[{"abstract":[{"text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"scopus_import":"1","intvolume":" 115","month":"06","publication_status":"published","language":[{"iso":"eng"}],"volume":115,"issue":"23","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"_id":"281","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-11T12:58:24Z","department":[{"_id":"GaTk"}],"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2018","isi":1,"publication":"PNAS","day":"05","page":"6088 - 6093","date_created":"2018-12-11T11:45:35Z","doi":"10.1073/pnas.1716659115","date_published":"2018-06-05T00:00:00Z","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"citation":{"chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"pmid":["29784812"],"isi":["000434114900071"]},"author":[{"full_name":"Granados, Alejandro","last_name":"Granados","first_name":"Alejandro"},{"full_name":"Pietsch, Julian","last_name":"Pietsch","first_name":"Julian"},{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez"},{"first_name":"Isebail","full_name":"Farquhar, Isebail","last_name":"Farquhar"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"last_name":"Swain","full_name":"Swain, Peter","first_name":"Peter"}],"publist_id":"7618","title":"Distributed and dynamic intracellular organization of extracellular information"},{"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062"}],"month":"01","intvolume":" 131","abstract":[{"text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","volume":131,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"620","department":[{"_id":"DaSi"}],"date_updated":"2023-09-11T12:57:13Z","publisher":"Company of Biologists","quality_controlled":"1","oa":1,"date_published":"2018-01-04T00:00:00Z","doi":"10.1242/jcs.207696","date_created":"2018-12-11T11:47:32Z","isi":1,"year":"2018","day":"04","publication":"Journal of Cell Science","article_number":"jcs207696","author":[{"full_name":"Yamamoto, Wataru","last_name":"Yamamoto","first_name":"Wataru"},{"last_name":"Wada","full_name":"Wada, Suguru","first_name":"Suguru"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"first_name":"Kaito","full_name":"Aoshima, Kaito","last_name":"Aoshima"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"last_name":"Toshima","full_name":"Toshima, Junko","first_name":"Junko"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"publist_id":"7184","article_processing_charge":"No","external_id":{"isi":["000424786900012"],"pmid":["29192062"]},"title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","citation":{"mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.","ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"citation":{"ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In Proceedings of the 21st International Conference on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132.","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: Proceedings of the 21st International Conference on Hybrid Systems. ACM; 2018:177-186. doi:10.1145/3178126.3178132","apa":"Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification for STL. In Proceedings of the 21st International Conference on Hybrid Systems (pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186.","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in Proceedings of the 21st International Conference on Hybrid Systems, Porto, Portugal, 2018, pp. 177–186.","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86, doi:10.1145/3178126.3178132."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7739","author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"}],"article_processing_charge":"No","external_id":{"isi":["000474781600020"]},"title":"Efficient parametric identification for STL","quality_controlled":"1","publisher":"ACM","oa":1,"isi":1,"has_accepted_license":"1","year":"2018","day":"11","publication":"Proceedings of the 21st International Conference on Hybrid Systems","page":"177 - 186","doi":"10.1145/3178126.3178132","date_published":"2018-04-11T00:00:00Z","date_created":"2018-12-11T11:45:04Z","_id":"182","type":"conference","conference":{"start_date":"2018-04-11","end_date":"2018-04-13","location":"Porto, Portugal","name":"HSCC: Hybrid Systems: Computation and Control"},"status":"public","date_updated":"2023-09-11T13:30:51Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:17Z","abstract":[{"text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","alternative_title":["HSCC Proceedings"],"month":"04","publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"publication_status":"published","file":[{"file_id":"7833","checksum":"81eabc96430e84336ea88310ac0a1ad0","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-05-14T12:18:29Z","file_name":"2018_HSCC_Bakhirkin.pdf","date_updated":"2020-07-14T12:45:17Z","file_size":5900421,"creator":"dernst"}],"language":[{"iso":"eng"}]},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis."