[{"publication_identifier":{"issn":["03044920"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.4077/CJP.2017.BAF469","quality_controlled":"1","external_id":{"pmid":["28847140"]},"publist_id":"7142","volume":60,"date_updated":"2021-01-12T08:07:28Z","date_created":"2018-12-11T11:47:40Z","author":[{"first_name":"Wuping","last_name":"Sun","full_name":"Sun, Wuping"},{"id":"34009CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Zhai","first_name":"Ming-Zhu","full_name":"Zhai, Ming-Zhu"},{"full_name":"Zhou, Qian","first_name":"Qian","last_name":"Zhou"},{"full_name":"Qian, Chengrui","last_name":"Qian","first_name":"Chengrui"},{"first_name":"Changyu","last_name":"Jiang","full_name":"Jiang, Changyu"}],"publisher":"Chinese Physiological Society","department":[{"_id":"RySh"}],"publication_status":"published","pmid":1,"year":"2017","article_processing_charge":"No","day":"31","scopus_import":1,"date_published":"2017-08-31T00:00:00Z","page":"207 - 214","article_type":"original","citation":{"ama":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469","ista":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 60(4), 207–214.","apa":"Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469","ieee":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp. 207–214, 2017.","mla":"Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology, vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:10.4077/CJP.2017.BAF469.","short":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology 60 (2017) 207–214.","chicago":"Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469."},"publication":"Chinese Journal of Physiology","issue":"4","abstract":[{"text":"It has been reported that nicotinamide-overload induces oxidative stress associated with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT) were also carried out in adult Sprague-Dawley rats treated with or without cumulative doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration significantly increased the plasma H2O2 levels associated with high insulin levels. Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration of nicotinic acid, another form of Vitamin B3, also significantly increased plasma insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic acid or nicotinamide impaired glucose metabolism. This study suggested that excess Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 60","ddc":["570"],"status":"public","title":"Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"643"},{"type":"journal_article","abstract":[{"text":"Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable.","lang":"eng"}],"issue":"307","_id":"642","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Localization errors in solving stochastic partial differential equations in the whole space","intvolume":" 86","oa_version":"Submitted Version","scopus_import":1,"day":"01","publication":"Mathematics of Computation","citation":{"ama":"Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397. doi:10.1090/mcom/3201","ista":"Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 86(307), 2373–2397.","ieee":"M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial differential equations in the whole space,” Mathematics of Computation, vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017.","apa":"Gerencser, M., & Gyöngy, I. (2017). Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. American Mathematical Society. https://doi.org/10.1090/mcom/3201","mla":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation, vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201.","short":"M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.","chicago":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation. American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201."},"page":"2373 - 2397","date_published":"2017-01-01T00:00:00Z","publist_id":"7144","year":"2017","publication_status":"published","department":[{"_id":"JaMa"}],"publisher":"American Mathematical Society","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","first_name":"Mate","full_name":"Gerencser, Mate"},{"last_name":"Gyöngy","first_name":"István","full_name":"Gyöngy, István"}],"date_created":"2018-12-11T11:47:40Z","date_updated":"2021-01-12T08:07:26Z","volume":86,"month":"01","publication_identifier":{"issn":["00255718"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.05535"}],"quality_controlled":"1","doi":"10.1090/mcom/3201","language":[{"iso":"eng"}]},{"author":[{"last_name":"Ashok","first_name":"Pranav","full_name":"Ashok, Pranav"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan"},{"full_name":"Meggendorfer, Tobias","first_name":"Tobias","last_name":"Meggendorfer"}],"volume":10426,"date_created":"2018-12-11T11:47:41Z","date_updated":"2021-01-12T08:07:32Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Springer","editor":[{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"},{"last_name":"Kunčak","first_name":"Viktor","full_name":"Kunčak, Viktor"}],"publication_status":"published","publist_id":"7135","ec_funded":1,"doi":"10.1007/978-3-319-63387-9_10","conference":{"name":"CAV: Computer Aided Verification","start_date":"2017-07-24","location":"Heidelberg, Germany","end_date":"2017-07-28"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.02326","open_access":"1"}],"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-331963386-2"]},"month":"07","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"645","intvolume":" 10426","status":"public","title":"Value iteration for long run average reward in markov decision processes","abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2017-07-13T00:00:00Z","citation":{"apa":"Ashok, P., Chatterjee, K., Daca, P., Kretinsky, J., & Meggendorfer, T. (2017). Value iteration for long run average reward in markov decision processes. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 201–221). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_10","ieee":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, and T. Meggendorfer, “Value iteration for long run average reward in markov decision processes,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 201–221.","ista":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration for long run average reward in markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 10426, 201–221.","ama":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration for long run average reward in markov decision processes. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:201-221. doi:10.1007/978-3-319-63387-9_10","chicago":"Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_10.","short":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221.","mla":"Ashok, Pranav, et al. Value Iteration for Long Run Average Reward in Markov Decision Processes. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 201–21, doi:10.1007/978-3-319-63387-9_10."},"page":"201 - 221","day":"13","scopus_import":1},{"publist_id":"7138","ec_funded":1,"year":"2017","publication_status":"published","publisher":"SIAM","department":[{"_id":"VlKo"}],"author":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"full_name":"Krokhin, Andrei","last_name":"Krokhin","first_name":"Andrei"},{"last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"}],"related_material":{"record":[{"relation":"other","status":"public","id":"1637"}]},"date_created":"2018-12-11T11:47:40Z","date_updated":"2023-02-23T10:07:49Z","volume":46,"month":"06","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1502.07327","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"doi":"10.1137/16M1091836","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"An instance of the valued constraint satisfaction problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P 6= NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in f0;1g corresponds to ordinary CSPs, where one deals only with the feasibility issue, and there is no optimization. This case is the subject of the algebraic CSP dichotomy conjecture predicting for which constraint languages CSPs are tractable (i.e., solvable in polynomial time) and for which they are NP-hard. The case when all allowed functions take only finite values corresponds to a finitevalued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Živný. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e., the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.","lang":"eng"}],"issue":"3","_id":"644","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The complexity of general-valued CSPs","status":"public","intvolume":" 46","oa_version":"Preprint","scopus_import":1,"day":"29","publication":"SIAM Journal on Computing","citation":{"ista":"Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued CSPs. SIAM Journal on Computing. 46(3), 1087–1110.","ieee":"V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” SIAM Journal on Computing, vol. 46, no. 3. SIAM, pp. 1087–1110, 2017.","apa":"Kolmogorov, V., Krokhin, A., & Rolinek, M. (2017). The complexity of general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16M1091836","ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. SIAM Journal on Computing. 2017;46(3):1087-1110. doi:10.1137/16M1091836","chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2017. https://doi.org/10.1137/16M1091836.","mla":"Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:10.1137/16M1091836.","short":"V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017) 1087–1110."},"page":"1087 - 1110","date_published":"2017-06-29T00:00:00Z"},{"scopus_import":1,"day":"01","page":"235 - 246","citation":{"apa":"Kuske, J., Swoboda, P., & Petra, S. (2017). A novel convex relaxation for non binary discrete tomography. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_19","ieee":"J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary discrete tomography,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246.","ista":"Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 235–246.","ama":"Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246. doi:10.1007/978-3-319-58771-4_19","chicago":"Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_19.","short":"J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 235–246.","mla":"Kuske, Jan, et al. A Novel Convex Relaxation for Non Binary Discrete Tomography. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:10.1007/978-3-319-58771-4_19."},"date_published":"2017-06-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations.","lang":"eng"}],"intvolume":" 10302","status":"public","title":"A novel convex relaxation for non binary discrete tomography","_id":"646","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","publication_identifier":{"isbn":["978-331958770-7"]},"month":"06","project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.03769","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-58771-4_19","conference":{"name":"SSVM: Scale Space and Variational Methods in Computer Vision","location":"Kolding, Denmark","start_date":"2017-06-04","end_date":"2017-06-08"},"ec_funded":1,"publist_id":"7132","department":[{"_id":"VlKo"}],"editor":[{"first_name":"François","last_name":"Lauze","full_name":"Lauze, François"},{"last_name":"Dong","first_name":"Yiqiu","full_name":"Dong, Yiqiu"},{"full_name":"Bjorholm Dahl, Anders","last_name":"Bjorholm Dahl","first_name":"Anders"}],"publisher":"Springer","publication_status":"published","year":"2017","volume":10302,"date_updated":"2021-01-12T08:07:34Z","date_created":"2018-12-11T11:47:41Z","author":[{"first_name":"Jan","last_name":"Kuske","full_name":"Kuske, Jan"},{"last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul"},{"last_name":"Petra","first_name":"Stefanie","full_name":"Petra, Stefanie"}]},{"author":[{"full_name":"Skórski, Maciej","first_name":"Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"date_created":"2018-12-11T11:47:42Z","date_updated":"2021-01-12T08:07:39Z","volume":10185,"year":"2017","publication_status":"published","editor":[{"full_name":"Jäger, Gerhard","first_name":"Gerhard","last_name":"Jäger"},{"full_name":"Steila, Silvia","last_name":"Steila","first_name":"Silvia"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"publist_id":"7125","conference":{"name":"TAMC: Theory and Applications of Models of Computation","end_date":"2017-04-22","location":"Bern, Switzerland","start_date":"2017-04-20"},"doi":"10.1007/978-3-319-55911-7_43","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/1186.pdf"}],"quality_controlled":"1","month":"04","publication_identifier":{"isbn":["978-331955910-0"]},"oa_version":"Submitted Version","_id":"648","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"On the complexity of breaking pseudoentropy","intvolume":" 10185","abstract":[{"text":"Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) differs from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2017-04-01T00:00:00Z","citation":{"chicago":"Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_43.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.","mla":"Skórski, Maciej. On the Complexity of Breaking Pseudoentropy. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:10.1007/978-3-319-55911-7_43.","ieee":"M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 600–613.","apa":"Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_43","ista":"Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 600–613.","ama":"Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:600-613. doi:10.1007/978-3-319-55911-7_43"},"page":"600 - 613","day":"01","scopus_import":1},{"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-58002-9_5","publication_identifier":{"eissn":["978-3-319-58002-9"],"isbn":["978-3-319-58001-2"]},"month":"10","department":[{"_id":"JaMa"}],"publisher":"Springer","editor":[{"last_name":"Najman","first_name":"Laurent","full_name":"Najman, Laurent"},{"first_name":"Pascal","last_name":"Romon","full_name":"Romon, Pascal"}],"publication_status":"published","year":"2017","volume":2184,"date_updated":"2022-05-24T07:01:33Z","date_created":"2018-12-11T11:47:42Z","author":[{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan"}],"publist_id":"7123","page":"159 - 174","citation":{"short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174.","mla":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:10.1007/978-3-319-58002-9_5.","chicago":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. https://doi.org/10.1007/978-3-319-58002-9_5.","ama":"Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. Modern Approaches to Discrete Curvature. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:10.1007/978-3-319-58002-9_5","ieee":"J. Maas, “Entropic Ricci curvature for discrete spaces,” in Modern Approaches to Discrete Curvature, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174.","apa":"Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman & P. Romon (Eds.), Modern Approaches to Discrete Curvature (Vol. 2184, pp. 159–174). Springer. https://doi.org/10.1007/978-3-319-58002-9_5","ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174."},"publication":"Modern Approaches to Discrete Curvature","date_published":"2017-10-05T00:00:00Z","series_title":"Lecture Notes in Mathematics","scopus_import":"1","article_processing_charge":"No","day":"05","intvolume":" 2184","title":"Entropic Ricci curvature for discrete spaces","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"649","oa_version":"None","type":"book_chapter","abstract":[{"text":"We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani.","lang":"eng"}]},{"publist_id":"7119","year":"2017","publication_status":"published","editor":[{"full_name":"Jäger, Gerhard","last_name":"Jäger","first_name":"Gerhard"},{"last_name":"Steila","first_name":"Silvia","full_name":"Steila, Silvia"}],"department":[{"_id":"KrPi"}],"publisher":"Springer","author":[{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski"}],"date_updated":"2021-01-12T08:07:46Z","date_created":"2018-12-11T11:47:42Z","volume":10185,"month":"01","publication_identifier":{"issn":["03029743"]},"main_file_link":[{"url":"https://eprint.iacr.org/2016/965.pdf","open_access":"1"}],"oa":1,"quality_controlled":"1","conference":{"end_date":"2017-04-22","start_date":"2017-04-20","location":"Bern, Switzerland","name":"TAMC: Theory and Applications of Models of Computation"},"doi":"10.1007/978-3-319-55911-7_42","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy.","lang":"eng"}],"_id":"650","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds","status":"public","intvolume":" 10185","oa_version":"Submitted Version","scopus_import":1,"day":"01","citation":{"mla":"Skórski, Maciej. A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 586–99, doi:10.1007/978-3-319-55911-7_42.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599.","chicago":"Skórski, Maciej. “A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds.” edited by Gerhard Jäger and Silvia Steila, 10185:586–99. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_42.","ama":"Skórski M. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:586-599. doi:10.1007/978-3-319-55911-7_42","ista":"Skórski M. 2017. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 586–599.","ieee":"M. Skórski, “A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 586–599.","apa":"Skórski, M. (2017). A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 586–599). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_42"},"page":"586 - 599","date_published":"2017-01-01T00:00:00Z"},{"_id":"6519","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Improved set-based symbolic algorithms for parity games","ddc":["004"],"intvolume":" 82","file":[{"checksum":"7c2c9d09970af79026d7e37d9b632ef8","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-04T12:56:52Z","file_id":"6520","relation":"main_file","creator":"kschuh","file_size":710185,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_LIPIcs-Chatterjee.pdf"}],"oa_version":"Published Version","type":"conference","abstract":[{"text":"Graph games with omega-regular winning conditions provide a mathematical framework to analyze a wide range of problems in the analysis of reactive systems and programs (such as the synthesis of reactive systems, program repair, and the verification of branching time properties). Parity conditions are canonical forms to specify omega-regular winning conditions. Graph games with parity conditions are equivalent to mu-calculus model checking, and thus a very important algorithmic problem. Symbolic algorithms are of great significance because they provide scalable algorithms for the analysis of large finite-state systems, as well as algorithms for the analysis of infinite-state systems with finite quotient. A set-based symbolic algorithm uses the basic set operations and the one-step predecessor operators. We consider graph games with n vertices and parity conditions with c priorities (equivalently, a mu-calculus formula with c alternations of least and greatest fixed points). While many explicit algorithms exist for graph games with parity conditions, for set-based symbolic algorithms there are only two algorithms (notice that we use space to refer to the number of sets stored by a symbolic algorithm): (a) the basic algorithm that requires O(n^c) symbolic operations and linear space; and (b) an improved algorithm that requires O(n^{c/2+1}) symbolic operations but also O(n^{c/2+1}) space (i.e., exponential space). In this work we present two set-based symbolic algorithms for parity games: (a) our first algorithm requires O(n^{c/2+1}) symbolic operations and only requires linear space; and (b) developing on our first algorithm, we present an algorithm that requires O(n^{c/3+1}) symbolic operations and only linear space. We also present the first linear space set-based symbolic algorithm for parity games that requires at most a sub-exponential number of symbolic operations. ","lang":"eng"}],"citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Set-Based Symbolic Algorithms for Parity Games,” Vol. 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017. https://doi.org/10.4230/LIPICS.CSL.2017.18.","mla":"Chatterjee, Krishnendu, et al. Improved Set-Based Symbolic Algorithms for Parity Games. Vol. 82, 18, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017, doi:10.4230/LIPICS.CSL.2017.18.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2017. Improved set-based symbolic algorithms for parity games. CSL: Conference on Computer Science Logic vol. 82, 18.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved set-based symbolic algorithms for parity games (Vol. 82). Presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden: Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik. https://doi.org/10.4230/LIPICS.CSL.2017.18","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Improved set-based symbolic algorithms for parity games,” presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden, 2017, vol. 82.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Improved set-based symbolic algorithms for parity games. In: Vol 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik; 2017. doi:10.4230/LIPICS.CSL.2017.18"},"date_published":"2017-08-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Dvorák, Wolfgang","first_name":"Wolfgang","last_name":"Dvorák"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}],"date_updated":"2023-02-14T10:08:25Z","date_created":"2019-06-04T12:42:43Z","volume":82,"article_number":"18","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"conference":{"name":"CSL: Conference on Computer Science Logic","end_date":"2017-08-24","start_date":"2017-08-20","location":"Stockholm, Sweden"},"doi":"10.4230/LIPICS.CSL.2017.18","language":[{"iso":"eng"}],"month":"08"},{"conference":{"name":"ISAAC: International Symposium on Algorithms and Computation","end_date":"2017-12-22","location":"Phuket, Thailand","start_date":"2017-12-09"},"doi":"10.4230/LIPICS.ISAAC.2017.34","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"},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"month":"12","author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774"}],"date_created":"2019-06-04T12:11:52Z","date_updated":"2021-01-12T08:07:51Z","volume":92,"year":"2017","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"article_number":"34","date_published":"2017-12-01T00:00:00Z","citation":{"short":"R. Fulek, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Fulek, Radoslav. Embedding Graphs into Embedded Graphs. Vol. 92, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ISAAC.2017.34.","chicago":"Fulek, Radoslav. “Embedding Graphs into Embedded Graphs,” Vol. 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ISAAC.2017.34.","ama":"Fulek R. Embedding graphs into embedded graphs. In: Vol 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ISAAC.2017.34","apa":"Fulek, R. (2017). Embedding graphs into embedded graphs (Vol. 92). Presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ISAAC.2017.34","ieee":"R. Fulek, “Embedding graphs into embedded graphs,” presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand, 2017, vol. 92.","ista":"Fulek R. 2017. Embedding graphs into embedded graphs. ISAAC: International Symposium on Algorithms and Computation vol. 92, 34."