJ. Mechanisms of zebrafish epiboly: A current view. In: Solnica-Krezel L, ed. <i>Gastrulation: From Embryonic Pattern to Form</i>. Vol 136. Current Topics in Developmental Biology. Elsevier; 2020:319-341. doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>","apa":"Bruce, A. E. E., &#38; Heisenberg, C.-P. J. (2020). Mechanisms of zebrafish epiboly: A current view. In L. Solnica-Krezel (Ed.), <i>Gastrulation: From Embryonic Pattern to Form</i> (Vol. 136, pp. 319–341). Elsevier. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>","short":"A.E.E. Bruce, C.-P.J. Heisenberg, in:, L. Solnica-Krezel (Ed.), Gastrulation: From Embryonic Pattern to Form, Elsevier, 2020, pp. 319–341.","ista":"Bruce AEE, Heisenberg C-PJ. 2020.Mechanisms of zebrafish epiboly: A current view. In: Gastrulation: From Embryonic Pattern to Form. vol. 136, 319–341.","chicago":"Bruce, Ashley E.E., and Carl-Philipp J Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” In <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, 136:319–41. Current Topics in Developmental Biology. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">https://doi.org/10.1016/bs.ctdb.2019.07.001</a>.","mla":"Bruce, Ashley E. E., and Carl-Philipp J. Heisenberg. “Mechanisms of Zebrafish Epiboly: A Current View.” <i>Gastrulation: From Embryonic Pattern to Form</i>, edited by Lilianna  Solnica-Krezel, vol. 136, Elsevier, 2020, pp. 319–41, doi:<a href=\"https://doi.org/10.1016/bs.ctdb.2019.07.001\">10.1016/bs.ctdb.2019.07.001</a>.","ieee":"A. E. E. Bruce and C.-P. J. Heisenberg, “Mechanisms of zebrafish epiboly: A current view,” in <i>Gastrulation: From Embryonic Pattern to Form</i>, vol. 136, L. Solnica-Krezel, Ed. Elsevier, 2020, pp. 319–341."},"publication_identifier":{"issn":["0070-2153"],"isbn":["9780128127988"]},"type":"book_chapter","date_updated":"2025-06-12T07:03:19Z","year":"2020","title":"Mechanisms of zebrafish epiboly: A current view","publisher":"Elsevier","series_title":"Current Topics in Developmental Biology","department":[{"_id":"CaHe"}],"page":"319-341","publication":"Gastrulation: From Embryonic Pattern to Form","status":"public","external_id":{"isi":["000611830600012"],"pmid":["31959293"]},"quality_controlled":"1","_id":"7410","article_processing_charge":"No","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"day":"01","date_created":"2020-01-30T09:24:06Z","publication_status":"published","intvolume":"       136"},{"intvolume":"        15","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012054","open_access":"1"}],"pmid":1,"date_created":"2020-01-30T10:12:04Z","day":"01","issue":"1","external_id":{"isi":["000494909300001"],"pmid":["31696764"]},"quality_controlled":"1","_id":"7416","article_processing_charge":"No","isi":1,"oa":1,"publisher":"Taylor & Francis","department":[{"_id":"JiFr"}],"publication":"Plant Signaling & Behavior","status":"public","date_updated":"2023-10-17T09:01:48Z","publication_identifier":{"issn":["1559-2324"]},"type":"journal_article","title":"Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation","year":"2020","oa_version":"Submitted Version","author":[{"last_name":"Sinclair","first_name":"Scott A","orcid":"0000-0002-4566-0593","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","full_name":"Sinclair, Scott A"},{"last_name":"Krämer","first_name":"U.","full_name":"Krämer, U."}],"abstract":[{"text":"Earlier, we demonstrated that transcript levels of METAL TOLERANCE PROTEIN2 (MTP2) and of HEAVY METAL ATPase2 (HMA2) increase strongly in roots of Arabidopsis upon prolonged zinc (Zn) deficiency and respond to shoot physiological Zn status, and not to the local Zn status in roots. This provided evidence for shoot-to-root communication in the acclimation of plants to Zn deficiency. Zn-deficient soils limit both the yield and quality of agricultural crops and can result in clinically relevant nutritional Zn deficiency in human populations. Implementing Zn deficiency during cultivation of the model plant Arabidopsis thaliana on agar-solidified media is difficult because trace element contaminations are present in almost all commercially available agars. Here, we demonstrate root morphological acclimations to Zn deficiency on agar-solidified medium following the effective removal of contaminants. These advancements allow reproducible phenotyping toward understanding fundamental plant responses to deficiencies of Zn and other essential trace elements.","lang":"eng"}],"citation":{"short":"S.A. Sinclair, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","ieee":"S. A. Sinclair and U. Krämer, “Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Taylor &#38; Francis, 2020.","mla":"Sinclair, Scott A., and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, 1687175, Taylor &#38; Francis, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>.","chicago":"Sinclair, Scott A, and U. Krämer. “Generation of Effective Zinc-Deficient Agar-Solidified Media Allows Identification of Root Morphology Changes in Response to Zinc Limitation.