[{"date_created":"2019-09-01T22:01:00Z","ec_funded":1,"date_published":"2017-02-21T00:00:00Z","publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","language":[{"iso":"eng"}],"day":"21","publication_status":"published","year":"2017","month":"02","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02995"}],"quality_controlled":"1","publisher":"International Conference on Learning Representations","scopus_import":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified."}],"department":[{"_id":"ChLa"}],"title":"Extrapolation and learning equations","external_id":{"arxiv":["1610.02995"]},"author":[{"full_name":"Martius, Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:09:17Z","citation":{"mla":"Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","apa":"Martius, G. S., & Lampert, C. (2017). Extrapolation and learning equations. In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. Toulon, France: International Conference on Learning Representations.","ama":"Martius GS, Lampert C. Extrapolation and learning equations. In: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations; 2017.","ieee":"G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, Toulon, France, 2017.","short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","chicago":"Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations, 2017.","ista":"Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations."},"project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"status":"public","conference":{"name":"ICLR: International Conference on Learning Representations","location":"Toulon, France","end_date":"2017-04-26","start_date":"2017-04-24"},"type":"conference","_id":"6841"},{"day":"01","publication":"Journal of Symbolic Logic","year":"2017","date_published":"2017-06-01T00:00:00Z","doi":"10.1017/jsl.2016.71","date_created":"2018-12-11T11:47:54Z","page":"420 - 452","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chatterjee K, Piterman N. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 2017;82(2):420-452. doi:10.1017/jsl.2016.71","apa":"Chatterjee, K., & Piterman, N. (2017). Obligation blackwell games and p-automata. Journal of Symbolic Logic. Cambridge University Press. https://doi.org/10.1017/jsl.2016.71","ieee":"K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” Journal of Symbolic Logic, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017.","short":"K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452.","mla":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:10.1017/jsl.2016.71.","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic. Cambridge University Press, 2017. https://doi.org/10.1017/jsl.2016.71."},"title":"Obligation blackwell games and p-automata","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Nir","full_name":"Piterman, Nir","last_name":"Piterman"}],"publist_id":"7026","article_processing_charge":"No","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1943-5886"],"issn":["0022-4812"]},"publication_status":"published","volume":82,"issue":"2","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic."}],"month":"06","intvolume":" 82","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1206.5174","open_access":"1"}],"date_updated":"2021-04-16T12:10:53Z","department":[{"_id":"KrCh"}],"_id":"684","status":"public","type":"journal_article"},{"has_accepted_license":"1","year":"2017","day":"01","publication":"Mechanisms of Development","page":"26 - 31","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.mod.2017.03.005","date_created":"2018-12-11T11:47:55Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"citation":{"mla":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 26–31, doi:10.1016/j.mod.2017.03.005.","ieee":"J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” Mechanisms of Development, vol. 145. Elsevier, pp. 26–31, 2017.","short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31.","ama":"Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. 2017;145:26-31. doi:10.1016/j.mod.2017.03.005","apa":"Briscoe, J., & Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.005","chicago":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.005.","ista":"Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7025","author":[{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"external_id":{"pmid":["28366718"]},"title":"The physics of development 100 years after D'Arcy Thompson's “on growth and form”","project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037"}],"publication_identifier":{"issn":["09254773"]},"publication_status":"published","file":[{"file_name":"2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf","date_created":"2019-04-17T07:58:48Z","file_size":652313,"date_updated":"2020-07-14T12:47:42Z","creator":"dernst","checksum":"727043d2e4199fbef6b3704e6d1ac105","file_id":"6335","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":145,"ec_funded":1,"abstract":[{"lang":"eng","text":"By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":1,"month":"06","intvolume":" 145","date_updated":"2021-01-12T08:09:20Z","ddc":["571"],"file_date_updated":"2020-07-14T12:47:42Z","department":[{"_id":"AnKi"}],"_id":"685","type":"journal_article","status":"public","pubrep_id":"985"},{"volume":77,"file":[{"date_created":"2018-12-12T10:11:03Z","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","date_updated":"2020-07-14T12:47:42Z","file_size":990546,"creator":"system","file_id":"4856","checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"]},"publication_status":"published","month":"06","intvolume":" 77","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. "}],"department":[{"_id":"HeEd"},{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:42Z","ddc":["514","516"],"date_updated":"2021-01-12T08:09:26Z","status":"public","pubrep_id":"895","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"Symposium on Computational Geometry, SoCG","start_date":"2017-07-04","end_date":"2017-07-07","location":"Brisbane, Australia"},"_id":"688","date_published":"2017-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2017.39","date_created":"2018-12-11T11:47:56Z","page":"391-3916","day":"01","has_accepted_license":"1","year":"2017","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"title":"Topological data analysis with Bregman divergences","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7021","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.39.","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","mla":"Edelsbrunner, Herbert, and Hubert Wagner. Topological Data Analysis with Bregman Divergences. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:10.4230/LIPIcs.SoCG.2017.39.","apa":"Edelsbrunner, H., & Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.39","ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:10.4230/LIPIcs.SoCG.2017.39","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916.","ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916."}},{"department":[{"_id":"TaHa"}],"date_updated":"2021-01-12T08:09:24Z","status":"public","type":"journal_article","_id":"687","volume":68,"issue":"2","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00335606"]},"publication_status":"published","month":"06","intvolume":" 68","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.7172"}],"oa_version":"Submitted Version","abstract":[{"text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs.","lang":"eng"}],"title":"The critical CoHA of a quiver with potential","publist_id":"7022","author":[{"full_name":"Davison, Ben","orcid":"0000-0002-8944-4390","last_name":"Davison","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87","first_name":"Ben"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053.","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703.","mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053.","ama":"Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703."},"project":[{"name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","call_identifier":"FP7","_id":"25E549F4-B435-11E9-9278-68D0E5697425"}],"date_published":"2017-06-01T00:00:00Z","doi":"10.1093/qmath/haw053","date_created":"2018-12-11T11:47:55Z","page":"635 - 703","day":"01","publication":"Quarterly Journal of Mathematics","year":"2017","publisher":"Oxford University Press","quality_controlled":"1","oa":1},{"publication":"Mechanisms of Development","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2017","publication_identifier":{"issn":["09254773"]},"date_created":"2018-12-11T11:47:55Z","volume":145,"doi":"10.1016/j.mod.2017.03.006","date_published":"2017-06-01T00:00:00Z","page":"32 - 37","oa_version":"None","abstract":[{"lang":"eng","text":"Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology."}],"intvolume":" 145","month":"06","quality_controlled":"1","scopus_import":1,"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37.","ieee":"C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017.","apa":"Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006","ama":"Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006","mla":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.","ista":"Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.","chicago":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006."},"date_updated":"2021-01-12T08:09:23Z","title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","department":[{"_id":"CaHe"}],"author":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"publist_id":"7024","_id":"686","status":"public","type":"journal_article"},{"_id":"689","article_number":"eaan8196","type":"journal_article","status":"public","citation":{"mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan8196.","apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan8196","ama":"Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196","short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017.","chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan8196.","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196."},"date_updated":"2021-01-12T08:09:29Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"7019","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"title":"Rett syndrome modeling goes simian","department":[{"_id":"GaNo"}],"abstract":[{"lang":"eng","text":"Rett syndrome modeling in monkey mirrors the human disorder."