},"day":"01","has_accepted_license":"1","scopus_import":1,"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2017_LIPIcs-Fulek.pdf","file_size":588982,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"6518","checksum":"fc7a643e29621c8bbe49d36b39081f31","date_created":"2019-06-04T12:20:35Z","date_updated":"2020-07-14T12:47:33Z"}],"_id":"6517","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Embedding graphs into embedded graphs","status":"public","ddc":["510"],"intvolume":" 92","abstract":[{"text":"A (possibly degenerate) drawing of a graph G in the plane is approximable by an embedding if it can be turned into an embedding by an arbitrarily small perturbation. We show that testing, whether a drawing of a planar graph G in the plane is approximable by an embedding, can be carried out in polynomial time, if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation system (or equivalently the faces) of the embedding of G and the choice of outer face are fixed. In other words, we show that c-planarity with embedded pipes is tractable for graphs with fixed embeddings. To the best of our knowledge an analogous result was previously known essentially only when G is a cycle.","lang":"eng"}],"type":"conference"},{"type":"conference","article_number":"7846789","publist_id":"7100","abstract":[{"text":"We present an approach that enables robots to self-organize their sensorimotor behavior from scratch without providing specific information about neither the robot nor its environment. This is achieved by a simple neural control law that increases the consistency between external sensor dynamics and internal neural dynamics of the utterly simple controller. In this way, the embodiment and the agent-environment coupling are the only source of individual development. We show how an anthropomorphic tendon driven arm-shoulder system develops different behaviors depending on that coupling. For instance: Given a bottle half-filled with water, the arm starts to shake it, driven by the physical response of the water. When attaching a brush, the arm can be manipulated into wiping a table, and when connected to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said to discover the affordances of the world. When allowing two (simulated) humanoid robots to interact physically, they engage into a joint behavior development leading to, for instance, spontaneous cooperation. More social effects are observed if the robots can visually perceive each other. Although, as an observer, it is tempting to attribute an apparent intentionality, there is nothing of the kind put in. As a conclusion, we argue that emergent behavior may be much less rooted in explicit intentions, internal motivations, or specific reward systems than is commonly believed.","lang":"eng"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publisher":"IEEE","publication_status":"published","title":"Dynamical self consistency leads to behavioral development and emergent social interactions in robots","status":"public","_id":"652","year":"2017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_updated":"2021-01-12T08:07:51Z","date_created":"2018-12-11T11:47:43Z","author":[{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"},{"full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","first_name":"Georg S"}],"scopus_import":1,"publication_identifier":{"isbn":["978-150905069-7"]},"month":"02","day":"07","quality_controlled":"1","citation":{"ista":"Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , 7846789.","apa":"Der, R., & Martius, G. S. (2017). Dynamical self consistency leads to behavioral development and emergent social interactions in robots. Presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France: IEEE. https://doi.org/10.1109/DEVLRN.2016.7846789","ieee":"R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral development and emergent social interactions in robots,” presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France, 2017.","ama":"Der R, Martius GS. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. In: IEEE; 2017. doi:10.1109/DEVLRN.2016.7846789","chicago":"Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots.” IEEE, 2017. https://doi.org/10.1109/DEVLRN.2016.7846789.","mla":"Der, Ralf, and Georg S. Martius. Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots. 7846789, IEEE, 2017, doi:10.1109/DEVLRN.2016.7846789.","short":"R. Der, G.S. Martius, in:, IEEE, 2017."},"language":[{"iso":"eng"}],"doi":"10.1109/DEVLRN.2016.7846789","date_published":"2017-02-07T00:00:00Z","conference":{"end_date":"2016-09-22","start_date":"2016-09-19","location":"Cergy-Pontoise, France","name":"ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics "}},{"volume":541,"oa_version":"None","date_created":"2018-12-11T11:47:43Z","date_updated":"2021-01-12T08:07:49Z","author":[{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"}],"department":[{"_id":"BjHo"}],"publisher":"Nature Publishing Group","intvolume":" 541","status":"public","publication_status":"published","title":"Fluid dynamics: Water flows out of touch","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"651","year":"2017","publist_id":"7116","issue":"7636","abstract":[{"lang":"eng","text":"Superhydrophobic surfaces reduce the frictional drag between water and solid materials, but this effect is often temporary. The realization of sustained drag reduction has applications for water vehicles and pipeline flows.\r\n\r\n"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/541161a","date_published":"2017-01-11T00:00:00Z","page":"161 - 162","quality_controlled":"1","citation":{"mla":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature, vol. 541, no. 7636, Nature Publishing Group, 2017, pp. 161–62, doi:10.1038/541161a.","short":"B. Hof, Nature 541 (2017) 161–162.","chicago":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/541161a.","ama":"Hof B. Fluid dynamics: Water flows out of touch. Nature. 2017;541(7636):161-162. doi:10.1038/541161a","ista":"Hof B. 2017. Fluid dynamics: Water flows out of touch. Nature. 