}],"month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1804.10985","open_access":"1"}],"scopus_import":"1","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-1-4503-5583-4"]},"ec_funded":1,"volume":"F138033","_id":"143","status":"public","conference":{"name":"LICS: Logic in Computer Science","start_date":"2018-07-09","end_date":"2018-07-12","location":"Oxford, United Kingdom"},"type":"conference","date_updated":"2023-09-11T13:23:42Z","department":[{"_id":"KrCh"}],"oa":1,"quality_controlled":"1","publisher":"IEEE","day":"09","year":"2018","isi":1,"date_created":"2018-12-11T11:44:51Z","date_published":"2018-07-09T00:00:00Z","doi":"10.1145/3209108.3209191","page":"185 - 194","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:10.1145/3209108.3209191","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194.","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","mla":"Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191."},"title":"Efficient algorithms for asymptotic bounds on termination time in VASS","external_id":{"isi":["000545262800020"]},"article_processing_charge":"No","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Antonín","full_name":"Kučera, Antonín","last_name":"Kučera"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr","last_name":"Novotny"},{"first_name":"Dominik","last_name":"Velan","full_name":"Velan, Dominik"},{"last_name":"Zuleger","full_name":"Zuleger, Florian","first_name":"Florian"}],"publist_id":"7780"},{"author":[{"first_name":"Pritish","full_name":"Mohapatra, Pritish","last_name":"Mohapatra"},{"last_name":"Rolinek","full_name":"Rolinek, Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"},{"first_name":"C V","last_name":"Jawahar","full_name":"Jawahar, C V"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M Pawan","full_name":"Kumar, M Pawan","last_name":"Kumar"}],"external_id":{"arxiv":["1604.08269"],"isi":["000457843603087"]},"article_processing_charge":"No","title":"Efficient optimization for rank-based loss functions","citation":{"ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389.","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"page":"3693-3701","doi":"10.1109/cvpr.2018.00389","date_published":"2018-06-28T00:00:00Z","date_created":"2018-12-11T11:45:33Z","isi":1,"year":"2018","day":"28","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","publisher":"IEEE","quality_controlled":"1","oa":1,"department":[{"_id":"VlKo"}],"date_updated":"2023-09-11T13:24:43Z","type":"conference","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","start_date":"2018-06-18","location":"Salt Lake City, UT, USA","end_date":"2018-06-22"},"status":"public","_id":"273","ec_funded":1,"publication_identifier":{"isbn":["9781538664209"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08269"}],"month":"06","abstract":[{"text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time.","lang":"eng"}],"oa_version":"Preprint"},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256.","date_published":"2018-10-19T00:00:00Z","doi":"10.1103/PhysRevLett.121.167601","date_created":"2018-12-11T11:45:38Z","day":"19","publication":"Physical Review Letters","isi":1,"year":"2018","article_number":"167601","title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","author":[{"first_name":"Alexander","last_name":"Zibrov","full_name":"Zibrov, Alexander"},{"last_name":"Peng","full_name":"Peng, Rao","orcid":"0000-0003-1250-0021","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","first_name":"Rao"},{"last_name":"Kometter","full_name":"Kometter, Carlos","first_name":"Carlos"},{"full_name":"Li, Jia","last_name":"Li","first_name":"Jia"},{"last_name":"Dean","full_name":"Dean, Cory","first_name":"Cory"},{"first_name":"Takashi","full_name":"Taniguchi, Takashi","last_name":"Taniguchi"},{"last_name":"Watanabe","full_name":"Watanabe, Kenji","first_name":"Kenji"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"Andrea","full_name":"Young, Andrea","last_name":"Young"}],"article_processing_charge":"No","external_id":{"arxiv":["1805.01038"],"isi":["000447307500007"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.167601","apa":"Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.167601","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018).","ieee":"A. Zibrov et al., “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","mla":"Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.167601.","ista":"Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.","chicago":"Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.167601."},"month":"10","intvolume":" 121","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1805.01038","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry."}],"issue":"16","volume":121,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"289","department":[{"_id":"MaSe"}],"date_updated":"2023-09-11T13:39:50Z"},{"isi":1,"year":"2018","day":"01","publication":"Frontiers in Bioscience - Landmark","page":"1391 - 1406","doi":"10.2741/4651","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:45:37Z","acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","quality_controlled":"1","publisher":"Frontiers in Bioscience","oa":1,"citation":{"short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.","ieee":"V. Salari et al., “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 2018;23(8):1391-1406. doi:10.2741/4651","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers in Bioscience. https://doi.org/10.2741/4651","mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651.","ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406.","chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark. Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Vahid","last_name":"Salari","full_name":"Salari, Vahid"},{"full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir"},{"first_name":"Michal","last_name":"Cifra","full_name":"Cifra, Michal"},{"first_name":"Christoph","full_name":"Simon, Christoph","last_name":"Simon"},{"last_name":"Scholkmann","full_name":"Scholkmann, Felix","first_name":"Felix"},{"first_name":"Zahra","full_name":"Alirezaei, Zahra","last_name":"Alirezaei"},{"first_name":"Jack","full_name":"Tuszynski, Jack","last_name":"Tuszynski"}],"article_processing_charge":"No","external_id":{"pmid":["29293441"],"isi":["000439042800001"]},"title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","project":[{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"}],"publication_status":"published","language":[{"iso":"eng"}],"issue":"8","volume":23,"ec_funded":1,"abstract":[{"lang":"eng","text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm"}],"month":"03","intvolume":" 23","date_updated":"2023-09-11T13:38:14Z","department":[{"_id":"JoFi"}],"_id":"287","type":"journal_article","status":"public"},{"abstract":[{"lang":"eng","text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0815"}],"scopus_import":"1","intvolume":" 65","month":"01","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"1","related_material":{"record":[{"relation":"earlier_version","id":"2157","status":"public"}]},"volume":65,"_id":"425","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-11T13:38:49Z","department":[{"_id":"UlWa"}],"oa":1,"publisher":"ACM","quality_controlled":"1","year":"2018","isi":1,"publication":"Journal of the ACM","day":"01","date_created":"2018-12-11T11:46:24Z","date_published":"2018-01-01T00:00:00Z","doi":"10.1145/3078632","article_number":"5","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"citation":{"ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1402.0815"],"isi":["000425685900006"]},"article_processing_charge":"No","publist_id":"7398","author":[{"full_name":"Matoušek, Jiří","last_name":"Matoušek","first_name":"Jiří"},{"first_name":"Eric","last_name":"Sedgwick","full_name":"Sedgwick, Eric"},{"orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"title":"Embeddability in the 3-Sphere is decidable"},{"citation":{"chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7250","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"}],"external_id":{"isi":["000440392900014"]},"article_processing_charge":"No","title":"Establishment in a new habitat by polygenic adaptation","project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Theoretical Population Biology","page":"110-127","doi":"10.1016/j.tpb.2017.11.007","date_published":"2018-07-01T00:00:00Z","date_created":"2018-12-11T11:47:12Z","publisher":"Academic Press","quality_controlled":"1","oa":1,"date_updated":"2023-09-11T13:41:22Z","ddc":["519","576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:09Z","_id":"564","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","publication_status":"published","file":[{"checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_id":"7199","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"bartonetheridge.pdf","date_created":"2019-12-21T09:36:39Z","creator":"nbarton","file_size":2287682,"date_updated":"2020-07-14T12:47:09Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"research_data","id":"9842","status":"public"}]},"issue":"7","volume":122,"license":"https://creativecommons.org/licenses/by-nc/4.0/","ec_funded":1,"abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"oa_version":"Submitted Version","scopus_import":"1","month":"07","intvolume":" 122"},{"project":[{"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":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Evolution of cooperation in stochastic games","article_processing_charge":"No","external_id":{"isi":["000438240900054"]},"author":[{"last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Šimsa","full_name":"Šimsa, Štepán","first_name":"Štepán"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"publist_id":"7764","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0277-x.","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” Nature, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:10.1038/s41586-018-0277-x.","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. Nature. 2018;559(7713):246-249. doi:10.1038/s41586-018-0277-x","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., & Nowak, M. (2018). Evolution of cooperation in stochastic games. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0277-x","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” Nature, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249."},"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","date_created":"2018-12-11T11:44:56Z","doi":"10.1038/s41586-018-0277-x","date_published":"2018-07-04T00:00:00Z","page":"246 - 249","publication":"Nature","day":"04","year":"2018","has_accepted_license":"1","isi":1,"status":"public","type":"journal_article","_id":"157","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:02Z","ddc":["000"],"date_updated":"2023-09-11T13:43:22Z","intvolume":" 559","month":"07","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas.","lang":"eng"}],"ec_funded":1,"volume":559,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/engineering-cooperation/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"7713","language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-19T08:09:57Z","file_name":"2018_Nature_Hilbe.pdf","date_updated":"2020-07-14T12:45:02Z","file_size":2834442,"creator":"dernst","checksum":"011ab905cf9a410bc2b96f15174d654d","file_id":"7049","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published"},{"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"month":"03","intvolume":" 10","scopus_import":"1","file":[{"file_id":"4667","checksum":"458a7c2c2e79528567edfeb0f326cbe0","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","date_created":"2018-12-12T10:08:07Z","creator":"system","file_size":691602,"date_updated":"2020-07-14T12:46:16Z"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":10,"license":"https://creativecommons.org/licenses/by/4.0/","_id":"384","status":"public","pubrep_id":"999","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)"},"ddc":["576"],"date_updated":"2023-09-11T13:56:52Z","file_date_updated":"2020-07-14T12:46:16Z","department":[{"_id":"FyKo"}],"acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"day":"01","publication":"Genome Biology and Evolution","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-03-01T00:00:00Z","doi":"10.1093/gbe/evy049","date_created":"2018-12-11T11:46:10Z","page":"928 - 938","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938."},"title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","publist_id":"7445","author":[{"first_name":"Peter","last_name":"Hönigschmid","full_name":"Hönigschmid, Peter"},{"full_name":"Bykova, Nadya","last_name":"Bykova","first_name":"Nadya"},{"first_name":"René","full_name":"Schneider, René","last_name":"Schneider"},{"last_name":"Ivankov","full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"first_name":"Dmitrij","last_name":"Frishman","full_name":"Frishman, Dmitrij"}],"article_processing_charge":"No","external_id":{"isi":["000429483700022"]}},{"oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","publication":"Genetics","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:47:12Z","date_published":"2018-03-01T00:00:00Z","doi":"10.1534/genetics.117.300638","page":"1231-1245","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245."},"title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","article_processing_charge":"No","external_id":{"isi":["000426219600025"]},"publist_id":"7251","author":[{"first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer"},{"full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander"},{"first_name":"David","full_name":"Field, David","last_name":"Field"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow."}],"intvolume":" 208","month":"03","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","issue":"3","volume":208,"related_material":{"record":[{"id":"200","status":"public","relation":"dissertation_contains"}]},"_id":"563","status":"public","type":"journal_article","date_updated":"2023-09-11T13:42:38Z","department":[{"_id":"NiBa"},{"_id":"ChLa"}]},{"publication_status":"published","publication_identifier":{"issn":["0167-7055"]},"language":[{"iso":"eng"}],"file":[{"file_size":54309947,"date_updated":"2020-10-08T08:38:23Z","creator":"wojtan","file_name":"exnbflip.pdf","date_created":"2020-10-08T08:38:23Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"8edb90da8a72395eb5d970580e0925b6","file_id":"8627"}],"ec_funded":1,"volume":37,"issue":"2","abstract":[{"text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","alternative_title":["Eurographics"],"intvolume":" 37","month":"05","date_updated":"2023-09-11T14:00:26Z","ddc":["006"],"department":[{"_id":"ChWo"}],"file_date_updated":"2020-10-08T08:38:23Z","_id":"135","type":"journal_article","article_type":"original","status":"public","year":"2018","isi":1,"has_accepted_license":"1","publication":"Computer Graphics Forum","day":"22","page":"169 - 177","date_created":"2018-12-11T11:44:49Z","date_published":"2018-05-22T00:00:00Z","doi":"10.1111/cgf.13351","oa":1,"publisher":"Wiley","quality_controlled":"1","citation":{"ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351","apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13351","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"isi":["000434085600016"]},"author":[{"first_name":"Takahiro","last_name":"Sato","full_name":"Sato, Takahiro"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"last_name":"Ando","full_name":"Ando, Ryoichi","first_name":"Ryoichi"}],"title":"Extended narrow band FLIP for liquid simulations","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425"}]},{"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","article_processing_charge":"No","external_id":{"isi":["000437171700017"]},"author":[{"first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bodova","full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171"},{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","last_name":"Pickup"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748."