}],"oa_version":"None","publisher":"American Association for the Advancement of Science","scopus_import":1,"quality_controlled":"1","intvolume":" 9","month":"06","year":"2017","publication_status":"published","publication_identifier":{"issn":["19466234"]},"publication":"Science Translational Medicine","language":[{"iso":"eng"}],"day":"07","date_created":"2018-12-11T11:47:56Z","doi":"10.1126/scitranslmed.aan8196","volume":9,"date_published":"2017-06-07T00:00:00Z","issue":"393"},{"_id":"693","status":"public","type":"journal_article","ddc":["570"],"date_updated":"2023-02-23T12:54:57Z","file_date_updated":"2020-07-14T12:47:44Z","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"pmid":1,"oa_version":"Published Version","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"intvolume":" 114","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"date_created":"2020-01-03T13:27:29Z","file_name":"2017_PNAS_Miki.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:44Z","file_size":2721544,"file_id":"7223","checksum":"2ab75d554f3df4a34d20fa8040589b7e","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["00278424"]},"issue":"26","volume":114,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","ieee":"T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017."},"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["28607047"]},"author":[{"last_name":"Miki","full_name":"Miki, Takafumi","first_name":"Takafumi"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315"},{"first_name":"Gerardo","full_name":"Malagon, Gerardo","last_name":"Malagon"},{"full_name":"Gomez, Laura","last_name":"Gomez","first_name":"Laura"},{"last_name":"Tabuchi","full_name":"Tabuchi, Katsuhiko","first_name":"Katsuhiko"},{"last_name":"Watanabe","full_name":"Watanabe, Masahiko","first_name":"Masahiko"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Marty, Alain","last_name":"Marty","first_name":"Alain"}],"publist_id":"7013","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","publication":"PNAS","day":"27","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:47:57Z","doi":"10.1073/pnas.1704470114","date_published":"2017-06-27T00:00:00Z","page":"E5246 - E5255"},{"date_published":"2017-07-01T00:00:00Z","doi":"10.1242/jcs.200899","date_created":"2018-12-11T11:47:58Z","page":"2172 - 2184","day":"01","publication":"Journal of Cell Science","has_accepted_license":"1","year":"2017","quality_controlled":"1","publisher":"Company of Biologists","oa":1,"title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","publist_id":"7008","author":[{"full_name":"Veß, Astrid","last_name":"Veß","first_name":"Astrid"},{"full_name":"Blache, Ulrich","last_name":"Blache","first_name":"Ulrich"},{"first_name":"Laura","full_name":"Leitner, Laura","last_name":"Leitner"},{"last_name":"Kurz","full_name":"Kurz, Angela","first_name":"Angela"},{"full_name":"Ehrenpfordt, Anja","last_name":"Ehrenpfordt","first_name":"Anja"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"first_name":"Guido","full_name":"Posern, Guido","last_name":"Posern"}],"external_id":{"pmid":["28515231"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.200899.","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:10.1242/jcs.200899.","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., & Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.200899","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 2017;130(13):2172-2184. doi:10.1242/jcs.200899","ieee":"A. Veß et al., “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” Journal of Cell Science, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184."},"volume":130,"issue":"13","file":[{"date_created":"2019-10-24T09:43:56Z","file_name":"2017_CellScience_Vess.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:45Z","file_size":10847596,"file_id":"6966","checksum":"42c81a0a4fc3128883b391c3af3f74bc","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00219533"]},"publication_status":"published","month":"07","intvolume":" 130","scopus_import":1,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells.","lang":"eng"}],"department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:45Z","ddc":["570"],"date_updated":"2021-01-12T08:09:41Z","status":"public","article_type":"original","type":"journal_article","_id":"694"},{"abstract":[{"text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. ","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"month":"07","intvolume":" 80","publication_identifier":{"issn":["18688969"]},"publication_status":"published","file":[{"date_created":"2018-12-12T10:08:40Z","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","creator":"system","date_updated":"2020-07-14T12:47:46Z","file_size":601004,"file_id":"4701","checksum":"e95618a001692f1af2d68f5fde43bc1f","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":80,"ec_funded":1,"_id":"697","type":"conference","conference":{"start_date":"2017-07-10","end_date":"2017-07-14","location":"Warsaw, Poland","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"893","date_updated":"2021-01-12T08:11:15Z","ddc":["005"],"file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"KrPi"}],"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2017","day":"01","doi":"10.4230/LIPIcs.ICALP.2017.39","date_published":"2017-07-01T00:00:00Z","date_created":"2018-12-11T11:47:59Z","article_number":"39","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ICALP.2017.39.","apa":"Pietrzak, K. Z., & Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2017.39","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.ICALP.2017.39","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. Non Uniform Attacks against Pseudoentropy. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.ICALP.2017.39."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","full_name":"Skórski, Maciej"}],"publist_id":"7003","title":"Non uniform attacks against pseudoentropy"},{"publisher":"American Society for Cell Biology","quality_controlled":"1","oa":1,"day":"07","publication":"Molecular Biology of the Cell","has_accepted_license":"1","year":"2017","doi":"10.1091/mbc.E16-12-0825","date_published":"2017-07-07T00:00:00Z","date_created":"2018-12-11T11:47:59Z","page":"1997 - 2009","project":[{"grant_number":"Y 903-N35","name":"Gaussian Graphical Models: Theory and Applications","_id":"2530CA10-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell. American Society for Cell Biology, 2017. https://doi.org/10.1091/mbc.E16-12-0825.","apa":"Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” Molecular Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825."},"title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","author":[{"last_name":"Wang","full_name":"Wang, Yejun","first_name":"Yejun"},{"first_name":"Mallika","full_name":"Nagarajan, Mallika","last_name":"Nagarajan"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"full_name":"Shivashankar, Gv","last_name":"Shivashankar","first_name":"Gv"}],"publist_id":"7001","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"month":"07","intvolume":" 28","scopus_import":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4844","checksum":"de01dac9e30970cfa6ae902480a4e04d","creator":"system","file_size":1086097,"date_updated":"2020-07-14T12:47:46Z","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","date_created":"2018-12-12T10:10:53Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10591524"]},"publication_status":"published","issue":"14","volume":28,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","_id":"698","status":"public","pubrep_id":"892","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","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)"},"ddc":["519"],"date_updated":"2021-01-12T08:11:17Z","file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"CaUh"}]},{"department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T08:11:21Z","status":"public","type":"journal_article","_id":"699","issue":"27","volume":114,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"publication_status":"published","month":"07","intvolume":" 114","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ","lang":"eng"}],"title":"The red queen and king in finite populations","author":[{"last_name":"Veller","full_name":"Veller, Carl","first_name":"Carl"},{"first_name":"Laura","full_name":"Hayward, Laura","last_name":"Hayward"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"},{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"}],"publist_id":"7002","external_id":{"pmid":["28630336"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114","apa":"Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114.","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114."},"doi":"10.1073/pnas.1702020114","date_published":"2017-07-03T00:00:00Z","date_created":"2018-12-11T11:48:00Z","page":"E5396 - E5405","day":"03","publication":"PNAS","year":"2017","quality_controlled":"1","publisher":"National Academy of Sciences","oa":1},{"article_number":"012404","project":[{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","grant_number":"707438","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.012404.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., & Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.012404","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.012404","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.012404.","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404."},"title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","publist_id":"6997","author":[{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh"},{"first_name":"Vahid","full_name":"Salari, Vahid","last_name":"Salari"},{"full_name":"Tuszynski, Jack","last_name":"Tuszynski","first_name":"Jack"},{"last_name":"Cifra","full_name":"Cifra, Michal","first_name":"Michal"},{"last_name":"Simon","full_name":"Simon, Christoph","first_name":"Christoph"}],"quality_controlled":"1","publisher":"American Institute of Physics","oa":1,"day":"12","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","year":"2017","doi":"10.1103/PhysRevE.96.012404","date_published":"2017-07-12T00:00:00Z","date_created":"2018-12-11T11:48:00Z","_id":"700","status":"public","type":"journal_article","date_updated":"2023-02-23T12:56:35Z","department":[{"_id":"JoFi"}],"oa_version":"Submitted Version","abstract":[{"text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.","lang":"eng"}],"month":"07","intvolume":" 96","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1612.07061.