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>.","ista":"Sinclair SA, Krämer U. 2020. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. Plant Signaling &#38; Behavior. 15(1), 1687175.","ama":"Sinclair SA, Krämer U. Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687175\">10.1080/15592324.2019.1687175</a>","apa":"Sinclair, S. A., &#38; Krämer, U. (2020). Generation of effective zinc-deficient agar-solidified media allows identification of root morphology changes in response to zinc limitation. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15592324.2019.1687175\">https://doi.org/10.1080/15592324.2019.1687175</a>"},"article_number":"1687175","scopus_import":"1","doi":"10.1080/15592324.2019.1687175","month":"01","volume":15,"date_published":"2020-01-01T00:00:00Z","language":[{"iso":"eng"}],"article_type":"original"},{"publication_status":"published","intvolume":"        15","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012154"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","pmid":1,"day":"01","date_created":"2020-01-30T10:14:14Z","external_id":{"isi":["000494907500001"],"pmid":["31696770"]},"quality_controlled":"1","article_processing_charge":"No","_id":"7417","isi":1,"publisher":"Informa UK Limited","department":[{"_id":"JiFr"}],"oa":1,"publication":"Plant Signaling & Behavior","status":"public","publication_identifier":{"issn":["1559-2324"]},"type":"journal_article","date_updated":"2023-09-06T15:23:04Z","year":"2020","title":"Regulation of acetylation of plant cell wall components is complex and responds to external stimuli","author":[{"full_name":"Sinclair, Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A","orcid":"0000-0002-4566-0593","last_name":"Sinclair"},{"first_name":"S.","last_name":"Gille","full_name":"Gille, S."},{"full_name":"Pauly, M.","last_name":"Pauly","first_name":"M."},{"full_name":"Krämer, U.","first_name":"U.","last_name":"Krämer"}],"oa_version":"Submitted Version","abstract":[{"text":"Previously, we reported that the allelic de-etiolated by zinc (dez) and trichome birefringence (tbr) mutants exhibit photomorphogenic development in the dark, which is enhanced by high Zn. TRICHOME BIREFRINGENCE-LIKE proteins had been implicated in transferring acetyl groups to various hemicelluloses. Pectin O-acetylation levels were lower in dark-grown dez seedlings than in the wild type. We observed Zn-enhanced photomorphogenesis in the dark also in the reduced wall acetylation 2 (rwa2-3) mutant, which exhibits lowered O-acetylation levels of cell wall macromolecules including pectins and xyloglucans, supporting a role for cell wall macromolecule O-acetylation in the photomorphogenic phenotypes of rwa2-3 and dez. Application of very short oligogalacturonides (vsOGs) restored skotomorphogenesis in dark-grown dez and rwa2-3. Here we demonstrate that in dez, O-acetylation of non-pectin cell wall components, notably of xyloglucan, is enhanced. Our results highlight the complexity of cell wall homeostasis and indicate against an influence of xyloglucan O-acetylation on light-dependent seedling development.","lang":"eng"}],"article_number":"e1687185","citation":{"ama":"Sinclair SA, Gille S, Pauly M, Krämer U. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. 2020;15(1). doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>","apa":"Sinclair, S. A., Gille, S., Pauly, M., &#38; Krämer, U. (2020). Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>","short":"S.A. Sinclair, S. Gille, M. Pauly, U. Krämer, Plant Signaling &#38; Behavior 15 (2020).","chicago":"Sinclair, Scott A, S. Gille, M. Pauly, and U. Krämer. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>. Informa UK Limited, 2020. <a href=\"https://doi.org/10.1080/15592324.2019.1687185\">https://doi.org/10.1080/15592324.2019.1687185</a>.","ista":"Sinclair SA, Gille S, Pauly M, Krämer U. 2020. Regulation of acetylation of plant cell wall components is complex and responds to external stimuli. Plant Signaling &#38; Behavior. 