},"project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:45:47Z","doi":"10.1534/genetics.118.300748","date_published":"2018-07-01T00:00:00Z","page":"861-883","publication":"Genetics","day":"01","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2023-09-11T13:57:43Z","status":"public","type":"journal_article","article_type":"original","_id":"316","ec_funded":1,"volume":209,"issue":"3","related_material":{"record":[{"relation":"research_data","status":"public","id":"9813"}],"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release","description":"News on IST Homepage"}]},"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 209","month":"07","main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants.","lang":"eng"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley, 2018. https://doi.org/10.1002/jez.b.22824.","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330, Wiley, 2018, pp. 254–64, doi:10.1002/jez.b.22824.","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","ieee":"M. Harrison et al., “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330. Wiley, pp. 254–264, 2018.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 2018;330:254-264. doi:10.1002/jez.b.22824","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley. https://doi.org/10.1002/jez.b.22824"},"title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","article_processing_charge":"No","external_id":{"pmid":["29998472"],"isi":["000443231000002"]},"publist_id":"7730","author":[{"last_name":"Harrison","full_name":"Harrison, Mark","first_name":"Mark"},{"last_name":"Arning","full_name":"Arning, Nicolas","first_name":"Nicolas"},{"last_name":"Kremer","full_name":"Kremer, Lucas","first_name":"Lucas"},{"last_name":"Ylla","full_name":"Ylla, Guillem","first_name":"Guillem"},{"last_name":"Belles","full_name":"Belles, Xavier","first_name":"Xavier"},{"last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich","first_name":"Erich"},{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"first_name":"Maria","full_name":"Puilachs, Maria","last_name":"Puilachs"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"first_name":"Coby","full_name":"Schal, Coby","last_name":"Schal"}],"publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","day":"11","year":"2018","isi":1,"date_created":"2018-12-11T11:45:06Z","date_published":"2018-07-11T00:00:00Z","doi":"10.1002/jez.b.22824","page":"254-264","oa":1,"publisher":"Wiley","quality_controlled":"1","date_updated":"2023-09-11T13:59:54Z","department":[{"_id":"BeVi"}],"_id":"190","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":330,"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"intvolume":" 330","month":"07","main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824"}],"scopus_import":"1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796","apa":"Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796","ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.","mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796."},"title":"Existence of positive solutions to stochastic thin-film equations","external_id":{"isi":["000426630900015"]},"article_processing_charge":"No","publist_id":"7425","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grün, Günther","last_name":"Grün","first_name":"Günther"}],"oa":1,"quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics ","publication":"SIAM Journal on Mathematical Analysis","day":"30","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:46:17Z","doi":"10.1137/16M1098796","date_published":"2018-01-30T00:00:00Z","page":"411 - 455","_id":"404","status":"public","type":"journal_article","article_type":"original","ddc":["510"],"date_updated":"2023-09-11T13:59:22Z","file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"JuFi"}],"oa_version":"Published Version","abstract":[{"text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n","lang":"eng"}],"intvolume":" 50","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-07T12:20:25Z","file_name":"2018_SIAM_Fischer.pdf","date_updated":"2020-07-14T12:46:22Z","file_size":557338,"creator":"dernst","file_id":"6992","checksum":"89a8eae7c52bb356c04f52b44bff4b5a","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","issue":"1","volume":50},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-11T13:57:42Z","citation":{"chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.","mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1"},"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"title":"Supplemental material for Bodova et al., 2018","author":[{"last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Priklopil","full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup"}],"article_processing_charge":"No","_id":"9813","status":"public","type":"research_data_reference","day":"30","year":"2018","doi":"10.25386/genetics.6148304.v1","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"316"}]},"date_published":"2018-04-30T00:00:00Z","date_created":"2021-08-06T13:04:32Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables."}],"month":"04","publisher":"Genetics Society of America","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}]},{"issue":"50","volume":115,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["00278424"]},"publication_status":"published","file":[{"file_name":"2018_PNAS_Kotlobay.pdf","date_created":"2019-02-05T15:21:40Z","file_size":1271988,"date_updated":"2020-07-14T12:47:11Z","creator":"dernst","file_id":"5926","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 115","abstract":[{"text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:47:11Z","date_updated":"2023-09-11T14:04:05Z","ddc":["580"],"type":"journal_article","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"},"status":"public","_id":"5780","page":"12728-12732","date_published":"2018-12-11T00:00:00Z","doi":"10.1073/pnas.1803615115","date_created":"2018-12-23T22:59:18Z","isi":1,"has_accepted_license":"1","year":"2018","day":"11","publication":"Proceedings of the National Academy of Sciences of the United States of America","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"author":[{"last_name":"Kotlobay","full_name":"Kotlobay, Alexey A.","first_name":"Alexey A."},{"last_name":"Sarkisyan","orcid":"0000-0002-5375-6341","full_name":"Sarkisyan, Karen","first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yuliana A.","last_name":"Mokrushina","full_name":"Mokrushina, Yuliana A."},{"first_name":"Marina","full_name":"Marcet-Houben, Marina","last_name":"Marcet-Houben"},{"full_name":"Serebrovskaya, Ekaterina O.","last_name":"Serebrovskaya","first_name":"Ekaterina O."},{"last_name":"Markina","full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M."},{"first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","orcid":"0000-0001-9139-5383","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Gorokhovatsky, Andrey Y.","last_name":"Gorokhovatsky","first_name":"Andrey Y."},{"first_name":"Andrey","last_name":"Vvedensky","full_name":"Vvedensky, Andrey"},{"last_name":"Purtov","full_name":"Purtov, Konstantin V.","first_name":"Konstantin V."},{"first_name":"Valentin N.","last_name":"Petushkov","full_name":"Petushkov, Valentin N."},{"first_name":"Natalja S.","last_name":"Rodionova","full_name":"Rodionova, Natalja S."},{"first_name":"Tatiana V.","full_name":"Chepurnyh, Tatiana V.","last_name":"Chepurnyh"},{"first_name":"Liliia","last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia"},{"last_name":"Guglya","full_name":"Guglya, Elena B.","first_name":"Elena B."},{"last_name":"Ziganshin","full_name":"Ziganshin, Rustam","first_name":"Rustam"},{"last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S."},{"full_name":"Kaskova, Zinaida M.","last_name":"Kaskova","first_name":"Zinaida M."},{"last_name":"Shender","full_name":"Shender, Victoria","first_name":"Victoria"},{"first_name":"Maxim","last_name":"Abakumov","full_name":"Abakumov, Maxim"},{"first_name":"Tatiana O.","full_name":"Abakumova, Tatiana O.","last_name":"Abakumova"},{"first_name":"Inna S.","full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya"},{"last_name":"Eroshkin","full_name":"Eroshkin, Fedor M.","first_name":"Fedor M."},{"full_name":"Zaraisky, Andrey G.","last_name":"Zaraisky","first_name":"Andrey G."},{"first_name":"Alexander S.","last_name":"Mishin","full_name":"Mishin, Alexander S."},{"first_name":"Sergey V.","last_name":"Dolgov","full_name":"Dolgov, Sergey V."},{"full_name":"Mitiouchkina, Tatiana Y.","last_name":"Mitiouchkina","first_name":"Tatiana Y."},{"first_name":"Eugene P.","last_name":"Kopantzev","full_name":"Kopantzev, Eugene P."},{"first_name":"Hans E.","last_name":"Waldenmaier","full_name":"Waldenmaier, Hans E."},{"full_name":"Oliveira, Anderson G.","last_name":"Oliveira","first_name":"Anderson G."},{"first_name":"Yuichi","last_name":"Oba","full_name":"Oba, Yuichi"},{"last_name":"Barsova","full_name":"Barsova, Ekaterina","first_name":"Ekaterina"},{"last_name":"Bogdanova","full_name":"Bogdanova, Ekaterina A.","first_name":"Ekaterina A."},{"first_name":"Toni","full_name":"Gabaldón, Toni","last_name":"Gabaldón"},{"full_name":"Stevani, Cassius V.","last_name":"Stevani","first_name":"Cassius V."},{"first_name":"Sergey","full_name":"Lukyanov, Sergey","last_name":"Lukyanov"},{"full_name":"Smirnov, Ivan V.","last_name":"Smirnov","first_name":"Ivan V."},{"full_name":"Gitelson, Josef I.","last_name":"Gitelson","first_name":"Josef I."