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["24700045"]},"publication_status":"published","volume":96,"issue":"1","ec_funded":1},{"author":[{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"first_name":"Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683"}],"publist_id":"6996","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","citation":{"chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics. International Press, 2017.","ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44.","mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics, vol. 24, no. 3, International Press, 2017, pp. 1–44.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” The Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, pp. 1–44, 2017.","ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 2017;24(3):1-44.","apa":"Kynčl, J., & Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. International Press."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"International Press","oa":1,"page":"1-44","date_published":"2017-07-14T00:00:00Z","date_created":"2018-12-11T11:48:00Z","has_accepted_license":"1","year":"2017","day":"14","publication":"The Electronic Journal of Combinatorics","type":"journal_article","status":"public","pubrep_id":"984","_id":"701","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:47Z","date_updated":"2021-01-12T08:11:28Z","ddc":["500"],"month":"07","intvolume":" 24","abstract":[{"text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2.","lang":"eng"}],"oa_version":"Submitted Version","volume":24,"issue":"3","publication_identifier":{"issn":["10778926"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5077","checksum":"a431e573e31df13bc0f66de3061006ec","creator":"system","date_updated":"2020-07-14T12:47:47Z","file_size":544042,"date_created":"2018-12-12T10:14:25Z","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf"}],"language":[{"iso":"eng"}]},{"day":"19","publication":"Science Translational Medicine","language":[{"iso":"eng"}],"publication_identifier":{"issn":["19466234"]},"year":"2017","publication_status":"published","doi":"10.1126/scitranslmed.aao0972","issue":"399","date_published":"2017-07-19T00:00:00Z","volume":9,"date_created":"2018-12-11T11:48:01Z","page":"eaao0972","oa_version":"None","abstract":[{"lang":"eng","text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n"}],"month":"07","intvolume":" 9","quality_controlled":"1","publisher":"American Association for the Advancement of Science","scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” Science Translational Medicine, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 2017;9(399):eaao0972. doi:10.1126/scitranslmed.aao0972","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao0972","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:10.1126/scitranslmed.aao0972.","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao0972."},"date_updated":"2021-01-12T08:11:31Z","department":[{"_id":"GaNo"}],"title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"}],"publist_id":"6993","_id":"702","status":"public","type":"journal_article"},{"page":"715 - 722","volume":22,"doi":"10.1111/gtc.12508","date_published":"2017-08-01T00:00:00Z","issue":"8","date_created":"2018-12-11T11:48:02Z","publication_identifier":{"issn":["13569597"]},"year":"2017","publication_status":"published","day":"01","publication":"Genes to Cells","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Wiley-Blackwell","scopus_import":1,"month":"08","intvolume":" 22","abstract":[{"lang":"eng","text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse."}],"oa_version":"None","author":[{"last_name":"Geng","full_name":"Geng, Xiaoqi","first_name":"Xiaoqi","id":"3395256A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tomohiko","full_name":"Maruo, Tomohiko","last_name":"Maruo"},{"full_name":"Mandai, Kenji","last_name":"Mandai","first_name":"Kenji"},{"first_name":"Irwan","full_name":"Supriyanto, Irwan","last_name":"Supriyanto"},{"last_name":"Miyata","full_name":"Miyata, Muneaki","first_name":"Muneaki"},{"first_name":"Shotaro","full_name":"Sakakibara, Shotaro","last_name":"Sakakibara"},{"last_name":"Mizoguchi","full_name":"Mizoguchi, Akira","first_name":"Akira"},{"first_name":"Yoshimi","full_name":"Takai, Yoshimi","last_name":"Takai"},{"first_name":"Masahiro","full_name":"Mori, Masahiro","last_name":"Mori"}],"publist_id":"6987","department":[{"_id":"PeJo"}],"title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","citation":{"mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:10.1111/gtc.12508.","ieee":"X. Geng et al., “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” Genes to Cells, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. Wiley-Blackwell. https://doi.org/10.1111/gtc.12508","ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 2017;22(8):715-722. doi:10.1111/gtc.12508","chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells. Wiley-Blackwell, 2017. https://doi.org/10.1111/gtc.12508.","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722."},"date_updated":"2021-01-12T08:11:37Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"706"},{"publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"doi":"10.1112/blms.12062","date_published":"2017-08-01T00:00:00Z","date_created":"2018-12-11T11:48:02Z","page":"690 - 693","day":"01","publication":"Bulletin of the London Mathematical Society","year":"2017","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"A tight estimate for the waist of the ball ","publist_id":"6982","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"first_name":"Roman","full_name":"Karasev, Roman","last_name":"Karasev"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society, vol. 49, no. 4, Wiley-Blackwell, 2017, pp. 690–93, doi:10.1112/blms.12062.","short":"A. Akopyan, R. Karasev, Bulletin of the London Mathematical Society 49 (2017) 690–693.","ieee":"A. Akopyan and R. Karasev, “A tight estimate for the waist of the ball ,” Bulletin of the London Mathematical Society, vol. 49, no. 4. Wiley-Blackwell, pp. 690–693, 2017.","apa":"Akopyan, A., & Karasev, R. (2017). A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. Wiley-Blackwell. https://doi.org/10.1112/blms.12062","ama":"Akopyan A, Karasev R. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 2017;49(4):690-693. doi:10.1112/blms.12062","chicago":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society. Wiley-Blackwell, 2017. https://doi.org/10.1112/blms.12062.","ista":"Akopyan A, Karasev R. 2017. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 49(4), 690–693."},"month":"08","intvolume":" 49","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.06279"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We answer a question of M. Gromov on the waist of the unit ball."}],"issue":"4","volume":49,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00246093"]},"publication_status":"published","status":"public","type":"journal_article","_id":"707","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T08:11:41Z"},{"ddc":["576","610"],"date_updated":"2021-01-12T08:11:45Z","department":[{"_id":"SaSi"}],"file_date_updated":"2020-07-14T12:47:49Z","_id":"708","status":"public","pubrep_id":"889","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"IST-2017-889-v1+1_journal.pbio.2001993.pdf","date_created":"2018-12-12T10:15:35Z","file_size":18155365,"date_updated":"2020-07-14T12:47:49Z","creator":"system","checksum":"0c974f430682dc832ea7b27ab5a93124","file_id":"5156","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15449173"]},"publication_status":"published","issue":"8","volume":15,"oa_version":"Published Version","abstract":[{"text":"In the developing and adult brain, oligodendrocyte precursor cells (OPCs) are influenced by neuronal activity: they are involved in synaptic signaling with neurons, and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing. An important question that has been unanswered is whether OPCs can discriminate different patterns of neuronal activity and respond to them in a distinct way. Here, we demonstrate in brain slices that the pattern of neuronal activity determines the functional changes triggered at synapses between axons and OPCs. Furthermore, we show that stimulation of the corpus callosum at different frequencies in vivo affects proliferation and differentiation of OPCs in a dissimilar way. Our findings suggest that neurons do not influence OPCs in “all-or-none” fashion but use their firing pattern to tune the response and behavior of these nonneuronal cells.","lang":"eng"}],"month":"08","intvolume":" 15","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. 2017. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 15(8), e2001993.","chicago":"Nagy, Balint, Anahit Hovhannisyan, Ruxandra Barzan, Ting Chen, and Maria Kukley. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001993.","ama":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 2017;15(8). doi:10.1371/journal.pbio.2001993","apa":"Nagy, B., Hovhannisyan, A., Barzan, R., Chen, T., & Kukley, M. (2017). Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001993","short":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, M. Kukley, PLoS Biology 15 (2017).","ieee":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, and M. Kukley, “Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum,” PLoS Biology, vol. 15, no. 8. Public Library of Science, 2017.","mla":"Nagy, Balint, et al. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology, vol. 15, no. 8, e2001993, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001993."