[{"oa":1,"issue":"6","date_updated":"2023-09-20T11:05:36Z","acknowledgement":"This work was partly supported by the starting grants ADAPT and BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012, ERC-2014-StG_638176 and ERC-2011-ADG_20110209).","date_published":"2017-09-01T00:00:00Z","month":"09","intvolume":" 36","year":"2017","page":"312 - 337","external_id":{"isi":["000408634200019"]},"day":"01","status":"public","ddc":["000"],"date_created":"2018-12-11T11:51:37Z","volume":36,"oa_version":"Submitted Version","isi":1,"publication":"Computer Graphics Forum","doi":"10.1111/cgf.12941","title":"Adaptive physically based models in computer graphics","author":[{"full_name":"Manteaux, Pierre","first_name":"Pierre","last_name":"Manteaux"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"},{"full_name":"Narain, Rahul","first_name":"Rahul","last_name":"Narain"},{"full_name":"Redon, Stéphane","last_name":"Redon","first_name":"Stéphane"},{"last_name":"Faure","first_name":"François","full_name":"Faure, François"},{"full_name":"Cani, Marie","first_name":"Marie","last_name":"Cani"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_name":"IST-2016-634-v1+1_starAdaptivity-cgf.pdf","date_created":"2018-12-12T10:16:21Z","date_updated":"2020-07-14T12:44:47Z","file_size":1434439,"creator":"system","content_type":"application/pdf","file_id":"5208","checksum":"7676e9a9ead6d58c3000988c97deb2ef","access_level":"open_access","relation":"main_file"}],"publisher":"Wiley-Blackwell","has_accepted_license":"1","pubrep_id":"634","language":[{"iso":"eng"}],"publist_id":"5873","department":[{"_id":"ChWo"}],"article_processing_charge":"No","quality_controlled":"1","_id":"1367","abstract":[{"text":"One of the major challenges in physically based modelling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes and particles. Applications range from fluids, through deformable bodies, to articulated solids.","lang":"eng"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:44:47Z","publication_identifier":{"issn":["01677055"]},"citation":{"mla":"Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37, doi:10.1111/cgf.12941.","apa":"Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., & Cani, M. (2017). Adaptive physically based models in computer graphics. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12941","chicago":"Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum. Wiley-Blackwell, 2017. https://doi.org/10.1111/cgf.12941.","short":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337.","ieee":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive physically based models in computer graphics,” Computer Graphics Forum, vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017.","ista":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.","ama":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 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Computer Graphics Forum. 2017;36(6):312-337. doi:10.1111/cgf.12941"},"publication_status":"published"},{"project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"}],"publication_status":"published","_id":"1407","quality_controlled":"1","citation":{"apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006.","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2. Elsevier, pp. 230–253, 2017.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006."},"type":"journal_article","scopus_import":"1","arxiv":1,"abstract":[{"lang":"eng","text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study."}],"language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"5800","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Mária","last_name":"Svoreňová","full_name":"Svoreňová, Mária"},{"orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan"},{"full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Cěrná","first_name":"Ivana","full_name":"Cěrná, Ivana"},{"first_name":"Cǎlin","last_name":"Belta","full_name":"Belta, Cǎlin"}],"publisher":"Elsevier","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1689"}]},"isi":1,"ec_funded":1,"oa_version":"Preprint","doi":"10.1016/j.nahs.2016.04.006","main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"publication":"Nonlinear Analysis: Hybrid Systems","date_created":"2018-12-11T11:51:50Z","day":"01","status":"public","volume":23,"year":"2017","page":"230 - 253","external_id":{"arxiv":["1410.5387"],"isi":["000390637000014"]},"date_updated":"2023-09-20T09:43:09Z","issue":"2","oa":1,"intvolume":" 23","month":"02","date_published":"2017-02-01T00:00:00Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"first_name":"Rajiv","last_name":"Khanna","full_name":"Khanna, Rajiv"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"},{"full_name":"Jaggi, Martin","first_name":"Martin","last_name":"Jaggi"}],"title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","publisher":"ML Research Press","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"FrLo"}],"_id":"14205","quality_controlled":"1","citation":{"mla":"Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017, pp. 860–68.","apa":"Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.","chicago":"Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 54:860–68. ML Research Press, 2017.","ama":"Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. Vol 54. ML Research Press; 2017:860-868.","short":"F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868.","ista":"Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.","ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868."