[{"type":"journal_article","abstract":[{"lang":"eng","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."}],"issue":"23","status":"public","title":"Distributed and dynamic intracellular organization of extracellular information","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"281","oa_version":"Preprint","scopus_import":"1","day":"05","article_processing_charge":"No","article_type":"original","page":"6088 - 6093","publication":"PNAS","citation":{"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","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.","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","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.","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 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.","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."},"date_published":"2018-06-05T00:00:00Z","publist_id":"7618","publication_status":"published","publisher":"National Academy of Sciences","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.).","year":"2018","pmid":1,"date_updated":"2023-09-11T12:58:24Z","date_created":"2018-12-11T11:45:35Z","volume":115,"author":[{"last_name":"Granados","first_name":"Alejandro","full_name":"Granados, Alejandro"},{"full_name":"Pietsch, Julian","last_name":"Pietsch","first_name":"Julian"},{"full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","last_name":"Cepeda Humerez"},{"last_name":"Farquhar","first_name":"Isebail","full_name":"Farquhar, Isebail"},{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"last_name":"Swain","first_name":"Peter","full_name":"Swain, Peter"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6473"}]},"month":"06","isi":1,"quality_controlled":"1","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"external_id":{"pmid":["29784812"],"isi":["000434114900071"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1716659115"},{"publist_id":"7184","article_number":"jcs207696","author":[{"full_name":"Yamamoto, Wataru","last_name":"Yamamoto","first_name":"Wataru"},{"first_name":"Suguru","last_name":"Wada","full_name":"Wada, Suguru"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"full_name":"Aoshima, Kaito","last_name":"Aoshima","first_name":"Kaito"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"volume":131,"date_created":"2018-12-11T11:47:32Z","date_updated":"2023-09-11T12:57:13Z","pmid":1,"year":"2018","department":[{"_id":"DaSi"}],"publisher":"Company of Biologists","publication_status":"published","month":"01","doi":"10.1242/jcs.207696","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062","open_access":"1"}],"external_id":{"isi":["000424786900012"],"pmid":["29192062"]},"quality_controlled":"1","isi":1,"issue":"1","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"}],"type":"journal_article","oa_version":"Published Version","_id":"620","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 131","status":"public","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2018-01-04T00:00:00Z","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.","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.","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","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.","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","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."},"publication":"Journal of Cell Science"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"11","citation":{"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.","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 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.","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.","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","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.","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"},"publication":"Proceedings of the 21st International Conference on Hybrid Systems","page":"177 - 186","date_published":"2018-04-11T00:00:00Z","type":"conference","alternative_title":["HSCC Proceedings"],"abstract":[{"lang":"eng","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."}],"_id":"182","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Efficient parametric identification for STL","ddc":["000"],"oa_version":"Submitted Version","file":[{"checksum":"81eabc96430e84336ea88310ac0a1ad0","date_updated":"2020-07-14T12:45:17Z","date_created":"2020-05-14T12:18:29Z","relation":"main_file","file_id":"7833","file_size":5900421,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_HSCC_Bakhirkin.pdf"}],"publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"month":"04","external_id":{"isi":["000474781600020"]},"oa":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"isi":1,"quality_controlled":"1","doi":"10.1145/3178126.3178132","conference":{"name":"HSCC: Hybrid Systems: Computation and Control","start_date":"2018-04-11","location":"Porto, Portugal","end_date":"2018-04-13"},"language":[{"iso":"eng"}],"publist_id":"7739","file_date_updated":"2020-07-14T12:45:17Z","year":"2018","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","author":[{"full_name":"Bakhirkin, Alexey","first_name":"Alexey","last_name":"Bakhirkin"},{"last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"}],"date_created":"2018-12-11T11:45:04Z","date_updated":"2023-09-11T13:30:51Z"},{"ec_funded":1,"publist_id":"7780","year":"2018","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IEEE","author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Kučera, Antonín","first_name":"Antonín","last_name":"Kučera"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr"},{"last_name":"Velan","first_name":"Dominik","full_name":"Velan, Dominik"},{"full_name":"Zuleger, Florian","last_name":"Zuleger","first_name":"Florian"}],"date_updated":"2023-09-11T13:23:42Z","date_created":"2018-12-11T11:44:51Z","volume":"F138033","month":"07","publication_identifier":{"isbn":["978-1-4503-5583-4"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10985"}],"oa":1,"external_id":{"isi":["000545262800020"]},"quality_controlled":"1","isi":1,"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"conference":{"start_date":"2018-07-09","location":"Oxford, United Kingdom","end_date":"2018-07-12","name":"LICS: Logic in Computer Science"},"doi":"10.1145/3209108.3209191","language":[{"iso":"eng"}],"type":"conference","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"abstract":[{"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.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"143","status":"public","title":"Efficient algorithms for asymptotic bounds on termination time in VASS","oa_version":"Preprint","scopus_import":"1","day":"09","article_processing_charge":"No","citation":{"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.","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.","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194.","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.","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","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.","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"},"page":"185 - 194","date_published":"2018-07-09T00:00:00Z"},{"scopus_import":"1","article_processing_charge":"No","day":"28","page":"3693-3701","citation":{"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.","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","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.","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","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.","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."},"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","date_published":"2018-06-28T00:00:00Z","type":"conference","abstract":[{"lang":"eng","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."}],"title":"Efficient optimization for rank-based loss functions","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"273","oa_version":"Preprint","publication_identifier":{"isbn":["9781538664209"]},"month":"06","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1604.08269"],"isi":["000457843603087"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08269"}],"language":[{"iso":"eng"}],"doi":"10.1109/cvpr.2018.00389","conference":{"name":"CVPR: Conference on Computer Vision and Pattern Recognition","end_date":"2018-06-22","start_date":"2018-06-18","location":"Salt Lake City, UT, USA"},"ec_funded":1,"department":[{"_id":"VlKo"}],"publisher":"IEEE","publication_status":"published","year":"2018","date_created":"2018-12-11T11:45:33Z","date_updated":"2023-09-11T13:24:43Z","author":[{"full_name":"Mohapatra, Pritish","first_name":"Pritish","last_name":"Mohapatra"},{"last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"full_name":"Jawahar, C V","first_name":"C V","last_name":"Jawahar"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"last_name":"Kumar","first_name":"M Pawan","full_name":"Kumar, M Pawan"}]},{"month":"10","main_file_link":[{"url":"https://arxiv.org/abs/1805.01038","open_access":"1"}],"external_id":{"arxiv":["1805.01038"],"isi":["000447307500007"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevLett.121.167601","language":[{"iso":"eng"}],"article_number":"167601","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.","year":"2018","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","author":[{"full_name":"Zibrov, Alexander","last_name":"Zibrov","first_name":"Alexander"},{"first_name":"Rao","last_name":"Peng","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","orcid":"0000-0003-1250-0021","full_name":"Peng, Rao"},{"full_name":"Kometter, Carlos","last_name":"Kometter","first_name":"Carlos"},{"full_name":"Li, Jia","first_name":"Jia","last_name":"Li"},{"first_name":"Cory","last_name":"Dean","full_name":"Dean, Cory"},{"full_name":"Taniguchi, Takashi","first_name":"Takashi","last_name":"Taniguchi"},{"first_name":"Kenji","last_name":"Watanabe","full_name":"Watanabe, Kenji"},{"full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827"},{"full_name":"Young, Andrea","last_name":"Young","first_name":"Andrea"}],"date_created":"2018-12-11T11:45:38Z","date_updated":"2023-09-11T13:39:50Z","volume":121,"scopus_import":"1","day":"19","article_processing_charge":"No","publication":"Physical Review Letters","citation":{"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","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.","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.","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","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.","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (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."},"article_type":"original","date_published":"2018-10-19T00:00:00Z","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"16","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"289","status":"public","title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","intvolume":" 121","oa_version":"Preprint"},{"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"287","intvolume":" 23","title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","status":"public","issue":"8","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."}],"type":"journal_article","date_published":"2018-03-01T00:00:00Z","citation":{"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.","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.","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.","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.","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","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.","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"},"publication":"Frontiers in Bioscience - Landmark","page":"1391 - 1406","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"full_name":"Salari, Vahid","first_name":"Vahid","last_name":"Salari"},{"full_name":"Barzanjeh, Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh"},{"last_name":"Cifra","first_name":"Michal","full_name":"Cifra, Michal"},{"full_name":"Simon, Christoph","first_name":"Christoph","last_name":"Simon"},{"last_name":"Scholkmann","first_name":"Felix","full_name":"Scholkmann, Felix"},{"last_name":"Alirezaei","first_name":"Zahra","full_name":"Alirezaei, Zahra"},{"last_name":"Tuszynski","first_name":"Jack","full_name":"Tuszynski, Jack"}],"volume":23,"date_created":"2018-12-11T11:45:37Z","date_updated":"2023-09-11T13:38:14Z","pmid":1,"year":"2018","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.","publisher":"Frontiers in Bioscience","department":[{"_id":"JoFi"}],"publication_status":"published","ec_funded":1,"doi":"10.2741/4651","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["29293441"],"isi":["000439042800001"]},"main_file_link":[{"url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm","open_access":"1"}],"project":[{"grant_number":"707438","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM"}],"isi":1,"quality_controlled":"1","month":"03"},{"language":[{"iso":"eng"}],"doi":"10.1145/3078632","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000425685900006"],"arxiv":["1402.0815"]},"main_file_link":[{"url":"https://arxiv.org/abs/1402.0815","open_access":"1"}],"month":"01","volume":65,"date_created":"2018-12-11T11:46:24Z","date_updated":"2023-09-11T13:38:49Z","related_material":{"record":[{"id":"2157","relation":"earlier_version","status":"public"}]},"author":[{"last_name":"Matoušek","first_name":"Jiří","full_name":"Matoušek, Jiří"},{"full_name":"Sedgwick, Eric","first_name":"Eric","last_name":"Sedgwick"},{"full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","last_name":"Tancer","first_name":"Martin"},{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"department":[{"_id":"UlWa"}],"publisher":"ACM","publication_status":"published","year":"2018","ec_funded":1,"publist_id":"7398","article_number":"5","date_published":"2018-01-01T00:00:00Z","article_type":"original","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.","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.","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","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.","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.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018)."},"publication":"Journal of the ACM","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 65","status":"public","title":"Embeddability in the 3-Sphere is decidable","_id":"425","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","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."}],"type":"journal_article"},{"date_published":"2018-07-01T00:00:00Z","publication":"Theoretical Population Biology","citation":{"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","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.","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 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","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.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 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."},"article_type":"original","page":"110-127","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"creator":"nbarton","file_size":2287682,"content_type":"application/pdf","access_level":"open_access","file_name":"bartonetheridge.pdf","checksum":"0b96f6db47e3e91b5e7d103b847c239d","date_created":"2019-12-21T09:36:39Z","date_updated":"2020-07-14T12:47:09Z","file_id":"7199","relation":"main_file"}],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"564","status":"public","title":"Establishment in a new habitat by polygenic adaptation","ddc":["519","576"],"intvolume":" 122","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."}],"issue":"7","type":"journal_article","doi":"10.1016/j.tpb.2017.11.007","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000440392900014"]},"quality_controlled":"1","isi":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"month":"07","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"related_material":{"record":[{"id":"9842","relation":"research_data","status":"public"}]},"date_created":"2018-12-11T11:47:12Z","date_updated":"2023-09-11T13:41:22Z","volume":122,"year":"2018","publication_status":"published","publisher":"Academic Press","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:09Z","ec_funded":1,"publist_id":"7250","license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"month":"07","doi":"10.1038/s41586-018-0277-x","language":[{"iso":"eng"}],"external_id":{"isi":["000438240900054"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"file_date_updated":"2020-07-14T12:45:02Z","ec_funded":1,"publist_id":"7764","author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian"},{"first_name":"Štepán","last_name":"Šimsa","full_name":"Šimsa, Štepán"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/engineering-cooperation/"}]},"date_updated":"2023-09-11T13:43:22Z","date_created":"2018-12-11T11:44:56Z","volume":559,"year":"2018","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"day":"04","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-07-04T00:00:00Z","publication":"Nature","citation":{"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.","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","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249.","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","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.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 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."},"page":"246 - 249","abstract":[{"lang":"eng","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."}],"issue":"7713","type":"journal_article","oa_version":"Submitted Version","file":[{"file_name":"2018_Nature_Hilbe.pdf","access_level":"open_access","file_size":2834442,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7049","date_created":"2019-11-19T08:09:57Z","date_updated":"2020-07-14T12:45:02Z","checksum":"011ab905cf9a410bc2b96f15174d654d"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"157","title":"Evolution of cooperation in stochastic games","status":"public","ddc":["000"],"intvolume":" 559"},{"status":"public","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","ddc":["576"],"intvolume":" 10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"384","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-12T10:08:07Z","checksum":"458a7c2c2e79528567edfeb0f326cbe0","relation":"main_file","file_id":"4667","content_type":"application/pdf","file_size":691602,"creator":"system","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","access_level":"open_access"}],"pubrep_id":"999","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3","page":"928 - 938","publication":"Genome Biology and Evolution","citation":{"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.","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","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.","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","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.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 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."},"date_published":"2018-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"FyKo"}],"year":"2018","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","date_updated":"2023-09-11T13:56:52Z","date_created":"2018-12-11T11:46:10Z","volume":10,"author":[{"last_name":"Hönigschmid","first_name":"Peter","full_name":"Hönigschmid, Peter"},{"full_name":"Bykova, Nadya","first_name":"Nadya","last_name":"Bykova"},{"full_name":"Schneider, René","last_name":"Schneider","first_name":"René"},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Frishman","first_name":"Dmitrij","full_name":"Frishman, Dmitrij"}],"license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:46:16Z","publist_id":"7445","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429483700022"]},"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evy049","month":"03"},{"publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"year":"2018","date_updated":"2023-09-11T13:42:38Z","date_created":"2018-12-11T11:47:12Z","volume":208,"author":[{"orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","first_name":"Harald","full_name":"Ringbauer, Harald"},{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Kolesnikov"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"id":"200","relation":"dissertation_contains","status":"public"}]},"publist_id":"7251","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000426219600025"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/205484v1","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300638","month":"03","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","status":"public","intvolume":" 208","_id":"563","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"3","page":"1231-1245","publication":"Genetics","citation":{"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","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.","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","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.","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.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","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."},"date_published":"2018-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"type":"journal_article","alternative_title":["Eurographics"],"abstract":[{"lang":"eng","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."}],"issue":"2","_id":"135","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["006"],"title":"Extended narrow band FLIP for liquid simulations","status":"public","intvolume":" 37","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"exnbflip.pdf","content_type":"application/pdf","file_size":54309947,"creator":"wojtan","relation":"main_file","file_id":"8627","checksum":"8edb90da8a72395eb5d970580e0925b6","success":1,"date_created":"2020-10-08T08:38:23Z","date_updated":"2020-10-08T08:38:23Z"}],"scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No","publication":"Computer Graphics Forum","citation":{"short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","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.","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","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.","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","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."},"article_type":"original","page":"169 - 177","date_published":"2018-05-22T00:00:00Z","file_date_updated":"2020-10-08T08:38:23Z","ec_funded":1,"year":"2018","publication_status":"published","publisher":"Wiley","department":[{"_id":"ChWo"}],"author":[{"last_name":"Sato","first_name":"Takahiro","full_name":"Sato, Takahiro"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"full_name":"Igarashi, Takeo","last_name":"Igarashi","first_name":"Takeo"},{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"}],"date_updated":"2023-09-11T14:00:26Z","date_created":"2018-12-11T11:44:49Z","volume":37,"month":"05","publication_identifier":{"issn":["0167-7055"]},"external_id":{"isi":["000434085600016"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"doi":"10.1111/cgf.13351","language":[{"iso":"eng"}]},{"date_updated":"2023-09-11T13:57:43Z","date_created":"2018-12-11T11:45:47Z","volume":209,"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarina","last_name":"Bodova","full_name":"Bodova, Katarina"},{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/"}],"record":[{"status":"public","relation":"research_data","id":"9813"}]},"publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"year":"2018","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.300748","quality_controlled":"1","isi":1,"project":[{"grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425","name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7"},{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"external_id":{"isi":["000437171700017"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/node/80098.abstract"}],"oa":1,"month":"07","oa_version":"Preprint","status":"public","title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","intvolume":" 209","_id":"316","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","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."}],"issue":"3","type":"journal_article","date_published":"2018-07-01T00:00:00Z","article_type":"original","page":"861-883","publication":"Genetics","citation":{"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","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.","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","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.","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."