15(1), e1687185.","ieee":"S. A. Sinclair, S. Gille, M. Pauly, and U. Krämer, “Regulation of acetylation of plant cell wall components is complex and responds to external stimuli,” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1. Informa UK Limited, 2020.","mla":"Sinclair, Scott A., et al. “Regulation of Acetylation of Plant Cell Wall Components Is Complex and Responds to External Stimuli.” <i>Plant Signaling &#38; Behavior</i>, vol. 15, no. 1, e1687185, Informa UK Limited, 2020, doi:<a href=\"https://doi.org/10.1080/15592324.2019.1687185\">10.1080/15592324.2019.1687185</a>."},"scopus_import":"1","doi":"10.1080/15592324.2019.1687185","month":"01","volume":15,"date_published":"2020-01-01T00:00:00Z","article_type":"original","language":[{"iso":"eng"}]},{"date_published":"2020-01-13T00:00:00Z","volume":101,"article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","doi":"10.1103/PhysRevB.101.020504","month":"01","author":[{"orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lopes","first_name":"P. L.S.","full_name":"Lopes, P. L.S."},{"full_name":"Hosur, Pavan","first_name":"Pavan","last_name":"Hosur"},{"full_name":"Gilbert, Matthew J.","last_name":"Gilbert","first_name":"Matthew J."},{"full_name":"Ghaemi, Pouyan","first_name":"Pouyan","last_name":"Ghaemi"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In the superconducting regime of FeTe(1−x)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1−x)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1−x)Sex."}],"article_number":"020504","citation":{"apa":"Ghazaryan, A., Lopes, P. L. S., Hosur, P., Gilbert, M. J., &#38; Ghaemi, P. (2020). Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>","ama":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. <i>Physical Review B</i>. 2020;101(2). doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>","mla":"Ghazaryan, Areg, et al. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>, vol. 101, no. 2, 020504, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">10.1103/PhysRevB.101.020504</a>.","ieee":"A. Ghazaryan, P. L. S. Lopes, P. Hosur, M. J. Gilbert, and P. Ghaemi, “Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors,” <i>Physical Review B</i>, vol. 101, no. 2. American Physical Society, 2020.","chicago":"Ghazaryan, Areg, P. L.S. Lopes, Pavan Hosur, Matthew J. Gilbert, and Pouyan Ghaemi. “Effect of Zeeman Coupling on the Majorana Vortex Modes in Iron-Based Topological Superconductors.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.101.020504\">https://doi.org/10.1103/PhysRevB.101.020504</a>.","ista":"Ghazaryan A, Lopes PLS, Hosur P, Gilbert MJ, Ghaemi P. 2020. Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors. Physical Review B. 101(2), 020504.","short":"A. Ghazaryan, P.L.S. Lopes, P. Hosur, M.J. Gilbert, P. Ghaemi, Physical Review B 101 (2020)."},"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"arxiv":1,"type":"journal_article","date_updated":"2025-07-10T11:54:37Z","year":"2020","title":"Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"oa":1,"publication":"Physical Review B","status":"public","quality_controlled":"1","external_id":{"arxiv":["1907.02077"],"isi":["000506843500001"]},"article_processing_charge":"No","_id":"7428","isi":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.02077"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","day":"13","date_created":"2020-02-02T23:01:01Z","publication_status":"published","intvolume":"       101"},{"ddc":["514"],"_id":"7460","article_processing_charge":"No","file":[{"file_name":"thesis_ist-final_noack.pdf","date_created":"2020-02-06T14:43:54Z","file_size":76195184,"checksum":"1df9f8c530b443c0e63a3f2e4fde412e","creator":"koelsboe","relation":"main_file","file_id":"7461","access_level":"open_access","date_updated":"2020-07-14T12:47:58Z","content_type":"application/pdf"},{"file_name":"latex-files.zip","checksum":"7a52383c812b0be64d3826546509e5a4","file_size":122103715,"date_created":"2020-02-06T14:52:45Z","description":"latex source