},"extern":"1","type":"conference","arxiv":1,"abstract":[{"text":"Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions.","lang":"eng"}],"publication_status":"published","date_updated":"2023-09-13T09:49:10Z","oa":1,"intvolume":" 54","month":"02","date_published":"2017-02-21T00:00:00Z","year":"2017","external_id":{"arxiv":["1702.06457"]},"page":"860-868","conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2017-04-20","end_date":"2017-04-22","location":"Fort Lauderdale, FL, United States"},"date_created":"2023-08-22T14:17:19Z","day":"21","status":"public","volume":54,"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.06457"}],"publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Greedy algorithms for cone constrained optimization with convergence guarantees","oa":1,"author":[{"full_name":"Locatello, Francesco","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"last_name":"Jaggi","first_name":"Martin","full_name":"Jaggi, Martin"}],"date_updated":"2023-09-13T08:32:23Z","month":"05","date_published":"2017-05-31T00:00:00Z","year":"2017","language":[{"iso":"eng"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2017-12-04","end_date":"2017-12-09","location":"Long Beach, CA, United States"},"department":[{"_id":"FrLo"}],"article_processing_charge":"No","external_id":{"arxiv":["1705.11041"]},"status":"public","quality_controlled":"1","day":"31","_id":"14206","date_created":"2023-08-22T14:17:38Z","type":"conference","arxiv":1,"abstract":[{"lang":"eng","text":"Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings."}],"citation":{"apa":"Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In Advances in Neural Information Processing Systems. Long Beach, CA, United States.","mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” Advances in Neural Information Processing Systems, 2017.","ama":"Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: Advances in Neural Information Processing Systems. ; 2017.","ista":"Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017.","ieee":"F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in Advances in Neural Information Processing Systems, Long Beach, CA, United States, 2017.","chicago":"Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In Advances in Neural Information Processing Systems, 2017."},"publication_identifier":{"isbn":["9781510860964"]},"extern":"1","oa_version":"Preprint","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1705.11041","open_access":"1"}],"publication":"Advances in Neural Information Processing Systems"},{"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"publication_status":"published","citation":{"apa":"Akopyan, A., & Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. Mathematical Association of America. https://doi.org/10.4169/amer.math.monthly.124.7.588","mla":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” The American Mathematical Monthly, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:10.4169/amer.math.monthly.124.7.588.","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596.","ieee":"A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” The American Mathematical Monthly, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017.","ista":"Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596.","ama":"Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 2017;124(7):588-596. doi:10.4169/amer.math.monthly.124.7.588","chicago":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” The American Mathematical Monthly. Mathematical Association of America, 2017. https://doi.org/10.4169/amer.math.monthly.124.7.588."},"publication_identifier":{"issn":["00029890"]},"type":"journal_article","scopus_import":"1","abstract":[{"text":"We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor ½ cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape.","lang":"eng"}],"arxiv":1,"_id":"909","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"HeEd"}],"publist_id":"6534","language":[{"iso":"eng"}],"article_type":"original","publisher":"Mathematical Association of America","author":[{"full_name":"Akopyan, Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"first_name":"Vladislav","last_name":"Vysotsky","full_name":"Vysotsky, Vladislav"}],"title":"On the lengths of curves passing through boundary points of a planar convex shape","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://arxiv.org/abs/1605.07997","open_access":"1"}],"doi":"10.4169/amer.math.monthly.124.7.588","publication":"The American Mathematical Monthly","isi":1,"oa_version":"Submitted Version","ec_funded":1,"volume":124,"date_created":"2018-12-11T11:49:09Z","status":"public","day":"01","page":"588 - 596","external_id":{"isi":["000413947300002"],"arxiv":["1605.07997"]},"year":"2017","month":"01","intvolume":" 124","date_published":"2017-01-01T00:00:00Z","date_updated":"2023-10-17T11:24:57Z","issue":"7","oa":1},{"quality_controlled":"1","_id":"910","type":"journal_article","file_date_updated":"2020-07-14T12:48:15Z","abstract":[{"text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n","lang":"eng"}],"scopus_import":"1","citation":{"apa":"Novak, S., & Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.","ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668.","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” Genetics. 