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"date_updated":"2023-09-11T13:59:54Z","date_created":"2018-12-11T11:45:06Z","volume":330,"author":[{"last_name":"Harrison","first_name":"Mark","full_name":"Harrison, Mark"},{"full_name":"Arning, Nicolas","last_name":"Arning","first_name":"Nicolas"},{"first_name":"Lucas","last_name":"Kremer","full_name":"Kremer, Lucas"},{"first_name":"Guillem","last_name":"Ylla","full_name":"Ylla, Guillem"},{"last_name":"Belles","first_name":"Xavier","full_name":"Belles, Xavier"},{"full_name":"Bornberg Bauer, Erich","first_name":"Erich","last_name":"Bornberg Bauer"},{"last_name":"Huylmans","first_name":"Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K"},{"last_name":"Jongepier","first_name":"Evelien","full_name":"Jongepier, Evelien"},{"full_name":"Puilachs, Maria","last_name":"Puilachs","first_name":"Maria"},{"full_name":"Richards, Stephen","first_name":"Stephen","last_name":"Richards"},{"last_name":"Schal","first_name":"Coby","full_name":"Schal, Coby"}],"publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Wiley","year":"2018","pmid":1,"publist_id":"7730","language":[{"iso":"eng"}],"doi":"10.1002/jez.b.22824","quality_controlled":"1","isi":1,"external_id":{"pmid":["29998472"],"isi":["000443231000002"]},"main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824"}],"oa":1,"month":"07","oa_version":"Submitted Version","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","status":"public","intvolume":" 330","_id":"190","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."}],"type":"journal_article","date_published":"2018-07-11T00:00:00Z","article_type":"original","page":"254-264","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","citation":{"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.","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.","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.","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","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.","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","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."},"day":"11","article_processing_charge":"No","scopus_import":"1"},{"date_published":"2018-01-30T00:00:00Z","publication":"SIAM Journal on Mathematical Analysis","citation":{"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.","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 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.","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","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","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."},"article_type":"original","page":"411 - 455","day":"30","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"file_id":"6992","relation":"main_file","date_created":"2019-11-07T12:20:25Z","date_updated":"2020-07-14T12:46:22Z","checksum":"89a8eae7c52bb356c04f52b44bff4b5a","file_name":"2018_SIAM_Fischer.pdf","access_level":"open_access","creator":"dernst","file_size":557338,"content_type":"application/pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"404","status":"public","ddc":["510"],"title":"Existence of positive solutions to stochastic thin-film equations","intvolume":" 50","abstract":[{"lang":"eng","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"}],"issue":"1","type":"journal_article","doi":"10.1137/16M1098796","language":[{"iso":"eng"}],"external_id":{"isi":["000426630900015"]},"oa":1,"isi":1,"quality_controlled":"1","month":"01","author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grün","first_name":"Günther","full_name":"Grün, Günther"}],"date_created":"2018-12-11T11:46:17Z","date_updated":"2023-09-11T13:59:22Z","volume":50,"year":"2018","publication_status":"published","department":[{"_id":"JuFi"}],"publisher":"Society for Industrial and Applied Mathematics ","file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7425"},{"month":"04","day":"30","article_processing_charge":"No","date_published":"2018-04-30T00:00:00Z","doi":"10.25386/genetics.6148304.v1","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.","mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","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.","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","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.","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"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"oa":1,"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."}],"type":"research_data_reference","date_created":"2021-08-06T13:04:32Z","date_updated":"2023-09-11T13:57:42Z","oa_version":"Published Version","author":[{"full_name":"Bod'ová, Katarína","first_name":"Katarína","last_name":"Bod'ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171"},{"last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","full_name":"Priklopil, Tadeas"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"}],"related_material":{"record":[{"id":"316","status":"public","relation":"used_in_publication"}]},"status":"public","title":"Supplemental material for Bodova et al., 2018","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"year":"2018","_id":"9813","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1271988,"access_level":"open_access","file_name":"2018_PNAS_Kotlobay.pdf","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","date_updated":"2020-07-14T12:47:11Z","date_created":"2019-02-05T15:21:40Z","file_id":"5926","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5780","ddc":["580"],"title":"Genetically encodable bioluminescent system from fungi","status":"public","intvolume":" 115","abstract":[{"lang":"eng","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."}],"issue":"50","type":"journal_article","date_published":"2018-12-11T00:00:00Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"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","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.","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.","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","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.","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.","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."},"page":"12728-12732","day":"11","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Kotlobay, Alexey A.","last_name":"Kotlobay","first_name":"Alexey A."},{"full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","last_name":"Sarkisyan","first_name":"Karen"},{"full_name":"Mokrushina, Yuliana A.","last_name":"Mokrushina","first_name":"Yuliana A."},{"full_name":"Marcet-Houben, Marina","first_name":"Marina","last_name":"Marcet-Houben"},{"full_name":"Serebrovskaya, Ekaterina O.","last_name":"Serebrovskaya","first_name":"Ekaterina O."},{"full_name":"Markina, Nadezhda M.","last_name":"Markina","first_name":"Nadezhda M."},{"last_name":"Gonzalez Somermeyer","first_name":"Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa"},{"full_name":"Gorokhovatsky, Andrey Y.","first_name":"Andrey Y.","last_name":"Gorokhovatsky"},{"first_name":"Andrey","last_name":"Vvedensky","full_name":"Vvedensky, Andrey"},{"full_name":"Purtov, Konstantin V.","first_name":"Konstantin V.","last_name":"Purtov"},{"last_name":"Petushkov","first_name":"Valentin N.","full_name":"Petushkov, Valentin N."},{"first_name":"Natalja S.","last_name":"Rodionova","full_name":"Rodionova, Natalja S."},{"last_name":"Chepurnyh","first_name":"Tatiana V.","full_name":"Chepurnyh, Tatiana V."},{"first_name":"Liliia","last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia"},{"last_name":"Guglya","first_name":"Elena B.","full_name":"Guglya, Elena B."},{"full_name":"Ziganshin, Rustam","first_name":"Rustam","last_name":"Ziganshin"},{"last_name":"Tsarkova","first_name":"Aleksandra S.","full_name":"Tsarkova, Aleksandra S."},{"full_name":"Kaskova, Zinaida M.","last_name":"Kaskova","first_name":"Zinaida M."},{"full_name":"Shender, Victoria","first_name":"Victoria","last_name":"Shender"},{"full_name":"Abakumov, Maxim","first_name":"Maxim","last_name":"Abakumov"},{"first_name":"Tatiana O.","last_name":"Abakumova","full_name":"Abakumova, Tatiana O."},{"last_name":"Povolotskaya","first_name":"Inna S.","full_name":"Povolotskaya, Inna S."},{"full_name":"Eroshkin, Fedor M.","last_name":"Eroshkin","first_name":"Fedor M."},{"last_name":"Zaraisky","first_name":"Andrey G.","full_name":"Zaraisky, Andrey G."},{"last_name":"Mishin","first_name":"Alexander S.","full_name":"Mishin, Alexander S."},{"full_name":"Dolgov, Sergey V.","first_name":"Sergey V.","last_name":"Dolgov"},{"last_name":"Mitiouchkina","first_name":"Tatiana Y.","full_name":"Mitiouchkina, Tatiana Y."},{"full_name":"Kopantzev, Eugene P.","last_name":"Kopantzev","first_name":"Eugene P."},{"full_name":"Waldenmaier, Hans E.","last_name":"Waldenmaier","first_name":"Hans E."},{"full_name":"Oliveira, Anderson G.","first_name":"Anderson G.","last_name":"Oliveira"},{"full_name":"Oba, Yuichi","first_name":"Yuichi","last_name":"Oba"},{"full_name":"Barsova, Ekaterina","last_name":"Barsova","first_name":"Ekaterina"},{"full_name":"Bogdanova, Ekaterina A.","first_name":"Ekaterina A.","last_name":"Bogdanova"},{"first_name":"Toni","last_name":"Gabaldón","full_name":"Gabaldón, Toni"},{"full_name":"Stevani, Cassius V.","last_name":"Stevani","first_name":"Cassius V."},{"full_name":"Lukyanov, Sergey","last_name":"Lukyanov","first_name":"Sergey"},{"full_name":"Smirnov, Ivan V.","last_name":"Smirnov","first_name":"Ivan V."},{"last_name":"Gitelson","first_name":"Josef I.","full_name":"Gitelson, Josef I."},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."}],"date_created":"2018-12-23T22:59:18Z","date_updated":"2023-09-11T14:04:05Z","volume":115,"year":"2018","publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"National Academy of Sciences","file_date_updated":"2020-07-14T12:47:11Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"10.1073/pnas.1803615115","language":[{"iso":"eng"}],"external_id":{"isi":["000452866000068"]},"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"isi":1,"quality_controlled":"1","month":"12","publication_identifier":{"issn":["00278424"]}},{"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."}],"issue":"14","type":"journal_article","file":[{"file_id":"5700","relation":"main_file","date_created":"2018-12-17T12:30:14Z","date_updated":"2020-07-14T12:46:26Z","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","file_name":"2018_PNAS_Salanenka.pdf","access_level":"open_access","creator":"dernst","file_size":1924101,"content_type":"application/pdf"}],"oa_version":"Published Version","title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","status":"public","ddc":["580"],"intvolume":" 115","_id":"428","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"03","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-04-03T00:00:00Z","page":" 3716 - 3721","publication":"PNAS","citation":{"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","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.","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","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.","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."},"file_date_updated":"2020-07-14T12:46:26Z","publist_id":"7395","ec_funded":1,"date_updated":"2023-09-11T14:06:34Z","date_created":"2018-12-11T11:46:25Z","volume":115,"author":[{"id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","first_name":"Yuliya","last_name":"Salanenka","full_name":"Salanenka, Yuliya"},{"first_name":"Inge","last_name":"Verstraeten","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7241-2328","full_name":"Verstraeten, Inge"},{"first_name":"Christian","last_name":"Löfke","full_name":"Löfke, Christian"},{"id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0","last_name":"Tabata","first_name":"Kaori","full_name":"Tabata, Kaori"},{"full_name":"Naramoto, Satoshi","first_name":"Satoshi","last_name":"Naramoto"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","orcid":"0000-0003-0619-7783","first_name":"Matous","last_name":"Glanc","full_name":"Glanc, Matous"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","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","year":"2018","month":"04","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1721760115","quality_controlled":"1","isi":1,"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000429012500073"]}},{"month":"09","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000445336600015"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-018-32628-3","article_number":"14247","file_date_updated":"2020-07-14T12:47:24Z","publist_id":"7992","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MaJö"}],"year":"2018","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_updated":"2023-09-11T14:02:55Z","volume":8,"author":[{"full_name":"Shabazi, Ali","last_name":"Shabazi","first_name":"Ali"},{"first_name":"Jeffery","last_name":"Kinnison","full_name":"Kinnison, Jeffery"},{"last_name":"Vescovi","first_name":"Rafael","full_name":"Vescovi, Rafael"},{"last_name":"Du","first_name":"Ming","full_name":"Du, Ming"},{"full_name":"Hill, Robert","first_name":"Robert","last_name":"Hill"},{"full_name":"Jösch, Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch"},{"full_name":"Takeno, Marc","first_name":"Marc","last_name":"Takeno"},{"full_name":"Zeng, Hongkui","last_name":"Zeng","first_name":"Hongkui"},{"first_name":"Nuno","last_name":"Da Costa","full_name":"Da Costa, Nuno"},{"first_name":"Jaime","last_name":"Grutzendler","full_name":"Grutzendler, Jaime"},{"first_name":"Narayanan","last_name":"Kasthuri","full_name":"Kasthuri, Narayanan"},{"full_name":"Scheirer, Walter","first_name":"Walter","last_name":"Scheirer"}],"related_material":{"link":[{"relation":"erratum","url":"http://doi.org/10.1038/s41598-018-36220-7"}]},"scopus_import":"1","day":"24","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"Scientific Reports","citation":{"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).","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.","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","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.","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","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"},"date_published":"2018-09-24T00:00:00Z","type":"journal_article","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"}],"issue":"1","title":"Flexible learning-free segmentation and reconstruction of neural volumes","ddc":["570"],"status":"public","intvolume":" 8","_id":"62","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"checksum":"1a14ae0666b82fbaa04bef110e3f6bf2","date_created":"2018-12-17T12:22:24Z","date_updated":"2020-07-14T12:47:24Z","file_id":"5699","relation":"main_file","creator":"dernst","file_size":4141645,"content_type":"application/pdf","access_level":"open_access","file_name":"2018_ScientificReports_Shahbazi.pdf"}]},{"file_date_updated":"2020-07-14T12:46:27Z","ec_funded":1,"publist_id":"7386","acknowledgement":"This work was supported by grants of the European Research Council (ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific support units at IST Austria for excellent technical support.\r\nWe thank the scientific support units at IST Austria for excellent technical support. ","year":"2018","publication_status":"published","department":[{"_id":"MiSi"},{"_id":"Bio"}],"publisher":"Wiley-Blackwell","author":[{"full_name":"Leithner, Alexander F","first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X"},{"full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz"},{"last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"De Vries, Ingrid"},{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"},{"full_name":"Haecker, Hans","first_name":"Hans","last_name":"Haecker"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"date_updated":"2023-09-11T14:01:18Z","date_created":"2018-12-11T11:46:28Z","volume":48,"month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000434963700016"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"doi":"10.1002/eji.201747358","acknowledged_ssus":[{"_id":"SSU"}],"language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity.","lang":"eng"}],"issue":"6","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"437","status":"public","ddc":["570"],"title":"Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration","intvolume":" 48","pubrep_id":"1067","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":590106,"access_level":"open_access","file_name":"IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf","checksum":"9d5b74cd016505aeb9a4c2d33bbedaeb","date_created":"2018-12-12T10:13:56Z","date_updated":"2020-07-14T12:46:27Z","file_id":"5044","relation":"main_file"}],"scopus_import":"1","day":"13","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"European Journal of Immunology","citation":{"apa":"Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., & Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201747358","ieee":"A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M. K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration,” European Journal of Immunology, vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.","ista":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077.","ama":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077. doi:10.1002/eji.201747358","chicago":"Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild, Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.","short":"A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K. Sixt, European Journal of Immunology 48 (2018) 1074–1077.","mla":"Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358."},"page":"1074 - 1077","date_published":"2018-02-13T00:00:00Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"617","intvolume":" 31","status":"public","title":"Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions."}],"citation":{"ama":"Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 2018;31(1):159-171. doi:10.1111/jeb.13211","ista":"Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 31(1), 159–171.","ieee":"M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211","mla":"Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31, no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211.","short":"M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018) 159–171.","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211."},"publication":"Journal of Evolutionary Biology","page":"159 - 171","article_type":"original","date_published":"2018-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","pmid":1,"year":"2018","acknowledgement":"We would like to thank Susann Wicke for performing the genome-wide SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG) priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR 872/1-1). ","department":[{"_id":"SyCr"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Kutzer, Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8696-6978","first_name":"Megan","last_name":"Kutzer"},{"full_name":"Kurtz, Joachim","last_name":"Kurtz","first_name":"Joachim"},{"full_name":"Armitage, Sophie","first_name":"Sophie","last_name":"Armitage"}],"volume":31,"date_created":"2018-12-11T11:47:31Z","date_updated":"2023-09-11T14:06:04Z","publist_id":"7187","external_id":{"isi":["000419307000014"],"pmid":["29150962"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13211"}],"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1111/jeb.13211","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"month":"01"},{"file_date_updated":"2020-07-14T12:47:13Z","article_number":"100","author":[{"last_name":"Tarlungeanu","first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","full_name":"Tarlungeanu, Dora-Clara"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"volume":50,"date_updated":"2023-09-11T14:04:41Z","date_created":"2019-01-27T22:59:11Z","pmid":1,"year":"2018","publisher":"Springer Nature","department":[{"_id":"GaNo"}],"publication_status":"published","publication_identifier":{"issn":["2092-6413"]},"month":"08","doi":"10.1038/s12276-018-0129-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["30089840"],"isi":["000441266700006"]},"quality_controlled":"1","isi":1,"issue":"8","abstract":[{"text":"Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered,\r\nthe etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype-\r\nbased diagnosis of individual patients has become a requisite. In this review we look at recent advancements in\r\ngenomic analysis and their translation into clinical practice.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"5893","relation":"main_file","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-01-28T15:18:02Z","checksum":"4498301c8c53097c9a1a8ef990936eb5","file_name":"2018_EMM_Tarlungeanu.pdf","access_level":"open_access","creator":"dernst","file_size":1237482,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5888","intvolume":" 50","title":"Genomics in neurodevelopmental disorders: an avenue to personalized medicine","status":"public","ddc":["570"],"article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","date_published":"2018-08-07T00:00:00Z","citation":{"ista":"Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8), 100.","ieee":"D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders: an avenue to personalized medicine,” Experimental & Molecular Medicine, vol. 50, no. 8. Springer Nature, 2018.","apa":"Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7","ama":"Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 2018;50(8). doi:10.1038/s12276-018-0129-7","chicago":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7.","mla":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.","short":"D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50 (2018)."},"publication":"Experimental & Molecular Medicine"},{"month":"05","doi":"10.1007/s11005-018-1091-y","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1712.06218"],"isi":["000446491500008"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"},{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:45:55Z","publist_id":"7586","ec_funded":1,"author":[{"first_name":"Douglas","last_name":"Lundholm","full_name":"Lundholm, Douglas"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"date_created":"2018-12-11T11:45:40Z","date_updated":"2023-09-11T14:01:57Z","volume":108,"acknowledgement":"Financial support from the Swedish Research Council, grant no. 2013-4734 (D. L.), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 694227, R. S.), and by the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R. S.), is gratefully acknowledged.","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"day":"11","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-05-11T00:00:00Z","publication":"Letters in Mathematical Physics","citation":{"chicago":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” Letters in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s11005-018-1091-y.","mla":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” Letters in Mathematical Physics, vol. 108, no. 11, Springer, 2018, pp. 2523–41, doi:10.1007/s11005-018-1091-y.","short":"D. Lundholm, R. Seiringer, Letters in Mathematical Physics 108 (2018) 2523–2541.","ista":"Lundholm D, Seiringer R. 2018. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 108(11), 2523–2541.","ieee":"D. Lundholm and R. Seiringer, “Fermionic behavior of ideal anyons,” Letters in Mathematical Physics, vol. 108, no. 11. Springer, pp. 2523–2541, 2018.","apa":"Lundholm, D., & Seiringer, R. (2018). Fermionic behavior of ideal anyons. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-018-1091-y","ama":"Lundholm D, Seiringer R. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 2018;108(11):2523-2541. doi:10.1007/s11005-018-1091-y"},"page":"2523-2541","abstract":[{"text":"We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional anyon gas. Our bounds are extensive in the particle number, as for fermions, and linear in the statistics parameter (Formula presented.). The lower bounds extend to Lieb–Thirring inequalities for all anyons except bosons.","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2018_LettMathPhys_Lundholm.pdf","access_level":"open_access","file_size":551996,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5698","date_created":"2018-12-17T12:14:17Z","date_updated":"2020-07-14T12:45:55Z","checksum":"8beb9632fa41bbd19452f55f31286a31"}],"_id":"295","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["510"],"title":"Fermionic behavior of ideal anyons","intvolume":" 108"},{"oa_version":"Submitted Version","_id":"555","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 50","title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","status":"public","abstract":[{"text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.","lang":"eng"}],"type":"journal_article","date_published":"2018-06-01T00:00:00Z","citation":{"mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural Biology, vol. 50, Elsevier, 2018, pp. 65–74, doi:10.1016/j.sbi.2017.12.002.","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” Current Opinion in Structural Biology. Elsevier, 2018. https://doi.org/10.1016/j.sbi.2017.12.002.