},"title":"Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum","publist_id":"6983","author":[{"last_name":"Nagy","full_name":"Nagy, Balint","orcid":"0000-0002-4002-4686","first_name":"Balint","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2"},{"last_name":"Hovhannisyan","full_name":"Hovhannisyan, Anahit","first_name":"Anahit"},{"first_name":"Ruxandra","last_name":"Barzan","full_name":"Barzan, Ruxandra"},{"full_name":"Chen, Ting","last_name":"Chen","first_name":"Ting"},{"last_name":"Kukley","full_name":"Kukley, Maria","first_name":"Maria"}],"article_number":"e2001993","day":"22","publication":"PLoS Biology","has_accepted_license":"1","year":"2017","doi":"10.1371/journal.pbio.2001993","date_published":"2017-08-22T00:00:00Z","date_created":"2018-12-11T11:48:03Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1},{"status":"public","type":"journal_article","_id":"709","title":"Gene expression changes of thermo sensitive transient receptor potential channels in obese mice","department":[{"_id":"RySh"}],"publist_id":"6981","author":[{"first_name":"Wuping","last_name":"Sun","full_name":"Sun, Wuping"},{"last_name":"Li","full_name":"Li, Chen","first_name":"Chen"},{"last_name":"Zhang","full_name":"Zhang, Yonghong","first_name":"Yonghong"},{"first_name":"Changyu","full_name":"Jiang, Changyu","last_name":"Jiang"},{"full_name":"Zhai, Ming-Zhu","last_name":"Zhai","first_name":"Ming-Zhu","id":"34009CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhou","full_name":"Zhou, Qian","first_name":"Qian"},{"last_name":"Xiao","full_name":"Xiao, Lizu","first_name":"Lizu"},{"last_name":"Deng","full_name":"Deng, Qiwen","first_name":"Qiwen"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sun, Wuping, et al. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International, vol. 41, no. 8, Wiley-Blackwell, 2017, pp. 908–13, doi:10.1002/cbin.10783.","short":"W. Sun, C. Li, Y. Zhang, C. Jiang, M.-Z. Zhai, Q. Zhou, L. Xiao, Q. Deng, Cell Biology International 41 (2017) 908–913.","ieee":"W. Sun et al., “Gene expression changes of thermo sensitive transient receptor potential channels in obese mice,” Cell Biology International, vol. 41, no. 8. Wiley-Blackwell, pp. 908–913, 2017.","apa":"Sun, W., Li, C., Zhang, Y., Jiang, C., Zhai, M.-Z., Zhou, Q., … Deng, Q. (2017). Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. Wiley-Blackwell. https://doi.org/10.1002/cbin.10783","ama":"Sun W, Li C, Zhang Y, et al. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 2017;41(8):908-913. doi:10.1002/cbin.10783","chicago":"Sun, Wuping, Chen Li, Yonghong Zhang, Changyu Jiang, Ming-Zhu Zhai, Qian Zhou, Lizu Xiao, and Qiwen Deng. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International. Wiley-Blackwell, 2017. https://doi.org/10.1002/cbin.10783.","ista":"Sun W, Li C, Zhang Y, Jiang C, Zhai M-Z, Zhou Q, Xiao L, Deng Q. 2017. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 41(8), 908–913."},"date_updated":"2021-01-12T08:11:47Z","intvolume":" 41","month":"08","scopus_import":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","oa_version":"None","abstract":[{"lang":"eng","text":"Adipose tissues play key roles in energy homeostasis. Brown adipocytes and beige adipocytes in white adipose tissue (WAT) share the similar characters of thermogenesis, both of them could be potential targets for obesity management. Several thermo-sensitive transient receptor potential channels (thermoTRPs) are shown to be involved in adipocyte biology. However, the expression pattern of thermoTRPs in adipose tissues from obese mice is still unknown. The mRNA expression of thermoTRPs in subcutaneous WAT (sWAT) and interscapular brown adipose tissue (iBAT) from lean and obese mice were measured using reverse transcriptase-quantitative PCRs (RT-qPCR). The results demonstrated that all 10 thermoTRPs are expressed in both iBAT and sWAT, and without significant difference in the mRNA expression level of thermoTRPs between these two tissues. Moreover, Trpv1 and Trpv3 mRNA expression levels in both iBAT and sWAT were significantly decreased in high fat diet (HFD)-induced obese mice and db/db (leptin receptor deficient) mice. Trpm2 mRNA expression level was significantly decreased only in sWAT from HFD-induced obese mice and db/db mice. On the other hand, Trpv2 and Trpv4 mRNA expression levels in iBAT and sWAT were significantly increased in HFD-induced obese mice and db/db mice. Taken together, we conclude that all 10 thermoTRPs are expressed in iBAT and sWAT. And several thermoTRPs differentially expressed in adipose tissues from HFD-induced obese mice and db/db mice, suggesting a potential involvement in anti-obesity regulations."}],"date_created":"2018-12-11T11:48:04Z","doi":"10.1002/cbin.10783","issue":"8","volume":41,"date_published":"2017-08-01T00:00:00Z","page":"908 - 913","publication":"Cell Biology International","language":[{"iso":"eng"}],"day":"01","publication_status":"published","year":"2017","publication_identifier":{"issn":["10656995"]}},{"article_number":"20","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"citation":{"chicago":"Obremski, Maciej, and Maciej Skórski. “Renyi Entropy Estimation Revisited,” Vol. 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20.","ista":"Obremski M, Skórski M. 2017. Renyi entropy estimation revisited. 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, LIPIcs, vol. 81, 20.","mla":"Obremski, Maciej, and Maciej Skórski. Renyi Entropy Estimation Revisited. Vol. 81, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20.","apa":"Obremski, M., & Skórski, M. (2017). Renyi entropy estimation revisited (Vol. 81). Presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20","ama":"Obremski M, Skórski M. Renyi entropy estimation revisited. In: Vol 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20","short":"M. Obremski, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"M. Obremski and M. Skórski, “Renyi entropy estimation revisited,” presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA, 2017, vol. 81."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6979","author":[{"full_name":"Obremski, Maciej","last_name":"Obremski","first_name":"Maciej"},{"last_name":"Skórski","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"}],"title":"Renyi entropy estimation revisited","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2017","day":"01","date_published":"2017-08-01T00:00:00Z","doi":"10.4230/LIPIcs.APPROX-RANDOM.2017.20","date_created":"2018-12-11T11:48:04Z","_id":"710","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Berkeley, USA","end_date":"2017-08-18","start_date":"2017-08-18","name":"20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX"},"status":"public","pubrep_id":"888","date_updated":"2021-01-12T08:11:50Z","ddc":["005","600"],"file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"KrPi"}],"abstract":[{"lang":"eng","text":"We revisit the problem of estimating entropy of discrete distributions from independent samples, studied recently by Acharya, Orlitsky, Suresh and Tyagi (SODA 2015), improving their upper and lower bounds on the necessary sample size n. For estimating Renyi entropy of order alpha, up to constant accuracy and error probability, we show the following * Upper bounds n = O(1) 2^{(1-1/alpha)H_alpha} for integer alpha>1, as the worst case over distributions with Renyi entropy equal to H_alpha. * Lower bounds n = Omega(1) K^{1-1/alpha} for any real alpha>1, with the constant being an inverse polynomial of the accuracy, as the worst case over all distributions on K elements. Our upper bounds essentially replace the alphabet size by a factor exponential in the entropy, which offers improvements especially in low or medium entropy regimes (interesting for example in anomaly detection). As for the lower bounds, our proof explicitly shows how the complexity depends on both alphabet and accuracy, partially solving the open problem posted in previous works. The argument for upper bounds derives a clean identity for the variance of falling-power sum of a multinomial distribution. Our approach for lower bounds utilizes convex optimization to find a distribution with possibly worse estimation performance, and may be of independent interest as a tool to work with Le Cam’s two point method. "}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"month":"08","intvolume":" 81","publication_identifier":{"issn":["18688969"]},"publication_status":"published","file":[{"checksum":"89225c7dcec2c93838458c9102858985","file_id":"4991","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:13:10Z","file_name":"IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf","creator":"system","date_updated":"2020-07-14T12:47:49Z","file_size":604813}],"language":[{"iso":"eng"}],"volume":81,"ec_funded":1},{"scopus_import":1,"intvolume":" 6","month":"08","abstract":[{"text":"To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta.","lang":"eng"}],"oa_version":"Published Version","volume":6,"publication_status":"published","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5020","checksum":"1ace3462e64a971b9ead896091829549","creator":"system","date_updated":"2020-07-14T12:47:50Z","file_size":6399510,"date_created":"2018-12-12T10:13:36Z","file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf"},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"6241dc31eeb87b03facadec3a53a6827","file_id":"5021","creator":"system","file_size":4264398,"date_updated":"2020-07-14T12:47:50Z","file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf","date_created":"2018-12-12T10:13:36Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"885","status":"public","_id":"713","file_date_updated":"2020-07-14T12:47:50Z","department":[{"_id":"GaNo"},{"_id":"SiHi"}],"date_updated":"2021-01-12T08:11:57Z","ddc":["576"],"oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_created":"2018-12-11T11:48:05Z","date_published":"2017-08-14T00:00:00Z","doi":"10.7554/eLife.25125","year":"2017","has_accepted_license":"1","publication":"eLife","day":"14","project":[{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"e25125","publist_id":"6971","author":[{"full_name":"Andergassen, Daniel","last_name":"Andergassen","first_name":"Daniel"},{"id":"4C66542E-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Dotter, Christoph","last_name":"Dotter"},{"full_name":"Wenzel, Dyniel","last_name":"Wenzel","first_name":"Dyniel"},{"full_name":"Sigl, Verena","last_name":"Sigl","first_name":"Verena"},{"last_name":"Bammer","full_name":"Bammer, Philipp","first_name":"Philipp"},{"first_name":"Markus","full_name":"Muckenhuber, Markus","last_name":"Muckenhuber"},{"last_name":"Mayer","full_name":"Mayer, Daniela","first_name":"Daniela"},{"full_name":"Kulinski, Tomasz","last_name":"Kulinski","first_name":"Tomasz"},{"first_name":"Hans","last_name":"Theussl","full_name":"Theussl, Hans"},{"last_name":"Penninger","full_name":"Penninger, Josef","first_name":"Josef"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"first_name":"Denise","full_name":"Barlow, Denise","last_name":"Barlow"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"full_name":"Hudson, Quanah","last_name":"Hudson","first_name":"Quanah"}],"title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","citation":{"short":"D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber, D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler, Q. Hudson, ELife 6 (2017).","ieee":"D. Andergassen et al., “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber, M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25125","ama":"Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 2017;6. doi:10.7554/eLife.25125","mla":"Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife, vol. 6, e25125, eLife Sciences Publications, 2017, doi:10.7554/eLife.25125.","ista":"Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 6, e25125.","chicago":"Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25125."