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In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset."}],"arxiv":1,"scopus_import":"1","publication_identifier":{"eisbn":["190172560X"]},"citation":{"apa":"Royer, A., Kolesnikov, A., & Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. https://doi.org/10.5244/c.31.85","mla":"Royer, Amélie, et al. Probabilistic Image Colorization. BMVA Press, 2017, p. 85.1-85.12, doi:10.5244/c.31.85.","ieee":"A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12.","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.","ista":"Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.","ama":"Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:10.5244/c.31.85","chicago":"Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. 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(2017). A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/1.4996580","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” Journal of Mathematical Physics, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:10.1063/1.4996580.","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity. Journal of Mathematical Physics. 58(8), 081901.","ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” Journal of Mathematical Physics, vol. 58, no. 8. AIP Publishing, 2017.","short":"A. Deuchert, Journal of Mathematical Physics 58 (2017).","ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. 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Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n","lang":"eng"}],"_id":"912","quality_controlled":"1","article_processing_charge":"No","publist_id":"6531","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"publisher":"AIP Publishing","title":"A lower bound for the BCS functional with boundary conditions at infinity","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Deuchert, Andreas","first_name":"Andreas","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","last_name":"Deuchert","orcid":"0000-0003-3146-6746"}],"main_file_link":[{"url":"https://arxiv.org/abs/1703.04616","open_access":"1"}],"doi":"10.1063/1.4996580","publication":" Journal of Mathematical Physics","isi":1,"ec_funded":1,"oa_version":"Submitted Version","volume":58,"date_created":"2018-12-11T11:49:10Z","status":"public","day":"01","external_id":{"isi":["000409197200015"]},"year":"2017","intvolume":" 58","month":"08","date_published":"2017-08-01T00:00:00Z","article_number":"081901","date_updated":"2024-02-28T13:07:56Z","issue":"8","oa":1},{"doi":"10.1098/rsos.170547","publication":"Royal Society Open Science","related_material":{"record":[{"id":"9853","status":"public","relation":"research_data"}]},"isi":1,"oa_version":"Published Version","volume":4,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576","592"],"date_created":"2018-12-11T11:49:10Z","day":"05","status":"public","external_id":{"isi":["000406670000025"]},"year":"2017","intvolume":" 4","month":"07","date_published":"2017-07-05T00:00:00Z","acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","article_number":"170547","date_updated":"2023-09-26T15:45:47Z","issue":"7","oa":1,"publication_status":"published","publication_identifier":{"issn":["20545703"]},"citation":{"apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., & Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.170547","mla":"Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:10.1098/rsos.170547.","ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547.","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017).","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” Royal Society Open Science, vol. 4, no. 7. Royal Society, The, 2017.","ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 2017;4(7). doi:10.1098/rsos.170547","chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” Royal Society Open Science. Royal Society, The, 2017. https://doi.org/10.1098/rsos.170547."},"file_date_updated":"2020-07-14T12:48:15Z","type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect."}],"_id":"914","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"SyCr"}],"publist_id":"6527","language":[{"iso":"eng"}],"pubrep_id":"849","has_accepted_license":"1","publisher":"Royal Society, The","file":[{"date_created":"2018-12-12T10:08:24Z","date_updated":"2020-07-14T12:48:15Z","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf","checksum":"351ae5e7a37e6e7d9295cd41146c4190","relation":"main_file","access_level":"open_access","creator":"system","file_size":530412,"file_id":"4684","content_type":"application/pdf"}],"author":[{"last_name":"Giehr","first_name":"Julia","full_name":"Giehr, Julia"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"first_name":"Alexandra","last_name":"Schrempf","full_name":"Schrempf, Alexandra"}],"title":"Ant queens increase their reproductive efforts after pathogen infection","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_published":"2017-07-01T00:00:00Z","month":"07","intvolume":" 2017","oa":1,"date_updated":"2023-09-26T15:43:27Z","conference":{"location":"Honolulu, HA, United States","end_date":"2017-07-26","start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition"},"external_id":{"isi":["000418371405009"]},"page":"4990-4999","year":"2017","volume":2017,"status":"public","day":"01","date_created":"2018-12-11T11:49:11Z","ddc":["000"],"doi":"10.1109/CVPR.2017.530","ec_funded":1,"oa_version":"Submitted Version","isi":1,"publisher":"IEEE","has_accepted_license":"1","author":[{"full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda"},{"full_name":"Andres, Bjoern","last_name":"Andres","first_name":"Bjoern"}],"title":"A message passing algorithm for the minimum cost multicut problem","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"access_level":"open_access","checksum":"7e51dacefa693574581a32da3eff63dc","relation":"main_file","creator":"dernst","file_size":883264,"file_id":"5849","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-01-18T12:52:46Z","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf"}],"department":[{"_id":"VlKo"}],"publist_id":"6526","article_processing_charge":"No","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes. We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:15Z","type":"conference","citation":{"short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","ieee":"P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999.","ista":"Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.","ama":"Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:10.1109/CVPR.2017.530","chicago":"Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.530.","apa":"Swoboda, P., & Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.530","mla":"Swoboda, Paul, and Bjoern Andres. A Message Passing Algorithm for the Minimum Cost Multicut Problem. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:10.1109/CVPR.2017.530."},"publication_identifier":{"isbn":["978-153860457-1"]},"quality_controlled":"1","_id":"915","publication_status":"published","project":[{"grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}]},{"has_accepted_license":"1","publisher":"IEEE","file":[{"file_name":"2017_CVPR_Swoboda2.pdf","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-01-18T12:49:38Z","creator":"dernst","file_size":944332,"file_id":"5848","content_type":"application/pdf","relation":"main_file","checksum":"e38a2740daad1ea178465843b5072906","access_level":"open_access"}],"author":[{"full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda"},{"first_name":"Carsten","last_name":"Rother","full_name":"Rother, Carsten"},{"last_name":"Abu Alhaija","first_name":"Carsten","full_name":"Abu Alhaija, Carsten"},{"first_name":"Dagmar","last_name":"Kainmueller","full_name":"Kainmueller, Dagmar"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","department":[{"_id":"VlKo"}],"publist_id":"6525","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-153860457-1"]},"citation":{"chicago":"Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.747.","ieee":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071.","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","ista":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.","ama":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:10.1109/CVPR.2017.747","mla":"Swoboda, Paul, et al. A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:10.1109/CVPR.2017.747.","apa":"Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., & Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.747"},"type":"conference","file_date_updated":"2020-07-14T12:48:15Z","scopus_import":"1","abstract":[{"lang":"eng","text":"We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each."}],"_id":"916","quality_controlled":"1","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7"}],"publication_status":"published","intvolume":" 2017","month":"01","date_published":"2017-01-01T00:00:00Z","date_updated":"2023-09-26T15:41:40Z","oa":1,"page":"7062-7071","external_id":{"isi":["000418371407018"]},"conference":{"end_date":"2017-07-26","start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition","location":"Honolulu, HA, United States"},"year":"2017","volume":2017,"ddc":["000"],"date_created":"2018-12-11T11:49:11Z","day":"01","status":"public","doi":"10.1109/CVPR.2017.747","isi":1,"ec_funded":1,"oa_version":"Submitted Version"},{"abstract":[{"text":"We propose a general dual ascent framework for Lagrangean decomposition of combinatorial problems. Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers.","lang":"eng"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:48:15Z","type":"conference","publication_identifier":{"isbn":["978-153860457-1"]},"citation":{"mla":"Swoboda, Paul, et al. A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:10.1109/CVPR.2017.526.","apa":"Swoboda, P., Kuske, J., & Savchynskyy, B. (2017). A dual ascent framework for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. https://doi.org/10.1109/CVPR.2017.526","chicago":"Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017. https://doi.org/10.1109/CVPR.2017.526.","ama":"Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:10.1109/CVPR.2017.526","ista":"Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4950–4960.","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.","ieee":"P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean decomposition of combinatorial problems,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960."},"quality_controlled":"1","_id":"917","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"publisher":"IEEE","has_accepted_license":"1","title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"first_name":"Jan","last_name":"Kuske","full_name":"Kuske, Jan"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"file":[{"file_name":"2017_CVPR_Swoboda.pdf","date_created":"2019-01-18T12:45:55Z","date_updated":"2020-07-14T12:48:15Z","creator":"dernst","file_size":898652,"file_id":"5847","content_type":"application/pdf","checksum":"72fd291046bd8e5717961bd68f6b6f03","relation":"main_file","access_level":"open_access"}],"department":[{"_id":"VlKo"}],"publist_id":"6524","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":2017,"status":"public","day":"01","ddc":["000"],"date_created":"2018-12-11T11:49:11Z","doi":"10.1109/CVPR.2017.526","oa_version":"Submitted Version","ec_funded":1,"isi":1,"date_published":"2017-07-01T00:00:00Z","intvolume":" 2017","month":"07","oa":1,"date_updated":"2023-09-26T15:41:11Z","conference":{"location":"Honolulu, HA, United States","start_date":"2017-07-21","end_date":"2017-07-26","name":"CVPR: Computer Vision and Pattern Recognition"},"external_id":{"isi":["000418371405005"]},"page":"4950-4960","year":"2017"},{"supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"status":"public","day":"02","date_created":"2018-12-11T11:49:18Z","ddc":["581","583","580"],"oa_version":"Published Version","related_material":{"record":[{"id":"1591","relation":"part_of_dissertation","status":"public"}]},"doi":"10.15479/AT:ISTA:th_842","degree_awarded":"PhD","oa":1,"date_updated":"2023-09-07T12:06:09Z","month":"06","alternative_title":["ISTA Thesis"],"date_published":"2017-06-02T00:00:00Z","year":"2017","page":"117","_id":"938","file_date_updated":"2020-07-14T12:48:15Z","type":"dissertation","abstract":[{"text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin.","lang":"eng"}],"citation":{"short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842","chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842.","apa":"Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842","mla":"Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842."},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file":[{"date_created":"2019-04-05T09:03:20Z","date_updated":"2020-07-14T12:48:15Z","file_name":"2017_Adamowski-Thesis_Source.docx","access_level":"closed","relation":"source_file","checksum":"193425764d9aaaed3ac57062a867b315","file_size":46903863,"creator":"dernst","file_id":"6215","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_size":8698888,"creator":"dernst","content_type":"application/pdf","file_id":"6216","checksum":"df5ab01be81f821e1b958596a1ec8d21","relation":"main_file","access_level":"open_access","file_name":"2017_Adamowski-Thesis.pdf","date_created":"2019-04-05T09:03:19Z","date_updated":"2020-07-14T12:48:15Z"}],"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","author":[{"first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","last_name":"Adamowski","full_name":"Adamowski, Maciek"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","pubrep_id":"842","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"6483","article_processing_charge":"No"},{"title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","author":[{"last_name":"Midya","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","full_name":"Midya, Bikashkali"},{"full_name":"Konotop, Vladimir","last_name":"Konotop","first_name":"Vladimir"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Physical Society","language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"6481","department":[{"_id":"MiLe"}],"_id":"939","quality_controlled":"1","citation":{"mla":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.033905.","apa":"Midya, B., & Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.033905","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.033905.","short":"B. Midya, V. Konotop, Physical Review Letters 119 (2017).","ieee":"B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” Physical Review Letters, vol. 119, no. 3. American Physical Society, 2017.","ista":"Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.","ama":"Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 2017;119(3). doi:10.1103/PhysRevLett.119.033905"},"publication_identifier":{"issn":["00319007"]},"type":"journal_article","scopus_import":"1","abstract":[{"text":"We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding.","lang":"eng"}],"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publication_status":"published","date_updated":"2023-09-26T15:39:46Z","issue":"3","oa":1,"intvolume":" 