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 2018;50:65-74. doi:10.1016/j.sbi.2017.12.002","ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74.","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” Current Opinion in Structural Biology, vol. 50. Elsevier, pp. 65–74, 2018.","apa":"Richter, R., Baranova, N. S., Day, A., & Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2017.12.002"},"publication":"Current Opinion in Structural Biology","page":"65 - 74","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","author":[{"last_name":"Richter","first_name":"Ralf","full_name":"Richter, Ralf"},{"full_name":"Baranova, Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","first_name":"Natalia","last_name":"Baranova"},{"first_name":"Anthony","last_name":"Day","full_name":"Day, Anthony"},{"first_name":"Jessica","last_name":"Kwok","full_name":"Kwok, Jessica"}],"volume":50,"date_created":"2018-12-11T11:47:09Z","date_updated":"2023-09-11T14:07:03Z","acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","year":"2018","publisher":"Elsevier","department":[{"_id":"MaLo"}],"publication_status":"published","publist_id":"7259","doi":"10.1016/j.sbi.2017.12.002","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://eprints.whiterose.ac.uk/125524/"}],"oa":1,"external_id":{"isi":["000443661300011"]},"isi":1,"quality_controlled":"1","month":"06"},{"date_published":"2018-02-05T00:00:00Z","publication":"Nature Ecology and Evolution","citation":{"chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0459-1.","mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Nature Ecology and Evolution, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:10.1038/s41559-017-0459-1.","short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566.","ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.","apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0459-1","ieee":"M. Harrison et al., “Hemimetabolous genomes reveal molecular basis of termite eusociality,” Nature Ecology and Evolution, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2018;2(3):557-566. doi:10.1038/s41559-017-0459-1"},"page":"557-566","day":"05","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","pubrep_id":"969","oa_version":"Published Version","file":[{"file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf","access_level":"open_access","content_type":"application/pdf","file_size":3730583,"creator":"system","relation":"main_file","file_id":"4731","date_created":"2018-12-12T10:09:08Z","date_updated":"2020-07-14T12:46:30Z","checksum":"874953136ac125e65f37971d3cabc5b7"}],"_id":"448","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576"],"status":"public","title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","intvolume":" 2","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"issue":"3","type":"journal_article","doi":"10.1038/s41559-017-0459-1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000426559600026"]},"isi":1,"quality_controlled":"1","month":"02","author":[{"full_name":"Harrison, Mark","first_name":"Mark","last_name":"Harrison"},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"first_name":"Hugh","last_name":"Robertson","full_name":"Robertson, Hugh"},{"last_name":"Arning","first_name":"Nicolas","full_name":"Arning, Nicolas"},{"first_name":"Tristan","last_name":"Bitard Feildel","full_name":"Bitard Feildel, Tristan"},{"last_name":"Chao","first_name":"Hsu","full_name":"Chao, Hsu"},{"first_name":"Christopher","last_name":"Childers","full_name":"Childers, Christopher"},{"full_name":"Dinh, Huyen","first_name":"Huyen","last_name":"Dinh"},{"last_name":"Doddapaneni","first_name":"Harshavardhan","full_name":"Doddapaneni, Harshavardhan"},{"last_name":"Dugan","first_name":"Shannon","full_name":"Dugan, Shannon"},{"last_name":"Gowin","first_name":"Johannes","full_name":"Gowin, Johannes"},{"first_name":"Carolin","last_name":"Greiner","full_name":"Greiner, Carolin"},{"last_name":"Han","first_name":"Yi","full_name":"Han, Yi"},{"full_name":"Hu, Haofu","first_name":"Haofu","last_name":"Hu"},{"full_name":"Hughes, Daniel","last_name":"Hughes","first_name":"Daniel"},{"full_name":"Huylmans, Ann K","first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961"},{"full_name":"Kemena, Karsten","first_name":"Karsten","last_name":"Kemena"},{"full_name":"Kremer, Lukas","first_name":"Lukas","last_name":"Kremer"},{"full_name":"Lee, Sandra","last_name":"Lee","first_name":"Sandra"},{"full_name":"López Ezquerra, Alberto","last_name":"López Ezquerra","first_name":"Alberto"},{"first_name":"Ludovic","last_name":"Mallet","full_name":"Mallet, Ludovic"},{"full_name":"Monroy Kuhn, Jose","first_name":"Jose","last_name":"Monroy Kuhn"},{"full_name":"Moser, Annabell","last_name":"Moser","first_name":"Annabell"},{"full_name":"Murali, Shwetha","last_name":"Murali","first_name":"Shwetha"},{"first_name":"Donna","last_name":"Muzny","full_name":"Muzny, Donna"},{"full_name":"Otani, Saria","first_name":"Saria","last_name":"Otani"},{"last_name":"Piulachs","first_name":"Maria","full_name":"Piulachs, Maria"},{"last_name":"Poelchau","first_name":"Monica","full_name":"Poelchau, Monica"},{"first_name":"Jiaxin","last_name":"Qu","full_name":"Qu, Jiaxin"},{"first_name":"Florentine","last_name":"Schaub","full_name":"Schaub, Florentine"},{"full_name":"Wada Katsumata, Ayako","first_name":"Ayako","last_name":"Wada Katsumata"},{"full_name":"Worley, Kim","first_name":"Kim","last_name":"Worley"},{"first_name":"Qiaolin","last_name":"Xie","full_name":"Xie, Qiaolin"},{"last_name":"Ylla","first_name":"Guillem","full_name":"Ylla, Guillem"},{"full_name":"Poulsen, Michael","last_name":"Poulsen","first_name":"Michael"},{"first_name":"Richard","last_name":"Gibbs","full_name":"Gibbs, Richard"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"},{"full_name":"Richards, Stephen","first_name":"Stephen","last_name":"Richards"},{"last_name":"Belles","first_name":"Xavier","full_name":"Belles, Xavier"},{"last_name":"Korb","first_name":"Judith","full_name":"Korb, Judith"},{"last_name":"Bornberg Bauer","first_name":"Erich","full_name":"Bornberg Bauer, Erich"}],"related_material":{"record":[{"id":"9841","relation":"research_data","status":"public"}]},"date_created":"2018-12-11T11:46:32Z","date_updated":"2023-09-11T14:10:57Z","volume":2,"year":"2018","acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","publication_status":"published","department":[{"_id":"BeVi"}],"publisher":"Springer Nature","file_date_updated":"2020-07-14T12:46:30Z","publist_id":"7375"},{"file_date_updated":"2020-07-14T12:47:54Z","ec_funded":1,"publist_id":"6957","author":[{"last_name":"Oliveto","first_name":"Pietro","full_name":"Oliveto, Pietro"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"last_name":"Pérez Heredia","first_name":"Jorge","full_name":"Pérez Heredia, Jorge"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora"}],"date_updated":"2023-09-11T14:11:35Z","date_created":"2018-12-11T11:48:09Z","volume":80,"year":"2018","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Springer","month":"05","doi":"10.1007/s00453-017-0369-2","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000428239300010"]},"quality_controlled":"1","isi":1,"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys."}],"issue":"5","type":"journal_article","pubrep_id":"1014","file":[{"date_updated":"2020-07-14T12:47:54Z","date_created":"2018-12-12T10:08:14Z","checksum":"7d92f5d7be81e387edeec4f06442791c","relation":"main_file","file_id":"4674","file_size":691245,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"723","status":"public","title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","ddc":["576"],"intvolume":" 80","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-01T00:00:00Z","publication":"Algorithmica","citation":{"ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633."},"page":"1604 - 1633"},{"publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"IEEE","year":"2018","date_updated":"2023-09-11T14:07:54Z","date_created":"2018-12-11T11:45:48Z","volume":40,"author":[{"full_name":"Darrell, Trevor","first_name":"Trevor","last_name":"Darrell"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"last_name":"Sebe","first_name":"Nico","full_name":"Sebe, Nico"},{"last_name":"Wu","first_name":"Ying","full_name":"Wu, Ying"},{"full_name":"Yan, Yan","first_name":"Yan","last_name":"Yan"}],"file_date_updated":"2020-07-14T12:46:03Z","publist_id":"7544","isi":1,"quality_controlled":"1","external_id":{"isi":["000428901200001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/TPAMI.2018.2804998","month":"05","status":"public","title":"Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis","ddc":["000"],"intvolume":" 40","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"321","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"7835","checksum":"b19c75da06faf3291a3ca47dfa50ef63","date_updated":"2020-07-14T12:46:03Z","date_created":"2020-05-14T12:50:48Z","access_level":"open_access","file_name":"2018_IEEE_Darrell.pdf","file_size":141724,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","abstract":[{"text":"The twelve papers in this special section focus on learning systems with shared information for computer vision and multimedia communication analysis. In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes containing a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with shared information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different levels of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems.","lang":"eng"}],"issue":"5","article_type":"original","page":"1029 - 1031","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","citation":{"ama":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(5):1029-1031. doi:10.1109/TPAMI.2018.2804998","apa":"Darrell, T., Lampert, C., Sebe, N., Wu, Y., & Yan, Y. (2018). Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2018.2804998","ieee":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, and Y. Yan, “Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 5. IEEE, pp. 1029–1031, 2018.","ista":"Darrell T, Lampert C, Sebe N, Wu Y, Yan Y. 2018. Guest editors’ introduction to the special section on learning with Shared information for computer vision and multimedia analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(5), 1029–1031.","short":"T. Darrell, C. Lampert, N. Sebe, Y. Wu, Y. Yan, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1029–1031.","mla":"Darrell, Trevor, et al. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 5, IEEE, 2018, pp. 1029–31, doi:10.1109/TPAMI.2018.2804998.","chicago":"Darrell, Trevor, Christoph Lampert, Nico Sebe, Ying Wu, and Yan Yan. “Guest Editors’ Introduction to the Special Section on Learning with Shared Information for Computer Vision and Multimedia Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2018.2804998."},"date_published":"2018-05-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"related_material":{"record":[{"id":"448","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Harrison, Mark C.","last_name":"Harrison","first_name":"Mark C."},{"first_name":"Evelien","last_name":"Jongepier","full_name":"Jongepier, Evelien"},{"last_name":"Robertson","first_name":"Hugh M.","full_name":"Robertson, Hugh M."},{"last_name":"Arning","first_name":"Nicolas","full_name":"Arning, Nicolas"},{"first_name":"Tristan","last_name":"Bitard-Feildel","full_name":"Bitard-Feildel, Tristan"},{"first_name":"Hsu","last_name":"Chao","full_name":"Chao, Hsu"},{"first_name":"Christopher P.","last_name":"Childers","full_name":"Childers, Christopher P."},{"last_name":"Dinh","first_name":"Huyen","full_name":"Dinh, Huyen"},{"first_name":"Harshavardhan","last_name":"Doddapaneni","full_name":"Doddapaneni, Harshavardhan"},{"full_name":"Dugan, Shannon","first_name":"Shannon","last_name":"Dugan"},{"last_name":"Gowin","first_name":"Johannes","full_name":"Gowin, Johannes"},{"first_name":"Carolin","last_name":"Greiner","full_name":"Greiner, Carolin"},{"full_name":"Han, Yi","first_name":"Yi","last_name":"Han"},{"last_name":"Hu","first_name":"Haofu","full_name":"Hu, Haofu"},{"full_name":"Hughes, Daniel S. T.","last_name":"Hughes","first_name":"Daniel S. T."},{"first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"full_name":"Kemena, Carsten","last_name":"Kemena","first_name":"Carsten"},{"full_name":"Kremer, Lukas P. M.","first_name":"Lukas P. M.","last_name":"Kremer"},{"last_name":"Lee","first_name":"Sandra L.","full_name":"Lee, Sandra L."},{"full_name":"Lopez-Ezquerra, Alberto","last_name":"Lopez-Ezquerra","first_name":"Alberto"},{"first_name":"Ludovic","last_name":"Mallet","full_name":"Mallet, Ludovic"},{"full_name":"Monroy-Kuhn, Jose M.","last_name":"Monroy-Kuhn","first_name":"Jose M."},{"full_name":"Moser, Annabell","first_name":"Annabell","last_name":"Moser"},{"first_name":"Shwetha C.","last_name":"Murali","full_name":"Murali, Shwetha C."},{"last_name":"Muzny","first_name":"Donna M.","full_name":"Muzny, Donna M."},{"full_name":"Otani, Saria","last_name":"Otani","first_name":"Saria"},{"first_name":"Maria-Dolors","last_name":"Piulachs","full_name":"Piulachs, Maria-Dolors"},{"full_name":"Poelchau, Monica","first_name":"Monica","last_name":"Poelchau"},{"first_name":"Jiaxin","last_name":"Qu","full_name":"Qu, Jiaxin"},{"full_name":"Schaub, Florentine","last_name":"Schaub","first_name":"Florentine"},{"full_name":"Wada-Katsumata, Ayako","last_name":"Wada-Katsumata","first_name":"Ayako"},{"last_name":"Worley","first_name":"Kim C.","full_name":"Worley, Kim C."},{"full_name":"Xie, Qiaolin","last_name":"Xie","first_name":"Qiaolin"},{"last_name":"Ylla","first_name":"Guillem","full_name":"Ylla, Guillem"},{"full_name":"Poulsen, Michael","first_name":"Michael","last_name":"Poulsen"},{"first_name":"Richard A.","last_name":"Gibbs","full_name":"Gibbs, Richard A."},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"first_name":"Xavier","last_name":"Belles","full_name":"Belles, Xavier"},{"full_name":"Korb, Judith","last_name":"Korb","first_name":"Judith"},{"first_name":"Erich","last_name":"Bornberg-Bauer","full_name":"Bornberg-Bauer, Erich"}],"oa_version":"Published Version","date_created":"2021-08-09T13:13:48Z","date_updated":"2023-09-11T14:10:56Z","_id":"9841","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","publisher":"Dryad","department":[{"_id":"BeVi"}],"title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","status":"public","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"type":"research_data_reference","doi":"10.5061/dryad.51d4r","date_published":"2018-12-12T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51d4r"}],"oa":1,"citation":{"ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:10.5061/dryad.51d4r","ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, 10.5061/dryad.51d4r.","ieee":"M. C. Harrison et al., “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","apa":"Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. Dryad. https://doi.org/10.5061/dryad.51d4r","mla":"Harrison, Mark C., et al. Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality. Dryad, 2018, doi:10.5061/dryad.51d4r.","short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018).","chicago":"Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. https://doi.org/10.5061/dryad.51d4r."},"article_processing_charge":"No","day":"12","month":"12"},{"citation":{"ieee":"M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.","apa":"Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489","ista":"Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP, vol. 53, 14–27.","ama":"Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489","chicago":"Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.","short":"M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.","mla":"Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489."},"page":"14 - 27","date_published":"2018-02-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"397","title":"Harnessing epoch-based reclamation for efficient range queries","status":"public","intvolume":" 53","oa_version":"None","type":"conference","alternative_title":["PPoPP"],"abstract":[{"lang":"eng","text":"Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. "}],"issue":"1","external_id":{"isi":["000446161100002"]},"quality_controlled":"1","isi":1,"conference":{"location":"Vienna, Austria","start_date":"2018-02-24","end_date":"2018-02-28","name":"PPoPP: Principles and Practice of Parallel Programming"},"doi":"10.1145/3178487.3178489","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"isbn":["978-1-4503-4982-6"]},"year":"2018","publication_status":"published","department":[{"_id":"DaAl"}],"publisher":"ACM","author":[{"last_name":"Arbel Raviv","first_name":"Maya","full_name":"Arbel Raviv, Maya"},{"last_name":"Brown","first_name":"Trevor A","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Trevor A"}],"date_updated":"2023-09-11T14:10:25Z","date_created":"2018-12-11T11:46:14Z","volume":53,"publist_id":"7430"},{"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2018.09.066","quality_controlled":"1","isi":1,"external_id":{"isi":["000448219500005"]},"tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"10","volume":25,"date_updated":"2023-09-11T14:13:32Z","date_created":"2018-12-11T11:44:16Z","author":[{"full_name":"Chen, Ting","last_name":"Chen","first_name":"Ting"},{"full_name":"Kula, Bartosz","last_name":"Kula","first_name":"Bartosz"},{"full_name":"Nagy, Balint","first_name":"Balint","last_name":"Nagy","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","orcid":"0000-0002-4002-4686"},{"last_name":"Barzan","first_name":"Ruxandra","full_name":"Barzan, Ruxandra"},{"last_name":"Gall","first_name":"Andrea","full_name":"Gall, Andrea"},{"last_name":"Ehrlich","first_name":"Ingrid","full_name":"Ehrlich, Ingrid"},{"first_name":"Maria","last_name":"Kukley","full_name":"Kukley, Maria"}],"department":[{"_id":"SaSi"}],"publisher":"Elsevier","publication_status":"published","year":"2018","acknowledgement":"This work was supported by Deutsche Forschungsgemeinschaft (DFG) grant KU2569/1-1 (to M.K.); DFG project EXC307Centre for Integrative Neuroscience (CIN), including grant Pool Project 2011-12 (jointly to M.K. and I.E.); and the Charitable Hertie Foundation (to I.E.). CIN is an Excellence Cluster funded by the DFG within the framework of the Excellence Initiative for 2008–2018. M.K. is supported by the Tistou & Charlotte Kerstan Foundation.","publist_id":"8023","file_date_updated":"2020-07-14T12:46:03Z","date_published":"2018-10-23T00:00:00Z","page":"852 - 861.e7","citation":{"ista":"Chen T, Kula B, Nagy B, Barzan R, Gall A, Ehrlich I, Kukley M. 2018. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 25(4), 852–861.e7.","apa":"Chen, T., Kula, B., Nagy, B., Barzan, R., Gall, A., Ehrlich, I., & Kukley, M. (2018). In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2018.09.066","ieee":"T. Chen et al., “In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2,” Cell Reports, vol. 25, no. 4. Elsevier, p. 852–861.e7, 2018.","ama":"Chen T, Kula B, Nagy B, et al. In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2. Cell Reports. 2018;25(4):852-861.e7. doi:10.1016/j.celrep.2018.09.066","chicago":"Chen, Ting, Bartosz Kula, Balint Nagy, Ruxandra Barzan, Andrea Gall, Ingrid Ehrlich, and Maria Kukley. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports. Elsevier, 2018. https://doi.org/10.1016/j.celrep.2018.09.066.","mla":"Chen, Ting, et al. “In Vivo Regulation of Oligodendrocyte Processor Cell Proliferation and Differentiation by the AMPA-Receptor Subunit GluA2.” Cell Reports, vol. 25, no. 4, Elsevier, 2018, p. 852–861.e7, doi:10.1016/j.celrep.2018.09.066.","short":"T. Chen, B. Kula, B. Nagy, R. Barzan, A. Gall, I. Ehrlich, M. Kukley, Cell Reports 25 (2018) 852–861.e7."},"publication":"Cell Reports","article_processing_charge":"No","has_accepted_license":"1","day":"23","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2018_CellReports_Chen.pdf","content_type":"application/pdf","file_size":4461997,"creator":"dernst","relation":"main_file","file_id":"5703","checksum":"d9f74277fd57176e04732707d575cf08","date_updated":"2020-07-14T12:46:03Z","date_created":"2018-12-17T12:42:57Z"}],"intvolume":" 25","ddc":["570"],"title":"In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"32","issue":"4","abstract":[{"text":"The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in vivo during the peak of myelination by targeting the GluA2 subunit. Expression of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered proliferation of OPCs and reduced their differentiation into oligodendrocytes. Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit (C-tail), a modification designed to affect the interaction between GluA2 and AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs, decreased the differentiation of OPCs without affecting their proliferation. These findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs, as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in the mouse corpus callosum, are important for balancing the response of OPCs to proliferation and differentiation cues. In the brain, oligodendrocyte precursor cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC synapses alters proliferation and differentiation of OPCs. This expands the traditional view of synaptic transmission by suggesting neurons also use synapses to modulate behavior of glia.","lang":"eng"}],"type":"journal_article"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5672","intvolume":" 215","status":"public","title":"IgM's exit route","ddc":["570"],"oa_version":"Published Version","file":[{"checksum":"687beea1d64c213f4cb9e3c29ec11a14","date_created":"2019-02-06T08:49:52Z","date_updated":"2020-07-14T12:47:09Z","file_id":"5931","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1216437,"access_level":"open_access","file_name":"2018_JournalExperMed_Reversat.pdf"}],"type":"journal_article","issue":"12","abstract":[{"text":"The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocyte-packed environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific micro-anatomical route via lymph node conduits.","lang":"eng"}],"citation":{"chicago":"Reversat, Anne, and Michael K Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20181934.","short":"A. Reversat, M.K. Sixt, Journal of Experimental Medicine 215 (2018) 2959–2961.","mla":"Reversat, Anne, and Michael K. Sixt. “IgM’s Exit Route.” Journal of Experimental Medicine, vol. 215, no. 12, Rockefeller University Press, 2018, pp. 2959–61, doi:10.1084/jem.20181934.","ieee":"A. Reversat and M. K. Sixt, “IgM’s exit route,” Journal of Experimental Medicine, vol. 215, no. 12. Rockefeller University Press, pp. 2959–2961, 2018.","apa":"Reversat, A., & Sixt, M. K. (2018). IgM’s exit route. Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20181934","ista":"Reversat A, Sixt MK. 2018. IgM’s exit route. Journal of Experimental Medicine. 215(12), 2959–2961.","ama":"Reversat A, Sixt MK. IgM’s exit route. Journal of Experimental Medicine. 2018;215(12):2959-2961. doi:10.1084/jem.20181934"},"publication":"Journal of Experimental Medicine","page":"2959-2961","date_published":"2018-11-20T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"20","year":"2018","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"}],"publication_status":"published","author":[{"orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne","full_name":"Reversat, Anne"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"volume":215,"date_created":"2018-12-16T22:59:18Z","date_updated":"2023-09-11T14:12:06Z","file_date_updated":"2020-07-14T12:47:09Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"external_id":{"isi":["000451920600002"]},"isi":1,"quality_controlled":"1","doi":"10.1084/jem.20181934","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00221007"]},"month":"11"},{"article_processing_charge":"No","month":"05","day":"01","scopus_import":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.wneu.2018.02.096","date_published":"2018-05-01T00:00:00Z","page":"e568-e578","quality_controlled":"1","isi":1,"citation":{"chicago":"Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery. Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096.","short":"P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.","mla":"Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.","ieee":"P. Dodier et al., “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.","apa":"Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096","ista":"Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578.","ama":"Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096"},"external_id":{"isi":["000432942700070"]},"publication":"World Neurosurgery","publist_id":"7431","abstract":[{"text":"Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices.","lang":"eng"}],"type":"journal_article","volume":13,"oa_version":"None","date_updated":"2023-09-11T14:12:33Z","date_created":"2018-12-11T11:46:15Z","author":[{"last_name":"Dodier","first_name":"Philippe","full_name":"Dodier, Philippe"},{"full_name":"Frischer, Josa","last_name":"Frischer","first_name":"Josa"},{"full_name":"Wang, Wei","last_name":"Wang","first_name":"Wei"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265","first_name":"Thomas","last_name":"Auzinger","full_name":"Auzinger, Thomas"},{"last_name":"Mallouhi","first_name":"Ammar","full_name":"Mallouhi, Ammar"},{"last_name":"Serles","first_name":"Wolfgang","full_name":"Serles, Wolfgang"},{"full_name":"Gruber, Andreas","last_name":"Gruber","first_name":"Andreas"},{"first_name":"Engelbert","last_name":"Knosp","full_name":"Knosp, Engelbert"},{"first_name":"Gerhard","last_name":"Bavinzski","full_name":"Bavinzski, Gerhard"}],"department":[{"_id":"BeBi"}],"publisher":"Elsevier","intvolume":" 13","title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","status":"public","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"398","year":"2018"},{"scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society. American Mathematical Society, 2018. https://doi.org/10.1090/tran/7292.","short":"A. Akopyan, A. Bobenko, Transactions of the American Mathematical Society 370 (2018) 2825–2854.","mla":"Akopyan, Arseniy, and Alexander Bobenko. “Incircular Nets and Confocal Conics.” Transactions of the American Mathematical Society, vol. 370, no. 4, American Mathematical Society, 2018, pp. 2825–54, doi:10.1090/tran/7292.","ieee":"A. Akopyan and A. Bobenko, “Incircular nets and confocal conics,” Transactions of the American Mathematical Society, vol. 370, no. 4. American Mathematical Society, pp. 2825–2854, 2018.","apa":"Akopyan, A., & Bobenko, A. (2018). Incircular nets and confocal conics. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7292","ista":"Akopyan A, Bobenko A. 2018. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 370(4), 2825–2854.","ama":"Akopyan A, Bobenko A. Incircular nets and confocal conics. Transactions of the American Mathematical Society. 2018;370(4):2825-2854. doi:10.1090/tran/7292"},"publication":"Transactions of the American Mathematical Society","page":"2825 - 2854","date_published":"2018-04-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"We consider congruences of straight lines in a plane with the combinatorics of the square grid, with all elementary quadrilaterals possessing an incircle. It is shown that all the vertices of such nets (we call them incircular or IC-nets) lie on confocal conics. Our main new results are on checkerboard IC-nets in the plane. These are congruences of straight lines in the plane with the combinatorics of the square grid, combinatorially colored as a checkerboard, such that all black coordinate quadrilaterals possess inscribed circles. We show how this larger class of IC-nets appears quite naturally in Laguerre geometry of oriented planes and spheres and leads to new remarkable incidence theorems. Most of our results are valid in hyperbolic and spherical geometries as well. We present also generalizations in spaces of higher dimension, called checkerboard IS-nets. The construction of these nets is based on a new 9 inspheres incidence theorem."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"458","intvolume":" 370","status":"public","title":"Incircular nets and confocal conics","oa_version":"Preprint","month":"04","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.04637"}],"external_id":{"isi":["000423197800019"]},"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","isi":1,"doi":"10.1090/tran/7292","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"7363","acknowledgement":"DFG Collaborative Research Center TRR 109 “Discretization in Geometry and Dynamics”; People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) REA grant agreement n◦[291734]","year":"2018","department":[{"_id":"HeEd"}],"publisher":"American Mathematical Society","publication_status":"published","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"first_name":"Alexander","last_name":"Bobenko","full_name":"Bobenko, Alexander"}],"volume":370,"date_updated":"2023-09-11T14:19:12Z","date_created":"2018-12-11T11:46:35Z"},{"author":[{"full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87","last_name":"Metzler","first_name":"Sina"},{"first_name":"Alexandra","last_name":"Schrempf","full_name":"Schrempf, Alexandra"},{"first_name":"Jürgen","last_name":"Heinze","full_name":"Heinze, Jürgen"}],"volume":107,"date_updated":"2023-09-12T07:43:26Z","date_created":"2018-12-11T11:46:25Z","year":"2018","acknowledgement":"Research with C. obscurior from Brazil was permitted by Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no. 20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1 ), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice concerning graphs. One referee made helpful comments on the manuscript.\r\n","publisher":"Elsevier","department":[{"_id":"SyCr"}],"publication_status":"published","publist_id":"7397","doi":"10.1016/j.jinsphys.2017.12.003","language":[{"iso":"eng"}],"external_id":{"isi":["000434751100034"]},"isi":1,"quality_controlled":"1","month":"05","oa_version":"None","_id":"426","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 107","title":"Individual- and ejaculate-specific sperm traits in ant males","status":"public","abstract":[{"lang":"eng","text":"Sperm cells are the most morphologically diverse cells across animal taxa. Within species, sperm and ejaculate traits have been suggested to vary with the male's competitive environment, e.g., level of sperm competition, female mating status and quality, and also with male age, body mass, physiological condition, and resource availability. Most previous studies have based their conclusions on the analysis of only one or a few ejaculates per male without investigating differences among the ejaculates of the same individual. This masks potential ejaculate-specific traits. Here, we provide data on the length, quantity, and viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior. Males of this ant species are relatively long-lived and can mate with large numbers of female sexuals throughout their lives. We analyzed all ejaculates across the individuals' lifespan and manipulated the availability of mating partners. Our study shows that both the number and size of sperm cells transferred during copulations differ among individuals and also among ejaculates of the same male. Sperm quality does not decrease with male age, but the variation in sperm number between ejaculates indicates that males need considerable time to replenish their sperm supplies. Producing many ejaculates in a short time appears to be traded-off against male longevity rather than sperm quality."}],"type":"journal_article","date_published":"2018-05-01T00:00:00Z","citation":{"ista":"Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.","apa":"Metzler, S., Schrempf, A., & Heinze, J. (2018). Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. Elsevier. https://doi.org/10.1016/j.jinsphys.2017.12.003","ieee":"S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific sperm traits in ant males,” Journal of Insect Physiology, vol. 107. Elsevier, pp. 284–290, 2018.","ama":"Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 2018;107:284-290. doi:10.1016/j.jinsphys.2017.12.003","chicago":"Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology. Elsevier, 2018. https://doi.org/10.1016/j.jinsphys.2017.12.003.","mla":"Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” Journal of Insect Physiology, vol. 107, Elsevier, 2018, pp. 284–90, doi:10.1016/j.jinsphys.2017.12.003.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290."},"publication":"Journal of Insect Physiology","page":"284-290","article_processing_charge":"No","day":"01","scopus_import":"1"},{"publication_identifier":{"isbn":["9783030046118"],"issn":["03029743"]},"month":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.04372"}],"oa":1,"external_id":{"arxiv":["1804.04372"],"isi":["000865933000002"]},"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF","_id":"264B3912-B435-11E9-9278-68D0E5697425","grant_number":"M02369"}],"quality_controlled":"1","isi":1,"doi":"10.1007/978-3-030-04612-5_2","conference":{"name":"14th International Conference on Web and Internet Economics, WINE","location":"Oxford, UK","start_date":"2018-12-15","end_date":"2018-12-17"},"language":[{"iso":"eng"}],"year":"2018","publisher":"Springer","department":[{"_id":"ToHe"}],"author":[{"full_name":"Avni, Guy","first_name":"Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus"}],"volume":11316,"date_created":"2018-12-30T22:59:14Z","date_updated":"2023-09-12T07:44:01Z","scopus_import":"1","article_processing_charge":"No","day":"21","citation":{"chicago":"Avni, Guy, Thomas A Henzinger, and Rasmus Ibsen-Jensen. “Infinite-Duration Poorman-Bidding Games,” 11316:21–36. Springer, 2018. https://doi.org/10.1007/978-3-030-04612-5_2.","mla":"Avni, Guy, et al. Infinite-Duration Poorman-Bidding Games. Vol. 11316, Springer, 2018, pp. 21–36, doi:10.1007/978-3-030-04612-5_2.","short":"G. Avni, T.A. Henzinger, R. Ibsen-Jensen, in:, Springer, 2018, pp. 21–36.","ista":"Avni G, Henzinger TA, Ibsen-Jensen R. 2018. Infinite-duration poorman-bidding games. 14th International Conference on Web and Internet Economics, WINE, LNCS, vol. 11316, 21–36.","ieee":"G. Avni, T. A. Henzinger, and R. Ibsen-Jensen, “Infinite-duration poorman-bidding games,” presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK, 2018, vol. 11316, pp. 21–36.","apa":"Avni, G., Henzinger, T. A., & Ibsen-Jensen, R. (2018). Infinite-duration poorman-bidding games (Vol. 11316, pp. 21–36). Presented at the 14th International Conference on Web and Internet Economics, WINE, Oxford, UK: Springer. https://doi.org/10.1007/978-3-030-04612-5_2","ama":"Avni G, Henzinger TA, Ibsen-Jensen R. Infinite-duration poorman-bidding games. In: Vol 11316. Springer; 2018:21-36. doi:10.1007/978-3-030-04612-5_2"},"page":"21-36","date_published":"2018-11-21T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"In two-player games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a non-terminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the “bank” rather than the other player. While poorman reachability games have been studied before, we present, for the first time, results on infinite-duration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman mean-payoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with random-turn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5788","intvolume":" 11316","status":"public","title":"Infinite-duration poorman-bidding games","oa_version":"Preprint"},{"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242333/"}],"external_id":{"isi":["000442483400046"],"pmid":["30158708"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41586-018-0396-4","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1476-4687"]},"year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"FlSc"}],"publisher":"Nature Publishing Group","author":[{"last_name":"Dick","first_name":"Robert","full_name":"Dick, Robert"},{"full_name":"Zadrozny, Kaneil K","last_name":"Zadrozny","first_name":"Kaneil K"},{"last_name":"Xu","first_name":"Chaoyi","full_name":"Xu, Chaoyi"},{"orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian","full_name":"Schur, Florian"},{"full_name":"Lyddon, Terri D","first_name":"Terri D","last_name":"Lyddon"},{"full_name":"Ricana, Clifton L","last_name":"Ricana","first_name":"Clifton L"},{"last_name":"Wagner","first_name":"Jonathan M","full_name":"Wagner, Jonathan M"},{"last_name":"Perilla","first_name":"Juan R","full_name":"Perilla, Juan R"},{"last_name":"Ganser","first_name":"Pornillos Barbie K","full_name":"Ganser, Pornillos Barbie K"},{"full_name":"Johnson, Marc C","first_name":"Marc C","last_name":"Johnson"},{"full_name":"Pornillos, Owen","last_name":"Pornillos","first_name":"Owen"},{"first_name":"Volker","last_name":"Vogt","full_name":"Vogt, Volker"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-018-0505-4"}]},"date_updated":"2023-09-12T07:44:37Z","date_created":"2018-12-11T11:44:53Z","volume":560,"publication":"Nature","citation":{"ieee":"R. Dick et al., “Inositol phosphates are assembly co-factors for HIV-1,” Nature, vol. 560, no. 7719. Nature Publishing Group, pp. 509–512, 2018.","apa":"Dick, R., Zadrozny, K. K., Xu, C., Schur, F. K., Lyddon, T. D., Ricana, C. L., … Vogt, V. (2018). Inositol phosphates are assembly co-factors for HIV-1. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0396-4","ista":"Dick R, Zadrozny KK, Xu C, Schur FK, Lyddon TD, Ricana CL, Wagner JM, Perilla JR, Ganser PBK, Johnson MC, Pornillos O, Vogt V. 2018. Inositol phosphates are assembly co-factors for HIV-1. Nature. 560(7719), 509–512.","ama":"Dick R, Zadrozny KK, Xu C, et al. Inositol phosphates are assembly co-factors for HIV-1. Nature. 2018;560(7719):509–512. doi:10.1038/s41586-018-0396-4","chicago":"Dick, Robert, Kaneil K Zadrozny, Chaoyi Xu, Florian KM Schur, Terri D Lyddon, Clifton L Ricana, Jonathan M Wagner, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0396-4.","short":"R. Dick, K.K. Zadrozny, C. Xu, F.K. Schur, T.D. Lyddon, C.L. Ricana, J.M. Wagner, J.R. Perilla, P.B.K. Ganser, M.C. Johnson, O. Pornillos, V. Vogt, Nature 560 (2018) 509–512.","mla":"Dick, Robert, et al. “Inositol Phosphates Are Assembly Co-Factors for HIV-1.” Nature, vol. 560, no. 7719, Nature Publishing Group, 2018, pp. 509–512, doi:10.1038/s41586-018-0396-4."},"article_type":"original","page":"509–512","date_published":"2018-08-29T00:00:00Z","scopus_import":"1","day":"29","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"150","title":"Inositol phosphates are assembly co-factors for HIV-1","status":"public","intvolume":" 560","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"A short, 14-amino-acid segment called SP1, located in the Gag structural protein1, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane2,3. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors4,5. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP6) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP6 interaction promotes the assembly of the mature capsid lattice. These studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.","lang":"eng"}],"issue":"7719"},{"date_published":"2018-06-01T00:00:00Z","page":"2827 - 2849","citation":{"ista":"Kalinin N, Shkolnikov M. 2018. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 38(6), 2827–2849.","apa":"Kalinin, N., & Shkolnikov, M. (2018). Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. AIMS. https://doi.org/10.3934/dcds.2018120","ieee":"N. Kalinin and M. Shkolnikov, “Introduction to tropical series and wave dynamic on them,” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6. AIMS, pp. 2827–2849, 2018.","ama":"Kalinin N, Shkolnikov M. Introduction to tropical series and wave dynamic on them. Discrete and Continuous Dynamical Systems- Series A. 2018;38(6):2827-2849. doi:10.3934/dcds.2018120","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A. AIMS, 2018. https://doi.org/10.3934/dcds.2018120.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Introduction to Tropical Series and Wave Dynamic on Them.” Discrete and Continuous Dynamical Systems- Series A, vol. 38, no. 6, AIMS, 2018, pp. 2827–49, doi:10.3934/dcds.2018120.","short":"N. Kalinin, M. Shkolnikov, Discrete and Continuous Dynamical Systems- Series A 38 (2018) 2827–2849."},"publication":"Discrete and Continuous Dynamical Systems- Series A","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 38","title":"Introduction to tropical series and wave dynamic on them","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"303","issue":"6","abstract":[{"text":"The theory of tropical series, that we develop here, firstly appeared in the study of the growth of pluriharmonic functions. Motivated by waves in sandpile models we introduce a dynamic on the set of tropical series, and it is experimentally observed that this dynamic obeys a power law. So, this paper serves as a compilation of results we need for other articles and also introduces several objects interesting by themselves.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3934/dcds.2018120","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000438818400007"],"arxiv":["1706.03062"]},"main_file_link":[{"url":"https://arxiv.org/abs/1706.03062","open_access":"1"}],"month":"06","volume":38,"date_updated":"2023-09-12T07:45:37Z","date_created":"2018-12-11T11:45:43Z","author":[{"last_name":"Kalinin","first_name":"Nikita","full_name":"Kalinin, Nikita"},{"full_name":"Shkolnikov, Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","first_name":"Mikhail","last_name":"Shkolnikov"}],"publisher":"AIMS","department":[{"_id":"TaHa"}],"publication_status":"published","year":"2018","acknowledgement":"The first author, Nikita Kalinin, is funded by SNCF PostDoc.Mobility grant 168647. Support from the Basic Research Program of the National Research University Higher School of Economics is gratefully acknowledged. The second author, Mikhail Shkolnikov, is supported in part by the grant 159240 of the Swiss National Science Foundation as well as by the National Center of Competence in Research SwissMAP of the Swiss National Science Foundation.","publist_id":"7576"},{"day":"06","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-06T00:00:00Z","publication":"Advances in Neural Information Processing Systems","citation":{"mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” Advances in Neural Information Processing Systems, vol. 31, Neural Information Processing Systems Foundation, 2018.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018.","chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In Advances in Neural Information Processing Systems, Vol. 31. Neural Information Processing Systems Foundation, 2018.","ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: Advances in Neural Information Processing Systems. Vol 31. Neural Information Processing Systems Foundation; 2018.","ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., & Rätsch, G. (2018). Boosting black box variational inference. In Advances in Neural Information Processing Systems (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 31."},"abstract":[{"lang":"eng","text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions."}],"type":"conference","oa_version":"Preprint","title":"Boosting black box variational inference","status":"public","intvolume":" 31","_id":"14202","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","publication_identifier":{"eissn":["1049-5258"],"isbn":["9781510884472"]},"language":[{"iso":"eng"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2018-12-08","location":"Montreal, Canada","start_date":"2018-12-03"},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02185"}],"external_id":{"arxiv":["1806.02185"]},"oa":1,"extern":"1","date_created":"2023-08-22T14:15:40Z","date_updated":"2023-09-13T07:38:24Z","volume":31,"author":[{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco"},{"full_name":"Dresdner, Gideon","last_name":"Dresdner","first_name":"Gideon"},{"full_name":"Khanna, Rajiv","first_name":"Rajiv","last_name":"Khanna"},{"full_name":"Valera, Isabel","first_name":"Isabel","last_name":"Valera"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}],"publication_status":"published","publisher":"Neural Information Processing Systems Foundation","department":[{"_id":"FrLo"}],"year":"2018"},{"title":"Boosting variational inference: An optimization perspective","status":"public","intvolume":" 84","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14201","oa_version":"Preprint","alternative_title":["PMLR"],"type":"conference","abstract":[{"lang":"eng","text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties."}],"page":"464-472","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","citation":{"chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, 84:464–72. ML Research Press, 2018.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, vol. 84, ML Research Press, 2018, pp. 464–72.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","apa":"Locatello, F., Khanna, R., Ghosh, J., & Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In Proceedings of the 21st International Conference on Artificial Intelligence and Statistics (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. Vol 84. ML Research Press; 2018:464-472."},"date_published":"2018-04-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","publication_status":"published","publisher":"ML Research Press","department":[{"_id":"FrLo"}],"year":"2018","date_created":"2023-08-22T14:15:20Z","date_updated":"2023-09-13T07:52:40Z","volume":84,"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco"},{"first_name":"Rajiv","last_name":"Khanna","full_name":"Khanna, Rajiv"},{"full_name":"Ghosh, Joydeep","first_name":"Joydeep","last_name":"Ghosh"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"}],"extern":"1","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01733"}],"external_id":{"arxiv":["1708.01733"]},"language":[{"iso":"eng"}],"conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","location":"Playa Blanca, Lanzarote","start_date":"2018-04-09","end_date":"2018-04-11"},"month":"04"},{"publication":"International Conference on Learning Representations","main_file_link":[{"url":"https://arxiv.org/abs/1806.02199","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1806.02199"]},"citation":{"chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States.","ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018."},"quality_controlled":"1","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2019-05-09","location":"New Orleans, LA, United States","start_date":"2019-05-06"},"date_published":"2018-06-06T00:00:00Z","language":[{"iso":"eng"}],"day":"06","month":"06","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14198","year":"2018","publication_status":"published","title":"SOM-VAE: Interpretable discrete representation learning on time series","status":"public","department":[{"_id":"FrLo"}],"author":[{"full_name":"Fortuin, Vincent","first_name":"Vincent","last_name":"Fortuin"},{"last_name":"Hüser","first_name":"Matthias","full_name":"Hüser, Matthias"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"first_name":"Heiko","last_name":"Strathmann","full_name":"Strathmann, Heiko"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"}],"date_created":"2023-08-22T14:12:48Z","date_updated":"2023-09-13T06:35:12Z","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data."}],"extern":"1"},{"extern":"1","department":[{"_id":"FrLo"}],"publisher":"ML Research Press","publication_status":"published","year":"2018","volume":80,"date_created":"2023-08-22T14:16:01Z","date_updated":"2023-09-13T08:13:39Z","author":[{"first_name":"Alp","last_name":"Yurtsever","full_name":"Yurtsever, Alp"},{"full_name":"Fercoq, Olivier","first_name":"Olivier","last_name":"Fercoq"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"full_name":"Cevher, Volkan","first_name":"Volkan","last_name":"Cevher"}],"month":"07","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1804.08544","open_access":"1"}],"external_id":{"arxiv":["1804.08544"]},"oa":1,"language":[{"iso":"eng"}],"conference":{"location":"Stockholm, Sweden","start_date":"2018-07-10","end_date":"2018-07-15","name":"ICML: International Conference on Machine Learning"},"alternative_title":["PMLR"],"type":"conference","abstract":[{"lang":"eng","text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework."}],"intvolume":" 80","status":"public","title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14203","oa_version":"Preprint","article_processing_charge":"No","day":"15","page":"5727-5736","citation":{"ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736.","chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36.","short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736."},"publication":"Proceedings of the 35th International Conference on Machine Learning","date_published":"2018-07-15T00:00:00Z"},{"publist_id":"7617","author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"date_created":"2018-12-11T11:45:36Z","date_updated":"2023-09-13T08:22:32Z","volume":209,"year":"2018","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","month":"08","doi":"10.1534/genetics.118.301018","language":[{"iso":"eng"}],"external_id":{"isi":["000440014100020"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"isi":1,"quality_controlled":"1","abstract":[{"text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Submitted Version","_id":"282","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Introgression of a block of genome under infinitesimal selection","intvolume":" 209","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","publication":"Genetics","citation":{"ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018."},"page":"1279 - 1303"},{"title":"Inverted leftover hash lemma","status":"public","intvolume":" 2018","_id":"108","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","alternative_title":["ISIT Proceedings"],"type":"conference","abstract":[{"text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes.","lang":"eng"}],"citation":{"mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654"},"date_published":"2018-08-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"IEEE","year":"2018","date_created":"2018-12-11T11:44:40Z","date_updated":"2023-09-13T08:23:18Z","volume":2018,"author":[{"full_name":"Obremski, Marciej","last_name":"Obremski","first_name":"Marciej"},{"full_name":"Skorski, Maciej","first_name":"Maciej","last_name":"Skorski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"publist_id":"7946","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000448139300368"]},"main_file_link":[{"url":"https://eprint.iacr.org/2017/507","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2018-06-22","location":"Vail, CO, USA","start_date":"2018-06-17 ","name":"ISIT: International Symposium on Information Theory"},"doi":"10.1109/ISIT.2018.8437654","month":"08"},{"month":"07","quality_controlled":"1","external_id":{"arxiv":["1803.09539"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.09539"}],"oa":1,"language":[{"iso":"eng"}],"extern":"1","department":[{"_id":"FrLo"}],"publisher":"ML Research Press","publication_status":"published","year":"2018","volume":80,"date_created":"2023-08-22T14:16:25Z","date_updated":"2023-09-13T08:19:05Z","author":[{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"first_name":"Anant","last_name":"Raj","full_name":"Raj, Anant"},{"full_name":"Karimireddy, Sai Praneeth","last_name":"Karimireddy","first_name":"Sai Praneeth"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"first_name":"Sebastian U.","last_name":"Stich","full_name":"Stich, Sebastian U."