files, figures","relation":"source_file","file_id":"7462","creator":"koelsboe","access_level":"closed","content_type":"application/x-zip-compressed","date_updated":"2020-07-14T12:47:58Z"}],"oa":1,"supervisor":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"department":[{"_id":"HeEd"},{"_id":"GradSch"}],"page":"155","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"status":"public","OA_place":"publisher","publication_status":"published","keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"10","date_created":"2020-02-06T14:56:53Z","tmp":{"image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","doi":"10.15479/AT:ISTA:7460","month":"02","date_published":"2020-02-10T00:00:00Z","corr_author":"1","file_date_updated":"2020-07-14T12:47:58Z","has_accepted_license":"1","language":[{"iso":"eng"}],"date_updated":"2026-04-08T07:23:21Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"title":"The hole system of triangulated shapes","related_material":{"record":[{"id":"6608","relation":"part_of_dissertation","status":"public"}]},"year":"2020","oa_version":"Published Version","author":[{"full_name":"Ölsböck, Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4672-8297","first_name":"Katharina","last_name":"Ölsböck"}],"citation":{"chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","mla":"Ölsböck, Katharina. <i>The Hole System of Triangulated Shapes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","apa":"Ölsböck, K. (2020). <i>The hole system of triangulated shapes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>"},"abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}]},{"oa":1,"file":[{"creator":"dernst","file_id":"7484","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:59Z","file_name":"2020_PLOSPatho_Dick.pdf","date_created":"2020-02-11T10:07:28Z","file_size":4551246,"checksum":"a297f54d1fef0efe4789ca00f37f241e"}],"publisher":"Public Library of Science","department":[{"_id":"FlSc"}],"publication":"PLOS Pathogens","status":"public","ddc":["570"],"quality_controlled":"1","external_id":{"pmid":["31986188"],"isi":["000510746400010"]},"_id":"7464","article_processing_charge":"No","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"day":"27","date_created":"2020-02-06T18:47:17Z","issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":"        16","publication_status":"published","volume":16,"date_published":"2020-01-27T00:00:00Z","has_accepted_license":"1","project":[{"call_identifier":"FWF","_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","name":"Structural conservation and diversity in retroviral capsid"}],"file_date_updated":"2020-07-14T12:47:59Z","corr_author":"1","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","doi":"10.1371/journal.ppat.1008277","month":"01","oa_version":"Published Version","author":[{"full_name":"Dick, Robert A.","first_name":"Robert A.","last_name":"Dick"},{"last_name":"Xu","first_name":"Chaoyi","full_name":"Xu, Chaoyi"},{"first_name":"Dustin R.","last_name":"Morado","full_name":"Morado, Dustin R."},{"id":"4D62F2A6-F248-11E8-B48F-1D18A9856A87","full_name":"Kravchuk, Vladyslav","last_name":"Kravchuk","first_name":"Vladyslav","orcid":"0000-0001-9523-9089"},{"full_name":"Ricana, Clifton L.","first_name":"Clifton L.","last_name":"Ricana"},{"last_name":"Lyddon","first_name":"Terri D.","full_name":"Lyddon, Terri D."},{"full_name":"Broad, Arianna M.","last_name":"Broad","first_name":"Arianna M."},{"full_name":"Feathers, J. Ryan","first_name":"J. Ryan","last_name":"Feathers"},{"full_name":"Johnson, Marc C.","first_name":"Marc C.","last_name":"Johnson"},{"full_name":"Vogt, Volker M.","last_name":"Vogt","first_name":"Volker M."},{"first_name":"Juan R.","last_name":"Perilla","full_name":"Perilla, Juan R."},{"full_name":"Briggs, John A. G.","last_name":"Briggs","first_name":"John A. G."},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078"}],"abstract":[{"text":"Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.","lang":"eng"}],"article_number":"e1008277","citation":{"ama":"Dick RA, Xu C, Morado DR, et al. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. 2020;16(1). doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>","apa":"Dick, R. A., Xu, C., Morado, D. R., Kravchuk, V., Ricana, C. L., Lyddon, T. D., … Schur, F. K. (2020). Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. <i>PLOS Pathogens</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>","short":"R.A. Dick, C. Xu, D.R. Morado, V. Kravchuk, C.L. Ricana, T.D. Lyddon, A.M. Broad, J.R. Feathers, M.C. Johnson, V.M. Vogt, J.R. Perilla, J.A.G. Briggs, F.K. Schur, PLOS Pathogens 16 (2020).","chicago":"Dick, Robert A., Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, Clifton L. Ricana, Terri D. Lyddon, Arianna M. Broad, et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.ppat.1008277\">https://doi.org/10.1371/journal.ppat.1008277</a>.","ista":"Dick RA, Xu C, Morado DR, Kravchuk V, Ricana CL, Lyddon TD, Broad AM, Feathers JR, Johnson MC, Vogt VM, Perilla JR, Briggs JAG, Schur FK. 2020. Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly. PLOS Pathogens. 16(1), e1008277.","ieee":"R. A. Dick <i>et al.</i>, “Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly,” <i>PLOS Pathogens</i>, vol. 16, no. 1. Public Library of Science, 2020.","mla":"Dick, Robert A., et al. “Structures of Immature EIAV Gag Lattices Reveal a Conserved Role for IP6 in Lentivirus Assembly.” <i>PLOS Pathogens</i>, vol. 16, no. 1, e1008277, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.ppat.1008277\">10.1371/journal.ppat.1008277</a>."},"date_updated":"2025-04-15T08:24:51Z","publication_identifier":{"issn":["1553-7374"]},"type":"journal_article","related_material":{"record":[{"relation":"research_data","status":"deleted","id":"9723"}]},"title":"Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly","year":"2020"},{"publication_status":"published","intvolume":"       293","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","issue":"4","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2020-02-09T23:00:50Z","day":"01","pmid":1,"external_id":{"isi":["000520609800009"],"pmid":["32081263"]},"quality_controlled":"1","ddc":["580"],"isi":1,"article_processing_charge":"No","_id":"7465","department":[{"_id":"JiFr"}],"publisher":"Elsevier","file":[{"relation":"main_file","file_id":"7471","creator":"dernst","date_updated":"2020-07-14T12:47:59Z","content_type":"application/pdf","access_level":"open_access","checksum":"f7f27c6a8fea985ceb9279be2204461c","file_size":3499069,"date_created":"2020-02-10T08:59:36Z","file_name":"2020_PlantScience_Mazur.pdf"}],"oa":1,"status":"public","publication":"Plant Science","type":"journal_article","publication_identifier":{"issn":["0168-9452"],"eissn":["1873-2259"]},"date_updated":"2026-04-07T14:18:57Z","year":"2020","title":"Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis","related_material":{"record":[{"id":"11626","relation":"dissertation_contains","status":"public"}]},"author":[{"first_name":"Ewa","last_name":"Mazur","full_name":"Mazur, Ewa"},{"orcid":"0000-0003-1286-7368","first_name":"Michelle C","last_name":"Gallei","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","full_name":"Adamowski, Maciek","last_name":"Adamowski","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin","last_name":"Han","first_name":"Huibin"},{"full_name":"Robert, Hélène S.","first_name":"Hélène S.","last_name":"Robert"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","citation":{"ama":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. 2020;293(4). doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>","apa":"Mazur, E., Gallei, M. C., Adamowski, M., Han, H., Robert, H. S., &#38; Friml, J. (2020). Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. <i>Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>","short":"E. Mazur, M.C. Gallei, M. Adamowski, H. Han, H.S. Robert, J. Friml, Plant Science 293 (2020).","mla":"Mazur, Ewa, et al. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>, vol. 293, no. 4, 110414, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">10.1016/j.plantsci.2020.110414</a>.","ieee":"E. Mazur, M. C. Gallei, M. Adamowski, H. Han, H. S. Robert, and J. Friml, “Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis,” <i>Plant Science</i>, vol. 293, no. 4. Elsevier, 2020.","ista":"Mazur E, Gallei MC, Adamowski M, Han H, Robert HS, Friml J. 2020. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. Plant Science. 293(4), 110414.","chicago":"Mazur, Ewa, Michelle C Gallei, Maciek Adamowski, Huibin Han, Hélène S. Robert, and Jiří Friml. “Clathrin-Mediated Trafficking and PIN Trafficking Are Required for Auxin Canalization and Vascular Tissue Formation in Arabidopsis.” <i>Plant Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.plantsci.2020.110414\">https://doi.org/10.1016/j.plantsci.2020.110414</a>."},"article_number":"110414","abstract":[{"lang":"eng","text":"The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization."}],"scopus_import":"1","doi":"10.1016/j.plantsci.2020.110414","month":"04","corr_author":"1","project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"file_date_updated":"2020-07-14T12:47:59Z","has_accepted_license":"1","ec_funded":1,"volume":293,"date_published":"2020-04-01T00:00:00Z","article_type":"original","language":[{"iso":"eng"}]},{"year":"2020","title":"Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila","type":"journal_article","publication_identifier":{"eissn":["2050-084X"]},"date_updated":"2026-04-03T09:24:34Z","article_number":"e51595","citation":{"mla":"Kierdorf, Katrin, et al. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>, vol. 9, e51595, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>.","ieee":"K. Kierdorf <i>et al.</i>, “Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","chicago":"Kierdorf, Katrin, Fabian Hersperger, Jessica Sharrock, Crystal M. Vincent, Pinar Ustaoglu, Jiawen Dou, Attila György, Olaf Groß, Daria E Siekhaus, and Marc S. Dionne. “Muscle Function and Homeostasis Require Cytokine Inhibition of AKT Activity in Drosophila.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>.","ista":"Kierdorf K, Hersperger F, Sharrock J, Vincent CM, Ustaoglu P, Dou J, György A, Groß O, Siekhaus DE, Dionne MS. 2020. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. eLife. 9, e51595.","short":"K. Kierdorf, F. Hersperger, J. Sharrock, C.M. Vincent, P. Ustaoglu, J. Dou, A. György, O. Groß, D.E. Siekhaus, M.S. Dionne, ELife 9 (2020).","apa":"Kierdorf, K., Hersperger, F., Sharrock, J., Vincent, C. M., Ustaoglu, P., Dou, J., … Dionne, M. S. (2020). Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.51595\">https://doi.org/10.7554/eLife.51595</a>","ama":"Kierdorf K, Hersperger F, Sharrock J, et al. Muscle function and homeostasis require cytokine inhibition of AKT activity in Drosophila. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.51595\">10.7554/eLife.51595</a>"},"abstract":[{"text":"Unpaired ligands are secreted signals that act via a GP130-like receptor, domeless, to activate JAK/STAT signalling in Drosophila. Like many mammalian cytokines, unpaireds can be activated by infection and other stresses and can promote insulin resistance in target tissues. However, the importance of this effect in non-inflammatory physiology is unknown. Here, we identify a requirement for unpaired-JAK signalling as a metabolic regulator in healthy adult Drosophila muscle. Adult muscles show basal JAK-STAT signalling activity in the absence of any immune challenge. Plasmatocytes (Drosophila macrophages) are an important source of this tonic signal. Loss of the dome receptor on adult muscles significantly reduces lifespan and causes local and systemic metabolic pathology. These pathologies result from hyperactivation of AKT and consequent deregulation of metabolism. Thus, we identify a cytokine signal that must be received in muscle to control AKT activity and metabolic homeostasis.","lang":"eng"}],"author":[{"first_name":"Katrin","last_name":"Kierdorf","full_name":"Kierdorf, Katrin"},{"full_name":"Hersperger, Fabian","first_name":"Fabian","last_name":"Hersperger"},{"full_name":"Sharrock, Jessica","first_name":"Jessica","last_name":"Sharrock"},{"first_name":"Crystal M.","last_name":"Vincent","full_name":"Vincent, Crystal M."},{"last_name":"Ustaoglu","first_name":"Pinar","full_name":"Ustaoglu, Pinar"},{"full_name":"Dou, Jiawen","last_name":"Dou","first_name":"Jiawen"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila","last_name":"György","orcid":"0000-0002-1819-198X","first_name":"Attila"},{"first_name":"Olaf","last_name":"Groß","full_name":"Groß, Olaf"},{"orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dionne, Marc S.","first_name":"Marc S.","last_name":"Dionne"}],"oa_version":"Published Version","month":"01","doi":"10.7554/eLife.51595","scopus_import":"1","article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:59Z","has_accepted_license":"1","project":[{"call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425","grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion"}],"date_published":"2020-01-20T00:00:00Z","volume":9,"publication_status":"published","intvolume":"         9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"20","date_created":"2020-02-09T23:00:51Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","isi":1,"_id":"7466","article_processing_charge":"No","external_id":{"isi":["000512304800001"]},"quality_controlled":"1","ddc":["570"],"status":"public","publication":"eLife","department":[{"_id":"DaSi"}],"publisher":"eLife Sciences Publications","oa":1,"file":[{"file_name":"2020_eLife_Kierdorf.pdf","date_created":"2020-02-10T08:53:16Z","file_size":4959933,"checksum":"3a072be843f416c7a7d532a51dc0addb","creator":"dernst","relation":"main_file","file_id":"7470","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:59Z"}]}]