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Nested weighted automata (NWA) present a robust and convenient automata-theoretic formalism for quantitative specifications. Previous works have considered NWA that processed input words only in the forward direction. It is natural to allow the automata to process input words backwards as well, for example, to measure the maximal or average time between a response and the preceding request. We therefore introduce and study bidirectional NWA that can process input words in both directions. First, we show that bidirectional NWA can express interesting quantitative properties that are not expressible by forward-only NWA. Second, for the fundamental decision problems of emptiness and universality, we establish decidability and complexity results for the new framework which match the best-known results for the special case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality is achieved at no additional computational complexity. This is in stark contrast to the unweighted case, where bidirectional finite automata are no more expressive but exponentially more succinct than their forward-only counterparts."}],"intvolume":" 85","month":"08","alternative_title":["LIPIcs"],"scopus_import":1,"language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:47:49Z","file_size":570294,"date_created":"2018-12-12T10:08:02Z","file_name":"IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d2bda4783821a6358333fe27f11f4737","file_id":"4661"}],"publication_status":"published","publication_identifier":{"issn":["18688969"]},"volume":85,"_id":"711","pubrep_id":"886","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2017-09-05","end_date":"2017-09-08","location":"Berlin, Germany","name":"28th International Conference on Concurrency Theory, CONCUR"},"type":"conference","ddc":["004","005"],"date_updated":"2021-01-12T08:11:53Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:49Z","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:48:04Z","doi":"10.4230/LIPIcs.CONCUR.2017.5","date_published":"2017-08-01T00:00:00Z","article_number":"5","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Bidirectional Nested Weighted Automata,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5.","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 5.","mla":"Chatterjee, Krishnendu, et al. Bidirectional Nested Weighted Automata. Vol. 85, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.5.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Bidirectional nested weighted automata (Vol. 85). Presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5","ama":"Chatterjee K, Henzinger TA, Otop J. Bidirectional nested weighted automata. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.5","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Bidirectional nested weighted automata,” presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany, 2017, vol. 85."},"title":"Bidirectional nested weighted automata","publist_id":"6976","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Otop","full_name":"Otop, Jan","first_name":"Jan"}]},{"_id":"712","type":"journal_article","status":"public","citation":{"apa":"Fischer, J. L. (2017). Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. Elsevier. https://doi.org/10.1016/j.na.2017.03.001","ama":"Fischer JL. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 2017;159:181-207. doi:10.1016/j.na.2017.03.001","ieee":"J. L. Fischer, “Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations,” Nonlinear Analysis: Theory, Methods and Applications, vol. 159. Elsevier, pp. 181–207, 2017.","short":"J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207.","mla":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications, vol. 159, Elsevier, 2017, pp. 181–207, doi:10.1016/j.na.2017.03.001.","ista":"Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207.","chicago":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications. Elsevier, 2017. https://doi.org/10.1016/j.na.2017.03.001."},"date_updated":"2021-01-12T08:11:55Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"6975","author":[{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L"}],"department":[{"_id":"JuFi"}],"title":"Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations","abstract":[{"text":"We establish a weak–strong uniqueness principle for solutions to entropy-dissipating reaction–diffusion equations: As long as a strong solution to the reaction–diffusion equation exists, any weak solution and even any renormalized solution must coincide with this strong solution. Our assumptions on the reaction rates are just the entropy condition and local Lipschitz continuity; in particular, we do not impose any growth restrictions on the reaction rates. Therefore, our result applies to any single reversible reaction with mass-action kinetics as well as to systems of reversible reactions with mass-action kinetics satisfying the detailed balance condition. Renormalized solutions are known to exist globally in time for reaction–diffusion equations with entropy-dissipating reaction rates; in contrast, the global-in-time existence of weak solutions is in general still an open problem–even for smooth data–, thereby motivating the study of renormalized solutions. The key ingredient of our result is a careful adjustment of the usual relative entropy functional, whose evolution cannot be controlled properly for weak solutions or renormalized solutions.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00730"}],"oa":1,"publisher":"Elsevier","scopus_import":1,"quality_controlled":"1","intvolume":" 159","month":"08","year":"2017","publication_status":"published","publication_identifier":{"issn":["0362546X"]},"language":[{"iso":"eng"}],"publication":"Nonlinear Analysis: Theory, Methods and Applications","day":"01","page":"181 - 207","date_created":"2018-12-11T11:48:05Z","volume":159,"date_published":"2017-08-01T00:00:00Z","doi":"10.1016/j.na.2017.03.001"},{"_id":"714","status":"public","type":"journal_article","article_type":"original","date_updated":"2021-01-12T08:12:00Z","department":[{"_id":"GaNo"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients."}],"month":"09","intvolume":" 178","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["03768716"]},"publication_status":"published","volume":178,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence, vol. 178, Elsevier, 2017, pp. 7–14, doi:10.1016/j.drugalcdep.2017.04.015.","apa":"Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. Elsevier. https://doi.org/10.1016/j.drugalcdep.2017.04.015","ama":"Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 2017;178:7-14. doi:10.1016/j.drugalcdep.2017.04.015","ieee":"G. Brailoiu et al., “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” Drug and Alcohol Dependence, vol. 178. Elsevier, pp. 7–14, 2017.","short":"G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.","chicago":"Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence. Elsevier, 2017. https://doi.org/10.1016/j.drugalcdep.2017.04.015.","ista":"Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14."},"title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens","author":[{"full_name":"Brailoiu, Gabriela","last_name":"Brailoiu","first_name":"Gabriela"},{"first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","last_name":"Deliu","full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293"},{"last_name":"Barr","full_name":"Barr, Jeffrey","first_name":"Jeffrey"},{"first_name":"Linda","last_name":"Console Bram","full_name":"Console Bram, Linda"},{"first_name":"Alexandra","full_name":"Ciuciu, Alexandra","last_name":"Ciuciu"},{"last_name":"Abood","full_name":"Abood, Mary","first_name":"Mary"},{"first_name":"Ellen","last_name":"Unterwald","full_name":"Unterwald, Ellen"},{"first_name":"Eugen","full_name":"Brǎiloiu, Eugen","last_name":"Brǎiloiu"}],"publist_id":"6967","article_processing_charge":"No","external_id":{"pmid":["28623807"]},"acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"01","publication":"Drug and Alcohol Dependence","year":"2017","doi":"10.1016/j.drugalcdep.2017.04.015","date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:48:05Z","page":"7 - 14"},{"publication_identifier":{"issn":["19466234"]},"publication_status":"published","year":"2017","day":"30","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","doi":"10.1126/scitranslmed.aao4218","volume":9,"date_published":"2017-08-30T00:00:00Z","issue":"405","date_created":"2018-12-11T11:48:06Z","abstract":[{"lang":"eng","text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome."}],"oa_version":"None","publisher":"American Association for the Advancement of Science","quality_controlled":"1","scopus_import":1,"month":"08","intvolume":" 9","citation":{"mla":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aao4218.","ama":"Novarino G. More excitation for Rett syndrome. Science Translational Medicine. 