},{"last_name":"Jaggi","first_name":"Martin","full_name":"Jaggi, Martin"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"3198-3207","citation":{"short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207.","chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press.","ieee":"F. Locatello et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 3198–3207.","ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207."},"publication":"Proceedings of the 35th International Conference on Machine Learning","date_published":"2018-07-01T00:00:00Z","alternative_title":["PMLR"],"type":"conference","abstract":[{"lang":"eng","text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives."}],"intvolume":" 80","status":"public","title":"On matching pursuit and coordinate descent","_id":"14204","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"date_published":"2018-07-18T00:00:00Z","page":"79 - 102","citation":{"ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","apa":"Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5.","mla":"Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102."},"has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2018_LNCS_Kragl.pdf","access_level":"open_access","file_size":1603844,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5705","date_created":"2018-12-17T12:52:12Z","date_updated":"2020-07-14T12:45:04Z","checksum":"c64fff560fe5a7532ec10626ad1c215e"}],"intvolume":" 10981","status":"public","ddc":["000"],"title":"Layered Concurrent Programs","_id":"160","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-96145-3_5","conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","location":"Oxford, UK","end_date":"2018-07-17"},"project":[{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000491481600005"]},"month":"07","volume":10981,"date_created":"2018-12-11T11:44:57Z","date_updated":"2023-09-13T08:45:09Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8332"}]},"author":[{"orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","first_name":"Bernhard","full_name":"Kragl, Bernhard"},{"last_name":"Qadeer","first_name":"Shaz","full_name":"Qadeer, Shaz"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","publist_id":"7761","file_date_updated":"2020-07-14T12:45:04Z"},{"abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"None","status":"public","title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","intvolume":" 4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"280","day":"28","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-28T00:00:00Z","page":"365 - 375","publication":"Nature Plants","citation":{"mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7","ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","ieee":"Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7"},"publist_id":"7619","date_updated":"2023-09-13T08:24:17Z","date_created":"2018-12-11T11:45:35Z","volume":4,"author":[{"full_name":"Gao, Zhen","first_name":"Zhen","last_name":"Gao"},{"last_name":"Daneva","first_name":"Anna","full_name":"Daneva, Anna"},{"id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","first_name":"Yuliya","last_name":"Salanenka","full_name":"Salanenka, Yuliya"},{"last_name":"Van Durme","first_name":"Matthias","full_name":"Van Durme, Matthias"},{"full_name":"Huysmans, Marlies","first_name":"Marlies","last_name":"Huysmans"},{"full_name":"Lin, Zongcheng","last_name":"Lin","first_name":"Zongcheng"},{"first_name":"Freya","last_name":"De Winter","full_name":"De Winter, Freya"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Karimi","first_name":"Mansour","full_name":"Karimi, Mansour"},{"full_name":"Van De Velde, Jan","first_name":"Jan","last_name":"Van De Velde"},{"last_name":"Vandepoele","first_name":"Klaas","full_name":"Vandepoele, Klaas"},{"first_name":"Davy","last_name":"Van De Walle","full_name":"Van De Walle, Davy"},{"full_name":"Dewettinck, Koen","first_name":"Koen","last_name":"Dewettinck"},{"last_name":"Lambrecht","first_name":"Bart","full_name":"Lambrecht, Bart"},{"full_name":"Nowack, Moritz","last_name":"Nowack","first_name":"Moritz"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JiFr"}],"acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","year":"2018","month":"05","language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0160-7","isi":1,"quality_controlled":"1","external_id":{"isi":["000435571000017"]}},{"year":"2018","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","publication_status":"published","publisher":"Elsevier","department":[{"_id":"CaGu"}],"author":[{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3768-877X","first_name":"Kathrin","last_name":"Tomasek","full_name":"Tomasek, Kathrin"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"date_created":"2018-12-11T11:46:50Z","date_updated":"2023-09-13T08:24:51Z","volume":268,"publist_id":"7317","external_id":{"isi":["000425715100006"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.jbiotec.2018.01.008","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"month":"02","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"503","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","status":"public","intvolume":" 268","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry."}],"publication":"Journal of Biotechnology","citation":{"chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008.","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","apa":"Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018.","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008"},"page":"40 - 52","date_published":"2018-02-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No"},{"doi":"10.1371/journal.pbio.2005971","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000443383300024"]},"quality_controlled":"1","isi":1,"month":"08","author":[{"first_name":"Waqas","last_name":"Chaudhry","full_name":"Chaudhry, Waqas"},{"full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","last_name":"Pleska"},{"last_name":"Shah","first_name":"Nilang","full_name":"Shah, Nilang"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"full_name":"Mccall, Ingrid","last_name":"Mccall","first_name":"Ingrid"},{"last_name":"Meyer","first_name":"Justin","full_name":"Meyer, Justin"},{"full_name":"Gupta, Animesh","first_name":"Animesh","last_name":"Gupta"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"},{"full_name":"Levin, Bruce","last_name":"Levin","first_name":"Bruce"}],"related_material":{"record":[{"id":"9810","status":"public","relation":"research_data"}]},"date_updated":"2023-09-13T08:45:41Z","date_created":"2018-12-11T11:44:32Z","volume":16,"year":"2018","publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:48:10Z","publist_id":"7972","article_number":"2005971","date_published":"2018-08-16T00:00:00Z","publication":"PLoS Biology","citation":{"short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971","ieee":"W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971."},"day":"16","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2018_Plos_Chaudhry.pdf","access_level":"open_access","file_size":4007095,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5706","date_updated":"2020-07-14T12:48:10Z","date_created":"2018-12-17T12:55:31Z","checksum":"527076f78265cd4ea192cd1569851587"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"82","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","status":"public","ddc":["570"],"intvolume":" 16","abstract":[{"text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”.","lang":"eng"}],"issue":"8","type":"journal_article"},{"month":"08","doi":"10.1145/3197517.3201325","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000448185000050"]},"quality_controlled":"1","isi":1,"project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:46:22Z","ec_funded":1,"publist_id":"8053","article_number":"89","author":[{"full_name":"Umetani, Nobuyuki","last_name":"Umetani","first_name":"Nobuyuki"},{"full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2018-12-11T11:44:06Z","date_updated":"2023-09-13T08:46:15Z","volume":37,"year":"2018","publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"day":"04","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-08-04T00:00:00Z","publication":"ACM Trans. Graph.","citation":{"mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","chicago":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89.","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","apa":"Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325"},"abstract":[{"text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body.","lang":"eng"}],"issue":"4","type":"journal_article","pubrep_id":"1049","file":[{"creator":"system","content_type":"application/pdf","file_size":22803163,"file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:22Z","date_created":"2018-12-12T10:16:28Z","checksum":"7a2243668f215821bc6aecad0320079a","file_id":"5216","relation":"main_file"}],"oa_version":"Submitted Version","_id":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Learning three-dimensional flow for interactive aerodynamic design","status":"public","ddc":["003","004"],"intvolume":" 37"},{"month":"04","quality_controlled":"1","isi":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"external_id":{"isi":["000474781600022"]},"language":[{"iso":"eng"}],"conference":{"name":"HSCC: Hybrid Systems: Computation and Control","start_date":"2018-04-11","location":"Porto, Portugal","end_date":"2018-04-13"},"doi":"10.1145/3178126.3178131","publist_id":"7738","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Association for Computing Machinery, Inc","year":"2018","acknowledgement":"This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway.","date_updated":"2023-09-13T08:48:46Z","date_created":"2018-12-11T11:45:04Z","author":[{"first_name":"Ezio","last_name":"Bartocci","full_name":"Bartocci, Ezio"},{"last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","full_name":"Ferrere, Thomas"},{"full_name":"Manjunath, Niveditha","last_name":"Manjunath","first_name":"Niveditha"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic"}],"scopus_import":"1","day":"11","article_processing_charge":"No","page":"197 - 206","citation":{"mla":"Bartocci, Ezio, et al. Localizing Faults in Simulink/Stateflow Models with STL. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:10.1145/3178126.3178131.","short":"E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, Inc, 2018, pp. 197–206.","chicago":"Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, Inc, 2018. https://doi.org/10.1145/3178126.3178131.","ama":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:10.1145/3178126.3178131","ista":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 197–206.","apa":"Bartocci, E., Ferrere, T., Manjunath, N., & Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing Machinery, Inc. https://doi.org/10.1145/3178126.3178131","ieee":"E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal, 2018, pp. 197–206."},"date_published":"2018-04-11T00:00:00Z","alternative_title":["HSCC Proceedings"],"type":"conference","abstract":[{"lang":"eng","text":"Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain."}],"title":"Localizing faults in simulink/stateflow models with STL","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"183","oa_version":"None"},{"date_created":"2018-12-11T11:47:13Z","date_updated":"2023-09-13T08:47:52Z","volume":28,"author":[{"full_name":"Alt, Johannes","first_name":"Johannes","last_name":"Alt","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László"},{"last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H"}],"related_material":{"record":[{"id":"149","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","year":"2018","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1214/17-AAP1302","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"external_id":{"isi":["000431721800005"],"arxiv":["1612.07776 "]},"main_file_link":[{"url":"https://arxiv.org/abs/1612.07776 ","open_access":"1"}],"oa":1,"month":"03","oa_version":"Preprint","status":"public","title":"Local inhomogeneous circular law","intvolume":" 28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"566","abstract":[{"lang":"eng","text":"We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n"}],"issue":"1","type":"journal_article","date_published":"2018-03-03T00:00:00Z","article_type":"original","page":"148-203","publication":"Annals Applied Probability ","citation":{"chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/17-AAP1302.","short":"J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203.","mla":"Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:10.1214/17-AAP1302.","apa":"Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular law. Annals Applied Probability . Institute of Mathematical Statistics. https://doi.org/10.1214/17-AAP1302","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018.","ista":"Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203.","ama":"Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302"},"day":"03","article_processing_charge":"No","scopus_import":"1"},{"date_published":"2018-09-01T00:00:00Z","page":"26 - 31","citation":{"mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:10.1007/s00283-018-9795-5.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):26-31. doi:10.1007/s00283-018-9795-5","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31.","apa":"Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces. Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018."},"publication":"Mathematical Intelligencer","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 40","status":"public","title":"Long geodesics on convex surfaces","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"106","issue":"3","abstract":[{"lang":"eng","text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s00283-018-9795-5","quality_controlled":"1","isi":1,"external_id":{"arxiv":["1702.05172"],"isi":["000444141200005"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.05172"}],"month":"09","volume":40,"date_created":"2018-12-11T11:44:40Z","date_updated":"2023-09-13T08:49:16Z","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"full_name":"Petrunin, Anton","last_name":"Petrunin","first_name":"Anton"}],"publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2018","publist_id":"7948"},{"month":"08","day":"16","article_processing_charge":"No","citation":{"ama":"Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:10.1371/journal.pbio.2005971.s008","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008","ieee":"W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 2018.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018).","mla":"Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008.","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008."},"date_published":"2018-08-16T00:00:00Z","doi":"10.1371/journal.pbio.2005971.s008","type":"research_data_reference","status":"public","title":"Numerical data used in figures","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"year":"2018","_id":"9810","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-13T08:45:41Z","date_created":"2021-08-06T12:43:44Z","oa_version":"Published Version","author":[{"first_name":"Waqas","last_name":"Chaudhry","full_name":"Chaudhry, Waqas"},{"orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros"},{"full_name":"Shah, Nilang","first_name":"Nilang","last_name":"Shah"},{"full_name":"Weiss, Howard","last_name":"Weiss","first_name":"Howard"},{"first_name":"Ingrid","last_name":"Mccall","full_name":"Mccall, Ingrid"},{"full_name":"Meyer, Justin","last_name":"Meyer","first_name":"Justin"},{"full_name":"Gupta, Animesh","first_name":"Animesh","last_name":"Gupta"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"82"}]}},{"acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","year":"2018","pmid":1,"publication_status":"published","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"},{"_id":"Bio"}],"author":[{"last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"full_name":"Johnson, Louise","first_name":"Louise","last_name":"Johnson"},{"full_name":"Leone, Dario","last_name":"Leone","first_name":"Dario"},{"full_name":"Májek, Peter","last_name":"Májek","first_name":"Peter"},{"full_name":"Vaahtomeri, Kari","first_name":"Kari","last_name":"Vaahtomeri","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518"},{"last_name":"Senfter","first_name":"Daniel","full_name":"Senfter, Daniel"},{"full_name":"Bukosza, Nora","last_name":"Bukosza","first_name":"Nora"},{"first_name":"Helga","last_name":"Schachner","full_name":"Schachner, Helga"},{"full_name":"Asfour, Gabriele","first_name":"Gabriele","last_name":"Asfour"},{"full_name":"Langer, Brigitte","last_name":"Langer","first_name":"Brigitte"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild"},{"last_name":"Parapatics","first_name":"Katja","full_name":"Parapatics, Katja"},{"full_name":"Hong, Young","last_name":"Hong","first_name":"Young"},{"last_name":"Bennett","first_name":"Keiryn","full_name":"Bennett, Keiryn"},{"first_name":"Renate","last_name":"Kain","full_name":"Kain, Renate"},{"full_name":"Detmar, Michael","first_name":"Michael","last_name":"Detmar"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Jackson, David","first_name":"David","last_name":"Jackson"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"}],"date_updated":"2023-09-13T08:51:29Z","date_created":"2018-12-11T11:45:33Z","volume":217,"file_date_updated":"2020-07-14T12:45:45Z","ec_funded":1,"publist_id":"7627","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["29650776"],"isi":["000438077800026"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"}],"doi":"10.1083/jcb.201612051","language":[{"iso":"eng"}],"month":"04","_id":"275","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","ddc":["570"],"intvolume":" 217","oa_version":"Published Version","file":[{"checksum":"9c7eba51a35c62da8c13f98120b64df4","date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-17T12:50:07Z","relation":"main_file","file_id":"5704","content_type":"application/pdf","file_size":2252043,"creator":"dernst","access_level":"open_access","file_name":"2018_JournalCellBiology_Brown.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"issue":"6","publication":"Journal of Cell Biology","citation":{"ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221. doi:10.1083/jcb.201612051","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051","ieee":"M. Brown et al., “Lymphatic exosomes promote dendritic cell migration along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051.","chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201612051."},"page":"2205 - 2221","date_published":"2018-04-12T00:00:00Z","scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No"},{"scopus_import":"1","article_processing_charge":"No","day":"16","page":"548 - 553","citation":{"short":"H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553.","mla":"Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:10.1038/s41477-018-0204-z.","chicago":"Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0204-z.","ama":"Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553. doi:10.1038/s41477-018-0204-z","ieee":"H. Robert et al., “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018.","apa":"Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z","ista":"Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553."},"publication":"Nature Plants","date_published":"2018-07-16T00:00:00Z","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development."}],"intvolume":" 4","title":"Maternal auxin supply contributes to early embryo patterning in Arabidopsis","status":"public","_id":"158","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Submitted Version","month":"07","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","oa":1,"external_id":{"pmid":["30013211"],"isi":["000443861300011"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30013211"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41477-018-0204-z","ec_funded":1,"publist_id":"7763","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"year":"2018","acknowledgement":"This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.;","volume":4,"date_updated":"2023-09-13T08:53:28Z","date_created":"2018-12-11T11:44:56Z","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/"}]},"author":[{"first_name":"Hélène","last_name":"Robert","full_name":"Robert, Hélène"},{"full_name":"Park, Chulmin","first_name":"Chulmin","last_name":"Park"},{"last_name":"Gutièrrez","first_name":"Carla","full_name":"Gutièrrez, Carla"},{"first_name":"Barbara","last_name":"Wójcikowska","full_name":"Wójcikowska, Barbara"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"full_name":"Novák, Ondřej","last_name":"Novák","first_name":"Ondřej"},{"full_name":"Chen, Junyi","first_name":"Junyi","last_name":"Chen"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"full_name":"Dresselhaus, Thomas","first_name":"Thomas","last_name":"Dresselhaus"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"},{"last_name":"Laux","first_name":"Thomas","full_name":"Laux, Thomas"}]},{"oa_version":"Submitted Version","file":[{"creator":"lsazanov","file_size":2185385,"content_type":"application/pdf","access_level":"open_access","file_name":"SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf","checksum":"ef6d2b4e1fd63948539639242610bfa6","date_created":"2019-11-07T12:55:20Z","date_updated":"2020-07-14T12:45:00Z","file_id":"6994","relation":"main_file"}],"status":"public","title":"Mammalian mitochondrial complex I structure and disease causing mutations","ddc":["572"],"intvolume":" 28","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"152","abstract":[{"text":"Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context.","lang":"eng"}],"issue":"10","type":"journal_article","date_published":"2018-07-26T00:00:00Z","article_type":"original","page":"835 - 867","publication":"Trends in Cell Biology","citation":{"ama":"Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006","ieee":"K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10. Elsevier, pp. 835–867, 2018.","apa":"Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2018.06.006","ista":"Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867.","short":"K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867.","mla":"Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006.","chicago":"Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier, 2018. https://doi.org/10.1016/j.tcb.2018.06.006."},"day":"26","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-13T08:51:56Z","date_created":"2018-12-11T11:44:54Z","volume":28,"author":[{"first_name":"Karol","last_name":"Fiedorczuk","id":"5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0","full_name":"Fiedorczuk, Karol"},{"orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A"}],"publication_status":"published","department":[{"_id":"LeSa"}],"publisher":"Elsevier","year":"2018","file_date_updated":"2020-07-14T12:45:00Z","publist_id":"7769","language":[{"iso":"eng"}],"doi":"10.1016/j.tcb.2018.06.006","isi":1,"quality_controlled":"1","tmp":{"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","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000445118200007"]},"month":"07"},{"abstract":[{"lang":"eng","text":"A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components."}],"type":"conference","oa_version":"Preprint","status":"public","title":"Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"310","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","page":"2341 - 2356","citation":{"mla":"Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM, 2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356."},"publist_id":"7555","ec_funded":1,"date_created":"2018-12-11T11:45:45Z","date_updated":"2023-09-13T08:50:16Z","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wolfgang","last_name":"Dvorák","full_name":"Dvorák, Wolfgang"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"ACM","year":"2018","month":"01","language":[{"iso":"eng"}],"conference":{"location":"New Orleans, Louisiana, United States","start_date":"2018-01-07","end_date":"2018-01-10","name":"SODA: Symposium on Discrete Algorithms"},"doi":"10.1137/1.9781611975031.151","isi":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.09148"}],"external_id":{"arxiv":["1711.09148"],"isi":["000483921200152"]},"oa":1},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"436","status":"public","title":"Manipulating the flow of thermal noise in quantum devices","intvolume":" 120","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits."}],"issue":"6","publication":"Physical Review Letters","citation":{"short":"S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018).","mla":"Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601.","chicago":"Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601.","ama":"Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601","ieee":"S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018.","apa":"Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601","ista":"Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601."