541(7636), 161–162.","ieee":"B. Hof, “Fluid dynamics: Water flows out of touch,” Nature, vol. 541, no. 7636. Nature Publishing Group, pp. 161–162, 2017.","apa":"Hof, B. (2017). Fluid dynamics: Water flows out of touch. Nature. Nature Publishing Group. https://doi.org/10.1038/541161a"},"publication":"Nature","publication_identifier":{"issn":["00280836"]},"day":"11","month":"01","scopus_import":1},{"page":"358 - 366","article_type":"original","citation":{"mla":"Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:10.1038/ng.3764.","short":"A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366.","chicago":"Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics. Nature Publishing Group, 2017. https://doi.org/10.1038/ng.3764.","ama":"Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 2017;49(3):358-366. doi:10.1038/ng.3764","ista":"Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366.","ieee":"A. Makohon Moore et al., “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” Nature Genetics, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017.","apa":"Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng.3764"},"publication":"Nature Genetics","date_published":"2017-03-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","intvolume":" 49","status":"public","ddc":["000"],"title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"653","oa_version":"Submitted Version","file":[{"file_size":908099,"content_type":"application/pdf","creator":"dernst","file_name":"2017_NatureGenetics_Makohon.pdf","access_level":"open_access","date_created":"2019-11-19T08:13:50Z","date_updated":"2020-07-14T12:47:33Z","checksum":"e442dc3b7420a36ec805e9bb45cc1a2e","relation":"main_file","file_id":"7050"}],"type":"journal_article","issue":"3","abstract":[{"text":"The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease.","lang":"eng"}],"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"quality_controlled":"1","oa":1,"external_id":{"pmid":["28092682"]},"language":[{"iso":"eng"}],"doi":"10.1038/ng.3764","publication_identifier":{"issn":["10614036"]},"month":"03","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"year":"2017","acknowledgement":"We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).","volume":49,"date_updated":"2022-06-10T09:55:08Z","date_created":"2018-12-11T11:47:43Z","author":[{"full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore","first_name":"Alvin"},{"first_name":"Ming","last_name":"Zhang","full_name":"Zhang, Ming"},{"first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"first_name":"Benjamin","last_name":"Allen","full_name":"Allen, Benjamin"},{"last_name":"Kundu","first_name":"Deepanjan","id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45","full_name":"Kundu, Deepanjan"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Fay","last_name":"Wong","full_name":"Wong, Fay"},{"full_name":"Jiao, Yuchen","first_name":"Yuchen","last_name":"Jiao"},{"full_name":"Kohutek, Zachary","last_name":"Kohutek","first_name":"Zachary"},{"full_name":"Hong, Jungeui","last_name":"Hong","first_name":"Jungeui"},{"full_name":"Attiyeh, Marc","first_name":"Marc","last_name":"Attiyeh"},{"full_name":"Javier, Breanna","last_name":"Javier","first_name":"Breanna"},{"full_name":"Wood, Laura","first_name":"Laura","last_name":"Wood"},{"last_name":"Hruban","first_name":"Ralph","full_name":"Hruban, Ralph"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"full_name":"Papadopoulos, Nickolas","last_name":"Papadopoulos","first_name":"Nickolas"},{"full_name":"Kinzler, Kenneth","last_name":"Kinzler","first_name":"Kenneth"},{"full_name":"Vogelstein, Bert","last_name":"Vogelstein","first_name":"Bert"},{"full_name":"Iacobuzio Donahue, Christine","last_name":"Iacobuzio Donahue","first_name":"Christine"}],"publist_id":"7092","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z"},{"type":"conference","abstract":[{"lang":"eng","text":"A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called \"depth-robustness\") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.\r\n*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n"}],"ec_funded":1,"title":"Practical graphs for optimal side-channel resistant memory-hard functions","status":"public","publication_status":"published","publisher":"ACM Press","department":[{"_id":"KrPi"}],"_id":"6527","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-06-06T13:21:29Z","date_updated":"2021-01-12T08:07:53Z","oa_version":"Submitted Version","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"},{"first_name":"Ben","last_name":"Harsha","full_name":"Harsha, Ben"}],"scopus_import":1,"month":"10","day":"30","publication_identifier":{"isbn":["9781450349468"]},"quality_controlled":"1","page":"1001-1017","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","oa":1,"citation":{"short":"J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017.","mla":"Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–17, doi:10.1145/3133956.3134031.","chicago":"Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, 1001–17. ACM Press, 2017. https://doi.org/10.1145/3133956.3134031.","ama":"Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant memory-hard functions. In: Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. ACM Press; 2017:1001-1017. doi:10.1145/3133956.3134031","ieee":"J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel resistant memory-hard functions,” in Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, Dallas, TX, USA, 2017, pp. 1001–1017.","apa":"Alwen, J. F., Blocki, J., & Harsha, B. (2017). Practical graphs for optimal side-channel resistant memory-hard functions. In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security (pp. 1001–1017). Dallas, TX, USA: ACM Press. https://doi.org/10.1145/3133956.3134031","ista":"Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1001–1017."},"main_file_link":[{"url":"https://eprint.iacr.org/2017/443","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2017-11-03","start_date":"2017-10-30","location":"Dallas, TX, USA","name":"CCS: Conference on Computer and Communications Security"},"doi":"10.1145/3133956.3134031","date_published":"2017-10-30T00:00:00Z"},{"publication":"Development","citation":{"mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:10.1242/dev.144915.","short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","chicago":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144915.","ama":"Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. Development. 