119","month":"07","date_published":"2017-07-18T00:00:00Z","article_number":"033905","year":"2017","external_id":{"isi":["000405718200012"]},"date_created":"2018-12-11T11:49:18Z","day":"18","status":"public","volume":119,"isi":1,"oa_version":"Submitted Version","ec_funded":1,"doi":"10.1103/PhysRevLett.119.033905","main_file_link":[{"url":"https://arxiv.org/abs/1706.04085 ","open_access":"1"}],"publication":"Physical Review Letters"},{"quality_controlled":"1","status":"public","day":"10","_id":"941","date_created":"2018-12-11T11:49:19Z","scopus_import":1,"abstract":[{"text":"Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ ","lang":"eng"}],"type":"conference","citation":{"apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis (pp. 376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225","mla":"Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379.","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa Barbara, CA, United States, 2017, pp. 376–379.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ACM; 2017:376-379. doi:10.1145/3092703.3098225","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225."},"oa_version":"None","publication":"Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis","publication_status":"published","doi":"10.1145/3092703.3098225","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Le, Xuan","last_name":"Le","first_name":"Xuan"},{"id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep","last_name":"Chu","full_name":"Chu, Duc Hiep"},{"full_name":"Lo, David","last_name":"Lo","first_name":"David"},{"full_name":"Le Goues, Claire","last_name":"Le Goues","first_name":"Claire"},{"full_name":"Visser, Willem","last_name":"Visser","first_name":"Willem"}],"title":"JFIX: Semantics-based repair of Java programs via symbolic PathFinder","date_updated":"2021-01-12T08:22:05Z","publisher":"ACM","date_published":"2017-07-10T00:00:00Z","month":"07","year":"2017","language":[{"iso":"eng"}],"publist_id":"6478","department":[{"_id":"ToHe"}],"conference":{"name":"ISSTA: International Symposium on Software Testing and Analysis","end_date":"2017-07-14","start_date":"2017-07-10","location":"Santa Barbara, CA, United States"},"page":"376 - 379 "},{"author":[{"full_name":"Le, Xuan","first_name":"Xuan","last_name":"Le"},{"full_name":"Chu, Duc Hiep","first_name":"Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87","last_name":"Chu"},{"full_name":"Lo, David","first_name":"David","last_name":"Lo"},{"full_name":"Le Goues, Claire","first_name":"Claire","last_name":"Le Goues"},{"full_name":"Visser, Willem","last_name":"Visser","first_name":"Willem"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"S3: Syntax- and semantic-guided repair synthesis via programming by examples","publisher":"ACM","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"ToHe"}],"publist_id":"6477","_id":"942","quality_controlled":"1","citation":{"mla":"Le, Xuan, et al. S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples. Vol. F130154, ACM, 2017, pp. 593–604, doi:10.1145/3106237.3106309.","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). S3: Syntax- and semantic-guided repair synthesis via programming by examples (Vol. F130154, pp. 593–604). Presented at the FSE: Foundations of Software Engineering, Paderborn, Germany: ACM. https://doi.org/10.1145/3106237.3106309","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “S3: Syntax- and Semantic-Guided Repair Synthesis via Programming by Examples,” F130154:593–604. ACM, 2017. https://doi.org/10.1145/3106237.3106309.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. S3: Syntax- and semantic-guided repair synthesis via programming by examples. In: Vol F130154. ACM; 2017:593-604. doi:10.1145/3106237.3106309","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “S3: Syntax- and semantic-guided repair synthesis via programming by examples,” presented at the FSE: Foundations of Software Engineering, Paderborn, Germany, 2017, vol. F130154, pp. 593–604.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, ACM, 2017, pp. 593–604.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. S3: Syntax- and semantic-guided repair synthesis via programming by examples. FSE: Foundations of Software Engineering vol. F130154, 593–604."