},"date_published":"2018-02-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"No","year":"2018","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"author":[{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423"},{"full_name":"Aquilina, Matteo","first_name":"Matteo","last_name":"Aquilina"},{"full_name":"Xuereb, André","last_name":"Xuereb","first_name":"André"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/","description":"News on IST Homepage","relation":"press_release"}]},"date_updated":"2023-09-13T08:52:27Z","date_created":"2018-12-11T11:46:28Z","volume":120,"article_number":"060601 ","publist_id":"7387","ec_funded":1,"external_id":{"isi":["000424382100004"],"arxiv":["1706.09051"]},"main_file_link":[{"url":"https://arxiv.org/abs/1706.09051","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Hybrid Optomechanical Technologies","grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425"},{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","call_identifier":"H2020"}],"doi":"10.1103/PhysRevLett.120.060601","language":[{"iso":"eng"}],"month":"02"},{"citation":{"ama":"Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600","ista":"Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600.","ieee":"S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","apa":"Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600","mla":"Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600.","short":"S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018).","chicago":"Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600."},"publication":"Journal of the Royal Society Interface","date_published":"2018-12-05T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"05","intvolume":" 15","title":"Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data","ddc":["570"],"status":"public","_id":"5858","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5925","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T14:46:44Z","checksum":"56eb4308a15b7190bff938fab1f780e8","file_name":"2018_Interface_Hross.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1464288,"creator":"dernst"}],"type":"journal_article","issue":"149","abstract":[{"text":"Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights.","lang":"eng"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000456783800011"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2018.0600","publication_identifier":{"issn":["17425689"]},"month":"12","department":[{"_id":"MiSi"}],"publisher":"Royal Society Publishing","publication_status":"published","year":"2018","volume":15,"date_created":"2019-01-20T22:59:18Z","date_updated":"2023-09-13T08:55:05Z","author":[{"first_name":"Sabrina","last_name":"Hross","full_name":"Hross, Sabrina"},{"full_name":"Theis, Fabian J.","first_name":"Fabian J.","last_name":"Theis"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"first_name":"Jan","last_name":"Hasenauer","full_name":"Hasenauer, Jan"}],"article_number":"20180600","file_date_updated":"2020-07-14T12:47:13Z"},{"year":"2018","acknowledgement":"This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145).","publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"American Physical Society","author":[{"full_name":"Varshney, Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3072-5999","first_name":"Atul","last_name":"Varshney"},{"full_name":"Steinberg, Victor","first_name":"Victor","last_name":"Steinberg"}],"date_created":"2018-12-11T11:44:10Z","date_updated":"2023-09-13T08:57:05Z","volume":3,"article_number":"103303","file_date_updated":"2020-07-14T12:45:04Z","ec_funded":1,"publist_id":"8039","external_id":{"isi":["000447469200001"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.1103/PhysRevFluids.3.103303","language":[{"iso":"eng"}],"month":"10","_id":"16","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Mixing layer instability and vorticity amplification in a creeping viscoelastic flow","ddc":["532"],"intvolume":" 3","pubrep_id":"1062","file":[{"access_level":"open_access","file_name":"IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf","creator":"system","file_size":1838431,"content_type":"application/pdf","file_id":"5043","relation":"main_file","checksum":"7fc0a2322214d1c04debef36d5bf2e8a","date_created":"2018-12-12T10:13:56Z","date_updated":"2020-07-14T12:45:04Z"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives."}],"issue":"10","publication":"Physical Review Fluids","citation":{"mla":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303.","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","chicago":"Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303.","ama":"Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303","ista":"Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303.","apa":"Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303","ieee":"A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018."},"article_type":"original","date_published":"2018-10-16T00:00:00Z","scopus_import":"1","day":"16","article_processing_charge":"No","has_accepted_license":"1"},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1721061115","quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"external_id":{"isi":["000447491300057"]},"oa":1,"month":"10","date_updated":"2023-09-13T08:57:38Z","date_created":"2018-12-11T11:44:19Z","volume":115,"author":[{"full_name":"Rybicki, Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","first_name":"Joel","last_name":"Rybicki"},{"full_name":"Kisdi, Eva","last_name":"Kisdi","first_name":"Eva"},{"last_name":"Anttila","first_name":"Jani","full_name":"Anttila, Jani"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"DaAl"}],"acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","year":"2018","file_date_updated":"2020-07-14T12:46:26Z","publist_id":"8011","ec_funded":1,"date_published":"2018-10-02T00:00:00Z","page":"10690 - 10695","publication":"PNAS","citation":{"mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115.","short":"J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695.","chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721061115.","ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695.","ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","apa":"Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115"},"day":"02","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2018_PNAS_Rybicki.pdf","creator":"dernst","file_size":4070777,"content_type":"application/pdf","file_id":"6258","relation":"main_file","checksum":"df7ac544a587c06b75692653b9fabd18","date_created":"2019-04-09T08:02:50Z","date_updated":"2020-07-14T12:46:26Z"}],"pubrep_id":"1063","ddc":["570","577"],"status":"public","title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"43","abstract":[{"lang":"eng","text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics."}],"issue":"42","type":"journal_article"},{"type":"journal_article","abstract":[{"text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery.","lang":"eng"}],"issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"13","status":"public","title":"Metamolds: Computational design of silicone molds","ddc":["004"],"intvolume":" 37","pubrep_id":"1038","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5374","date_created":"2018-12-12T10:18:52Z","date_updated":"2020-07-14T12:44:43Z","checksum":"61d46273dca4de626accef1d17a0aaad","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","access_level":"open_access","file_size":91939066,"content_type":"application/pdf","creator":"system"}],"scopus_import":"1","day":"04","has_accepted_license":"1","article_processing_charge":"No","publication":"ACM Trans. Graph.","citation":{"chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.","short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018).","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni, P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201381","ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.","ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381"},"date_published":"2018-08-04T00:00:00Z","article_number":"136","file_date_updated":"2020-07-14T12:44:43Z","ec_funded":1,"publist_id":"8043","year":"2018","publication_status":"published","publisher":"ACM","department":[{"_id":"BeBi"}],"author":[{"last_name":"Alderighi","first_name":"Thomas","full_name":"Alderighi, Thomas"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"full_name":"Giorgi, Daniela","first_name":"Daniela","last_name":"Giorgi"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/","description":"News on IST Homepage","relation":"press_release"}]},"date_created":"2018-12-11T11:44:09Z","date_updated":"2023-09-13T08:56:07Z","volume":37,"month":"08","oa":1,"external_id":{"isi":["000448185000097"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"doi":"10.1145/3197517.3201381","language":[{"iso":"eng"}]},{"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30061718"}],"external_id":{"pmid":["30061718 "],"isi":["000442174500013"]},"quality_controlled":"1","isi":1,"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"}],"doi":"10.1038/s41589-018-0108-2","language":[{"iso":"eng"}],"publist_id":"7786","year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"HaJa"}],"publisher":"Nature Publishing Group","author":[{"last_name":"Zhang","first_name":"William","full_name":"Zhang, William"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"last_name":"Mitchell","first_name":"Joshua","full_name":"Mitchell, Joshua"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"full_name":"Wulff, Andreas","last_name":"Wulff","first_name":"Andreas"},{"last_name":"Vongsouthi","first_name":"Vanessa","full_name":"Vongsouthi, Vanessa"},{"full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","last_name":"Sanchez Romero"},{"last_name":"Gulakova","first_name":"Polina","full_name":"Gulakova, Polina"},{"full_name":"Minge, Daniel","last_name":"Minge","first_name":"Daniel"},{"last_name":"Breithausen","first_name":"Björn","full_name":"Breithausen, Björn"},{"last_name":"Schoch","first_name":"Susanne","full_name":"Schoch, Susanne"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"}],"date_updated":"2023-09-13T08:58:05Z","date_created":"2018-12-11T11:44:49Z","volume":14,"scopus_import":"1","day":"30","article_processing_charge":"No","publication":"Nature Chemical Biology","citation":{"short":"W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869.","mla":"Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2.","chicago":"Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2.","ama":"Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2","apa":"Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2","ieee":"W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018.","ista":"Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869."},"article_type":"original","page":"861 - 869","date_published":"2018-07-30T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli."}],"issue":"9","_id":"137","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS","intvolume":" 14","oa_version":"Submitted Version"},{"publication_identifier":{"issn":["0091679X"]},"month":"07","isi":1,"quality_controlled":"1","external_id":{"isi":["000452412300006"],"pmid":["30165964"]},"language":[{"iso":"eng"}],"doi":"10.1016/bs.mcb.2018.07.004","publist_id":"7768","publisher":"Academic Press","department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"publication_status":"published","pmid":1,"year":"2018","volume":147,"date_updated":"2023-09-13T08:56:35Z","date_created":"2018-12-11T11:44:54Z","author":[{"full_name":"Renkawitz, Jörg","last_name":"Renkawitz","first_name":"Jörg","orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","first_name":"Anne","last_name":"Reversat"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X","first_name":"Alexander F","last_name":"Leithner","full_name":"Leithner, Alexander F"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"}],"scopus_import":"1","article_processing_charge":"No","day":"27","page":"79 - 91","citation":{"ista":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.","apa":"Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91). Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004","ieee":"J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91.","ama":"Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004","chicago":"Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91. Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004.","mla":"Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004.","short":"J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91."},"publication":"Methods in Cell Biology","date_published":"2018-07-27T00:00:00Z","type":"book_chapter","abstract":[{"lang":"eng","text":"Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters."}],"intvolume":" 147","status":"public","title":"Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"153","oa_version":"None"},{"external_id":{"isi":["000446579900002"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2018.09.014"}],"isi":1,"quality_controlled":"1","doi":"10.1016/j.devcel.2018.09.014","language":[{"iso":"eng"}],"month":"10","acknowledgement":"Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants.","year":"2018","publisher":"Cell Press","department":[{"_id":"CaHe"}],"publication_status":"published","author":[{"full_name":"Nunes Pinheiro, Diana C","id":"2E839F16-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4333-7503","first_name":"Diana C","last_name":"Nunes Pinheiro"},{"full_name":"Bellaïche, Yohanns","first_name":"Yohanns","last_name":"Bellaïche"}],"volume":47,"date_created":"2018-12-11T11:44:23Z","date_updated":"2023-09-13T08:54:38Z","publist_id":"8000","citation":{"ista":"Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19.","apa":"Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014","ieee":"D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” Developmental Cell, vol. 47, no. 1. Cell Press, pp. 3–19, 2018.","ama":"Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19. doi:10.1016/j.devcel.2018.09.014","chicago":"Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014.","mla":"Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014.","short":"D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19."},"publication":"Developmental Cell","page":"3 - 19","article_type":"review","date_published":"2018-10-08T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"08","_id":"54","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 47","title":"Mechanical force-driven adherents junction remodeling and epithelial dynamics","status":"public","oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics.","lang":"eng"}]},{"day":"07","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-06-07T00:00:00Z","article_type":"original","publication":"PLoS One","citation":{"chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:10.1371/journal.pone.0198330.","ieee":"C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science, 2018.","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330.","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330"},"abstract":[{"text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-17T14:10:32Z","checksum":"95fc5dc3938b3ad3b7697d10c83cc143","relation":"main_file","file_id":"5709","content_type":"application/pdf","file_size":7682167,"creator":"dernst","file_name":"2018_Plos_Frick.pdf","access_level":"open_access"}],"status":"public","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","ddc":["570"],"intvolume":" 13","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"276","month":"06","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0198330","isi":1,"quality_controlled":"1","external_id":{"isi":["000434384900031"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2020-07-14T12:45:45Z","publist_id":"7626","article_number":"e0198330","date_created":"2018-12-11T11:45:34Z","date_updated":"2023-09-13T09:00:15Z","volume":13,"author":[{"last_name":"Frick","first_name":"Corina","full_name":"Frick, Corina"},{"full_name":"Dettinger, Philip","first_name":"Philip","last_name":"Dettinger"},{"orcid":"0000-0003-2856-3369","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz","first_name":"Jörg","full_name":"Renkawitz, Jörg"},{"full_name":"Jauch, Annaïse","first_name":"Annaïse","last_name":"Jauch"},{"first_name":"Christoph","last_name":"Berger","full_name":"Berger, Christoph"},{"last_name":"Recher","first_name":"Mike","full_name":"Recher, Mike"},{"full_name":"Schroeder, Timm","first_name":"Timm","last_name":"Schroeder"},{"last_name":"Mehling","first_name":"Matthias","full_name":"Mehling, Matthias"}],"publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"Public Library of Science","year":"2018","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."},{"publist_id":"7616","file_date_updated":"2020-07-14T12:45:49Z","article_number":"8754","author":[{"full_name":"Ceinos, Rosa Maria","last_name":"Ceinos","first_name":"Rosa Maria"},{"first_name":"Elena","last_name":"Frigato","full_name":"Frigato, Elena"},{"last_name":"Pagano","first_name":"Cristina","full_name":"Pagano, Cristina"},{"full_name":"Frohlich, Nadine","first_name":"Nadine","last_name":"Frohlich"},{"last_name":"Negrini","first_name":"Pietro","full_name":"Negrini, Pietro"},{"first_name":"Nicola","last_name":"Cavallari","id":"457160E6-F248-11E8-B48F-1D18A9856A87","full_name":"Cavallari, Nicola"},{"first_name":"Daniela","last_name":"Vallone","full_name":"Vallone, Daniela"},{"first_name":"Silvia","last_name":"Fuselli","full_name":"Fuselli, Silvia"},{"full_name":"Bertolucci, Cristiano","first_name":"Cristiano","last_name":"Bertolucci"},{"last_name":"Foulkes","first_name":"Nicholas S","full_name":"Foulkes, Nicholas S"}],"volume":8,"date_updated":"2023-09-13T08:59:27Z","date_created":"2018-12-11T11:45:36Z","year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"EvBe"}],"publication_status":"published","month":"06","doi":"10.1038/s41598-018-27080-2","language":[{"iso":"eng"}],"external_id":{"isi":["000434640800008"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"issue":"1","abstract":[{"text":"Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"5707","relation":"main_file","checksum":"9c3942d772f84f3df032ffde0ed9a8ea","date_created":"2018-12-17T13:04:46Z","date_updated":"2020-07-14T12:45:49Z","access_level":"open_access","file_name":"2018_ScientificReports_Ceinos.pdf","creator":"dernst","file_size":1855324,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"283","intvolume":" 8","status":"public","title":"Mutations in blind cavefish target the light regulated circadian clock gene period 2","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2018-06-08T00:00:00Z","citation":{"ama":"Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-27080-2","apa":"Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-27080-2","ieee":"R. M. Ceinos et al., “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ista":"Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.","short":"R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).","mla":"Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2.","chicago":"Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-27080-2."},"publication":"Scientific Reports"},{"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","year":"2018","volume":11022,"date_created":"2018-12-11T11:44:31Z","date_updated":"2023-09-13T08:58:34Z","author":[{"full_name":"Elgyütt, Adrian","first_name":"Adrian","last_name":"Elgyütt","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","first_name":"Thomas"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"publist_id":"7973","file_date_updated":"2020-10-09T06:24:21Z","project":[{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000884993200004"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-00151-3_4","conference":{"start_date":"2018-09-04","location":"Beijing, China","end_date":"2018-09-06","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"month":"08","intvolume":" 11022","status":"public","title":"Monitoring temporal logic with clock variables","ddc":["000"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"81","oa_version":"Submitted Version","file":[{"date_updated":"2020-10-09T06:24:21Z","date_created":"2020-10-09T06:24:21Z","success":1,"checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","file_id":"8638","relation":"main_file","creator":"dernst","file_size":537219,"content_type":"application/pdf","file_name":"2018_LNCS_Elgyuett.pdf","access_level":"open_access"}],"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,"}],"page":"53 - 70","citation":{"short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70.","mla":"Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.","chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.","ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","apa":"Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70."},"date_published":"2018-08-26T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26"},{"month":"09","external_id":{"isi":["000475627800005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"doi":"10.1007/s00446-018-0342-6","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:48:01Z","publist_id":"7978","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"DaAl"}],"author":[{"first_name":"Christoph","last_name":"Lenzen","full_name":"Lenzen, Christoph"},{"last_name":"Rybicki","first_name":"Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","full_name":"Rybicki, Joel"}],"date_created":"2018-12-11T11:44:30Z","date_updated":"2023-09-13T09:01:06Z","scopus_import":"1","day":"12","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Distributed Computing","citation":{"ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6."},"date_published":"2018-09-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"76","ddc":["000"],"title":"Near-optimal self-stabilising counting and firing squads","status":"public","oa_version":"Published Version","file":[{"checksum":"872db70bba9b401500abe3c6ae2f1a61","date_created":"2018-12-17T14:21:22Z","date_updated":"2020-07-14T12:48:01Z","relation":"main_file","file_id":"5711","file_size":799337,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2018_DistributedComputing_Lenzen.pdf"}]},{"file_date_updated":"2020-07-14T12:46:38Z","ec_funded":1,"publist_id":"7289","date_created":"2018-12-11T11:46:59Z","date_updated":"2023-09-13T08:59:00Z","volume":68,"author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Elsevier","year":"2018","month":"03","language":[{"iso":"eng"}],"doi":"10.1016/j.comgeo.2017.06.014","quality_controlled":"1","isi":1,"project":[{"name":"Topological Complex Systems","call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000415778300010"]},"oa":1,"abstract":[{"text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","file":[{"creator":"dernst","content_type":"application/pdf","file_size":708357,"file_name":"2018_Edelsbrunner.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:38Z","date_created":"2019-02-12T06:47:52Z","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","file_id":"5953","relation":"main_file"}],"ddc":["000"],"title":"Multiple covers with balls I: Inclusion–exclusion","status":"public","intvolume":" 68","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"530","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-03-01T00:00:00Z","page":"119 - 133","publication":"Computational Geometry: Theory and Applications","citation":{"ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014."}},{"month":"04","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.97.043812","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000429454000015"],"arxiv":["1712.10127"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1712.10127"}],"publist_id":"7572","article_number":" 043812 ","date_created":"2018-12-11T11:45:44Z","date_updated":"2023-09-13T09:00:41Z","volume":97,"author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Makarov, Alexander","last_name":"Makarov","first_name":"Alexander"},{"full_name":"Yudson, Vladimir","first_name":"Vladimir","last_name":"Yudson"}],"publication_status":"published","publisher":"American Physical Society","department":[{"_id":"JoFi"}],"year":"2018","acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","day":"09","article_processing_charge":"No","scopus_import":"1","date_published":"2018-04-09T00:00:00Z","article_type":"original","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812.","ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","apa":"Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812.","mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812.","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018)."