2017;9(405). doi:10.1126/scitranslmed.aao4218","apa":"Novarino, G. (2017). More excitation for Rett syndrome. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218","ieee":"G. Novarino, “More excitation for Rett syndrome,” Science Translational Medicine, vol. 9, no. 405. American Association for the Advancement of Science, 2017.","short":"G. Novarino, Science Translational Medicine 9 (2017).","chicago":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218.","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218."},"date_updated":"2021-01-12T08:12:04Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6968","title":"More excitation for Rett syndrome","department":[{"_id":"GaNo"}],"_id":"715","article_number":"aao4218","type":"journal_article","status":"public"},{"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"citation":{"apa":"Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408","ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):34. doi:10.1145/3121408","short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.","ieee":"K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017.","mla":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408.","ista":"Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"publist_id":"6964","external_id":{"arxiv":["1201.2829"]},"title":"The complexity of mean-payoff pushdown games","publisher":"ACM","quality_controlled":"1","oa":1,"year":"2017","day":"01","publication":"Journal of the ACM","page":"34","doi":"10.1145/3121408","date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:48:06Z","_id":"716","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-01-12T08:12:08Z","department":[{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.2829"}],"month":"09","intvolume":" 64","publication_identifier":{"issn":["00045411"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":64,"issue":"5","ec_funded":1},{"publisher":"Academic Press","quality_controlled":"1","oa":1,"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.","date_published":"2017-09-01T00:00:00Z","doi":"10.1016/j.jcss.2017.04.005","date_created":"2018-12-11T11:48:07Z","page":"236 - 259","day":"01","publication":"Journal of Computer and System Sciences","year":"2017","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"title":"Hyperplane separation technique for multidimensional mean-payoff games","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"publist_id":"6963","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259. doi:10.1016/j.jcss.2017.04.005","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic Press, pp. 236–259, 2017.","short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","mla":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences, vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005.","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences. Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005."},"month":"09","intvolume":" 88","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1210.3141"}],"oa_version":"Preprint","abstract":[{"text":"We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard.","lang":"eng"}],"volume":88,"related_material":{"record":[{"status":"public","id":"2329","relation":"earlier_version"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"717","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T10:38:15Z"},{"quality_controlled":"1","publisher":"Springer","scopus_import":1,"month":"09","intvolume":" 54","abstract":[{"lang":"eng","text":"The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains."}],"oa_version":"None","page":"543 - 544","issue":"6","volume":54,"date_published":"2017-09-01T00:00:00Z","doi":"10.1007/s00236-017-0299-0","date_created":"2018-12-11T11:48:07Z","publication_identifier":{"issn":["00015903"]},"publication_status":"published","year":"2017","day":"01","publication":"Acta Informatica","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"719","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Ehlers, Rüdiger","last_name":"Ehlers","first_name":"Rüdiger"}],"publist_id":"6961","title":"Special issue: Synthesis and SYNT 2014","department":[{"_id":"KrCh"}],"citation":{"short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica. 2017;54(6):543-544. doi:10.1007/s00236-017-0299-0","apa":"Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0","mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:10.1007/s00236-017-0299-0.","ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0."},"date_updated":"2021-01-12T08:12:18Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2018-12-11T11:48:08Z","doi":"10.1371/journal.pcbi.1005763","date_published":"2017-09-19T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"PLoS Computational Biology","day":"19","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","article_processing_charge":"Yes","author":[{"full_name":"Humplik, Jan","last_name":"Humplik","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"publist_id":"6960","title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","citation":{"mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763","apa":"Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"},{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes"}],"article_number":"e1005763","volume":13,"issue":"9","publication_status":"published","publication_identifier":{"issn":["1553734X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5352","checksum":"81107096c19771c36ddbe6f0282a3acb","file_size":14167050,"date_updated":"2020-07-14T12:47:53Z","creator":"system","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","date_created":"2018-12-12T10:18:30Z"}],"scopus_import":1,"intvolume":" 13","month":"09","abstract":[{"text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:53Z","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T08:12:21Z","ddc":["530","571"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"884","status":"public","_id":"720"},{"type":"journal_article","status":"public","_id":"721","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T08:12:24Z","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1512.03703","open_access":"1"}],"month":"09","intvolume":" 70","abstract":[{"text":"Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur.","lang":"eng"}],"oa_version":"Submitted Version","issue":"9","volume":70,"ec_funded":1,"publication_identifier":{"issn":["00103640"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"publist_id":"6959","author":[{"first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","full_name":"Ajanki, Oskari H","last_name":"Ajanki"},{"last_name":"Krüger","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"}],"title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","citation":{"ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639","apa":"Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639","ieee":"O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” Communications on Pure and Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705.","mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639.","ista":"Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705.","chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"page":"1672 - 1705","date_published":"2017-09-01T00:00:00Z","doi":"10.1002/cpa.21639","date_created":"2018-12-11T11:48:08Z","year":"2017","day":"01","publication":"Communications on Pure and Applied Mathematics"},{"pubrep_id":"982","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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"},"type":"journal_article","_id":"722","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:54Z","ddc":["581"],"date_updated":"2021-01-12T08:12:29Z","intvolume":" 27","month":"09","scopus_import":1,"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises."}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"issue":"17","volume":27,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-04-17T07:46:40Z","file_name":"2017_CurrentBiology_Morris.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:54Z","file_size":1576593,"file_id":"6332","checksum":"e45588b21097b408da6276a3e5eedb2e","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["09609822"]},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"title":"Shaping 3D root system architecture","external_id":{"pmid":["28898665"]},"publist_id":"6956","author":[{"last_name":"Morris","full_name":"Morris, Emily","first_name":"Emily"},{"full_name":"Griffiths, Marcus","last_name":"Griffiths","first_name":"Marcus"},{"last_name":"Golebiowska","full_name":"Golebiowska, Agata","first_name":"Agata"},{"last_name":"Mairhofer","full_name":"Mairhofer, Stefan","first_name":"Stefan"},{"full_name":"Burr Hersey, Jasmine","last_name":"Burr Hersey","first_name":"Jasmine"},{"first_name":"Tatsuaki","full_name":"Goh, Tatsuaki","last_name":"Goh"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247"},{"first_name":"Brian","last_name":"Atkinson","full_name":"Atkinson, Brian"},{"full_name":"Sturrock, Craig","last_name":"Sturrock","first_name":"Craig"},{"full_name":"Lynch, Jonathan","last_name":"Lynch","first_name":"Jonathan"},{"first_name":"Kris","last_name":"Vissenberg","full_name":"Vissenberg, Kris"},{"full_name":"Ritz, Karl","last_name":"Ritz","first_name":"Karl"},{"last_name":"Wells","full_name":"Wells, Darren","first_name":"Darren"},{"last_name":"Mooney","full_name":"Mooney, Sacha","first_name":"Sacha"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043","ieee":"E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043.","ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930.","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043."},"oa":1,"quality_controlled":"1","publisher":"Cell Press","date_created":"2018-12-11T11:48:08Z","doi":"10.1016/j.cub.2017.06.043","date_published":"2017-09-11T00:00:00Z","page":"R919 - R930","publication":"Current Biology","day":"11","year":"2017","has_accepted_license":"1"},{"abstract":[{"lang":"eng","text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species."