},"publication_identifier":{"isbn":["978-145035105-8"]},"type":"conference","scopus_import":"1","abstract":[{"lang":"eng","text":"A notable class of techniques for automatic program repair is known as semantics-based. Such techniques, e.g., Angelix, infer semantic specifications via symbolic execution, and then use program synthesis to construct new code that satisfies those inferred specifications. However, the obtained specifications are naturally incomplete, leaving the synthesis engine with a difficult task of synthesizing a general solution from a sparse space of many possible solutions that are consistent with the provided specifications but that do not necessarily generalize. We present S3, a new repair synthesis engine that leverages programming-by-examples methodology to synthesize high-quality bug repairs. The novelty in S3 that allows it to tackle the sparse search space to create more general repairs is three-fold: (1) A systematic way to customize and constrain the syntactic search space via a domain-specific language, (2) An efficient enumeration-based search strategy over the constrained search space, and (3) A number of ranking features based on measures of the syntactic and semantic distances between candidate solutions and the original buggy program. We compare S3’s repair effectiveness with state-of-the-art synthesis engines Angelix, Enumerative, and CVC4. S3 can successfully and correctly fix at least three times more bugs than the best baseline on datasets of 52 bugs in small programs, and 100 bugs in real-world large programs. "}],"project":[{"grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","date_updated":"2023-09-26T15:38:36Z","month":"09","date_published":"2017-09-01T00:00:00Z","year":"2017","page":"593 - 604","external_id":{"isi":["000414279300055"]},"conference":{"name":"FSE: Foundations of Software Engineering","end_date":"2017-09-08","start_date":"2017-09-04","location":"Paderborn, Germany"},"date_created":"2018-12-11T11:49:19Z","day":"01","status":"public","volume":"F130154","isi":1,"oa_version":"None","doi":"10.1145/3106237.3106309"},{"date_updated":"2023-09-26T15:38:05Z","oa":1,"issue":"6345","date_published":"2017-06-30T00:00:00Z","month":"06","intvolume":" 356","year":"2017","external_id":{"pmid":["28663499"],"isi":["000404351500036"]},"page":"1379 - 1383","date_created":"2018-12-11T11:49:20Z","day":"30","status":"public","volume":356,"pmid":1,"ec_funded":1,"oa_version":"Submitted Version","isi":1,"publication":"Science","doi":"10.1126/science.aam5887","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Zagórski, Marcin P","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","last_name":"Zagórski"},{"last_name":"Tabata","first_name":"Yoji","full_name":"Tabata, Yoji"},{"full_name":"Brandenberg, Nathalie","last_name":"Brandenberg","first_name":"Nathalie"},{"full_name":"Lutolf, Matthias","first_name":"Matthias","last_name":"Lutolf"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455"},{"last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"},{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"},{"full_name":"Kicheva, Anna","first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","last_name":"Kicheva"}],"title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"AnKi"},{"_id":"GaTk"}],"publist_id":"6474","_id":"943","quality_controlled":"1","publication_identifier":{"issn":["00368075"]},"citation":{"short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.","ista":"Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383.","ieee":"M. P. Zagórski et al., “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” Science, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017.","ama":"Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 2017;356(6345):1379-1383. doi:10.1126/science.aam5887","chicago":"Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5887.","apa":"Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aam5887","mla":"Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887."},"scopus_import":"1","abstract":[{"lang":"eng","text":"Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation."}],"type":"journal_article","project":[{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF"},{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020"},{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"201439"}],"publication_status":"published"},{"page":"517 - 533.e3","external_id":{"isi":["000400466700011"]},"year":"2017","intvolume":" 94","month":"05","date_published":"2017-05-03T00:00:00Z","date_updated":"2023-09-26T15:37:02Z","issue":"3","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"doi":"10.1016/j.neuron.2017.04.012","publication":"Neuron","isi":1,"ec_funded":1,"oa_version":"None","volume":94,"date_created":"2018-12-11T11:49:20Z","status":"public","day":"03","article_processing_charge":"No","publist_id":"6473","department":[{"_id":"SiHi"},{"_id":"MaJö"}],"language":[{"iso":"eng"}],"publisher":"Cell Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","orcid":"0000-0002-8483-8753","last_name":"Beattie"},{"full_name":"Postiglione, Maria P","first_name":"Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","last_name":"Postiglione"},{"full_name":"Burnett, Laura","first_name":"Laura","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","last_name":"Burnett"},{"full_name":"Laukoter, Susanne","last_name":"Laukoter","orcid":"0000-0002-7903-3010","first_name":"Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"full_name":"Pauler, Florian","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"full_name":"Xiao, Guanxi","last_name":"Xiao","first_name":"Guanxi"},{"last_name":"Klezovitch","first_name":"Olga","full_name":"Klezovitch, Olga"},{"last_name":"Vasioukhin","first_name":"Valeri","full_name":"Vasioukhin, Valeri"},{"last_name":"Ghashghaei","first_name":"Troy","full_name":"Ghashghaei, Troy"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"title":"Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells","project":[{"grant_number":"618444","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","_id":"25D61E48-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"}],"publication_status":"published","publication_identifier":{"issn":["08966273"]},"citation":{"mla":"Beattie, Robert J., et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron, vol. 94, no. 3, Cell Press, 2017, p. 517–533.e3, doi:10.1016/j.neuron.2017.04.012.","apa":"Beattie, R. J., Postiglione, M. P., Burnett, L., Laukoter, S., Streicher, C., Pauler, F., … Hippenmeyer, S. (2017). Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2017.04.012","chicago":"Beattie, Robert J, Maria P Postiglione, Laura Burnett, Susanne Laukoter, Carmen Streicher, Florian Pauler, Guanxi Xiao, et al. “Mosaic Analysis with Double Markers Reveals Distinct Sequential Functions of Lgl1 in Neural Stem Cells.” Neuron. Cell Press, 2017. https://doi.org/10.1016/j.neuron.2017.04.012.","ista":"Beattie RJ, Postiglione MP, Burnett L, Laukoter S, Streicher C, Pauler F, Xiao G, Klezovitch O, Vasioukhin V, Ghashghaei T, Hippenmeyer S. 2017. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 94(3), 517–533.e3.","short":"R.J. Beattie, M.P. Postiglione, L. Burnett, S. Laukoter, C. Streicher, F. Pauler, G. Xiao, O. Klezovitch, V. Vasioukhin, T. Ghashghaei, S. Hippenmeyer, Neuron 94 (2017) 517–533.e3.","ieee":"R. J. Beattie et al., “Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells,” Neuron, vol. 94, no. 3. Cell Press, p. 517–533.e3, 2017.","ama":"Beattie RJ, Postiglione MP, Burnett L, et al. Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells. Neuron. 2017;94(3):517-533.e3. doi:10.1016/j.neuron.2017.04.012"},"type":"journal_article","abstract":[{"lang":"eng","text":"The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms."}],"scopus_import":"1","_id":"944","quality_controlled":"1"},{"publication_identifier":{"eissn":["2050-084X"]},"extern":"1","citation":{"chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674.","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674"},"file_date_updated":"2021-06-02T14:33:36Z","type":"journal_article","abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"scopus_import":"1","_id":"9445","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"eLife Sciences Publications","file":[{"content_type":"application/pdf","file_id":"9446","creator":"cziletti","file_size":1603102,"access_level":"open_access","checksum":"4cfcdd67511ae4aed3d993550e46e146","relation":"main_file","success":1,"file_name":"2017_eLife_Lyons.pdf","date_updated":"2021-06-02T14:33:36Z","date_created":"2021-06-02T14:33:36Z"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","author":[{"full_name":"Lyons, David B","last_name":"Lyons","first_name":"David B"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"article_processing_charge":"No","department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"article_type":"original","pmid":1,"volume":6,"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2021-06-02T14:28:58Z","status":"public","day":"15","doi":"10.7554/elife.30674","publication":"eLife","oa_version":"Published Version","month":"11","intvolume":" 6","date_published":"2017-11-15T00:00:00Z","article_number":"e30674","date_updated":"2021-12-14T07:54:36Z","oa":1,"external_id":{"pmid":["29140247"]},"year":"2017"},{"oa_version":"Published Version","isi":1,"publication":"Molecular Biology and Evolution","doi":"10.1093/molbev/msx190","day":"06","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570","576"],"date_created":"2018-12-11T11:49:20Z","volume":34,"year":"2017","external_id":{"isi":["000411814800016"]},"page":"2637 - 2649","oa":1,"issue":"10","date_updated":"2023-09-26T15:36:34Z","date_published":"2017-07-06T00:00:00Z","month":"07","intvolume":" 34","publication_status":"published","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","call_identifier":"FWF"}],"quality_controlled":"1","_id":"945","abstract":[{"text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.","lang":"eng"}],"scopus_import":"1","type":"journal_article","file_date_updated":"2020-07-14T12:48:15Z","citation":{"chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2017. https://doi.org/10.1093/molbev/msx190.","ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017.","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:10.1093/molbev/msx190.","apa":"Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190"},"publication_identifier":{"issn":["07374038"]},"pubrep_id":"848","language":[{"iso":"eng"}],"publist_id":"6472","department":[{"_id":"BeVi"}],"article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Huylmans, Ann K","last_name":"Huylmans","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"full_name":"Macon, Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_size":462863,"creator":"system","file_id":"4810","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"009fd68043211d645ceb9d1de28274f2","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-12T10:10:23Z"}],"publisher":"Oxford University Press","has_accepted_license":"1"}]