},"abstract":[{"lang":"eng","text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. "}],"issue":"4","type":"journal_article","oa_version":"Submitted Version","title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","status":"public","intvolume":" 97","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"307"},{"month":"05","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000433986200001"]},"project":[{"grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"doi":"10.1186/s13059-018-1434-0","language":[{"iso":"eng"}],"article_number":"67","ec_funded":1,"publist_id":"7620","file_date_updated":"2020-07-14T12:45:47Z","year":"2018","publisher":"BioMed Central","department":[{"_id":"FyKo"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"9811"},{"status":"public","relation":"research_data","id":"9812"}]},"author":[{"last_name":"Zapata","first_name":"Luis","full_name":"Zapata, Luis"},{"first_name":"Oriol","last_name":"Pich","full_name":"Pich, Oriol"},{"full_name":"Serrano, Luis","last_name":"Serrano","first_name":"Luis"},{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"full_name":"Ossowski, Stephan","first_name":"Stephan","last_name":"Ossowski"},{"last_name":"Schaefer","first_name":"Martin","full_name":"Schaefer, Martin"}],"volume":19,"date_created":"2018-12-11T11:45:35Z","date_updated":"2023-09-13T09:01:32Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"31","citation":{"ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0."},"publication":"Genome Biology","date_published":"2018-05-31T00:00:00Z","type":"journal_article","abstract":[{"text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"279","intvolume":" 19","status":"public","ddc":["570"],"title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5708","checksum":"f3e4922486bd9bf1483271bdbed394a7","date_created":"2018-12-17T14:05:01Z","date_updated":"2020-07-14T12:45:47Z","access_level":"open_access","file_name":"2018_GenomeBiology_Zapata.pdf","file_size":1414722,"content_type":"application/pdf","creator":"dernst"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","citation":{"ista":"Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044.","ieee":"S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018.","apa":"Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044","ama":"Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044","chicago":"Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044.","mla":"Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044.","short":"S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018)."},"publication":"The EMBO Journal","article_type":"original","issue":"15","abstract":[{"lang":"eng","text":"Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins."}],"type":"journal_article","file":[{"creator":"dernst","file_size":2846470,"content_type":"application/pdf","file_name":"2018_EMBO_Truckenbrodt.pdf","access_level":"open_access","date_created":"2018-12-17T14:17:29Z","date_updated":"2020-07-14T12:44:56Z","checksum":"a540feb6c9af6aefc78de531461a8835","file_id":"5710","relation":"main_file"}],"oa_version":"Published Version","_id":"145","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 37","title":"Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission","status":"public","ddc":["570"],"publication_identifier":{"issn":["0261-4189"]},"month":"08","doi":"10.15252/embj.201798044","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["29950309"],"isi":["000440416900005"]},"quality_controlled":"1","isi":1,"publist_id":"7778","file_date_updated":"2020-07-14T12:44:56Z","article_number":"e98044","author":[{"id":"45812BD4-F248-11E8-B48F-1D18A9856A87","last_name":"Truckenbrodt","first_name":"Sven M","full_name":"Truckenbrodt, Sven M"},{"full_name":"Viplav, Abhiyan","last_name":"Viplav","first_name":"Abhiyan"},{"last_name":"Jähne","first_name":"Sebsatian","full_name":"Jähne, Sebsatian"},{"first_name":"Angela","last_name":"Vogts","full_name":"Vogts, Angela"},{"last_name":"Denker","first_name":"Annette","full_name":"Denker, Annette"},{"full_name":"Wildhagen, Hanna","first_name":"Hanna","last_name":"Wildhagen"},{"last_name":"Fornasiero","first_name":"Eugenio","full_name":"Fornasiero, Eugenio"},{"last_name":"Rizzoli","first_name":"Silvio","full_name":"Rizzoli, Silvio"}],"volume":37,"date_updated":"2023-09-13T09:02:48Z","date_created":"2018-12-11T11:44:52Z","pmid":1,"acknowledgement":"We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A).","year":"2018","department":[{"_id":"JoDa"}],"publisher":"Wiley","publication_status":"published"},{"publist_id":"7359","file_date_updated":"2020-07-14T12:46:32Z","department":[{"_id":"JiFr"}],"publisher":"Wiley-Blackwell","publication_status":"published","pmid":1,"year":"2018","acknowledgement":"This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ","volume":41,"date_created":"2018-12-11T11:46:36Z","date_updated":"2023-09-13T09:03:18Z","author":[{"first_name":"Ligang","last_name":"Fan","full_name":"Fan, Ligang"},{"full_name":"Zhao, Lei","last_name":"Zhao","first_name":"Lei"},{"last_name":"Hu","first_name":"Wei","full_name":"Hu, Wei"},{"full_name":"Li, Weina","first_name":"Weina","last_name":"Li"},{"last_name":"Novák","first_name":"Ondřej","full_name":"Novák, Ondřej"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"first_name":"Sibu","last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"},{"first_name":"Jinbo","last_name":"Shen","full_name":"Shen, Jinbo"},{"last_name":"Jiang","first_name":"Liwen","full_name":"Jiang, Liwen"},{"full_name":"Qiu, Quan","first_name":"Quan","last_name":"Qiu"}],"month":"05","isi":1,"quality_controlled":"1","external_id":{"pmid":["29360148"],"isi":["000426870500012"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/pce.13153","type":"journal_article","abstract":[{"lang":"eng","text":"AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. "}],"intvolume":" 41","title":"NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development","ddc":["580"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"462","file":[{"checksum":"6a20f843565f962cb20281cdf5e40914","date_updated":"2020-07-14T12:46:32Z","date_created":"2019-11-18T16:22:22Z","file_id":"7042","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1937976,"access_level":"open_access","file_name":"2018_PlantCellEnv_Fan.pdf"}],"oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"850 - 864","article_type":"original","citation":{"chicago":"Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153.","mla":"Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153.","short":"L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864.","ista":"Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864.","apa":"Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153","ieee":"L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018.","ama":"Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153"},"publication":"Plant, Cell and Environment","date_published":"2018-05-01T00:00:00Z"},{"year":"2018","acknowledgement":"S.Altmeyer is a Serra Húnter Fellow","publication_status":"published","publisher":"Elsevier","department":[{"_id":"BjHo"}],"author":[{"id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5964-0203","first_name":"Sebastian","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian"}],"date_updated":"2023-09-13T09:03:44Z","date_created":"2018-12-11T11:46:56Z","volume":452,"file_date_updated":"2020-07-14T12:46:37Z","publist_id":"7297","oa":1,"external_id":{"isi":["000425547700061"]},"isi":1,"quality_controlled":"1","doi":"10.1016/j.jmmm.2017.12.073","language":[{"iso":"eng"}],"month":"04","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"519","ddc":["530"],"status":"public","title":"Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow","intvolume":" 452","oa_version":"Submitted Version","file":[{"creator":"dernst","file_size":17309535,"content_type":"application/pdf","file_name":"2018_Magnetism_Altmeyer.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:37Z","date_created":"2020-05-14T14:41:17Z","checksum":"431f5cd4a628d7ca21161f82b14ccb4f","file_id":"7838","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. "}],"publication":"Journal of Magnetism and Magnetic Materials","citation":{"ama":"Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073","apa":"Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073","ieee":"S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018.","ista":"Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441.","short":"S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441.","mla":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073.","chicago":"Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073."},"article_type":"original","page":"427 - 441","date_published":"2018-04-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1"},{"abstract":[{"text":"We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 11275","title":"New approaches for almost-sure termination of probabilistic programs","status":"public","_id":"5679","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-12-01T00:00:00Z","page":"181-201","citation":{"short":"M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201.","mla":"Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11.","chicago":"Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11.","ama":"Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11","ieee":"M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201.","apa":"Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11","ista":"Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201."},"volume":11275,"date_created":"2018-12-16T22:59:20Z","date_updated":"2023-09-13T09:02:22Z","author":[{"last_name":"Huang","first_name":"Mingzhang","full_name":"Huang, Mingzhang"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"editor":[{"first_name":"Sukyoung","last_name":"Ryu","full_name":"Ryu, Sukyoung"}],"year":"2018","publication_identifier":{"isbn":["9783030027674"],"issn":["03029743"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-02768-1_11","conference":{"start_date":"2018-12-02","location":"Wellington, New Zealand","end_date":"2018-12-06","name":"16th Asian Symposium on Programming Languages and Systems, APLAS"},"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1806.06683"}],"oa":1,"external_id":{"arxiv":["1806.06683"],"isi":["000916310900011"]}},{"isi":1,"quality_controlled":"1","external_id":{"isi":["000427101600018"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.conb.2017.12.005","month":"02","publisher":"Elsevier","department":[{"_id":"GaNo"}],"publication_status":"published","year":"2018","volume":48,"date_updated":"2023-09-13T09:01:56Z","date_created":"2018-12-11T11:47:06Z","author":[{"full_name":"Sacco, Roberto","last_name":"Sacco","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cacci","first_name":"Emanuele","full_name":"Cacci, Emanuele"},{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"publist_id":"7268","page":"131 - 138","citation":{"chicago":"Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier, 2018. https://doi.org/10.1016/j.conb.2017.12.005.","mla":"Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005.","short":"R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138.","ista":"Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138.","ieee":"R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier, pp. 131–138, 2018.","apa":"Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005","ama":"Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005"},"publication":"Current Opinion in Neurobiology","date_published":"2018-02-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 48","title":"Neural stem cells in neuropsychiatric disorders","status":"public","_id":"546","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies."}]},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"This document contains the full list of genes with their respective significance and dN/dS values. 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(2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","mla":"Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1."},"oa":1,"date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401414.v1"},{"publisher":"Springer Nature","department":[{"_id":"FyKo"}],"status":"public","title":"Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9811","year":"2018","oa_version":"Preprint","date_updated":"2023-09-13T09:01:31Z","date_created":"2021-08-06T12:53:49Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"279"}]},"author":[{"first_name":"Luis","last_name":"Zapata","full_name":"Zapata, Luis"},{"full_name":"Pich, Oriol","first_name":"Oriol","last_name":"Pich"},{"first_name":"Luis","last_name":"Serrano","full_name":"Serrano, Luis"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Kondrashov, Fyodor"},{"full_name":"Ossowski, Stephan","last_name":"Ossowski","first_name":"Stephan"},{"last_name":"Schaefer","first_name":"Martin","full_name":"Schaefer, Martin"}],"type":"research_data_reference","abstract":[{"text":"This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb)","lang":"eng"}],"citation":{"ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018).","mla":"Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1."},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.6401390.v1","open_access":"1"}],"oa":1,"date_published":"2018-05-31T00:00:00Z","doi":"10.6084/m9.figshare.6401390.v1","article_processing_charge":"No","month":"05","day":"31"},{"quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000450976700002"]},"language":[{"iso":"eng"}],"doi":"10.1186/s12864-018-5173-0","publication_identifier":{"issn":["1471-2164"]},"month":"11","department":[{"_id":"SiHi"}],"publisher":"BioMed Central","publication_status":"published","year":"2018","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","volume":19,"date_updated":"2023-09-13T09:10:47Z","date_created":"2018-12-11T11:44:12Z","related_material":{"record":[{"id":"9807","status":"public","relation":"research_data"},{"id":"9808","status":"public","relation":"research_data"}]},"author":[{"full_name":"Higareda Almaraz, Juan","first_name":"Juan","last_name":"Higareda Almaraz"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"full_name":"Giroud, Maude","first_name":"Maude","last_name":"Giroud"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"full_name":"Gerhalter, Teresa","first_name":"Teresa","last_name":"Gerhalter"},{"full_name":"Herzig, Stephan","first_name":"Stephan","last_name":"Herzig"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"publist_id":"8035","file_date_updated":"2020-07-14T12:45:23Z","article_type":"original","citation":{"short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1)."},"publication":"BMC Genomics","date_published":"2018-11-03T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"03","intvolume":" 19","status":"public","ddc":["570"],"title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","_id":"20","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_name":"2018_BMCGenomics_Higareda.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":4629784,"file_id":"5712","relation":"main_file","date_created":"2018-12-17T14:52:57Z","date_updated":"2020-07-14T12:45:23Z","checksum":"a56516e734dab589dc7f3e1915973b4d"}],"type":"journal_article","issue":"1","abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}]},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","article_type":"original","publication":"Journal of the ACM","citation":{"apa":"Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018.","ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.","short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432."},"abstract":[{"text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Preprint","status":"public","title":"Non-malleable codes","intvolume":" 65","_id":"107","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"08","language":[{"iso":"eng"}],"doi":"10.1145/3178432","quality_controlled":"1","isi":1,"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"},{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2009/608"}],"external_id":{"isi":["000442938200004"]},"oa":1,"ec_funded":1,"publist_id":"7947","article_number":"20","date_updated":"2023-09-13T09:05:17Z","date_created":"2018-12-11T11:44:40Z","volume":65,"author":[{"last_name":"Dziembowski","first_name":"Stefan","full_name":"Dziembowski, Stefan"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Wichs, Daniel","first_name":"Daniel","last_name":"Wichs"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"KrPi"}],"year":"2018"},{"type":"journal_article","abstract":[{"lang":"eng","text":"In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge."}],"issue":"12","_id":"5676","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Occluding junctions as novel regulators of tissue mechanics during wound repair","status":"public","intvolume":" 217","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Journal of Cell Biology","citation":{"ama":"Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048","ista":"Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283.","ieee":"L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018.","apa":"Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048","mla":"Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048.","short":"L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283.","chicago":"Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048."},"page":"4267-4283","date_published":"2018-12-01T00:00:00Z","ec_funded":1,"year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Rockefeller University Press","author":[{"first_name":"Lara","last_name":"Carvalho","full_name":"Carvalho, Lara"},{"full_name":"Patricio, Pedro","last_name":"Patricio","first_name":"Pedro"},{"full_name":"Ponte, Susana","first_name":"Susana","last_name":"Ponte"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"last_name":"Almeida","first_name":"Luis","full_name":"Almeida, Luis"},{"full_name":"Nunes, André S.","first_name":"André S.","last_name":"Nunes"},{"full_name":"Araújo, Nuno A.M.","last_name":"Araújo","first_name":"Nuno A.M."},{"full_name":"Jacinto, Antonio","first_name":"Antonio","last_name":"Jacinto"}],"date_updated":"2023-09-13T09:11:17Z","date_created":"2018-12-16T22:59:19Z","volume":217,"month":"12","publication_identifier":{"issn":["00219525"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30228162"}],"external_id":{"isi":["000451960800018"],"pmid":["30228162 "]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"doi":"10.1083/jcb.201804048","language":[{"iso":"eng"}]},{"author":[{"full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Vincent, Damien","last_name":"Vincent","first_name":"Damien"},{"first_name":"Ilya","last_name":"Tolstikhin","full_name":"Tolstikhin, Ilya"},{"full_name":"Ratsch, Gunnar","first_name":"Gunnar","last_name":"Ratsch"},{"full_name":"Gelly, Sylvain","first_name":"Sylvain","last_name":"Gelly"},{"full_name":"Scholkopf, Bernhard","last_name":"Scholkopf","first_name":"Bernhard"}],"oa_version":"Preprint","date_created":"2023-08-22T14:25:34Z","date_updated":"2023-09-13T09:08:24Z","_id":"14224","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"FrLo"}],"publication_status":"published","status":"public","title":"Clustering meets implicit generative models","abstract":[{"lang":"eng","text":"Clustering is a cornerstone of unsupervised learning which can be thought as disentangling multiple generative mechanisms underlying the data. In this paper we introduce an algorithmic framework to train mixtures of implicit generative models which we particularize for variational autoencoders. Relying on an additional set of discriminators, we propose a competitive procedure in which the models only need to approximate the portion of the data distribution from which they can produce realistic samples. As a byproduct, each model is simpler to train, and a clustering interpretation arises naturally from the partitioning of the training points among the models. We empirically show that our approach splits the training distribution in a reasonable way and increases the quality of the generated samples."}],"extern":"1","type":"conference","date_published":"2018-05-01T00:00:00Z","conference":{"end_date":"2018-05-03","location":"Vancouver, Canada","start_date":"2018-04-30","name":"International Conference on Machine Learning"},"language":[{"iso":"eng"}],"citation":{"ista":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018. Clustering meets implicit generative models. 6th International Conference on Learning Representations. International Conference on Machine Learning.","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., & Scholkopf, B. (2018). Clustering meets implicit generative models. In 6th International Conference on Learning Representations. Vancouver, Canada.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf, “Clustering meets implicit generative models,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","ama":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering meets implicit generative models. In: 6th International Conference on Learning Representations. ; 2018.","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.” In 6th International Conference on Learning Representations, 2018.","mla":"Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” 6th International Conference on Learning Representations, 2018.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 2018."},"oa":1,"external_id":{"arxiv":["1804.11130"]},"main_file_link":[{"url":"https://arxiv.org/abs/1804.11130","open_access":"1"}],"publication":"6th International Conference on Learning Representations","quality_controlled":"1","article_processing_charge":"No","month":"05","day":"01","scopus_import":"1"},{"type":"research_data_reference","abstract":[{"text":"Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb).","lang":"eng"}],"_id":"9807","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","publisher":"Springer Nature","department":[{"_id":"SiHi"}],"title":"Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","status":"public","related_material":{"record":[{"id":"20","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Juan","last_name":"Higareda Almaraz","full_name":"Higareda Almaraz, Juan"},{"last_name":"Karbiener","first_name":"Michael","full_name":"Karbiener, Michael"},{"first_name":"Maude","last_name":"Giroud","full_name":"Giroud, Maude"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"first_name":"Teresa","last_name":"Gerhalter","full_name":"Gerhalter, Teresa"},{"full_name":"Herzig, Stephan","last_name":"Herzig","first_name":"Stephan"},{"first_name":"Marcel","last_name":"Scheideler","full_name":"Scheideler, Marcel"}],"oa_version":"Published Version","date_created":"2021-08-06T12:26:53Z","date_updated":"2023-09-13T09:10:47Z","article_processing_charge":"No","month":"11","day":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295339.v1"}],"citation":{"short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","mla":"Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1","ieee":"J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1."},"oa":1,"doi":"10.6084/m9.figshare.7295339.v1","date_published":"2018-11-03T00:00:00Z"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9808","year":"2018","title":"Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","status":"public","publisher":"Springer Nature","department":[{"_id":"SiHi"}],"author":[{"last_name":"Higareda Almaraz","first_name":"Juan","full_name":"Higareda Almaraz, Juan"},{"first_name":"Michael","last_name":"Karbiener","full_name":"Karbiener, Michael"},{"full_name":"Giroud, Maude","first_name":"Maude","last_name":"Giroud"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","last_name":"Pauler","full_name":"Pauler, Florian"},{"full_name":"Gerhalter, Teresa","first_name":"Teresa","last_name":"Gerhalter"},{"first_name":"Stephan","last_name":"Herzig","full_name":"Herzig, Stephan"},{"full_name":"Scheideler, Marcel","last_name":"Scheideler","first_name":"Marcel"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"20"}]},"date_updated":"2023-09-13T09:10:47Z","date_created":"2021-08-06T12:31:57Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"lang":"eng","text":"Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb)."}],"citation":{"short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018).","mla":"Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.","chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1","ieee":"J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7295369.v1"}],"doi":"10.6084/m9.figshare.7295369.v1","date_published":"2018-11-03T00:00:00Z","month":"11","day":"03","article_processing_charge":"No"},{"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"},{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/783"}],"oa":1,"external_id":{"isi":["000516620100005"]},"language":[{"iso":"eng"}],"doi":"10.1145/3196494.3196534","conference":{"name":"ASIACCS: Asia Conference on Computer and Communications Security ","location":"Incheon, Republic of Korea","start_date":"2018-06-04","end_date":"2018-06-08"},"month":"06","publisher":"ACM","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"publication_status":"published","acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","year":"2018","date_created":"2018-12-11T11:45:07Z","date_updated":"2023-09-13T09:13:12Z","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gazi, Peter","first_name":"Peter","last_name":"Gazi"},{"full_name":"Kamath Hosdurg, Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","last_name":"Kamath Hosdurg"},{"id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","last_name":"Klein","full_name":"Klein, Karen"},{"full_name":"Osang, Georg F","last_name":"Osang","first_name":"Georg F","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Reyzin","first_name":"Lenoid","full_name":"Reyzin, Lenoid"},{"first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","first_name":"Michal","full_name":"Rybar, Michal"}],"ec_funded":1,"publist_id":"7723","page":"51 - 65","citation":{"mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534.","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings of the 2018 on Asia Conference on Computer and Communication Security, 51–65. ACM, 2018. https://doi.org/10.1145/3196494.3196534.","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In Proceedings of the 2018 on Asia Conference on Computer and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534","ieee":"J. F. Alwen et al., “On the memory hardness of data independent password hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65."