}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/"}],"scopus_import":1,"intvolume":" 114","month":"09","publication_status":"published","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"volume":114,"issue":"38","_id":"725","type":"journal_article","status":"public","date_updated":"2021-01-12T08:12:36Z","department":[{"_id":"GaTk"}],"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2017","publication":"PNAS","day":"19","page":"10149 - 10154","date_created":"2018-12-11T11:48:10Z","date_published":"2017-09-19T00:00:00Z","doi":"10.1073/pnas.1703817114","citation":{"ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114","apa":"Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28874581"]},"publist_id":"6953","author":[{"full_name":"Harpaz, Roy","last_name":"Harpaz","first_name":"Roy"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"}],"title":"Discrete modes of social information processing predict individual behavior of fish in a group"},{"main_file_link":[{"url":"https://arxiv.org/abs/1701.02744","open_access":"1"}],"scopus_import":1,"intvolume":" 96","month":"09","abstract":[{"text":"We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic.","lang":"eng"}],"oa_version":"Submitted Version","volume":96,"issue":"10","publication_status":"published","publication_identifier":{"issn":["24699950"]},"language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"724","department":[{"_id":"MaSe"}],"date_updated":"2021-01-12T08:12:35Z","oa":1,"publisher":"American Physical Society","quality_controlled":"1","acknowledgement":"We would like to thank Dmitry Abanin, Christophe De\r\nBeule, Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions. Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1.","date_created":"2018-12-11T11:48:09Z","date_published":"2017-09-13T00:00:00Z","doi":"10.1103/PhysRevB.96.104203","year":"2017","publication":"Physical Review B","day":"13","article_number":"104203","author":[{"last_name":"Hetterich","full_name":"Hetterich, Daniel","first_name":"Daniel"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"full_name":"Domínguez, Fernando","last_name":"Domínguez","first_name":"Fernando"},{"first_name":"Frank","last_name":"Pollmann","full_name":"Pollmann, Frank"},{"last_name":"Trauzettel","full_name":"Trauzettel, Björn","first_name":"Björn"}],"publist_id":"6955","title":"Noninteracting central site model localization and logarithmic entanglement growth","citation":{"ama":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203","apa":"Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203","short":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017).","ieee":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” Physical Review B, vol. 96, no. 10. American Physical Society, 2017.","mla":"Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203.","ista":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 96(10), 104203.","chicago":"Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104203."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"None","abstract":[{"lang":"eng","text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently."}],"intvolume":" 9","month":"10","scopus_import":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","day":"11","publication_status":"published","year":"2017","publication_identifier":{"issn":["19466234"]},"date_created":"2018-12-11T11:48:12Z","doi":"10.1126/scitranslmed.aap8168","issue":"411","date_published":"2017-10-11T00:00:00Z","volume":9,"article_number":"eaap8168","_id":"731","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:12:57Z","citation":{"mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aap8168.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “The science of love in ASD and ADHD,” Science Translational Medicine, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). The science of love in ASD and ADHD. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aap8168","ama":"Novarino G. The science of love in ASD and ADHD. Science Translational Medicine. 2017;9(411). doi:10.1126/scitranslmed.aap8168","chicago":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aap8168.","ista":"Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168."},"department":[{"_id":"GaNo"}],"title":"The science of love in ASD and ADHD","publist_id":"6938","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}]},{"oa":1,"quality_controlled":"1","publisher":"Elsevier","page":"102-119","date_created":"2020-01-25T15:55:39Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.ymthe.2016.10.005","year":"2017","has_accepted_license":"1","publication":"Molecular Therapy","day":"01","article_processing_charge":"No","external_id":{"pmid":["28129106"]},"author":[{"full_name":"Smole, Anže","last_name":"Smole","first_name":"Anže"},{"first_name":"Duško","full_name":"Lainšček, Duško","last_name":"Lainšček"},{"full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","first_name":"Urban"},{"last_name":"Horvat","full_name":"Horvat, Simon","first_name":"Simon"},{"last_name":"Jerala","full_name":"Jerala, Roman","first_name":"Roman"}],"title":"A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation","citation":{"chicago":"Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.","ista":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 25(1), 102–119.","mla":"Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier, 2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005.","apa":"Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017). A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005","ama":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005","short":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119.","ieee":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation,” Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 25","month":"01","abstract":[{"lang":"eng","text":"Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy."}],"oa_version":"Published Version","pmid":1,"volume":25,"issue":"1","publication_status":"published","publication_identifier":{"issn":["1525-0016"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:56Z","file_size":3404806,"date_created":"2020-03-03T10:55:13Z","file_name":"2017_MolecularTherapy_Smole.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7561","checksum":"ea8b1b28606dd1edab7379ba4fa3641f"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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"},"article_type":"original","type":"journal_article","status":"public","_id":"7360","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"MaLo"}],"date_updated":"2021-01-12T08:13:14Z","ddc":["570"]},{"date_updated":"2021-01-12T08:13:55Z","citation":{"ieee":"J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial volunteer allocation needs realistic distances,” in 2017 IEEE International Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.","short":"J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763.","ama":"Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer allocation needs realistic distances. In: 2017 IEEE International Conference on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375","apa":"Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal geospatial volunteer allocation needs realistic distances. In 2017 IEEE International Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375","mla":"Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–63, doi:10.1109/BigData.2017.8258375.","ista":"Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial volunteer allocation needs realistic distances. 2017 IEEE International Conference on Big Data. Big Data, 3760–3763.","chicago":"Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017 IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6906","author":[{"id":"49BC895A-F248-11E8-B48F-1D18A9856A87","first_name":"Jasmin","full_name":"Pielorz, Jasmin","last_name":"Pielorz"},{"full_name":"Prandtstetter, Matthias","last_name":"Prandtstetter","first_name":"Matthias"},{"last_name":"Straub","full_name":"Straub, Markus","first_name":"Markus"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"}],"department":[{"_id":"ChLa"}],"title":"Optimal geospatial volunteer allocation needs realistic distances","_id":"750","conference":{"end_date":"2017-12-14","location":"Boston, MA, United States","start_date":"2017-12-11","name":"Big Data"},"type":"conference","status":"public","publication_status":"published","year":"2017","publication_identifier":{"isbn":["978-153862714-3"]},"publication":"2017 IEEE International Conference on Big Data","language":[{"iso":"eng"}],"day":"01","page":"3760 - 3763","date_created":"2018-12-11T11:48:18Z","doi":"10.1109/BigData.2017.8258375","date_published":"2017-12-01T00:00:00Z","abstract":[{"lang":"eng","text":"Modern communication technologies allow first responders to contact thousands of potential volunteers simultaneously for support during a crisis or disaster event. However, such volunteer efforts must be well coordinated and monitored, in order to offer an effective relief to the professionals. In this paper we extend earlier work on optimally assigning volunteers to selected landmark locations. In particular, we emphasize the aspect that obtaining good assignments requires not only advanced computational tools, but also a realistic measure of distance between volunteers and landmarks. Specifically, we propose the use of the Open Street Map (OSM) driving distance instead of he previously used flight distance. We find the OSM driving distance to be better aligned with the interests of volunteers and first responders. Furthermore, we show that relying on the flying distance leads to a substantial underestimation of the number of required volunteers, causing negative side effects in case of an actual crisis situation."}],"oa_version":"None","scopus_import":1,"publisher":"IEEE","quality_controlled":"1","month":"12"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663.","short":"R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017).","ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.","apa":"Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663","ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 2017;24(3). doi:10.37236/6663","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics. International Press, 2017. https://doi.org/10.37236/6663.","ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18."