},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yampolsky, Ilia V.","last_name":"Yampolsky","first_name":"Ilia V."}],"external_id":{"isi":["000452866000068"]},"article_processing_charge":"No","title":"Genetically encodable bioluminescent system from fungi","citation":{"chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115.","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","ieee":"A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"isi":1,"has_accepted_license":"1","year":"2018","day":"03","publication":"PNAS","page":" 3716 - 3721","doi":"10.1073/pnas.1721760115","date_published":"2018-04-03T00:00:00Z","date_created":"2018-12-11T11:46:25Z","acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"citation":{"mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, PNAS 115 (2018) 3716–3721.","ieee":"Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” PNAS, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721760115","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 2018;115(14):3716-3721. doi:10.1073/pnas.1721760115","chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115.","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","last_name":"Salanenka","full_name":"Salanenka, Yuliya"},{"orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge"},{"first_name":"Christian","full_name":"Löfke, Christian","last_name":"Löfke"},{"full_name":"Tabata, Kaori","last_name":"Tabata","first_name":"Kaori","id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0"},{"first_name":"Satoshi","full_name":"Naramoto, Satoshi","last_name":"Naramoto"},{"first_name":"Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","last_name":"Glanc","full_name":"Glanc, Matous","orcid":"0000-0003-0619-7783"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"publist_id":"7395","external_id":{"isi":["000429012500073"]},"article_processing_charge":"No","title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","file":[{"file_size":1924101,"date_updated":"2020-07-14T12:46:26Z","creator":"dernst","file_name":"2018_PNAS_Salanenka.pdf","date_created":"2018-12-17T12:30:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","file_id":"5700"}],"language":[{"iso":"eng"}],"issue":"14","volume":115,"ec_funded":1,"abstract":[{"lang":"eng","text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses."}],"oa_version":"Published Version","scopus_import":"1","month":"04","intvolume":" 115","date_updated":"2023-09-11T14:06:34Z","ddc":["580"],"file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"JiFr"}],"_id":"428","type":"journal_article","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"},"status":"public"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"62","department":[{"_id":"MaJö"}],"file_date_updated":"2020-07-14T12:47:24Z","ddc":["570"],"date_updated":"2023-09-11T14:02:55Z","intvolume":" 8","month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.","lang":"eng"}],"related_material":{"link":[{"url":"http://doi.org/10.1038/s41598-018-36220-7","relation":"erratum"}]},"volume":8,"issue":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:24Z","file_size":4141645,"date_created":"2018-12-17T12:22:24Z","file_name":"2018_ScientificReports_Shahbazi.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5699","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2"}],"publication_status":"published","article_number":"14247","title":"Flexible learning-free segmentation and reconstruction of neural volumes","external_id":{"isi":["000445336600015"]},"article_processing_charge":"No","publist_id":"7992","author":[{"first_name":"Ali","full_name":"Shabazi, Ali","last_name":"Shabazi"},{"first_name":"Jeffery","full_name":"Kinnison, Jeffery","last_name":"Kinnison"},{"first_name":"Rafael","last_name":"Vescovi","full_name":"Vescovi, Rafael"},{"full_name":"Du, Ming","last_name":"Du","first_name":"Ming"},{"first_name":"Robert","full_name":"Hill, Robert","last_name":"Hill"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330"},{"full_name":"Takeno, Marc","last_name":"Takeno","first_name":"Marc"},{"full_name":"Zeng, Hongkui","last_name":"Zeng","first_name":"Hongkui"},{"last_name":"Da Costa","full_name":"Da Costa, Nuno","first_name":"Nuno"},{"last_name":"Grutzendler","full_name":"Grutzendler, Jaime","first_name":"Jaime"},{"full_name":"Kasthuri, Narayanan","last_name":"Kasthuri","first_name":"Narayanan"},{"last_name":"Scheirer","full_name":"Scheirer, Walter","first_name":"Walter"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-32628-3.","ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.","mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:10.1038/s41598-018-32628-3.","short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3","apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3"},"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.","date_created":"2018-12-11T11:44:25Z","date_published":"2018-09-24T00:00:00Z","doi":"10.1038/s41598-018-32628-3","publication":"Scientific Reports","day":"24","year":"2018","isi":1,"has_accepted_license":"1"}]