},"publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","date_published":"2018-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","status":"public","title":"On the memory hardness of data independent password hashing functions","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"193","oa_version":"Submitted Version","type":"conference","abstract":[{"lang":"eng","text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF."}]},{"abstract":[{"lang":"eng","text":"We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"300","intvolume":" 10820","title":"On the bit security of cryptographic primitives","status":"public","article_processing_charge":"No","day":"31","scopus_import":"1","date_published":"2018-03-31T00:00:00Z","citation":{"ama":"Micciancio D, Walter M. On the bit security of cryptographic primitives. In: Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1","apa":"Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1","ieee":"D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10820, pp. 3–28.","ista":"Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives. Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.","short":"D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28.","mla":"Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1.","chicago":"Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1."},"page":"3 - 28","publist_id":"7581","ec_funded":1,"author":[{"full_name":"Micciancio, Daniele","first_name":"Daniele","last_name":"Micciancio"},{"full_name":"Walter, Michael","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3186-2482","first_name":"Michael","last_name":"Walter"}],"volume":10820,"date_created":"2018-12-11T11:45:42Z","date_updated":"2023-09-13T09:12:04Z","acknowledgement":"Research supported in part by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views, position or policy of the Government. The second author was also supported by the European Research Council, ERC consolidator grant (682815 - TOCNeT).","year":"2018","department":[{"_id":"KrPi"}],"publisher":"Springer","publication_status":"published","month":"03","doi":"10.1007/978-3-319-78381-9_1","conference":{"name":"Eurocrypt: Advances in Cryptology","end_date":"2018-05-03","location":"Tel Aviv, Israel","start_date":"2018-04-29"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/077"}],"external_id":{"isi":["000517097500001"]},"oa":1,"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"isi":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1137/16M1097201","quality_controlled":"1","isi":1,"project":[{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf","open_access":"1"}],"external_id":{"isi":["000428958900038"]},"month":"03","publication_identifier":{"issn":["08954801"]},"date_updated":"2023-09-13T09:34:38Z","date_created":"2018-12-11T11:45:46Z","volume":32,"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Iglesias Ham, Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","last_name":"Iglesias Ham","first_name":"Mabel"}],"publication_status":"published","publisher":"Society for Industrial and Applied Mathematics ","department":[{"_id":"HeEd"}],"acknowledgement":"This work was partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35 of the Austrian Science Fund (FWF).","year":"2018","publist_id":"7553","date_published":"2018-03-29T00:00:00Z","article_type":"original","page":"750 - 782","publication":"SIAM J Discrete Math","citation":{"ama":"Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201","ista":"Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society for Industrial and Applied Mathematics , pp. 750–782, 2018.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1097201","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201.","short":"H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201."},"day":"29","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","title":"On the optimality of the FCC lattice for soft sphere packing","status":"public","intvolume":" 32","_id":"312","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice."}],"issue":"1","type":"journal_article"},{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","article_type":"original","page":"412-414","publication":"Comptes Rendus Mathematique","citation":{"chicago":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005.","mla":"Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005.","short":"A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414.","ista":"Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414.","ieee":"A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018.","apa":"Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005","ama":"Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005"},"abstract":[{"text":"We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Preprint","status":"public","title":"On the number of non-hexagons in a planar tiling","intvolume":" 356","_id":"409","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"04","publication_identifier":{"issn":["1631073X"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.crma.2018.03.005","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1805.01652","open_access":"1"}],"external_id":{"isi":["000430402700009"],"arxiv":["1805.01652"]},"publist_id":"7420","date_updated":"2023-09-13T09:34:12Z","date_created":"2018-12-11T11:46:19Z","volume":356,"author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"HeEd"}],"year":"2018"},{"month":"03","doi":"10.1038/s41562-018-0320-9","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000446612000016"]},"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"quality_controlled":"1","ec_funded":1,"publist_id":"7404","file_date_updated":"2020-07-14T12:46:25Z","related_material":{"link":[{"url":"http://doi.org/10.1038/s41562-018-0342-3","relation":"erratum"}]},"author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"volume":2,"date_created":"2018-12-11T11:46:22Z","date_updated":"2023-09-13T09:38:54Z","year":"2018","publisher":"Nature Publishing Group","department":[{"_id":"KrCh"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"19","scopus_import":"1","date_published":"2018-03-19T00:00:00Z","citation":{"ista":"Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477.","ieee":"C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018.","apa":"Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9","ama":"Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9","chicago":"Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9.","mla":"Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9.","short":"C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477."},"publication":"Nature Human Behaviour","page":"469–477","article_type":"review","abstract":[{"text":"Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","file":[{"checksum":"571b8cc0ba14e8d5d8b18e439a9835eb","date_created":"2019-11-19T08:19:51Z","date_updated":"2020-07-14T12:46:25Z","file_id":"7052","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":598033,"access_level":"open_access","file_name":"2018_NatureHumanBeh_Hilbe.pdf"}],"_id":"419","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 2","ddc":["000"],"status":"public","title":"Partners and rivals in direct reciprocity"},{"publication_identifier":{"isbn":["978-3-030-00150-6"]},"month":"08","external_id":{"isi":["000884993200013"]},"oa":1,"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"doi":"10.1007/978-3-030-00151-3_13","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","location":"Bejing, China","start_date":"2018-09-04","end_date":"2018-09-06"},"language":[{"iso":"eng"}],"publist_id":"7976","file_date_updated":"2020-07-14T12:48:03Z","year":"2018","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143"},{"full_name":"Nickovic, Dejan","first_name":"Dejan","last_name":"Nickovic"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"first_name":"Eugene","last_name":"Asarin","full_name":"Asarin, Eugene"}],"volume":11022,"date_created":"2018-12-11T11:44:31Z","date_updated":"2023-09-13T09:35:46Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26","citation":{"short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232.","mla":"Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13.","ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232."},"page":"215 - 232","date_published":"2018-08-26T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.","lang":"eng"}],"_id":"78","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 11022","ddc":["000"],"title":"Online timed pattern matching using automata","status":"public","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:48:03Z","date_created":"2020-05-14T11:34:34Z","checksum":"436b7574934324cfa7d1d3986fddc65b","file_id":"7831","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":374851,"file_name":"2018_LNCS_Bakhirkin.pdf","access_level":"open_access"}]},{"article_number":"5690","file_date_updated":"2020-07-14T12:46:02Z","publist_id":"7548","year":"2018","publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"Nature Publishing Group","author":[{"id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","last_name":"Brauns","first_name":"Matthias","full_name":"Brauns, Matthias"},{"full_name":"Amitonov, Sergey","last_name":"Amitonov","first_name":"Sergey"},{"full_name":"Spruijtenburg, Paul","last_name":"Spruijtenburg","first_name":"Paul"},{"full_name":"Zwanenburg, Floris","last_name":"Zwanenburg","first_name":"Floris"}],"date_updated":"2023-09-13T09:38:00Z","date_created":"2018-12-11T11:45:47Z","volume":8,"month":"04","external_id":{"isi":["000429404300013"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1038/s41598-018-24004-y","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack.","lang":"eng"}],"issue":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"317","title":"Palladium gates for reproducible quantum dots in silicon","ddc":["539"],"status":"public","intvolume":" 8","pubrep_id":"1016","file":[{"file_name":"IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1850530,"creator":"system","relation":"main_file","file_id":"5256","date_created":"2018-12-12T10:17:04Z","date_updated":"2020-07-14T12:46:02Z","checksum":"20af238ca4ba6491b77270be8d826bf5"}],"oa_version":"Published Version","scopus_import":"1","day":"09","has_accepted_license":"1","article_processing_charge":"No","publication":"Scientific Reports","citation":{"chicago":"Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y.","mla":"Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y.","short":"M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018).","ista":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690.","ieee":"M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","apa":"Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y","ama":"Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y"},"date_published":"2018-04-09T00:00:00Z"},{"date_published":"2018-11-29T00:00:00Z","publication":"The FASEB Journal","citation":{"chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443.","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443.","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821.","ieee":"Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443"},"article_type":"original","page":"6808-6821","day":"29","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"194","status":"public","title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","intvolume":" 32","abstract":[{"lang":"eng","text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion."}],"issue":"12","type":"journal_article","doi":"10.1096/fj.201800443","language":[{"iso":"eng"}],"external_id":{"pmid":["29939785"],"isi":["000449359700035"]},"oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.1096/fj.201800443"}],"isi":1,"quality_controlled":"1","project":[{"_id":"25E3D34E-B435-11E9-9278-68D0E5697425","name":"Individual function and social role of oxytocin-like neuropeptides in ants"}],"month":"11","publication_identifier":{"issn":["08926638"]},"author":[{"full_name":"Liutkeviciute, Zita","last_name":"Liutkeviciute","first_name":"Zita"},{"full_name":"Gil Mansilla, Esther","first_name":"Esther","last_name":"Gil Mansilla"},{"full_name":"Eder, Thomas","last_name":"Eder","first_name":"Thomas"},{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Giulia Di Giglio","first_name":"Maria","full_name":"Giulia Di Giglio, Maria"},{"full_name":"Muratspahić, Edin","first_name":"Edin","last_name":"Muratspahić"},{"full_name":"Grebien, Florian","last_name":"Grebien","first_name":"Florian"},{"last_name":"Rattei","first_name":"Thomas","full_name":"Rattei, Thomas"},{"full_name":"Muttenthaler, Markus","last_name":"Muttenthaler","first_name":"Markus"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"},{"first_name":"Christian","last_name":"Gruber","full_name":"Gruber, Christian"}],"date_created":"2018-12-11T11:45:08Z","date_updated":"2023-09-13T09:37:32Z","volume":32,"year":"2018","pmid":1,"publication_status":"published","publisher":"FASEB","department":[{"_id":"SyCr"}],"publist_id":"7721"},{"scopus_import":"1","day":"16","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature Chemical Biology","citation":{"mla":"Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8.","short":"T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767.","chicago":"Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8.","ama":"Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8","ista":"Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767.","apa":"Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8","ieee":"T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018."},"article_type":"original","page":"764 - 767","date_published":"2018-07-16T00:00:00Z","type":"journal_article","abstract":[{"text":"L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control.","lang":"eng"}],"issue":"8","_id":"159","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Optical control of L-type Ca2+ channels using a diltiazem photoswitch","ddc":["570"],"intvolume":" 14","file":[{"content_type":"application/pdf","file_size":6321000,"creator":"dernst","file_name":"2018_NatureChemicalBiology_Fehrentz.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:03Z","date_created":"2020-05-14T12:14:09Z","checksum":"d42935094ec845f54a0688bf12986d62","relation":"main_file","file_id":"7832"}],"oa_version":"Submitted Version","month":"07","external_id":{"isi":["000438970200010"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1038/s41589-018-0090-8","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:03Z","publist_id":"7762","year":"2018","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JoDa"}],"author":[{"first_name":"Timm","last_name":"Fehrentz","full_name":"Fehrentz, Timm"},{"full_name":"Huber, Florian","last_name":"Huber","first_name":"Florian"},{"last_name":"Hartrampf","first_name":"Nina","full_name":"Hartrampf, Nina"},{"full_name":"Bruegmann, Tobias","first_name":"Tobias","last_name":"Bruegmann"},{"full_name":"Frank, James","first_name":"James","last_name":"Frank"},{"first_name":"Nicholas","last_name":"Fine","full_name":"Fine, Nicholas"},{"first_name":"Daniela","last_name":"Malan","full_name":"Malan, Daniela"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"},{"full_name":"Tikhonov, Denis","first_name":"Denis","last_name":"Tikhonov"},{"first_name":"Maritn","last_name":"Sumser","full_name":"Sumser, Maritn"},{"full_name":"Sasse, Philipp","last_name":"Sasse","first_name":"Philipp"},{"full_name":"Hodson, David","last_name":"Hodson","first_name":"David"},{"full_name":"Zhorov, Boris","last_name":"Zhorov","first_name":"Boris"},{"first_name":"Nikolaj","last_name":"Klocker","full_name":"Klocker, Nikolaj"},{"full_name":"Trauner, Dirk","last_name":"Trauner","first_name":"Dirk"}],"related_material":{"link":[{"url":"https://doi.org/10.1038/s41589-021-00744-3","relation":"erratum"}]},"date_created":"2018-12-11T11:44:56Z","date_updated":"2023-09-13T09:36:35Z","volume":14},{"title":"Parameter-independent strategies for pMDPs via POMDPs","status":"public","intvolume":" 11024","_id":"79","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol.","lang":"eng"}],"page":"53-70","citation":{"mla":"Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4.","short":"S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70.","chicago":"Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4.","ama":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4","ista":"Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.","ieee":"S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.","apa":"Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4"},"date_published":"2018-08-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Springer","year":"2018","date_updated":"2023-09-13T09:38:28Z","date_created":"2018-12-11T11:44:31Z","volume":11024,"author":[{"full_name":"Arming, Sebastian","first_name":"Sebastian","last_name":"Arming"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Katoen","first_name":"Joost P","id":"4524F760-F248-11E8-B48F-1D18A9856A87","full_name":"Katoen, Joost P"},{"first_name":"Ana","last_name":"Sokolova","full_name":"Sokolova, Ana"}],"publist_id":"7975","isi":1,"quality_controlled":"1","external_id":{"isi":["000548912200004"],"arxiv":["1806.05126"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.05126"}],"language":[{"iso":"eng"}],"conference":{"location":"Beijing, China","start_date":"2018-09-04","end_date":"2018-09-07","name":"QEST: Quantitative Evaluation of Systems"},"doi":"10.1007/978-3-319-99154-2_4","month":"08"},{"article_processing_charge":"No","day":"30","month":"04","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.1804.11130","date_published":"2018-04-30T00:00:00Z","external_id":{"arxiv":["1804.11130"]},"citation":{"ama":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv. doi:10.48550/arXiv.1804.11130","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” arXiv. .","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., & Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. arXiv. https://doi.org/10.48550/arXiv.1804.11130","ista":"Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130.","short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.).","mla":"Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” ArXiv, 1804.11130, doi:10.48550/arXiv.1804.11130.","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1804.11130."},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1804.11130","open_access":"1"}],"publication":"arXiv","extern":"1","abstract":[{"lang":"eng","text":"A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples."}],"type":"preprint","article_number":"1804.11130","oa_version":"Preprint","date_updated":"2023-09-13T12:23:03Z","date_created":"2023-09-13T12:20:49Z","author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Vincent, Damien","first_name":"Damien","last_name":"Vincent"},{"last_name":"Tolstikhin","first_name":"Ilya","full_name":"Tolstikhin, Ilya"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"}],"department":[{"_id":"FrLo"}],"title":"Competitive training of mixtures of independent deep generative models","status":"public","publication_status":"submitted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14327","year":"2018"},{"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2018-05-01T00:00:00Z","citation":{"ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018.","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7.","chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7."},"publication":"Annales Henri Poincare","page":"1507 - 1527","issue":"5","abstract":[{"text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case.","lang":"eng"}],"type":"journal_article","pubrep_id":"1011","file":[{"relation":"main_file","file_id":"4966","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","date_created":"2018-12-12T10:12:47Z","date_updated":"2020-07-14T12:46:22Z","access_level":"open_access","file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","file_size":582680,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","_id":"400","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 19","status":"public","ddc":["510"],"title":"Persistence of translational symmetry in the BCS model with radial pair interaction","month":"05","doi":"10.1007/s00023-018-0665-7","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000429799900008"]},"oa":1,"project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"quality_controlled":"1","isi":1,"ec_funded":1,"publist_id":"7429","file_date_updated":"2020-07-14T12:46:22Z","author":[{"full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","first_name":"Andreas"},{"first_name":"Alissa","last_name":"Geisinge","full_name":"Geisinge, Alissa"},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"full_name":"Loss, Michael","last_name":"Loss","first_name":"Michael"}],"volume":19,"date_updated":"2023-09-15T12:04:15Z","date_created":"2018-12-11T11:46:15Z","year":"2018","publisher":"Springer","department":[{"_id":"RoSe"}],"publication_status":"published"},{"scopus_import":"1","day":"07","article_processing_charge":"Yes","has_accepted_license":"1","publication":"PLoS One","citation":{"ista":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3).","apa":"Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049","ieee":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018.","ama":"Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049","chicago":"Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.","mla":"Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.","short":"K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018)."},"date_published":"2018-03-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. "}],"issue":"3","ddc":["530","571"],"status":"public","title":"Probabilistic models of individual and collective animal behavior","intvolume":" 13","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"406","oa_version":"Submitted Version","file":[{"file_id":"5165","relation":"main_file","date_created":"2018-12-12T10:15:43Z","date_updated":"2020-07-14T12:46:22Z","checksum":"684229493db75b43e98a46cd922da497","file_name":"IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf","access_level":"open_access","creator":"system","file_size":6887358,"content_type":"application/pdf"}],"pubrep_id":"995","month":"03","isi":1,"quality_controlled":"1","project":[{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000426896800032"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0193049","file_date_updated":"2020-07-14T12:46:22Z","publist_id":"7423","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"year":"2018","acknowledgement":"This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES).","date_created":"2018-12-11T11:46:18Z","date_updated":"2023-09-15T12:06:19Z","volume":13,"author":[{"first_name":"Katarína","last_name":"Bod’Ová","full_name":"Bod’Ová, Katarína"},{"id":"315BCD80-F248-11E8-B48F-1D18A9856A87","last_name":"Mitchell","first_name":"Gabriel","full_name":"Mitchell, Gabriel"},{"full_name":"Harpaz, Roy","first_name":"Roy","last_name":"Harpaz"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"related_material":{"record":[{"id":"9831","status":"public","relation":"research_data"}]}},{"type":"journal_article","issue":"2","abstract":[{"text":"Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"457","intvolume":" 2","title":"Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity","status":"public","oa_version":"None","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z","ieee":"M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018.","apa":"Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z","ista":"Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366.","short":"M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366.","mla":"Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z.","chicago":"Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z."},"publication":"Nature Ecology and Evolution","page":"359 - 366","date_published":"2018-02-01T00:00:00Z","ec_funded":1,"publist_id":"7364","year":"2018","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Springer Nature","publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"202"}]},"author":[{"last_name":"Pleska","first_name":"Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros"},{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","last_name":"Lang"},{"full_name":"Refardt, Dominik","first_name":"Dominik","last_name":"Refardt"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"volume":2,"date_updated":"2023-09-15T12:04:57Z","date_created":"2018-12-11T11:46:35Z","month":"02","external_id":{"isi":["000426516400027"]},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"_id":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41559-017-0424-z","language":[{"iso":"eng"}]}]