},"title":"Unified Hanani Tutte theorem","article_processing_charge":"No","publist_id":"6859","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"},{"full_name":"Pálvölgyi, Dömötör","last_name":"Pálvölgyi","first_name":"Dömötör"}],"article_number":"P3.18","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication":"Electronic Journal of Combinatorics","day":"28","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:48:32Z","date_published":"2017-07-28T00:00:00Z","doi":"10.37236/6663","oa":1,"quality_controlled":"1","publisher":"International Press","ddc":["000"],"date_updated":"2022-03-18T12:58:53Z","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:06Z","_id":"795","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:48:06Z","file_size":236944,"date_created":"2019-01-18T14:04:08Z","file_name":"2017_ElectrCombi_Fulek.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5853","checksum":"ef320cff0f062051e858f929be6a3581"}],"publication_status":"published","publication_identifier":{"issn":["10778926"]},"ec_funded":1,"issue":"3","volume":24,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof."}],"intvolume":" 24","month":"07","scopus_import":"1"},{"_id":"797","status":"public","article_type":"original","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit. Wiley, 2017. https://doi.org/10.1002/piuz.201770305.","ieee":"J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit. Wiley. https://doi.org/10.1002/piuz.201770305","ama":"Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113. doi:10.1002/piuz.201770305","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305."},"date_updated":"2022-03-24T09:16:20Z","title":"Photonenblockade aufgelöst","department":[{"_id":"JoFi"}],"publist_id":"6856","author":[{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"article_processing_charge":"No","oa_version":"None","abstract":[{"lang":"ger","text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden."}],"month":"05","intvolume":" 48","quality_controlled":"1","publisher":"Wiley","day":"01","language":[{"iso":"eng"}],"publication":"Physik in unserer Zeit","year":"2017","publication_status":"published","doi":"10.1002/piuz.201770305","issue":"3","volume":48,"date_published":"2017-05-01T00:00:00Z","date_created":"2018-12-11T11:48:33Z","page":"111 - 113"},{"publication_status":"published","publication_identifier":{"issn":["10222588"]},"language":[{"iso":"eng"}],"file":[{"file_size":125065,"date_updated":"2020-07-14T12:48:09Z","creator":"dernst","file_name":"2017_VOEB_Andrae.pdf","date_created":"2019-01-18T13:39:26Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"558c18bcf5580d87dd371ec626d52075","file_id":"5851"}],"issue":"2","volume":70,"abstract":[{"lang":"eng","text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 70","month":"08","date_updated":"2021-01-12T08:16:45Z","ddc":["020"],"file_date_updated":"2020-07-14T12:48:09Z","department":[{"_id":"E-Lib"}],"_id":"807","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","year":"2017","has_accepted_license":"1","popular_science":"1","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","day":"01","page":"274 - 280","date_created":"2018-12-11T11:48:36Z","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1898","oa":1,"publisher":"VÖB","citation":{"ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898","apa":"Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898","ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1898."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Magdalena","full_name":"Andrae, Magdalena","last_name":"Andrae"},{"orcid":"0000-0001-8126-0426","full_name":"Villányi, Márton","last_name":"Villányi","first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6843","title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 70 (2017) 200–207.","ieee":"B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","ama":"Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207. doi:10.31263/voebm.v70i2.1678","apa":"Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1678","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1678."},"title":"Metadata for research data in practice","author":[{"id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614","last_name":"Petritsch"}],"publist_id":"6823","oa":1,"publisher":"VÖB","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:48:42Z","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1678","page":"200 - 207","_id":"825","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["020"],"date_updated":"2021-01-12T08:17:44Z","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:48:11Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep."}],"intvolume":" 70","month":"08","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5850","checksum":"7c4544d07efa2c2add8612b489abb4e2","creator":"dernst","date_updated":"2020-07-14T12:48:11Z","file_size":7843975,"date_created":"2019-01-18T13:32:17Z","file_name":"2017_VOEB_Petritsch.pdf"}],"publication_status":"published","publication_identifier":{"issn":["10222588"]},"issue":"2","volume":70},{"status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"9445","department":[{"_id":"DaZi"}],"file_date_updated":"2021-06-02T14:33:36Z","extern":"1","ddc":["570"],"date_updated":"2021-12-14T07:54:36Z","month":"11","intvolume":" 6","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation.","lang":"eng"}],"volume":6,"file":[{"success":1,"checksum":"4cfcdd67511ae4aed3d993550e46e146","file_id":"9446","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_eLife_Lyons.pdf","date_created":"2021-06-02T14:33:36Z","creator":"cziletti","file_size":1603102,"date_updated":"2021-06-02T14:33:36Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","article_number":"e30674","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","author":[{"first_name":"David B","full_name":"Lyons, David B","last_name":"Lyons"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"external_id":{"pmid":["29140247"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674."},"publisher":"eLife Sciences Publications","quality_controlled":"1","oa":1,"date_published":"2017-11-15T00:00:00Z","doi":"10.7554/elife.30674","date_created":"2021-06-02T14:28:58Z","day":"15","publication":"eLife","has_accepted_license":"1","year":"2017"},{"page":"71 - 87","date_created":"2018-12-11T11:49:24Z","doi":"10.1007/978-1-4939-6940-1_5","date_published":"2017-03-15T00:00:00Z","year":"2017","publication":"Synthetic Protein Switches","day":"15","quality_controlled":"1","publisher":"Springer","publist_id":"6451","author":[{"first_name":"Ben","full_name":"Clifton, Ben","last_name":"Clifton"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada"},{"last_name":"Herde","full_name":"Herde, Michel","first_name":"Michel"},{"first_name":"Christian","full_name":"Henneberger, Christian","last_name":"Henneberger"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jackson","full_name":"Jackson, Colin","first_name":"Colin"}],"title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","editor":[{"first_name":"Viktor","full_name":"Stein, Viktor","last_name":"Stein"}],"citation":{"chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"volume":1596,"publication_status":"published","publication_identifier":{"issn":["10643745"]},"language":[{"iso":"eng"}],"scopus_import":1,"alternative_title":["Methods in Molecular Biology"],"intvolume":" 1596","month":"03","abstract":[{"lang":"eng","text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors."}],"oa_version":"None","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T08:22:13Z","type":"book_chapter","status":"public","_id":"957","series_title":"Synthetic Protein Switches"},{"ddc":["004"],"date_updated":"2023-02-23T12:35:50Z","file_date_updated":"2020-07-14T12:48:18Z","department":[{"_id":"ToHe"}],"_id":"963","pubrep_id":"829","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"start_date":"2017-08-21","location":"Aalborg, Denmark","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"type":"conference","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5059","checksum":"f55eaf7f3c36ea07801112acfedd17d5","date_updated":"2020-07-14T12:48:18Z","file_size":369730,"creator":"system","date_created":"2018-12-12T10:14:10Z","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf"}],"publication_status":"published","publication_identifier":{"issn":["18688969"]},"volume":83,"related_material":{"record":[{"relation":"later_version","id":"6005","status":"public"}]},"oa_version":"Published Version","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ","lang":"eng"}],"intvolume":" 83","month":"06","alternative_title":["LIPIcs"],"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37."},"title":"Timed network games with clocks","publist_id":"6438","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni"},{"last_name":"Guha","full_name":"Guha, Shibashis","first_name":"Shibashis"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"article_number":"37","project":[{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:49:26Z","date_published":"2017-06-01T00:00:00Z","doi":"10.4230/LIPIcs.MFCS.2017.37","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-21T16:34:41Z","citation":{"chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.","mla":"Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 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A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. 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Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed."}],"oa_version":"Published Version","author":[{"first_name":"Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"last_name":"Dal Co","full_name":"Dal Co, Alma","first_name":"Alma"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller"},{"first_name":"Sten","full_name":"Littmann, Sten","last_name":"Littmann"},{"first_name":"Marcel","last_name":"Kuypers","full_name":"Kuypers, Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"publist_id":"7275","title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","citation":{"ieee":"N. 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