2017;144(5):733-736. doi:10.1242/dev.144915","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736.","ieee":"A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” Development, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017.","apa":"Kicheva, A., & Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. Development. Company of Biologists. https://doi.org/10.1242/dev.144915"},"page":"733 - 736","date_published":"2017-03-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"654","title":"Creating to understand – developmental biology meets engineering in Paris","ddc":["571"],"status":"public","intvolume":" 144","pubrep_id":"987","file":[{"creator":"system","file_size":228206,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","checksum":"eef22a0f42a55b232cb2d1188a2322cb","date_created":"2018-12-12T10:15:20Z","date_updated":"2020-07-14T12:47:33Z","file_id":"5139","relation":"main_file"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations."}],"issue":"5","oa":1,"quality_controlled":"1","project":[{"grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"}],"doi":"10.1242/dev.144915","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["09501991"]},"year":"2017","publication_status":"published","department":[{"_id":"AnKi"}],"publisher":"Company of Biologists","author":[{"full_name":"Kicheva, Anna","last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rivron","first_name":"Nicolas","full_name":"Rivron, Nicolas"}],"date_updated":"2021-01-12T08:07:54Z","date_created":"2018-12-11T11:47:44Z","volume":144,"file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"publist_id":"7089"},{"scopus_import":1,"day":"09","publication":"2017 IEEE International Symposium on Information Theory (ISIT)","citation":{"mla":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” 2017 IEEE International Symposium on Information Theory (ISIT), 8006529, IEEE, 2017, doi:10.1109/isit.2017.8006529.","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017.","chicago":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In 2017 IEEE International Symposium on Information Theory (ISIT). IEEE, 2017. https://doi.org/10.1109/isit.2017.8006529.","ama":"Skórski M. On the complexity of estimating Rènyi divergences. In: 2017 IEEE International Symposium on Information Theory (ISIT). IEEE; 2017. doi:10.1109/isit.2017.8006529","ista":"Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017 IEEE International Symposium on Information Theory (ISIT). ISIT: International Symposium on Information Theory, 8006529.","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017.","apa":"Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In 2017 IEEE International Symposium on Information Theory (ISIT). Aachen, Germany: IEEE. https://doi.org/10.1109/isit.2017.8006529"},"date_published":"2017-08-09T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity."}],"title":"On the complexity of estimating Rènyi divergences","status":"public","_id":"6526","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"08","publication_identifier":{"isbn":["9781509040964"]},"quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"external_id":{"arxiv":["1702.01666"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.01666"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2017-06-30","start_date":"2017-06-25","location":"Aachen, Germany","name":"ISIT: International Symposium on Information Theory"},"doi":"10.1109/isit.2017.8006529","article_number":"8006529","ec_funded":1,"publication_status":"published","publisher":"IEEE","department":[{"_id":"KrPi"}],"year":"2017","date_updated":"2021-01-12T08:07:53Z","date_created":"2019-06-06T12:53:09Z","author":[{"last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej"}]},{"department":[{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2017","volume":6,"date_updated":"2021-01-12T08:07:55Z","date_created":"2018-12-11T11:47:44Z","author":[{"full_name":"Renault, Thibaud","first_name":"Thibaud","last_name":"Renault"},{"first_name":"Anthony","last_name":"Abraham","full_name":"Abraham, Anthony"},{"orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"full_name":"Paradis, Guillaume","last_name":"Paradis","first_name":"Guillaume"},{"full_name":"Rainville, Simon","first_name":"Simon","last_name":"Rainville"},{"last_name":"Charpentier","first_name":"Emmanuelle","full_name":"Charpentier, Emmanuelle"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tu, Yuhai","last_name":"Tu","first_name":"Yuhai"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"full_name":"Keener, James","first_name":"James","last_name":"Keener"},{"full_name":"Minamino, Tohru","last_name":"Minamino","first_name":"Tohru"},{"full_name":"Erhardt, Marc","last_name":"Erhardt","first_name":"Marc"}],"article_number":"e23136","publist_id":"7082","file_date_updated":"2020-07-14T12:47:33Z","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,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.23136","publication_identifier":{"issn":["2050084X"]},"month":"03","intvolume":" 6","ddc":["579"],"title":"Bacterial flagella grow through an injection diffusion mechanism","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"655","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:08:53Z","date_updated":"2020-07-14T12:47:33Z","checksum":"39e1c3e82ddac83a30422fa72fa1a383","file_id":"4716","relation":"main_file","creator":"system","file_size":5520359,"content_type":"application/pdf","file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","access_level":"open_access"},{"relation":"main_file","file_id":"4717","date_created":"2018-12-12T10:08:54Z","date_updated":"2020-07-14T12:47:33Z","checksum":"a6d542253028f52e00aa29739ddffe8f","file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf","access_level":"open_access","file_size":11242920,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"904","type":"journal_article","abstract":[{"lang":"eng","text":"The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell."}],"citation":{"ieee":"T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier, E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.23136","ista":"Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella grow through an injection diffusion mechanism. eLife. 6, e23136.","ama":"Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through an injection diffusion mechanism. eLife. 2017;6. doi:10.7554/eLife.23136","chicago":"Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.23136.","short":"T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).","mla":"Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife, vol. 6, e23136, eLife Sciences Publications, 2017, doi:10.7554/eLife.23136."},"publication":"eLife","date_published":"2017-03-06T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"06"},{"publication_identifier":{"issn":["00278424"]},"month":"03","doi":"10.1073/pnas.1616493114","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/"}],"external_id":{"pmid":["28265057"]},"quality_controlled":"1","publist_id":"7076","author":[{"last_name":"Möller","first_name":"Barbara","full_name":"Möller, Barbara"},{"full_name":"Ten Hove, Colette","first_name":"Colette","last_name":"Ten Hove"},{"first_name":"Daoquan","last_name":"Xiang","full_name":"Xiang, Daoquan"},{"full_name":"Williams, Nerys","last_name":"Williams","first_name":"Nerys"},{"last_name":"López","first_name":"Lorena","full_name":"López, Lorena"},{"full_name":"Yoshida, Saiko","first_name":"Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Margot","last_name":"Smit","full_name":"Smit, Margot"},{"full_name":"Datla, Raju","first_name":"Raju","last_name":"Datla"},{"full_name":"Weijers, Dolf","last_name":"Weijers","first_name":"Dolf"}],"volume":114,"date_updated":"2021-01-12T08:08:02Z","date_created":"2018-12-11T11:47:45Z","pmid":1,"year":"2017","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","publication_status":"published","day":"21","scopus_import":1,"date_published":"2017-03-21T00:00:00Z","citation":{"ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 2017;114(12):E2533-E2539. doi:10.1073/pnas.1616493114","ieee":"B. Möller et al., “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” PNAS, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017.","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1616493114","ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.","mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:10.1073/pnas.1616493114.","chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1616493114."},"publication":"PNAS","page":"E2533 - E2539","issue":"12","abstract":[{"text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"657","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 114","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","status":"public"},{"type":"journal_article","article_number":"eaam9867","issue":"381","publist_id":"7079","abstract":[{"text":"Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"656","year":"2017","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","intvolume":" 9","title":"Modeling Alzheimer's disease in mice with human neurons","status":"public","publication_status":"published","author":[{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"}],"volume":9,"oa_version":"None","date_updated":"2021-01-12T08:07:59Z","date_created":"2018-12-11T11:47:45Z","scopus_import":1,"publication_identifier":{"issn":["19466234"]},"day":"15","month":"03","citation":{"chicago":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aam9867.","mla":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine, vol. 9, no. 381, eaam9867, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aam9867.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ista":"Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 9(381), eaam9867.","apa":"Novarino, G. (2017). Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aam9867","ieee":"G. Novarino, “Modeling Alzheimer’s disease in mice with human neurons,” Science Translational Medicine, vol. 9, no. 381. American Association for the Advancement of Science, 2017.","ama":"Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867"},"publication":"Science Translational Medicine","quality_controlled":"1","date_published":"2017-03-15T00:00:00Z","doi":"10.1126/scitranslmed.aam9867","language":[{"iso":"eng"}]},{"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"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,"language":[{"iso":"eng"}],"doi":"10.3389/fnbot.2017.00008","publication_identifier":{"issn":["16625218"]},"month":"03","publisher":"Frontiers Research Foundation","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publication_status":"published","year":"2017","volume":11,"date_updated":"2021-01-12T08:08:04Z","date_created":"2018-12-11T11:47:45Z","author":[{"full_name":"Der, Ralf","first_name":"Ralf","last_name":"Der"},{"full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"article_number":"00008","publist_id":"7078","ec_funded":1,"file_date_updated":"2020-07-14T12:47:33Z","citation":{"chicago":"Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fnbot.2017.00008.","mla":"Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:10.3389/fnbot.2017.00008.","short":"R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).","ista":"Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.","ieee":"R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” Frontiers in Neurorobotics, vol. 11, no. MAR. Frontiers Research Foundation, 2017.","apa":"Der, R., & Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. Frontiers Research Foundation. https://doi.org/10.3389/fnbot.2017.00008","ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008"},"publication":"Frontiers in Neurorobotics","date_published":"2017-03-16T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"Yes","day":"16","intvolume":" 11","ddc":["006"],"status":"public","title":"Self organized behavior generation for musculoskeletal robots","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"658","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","content_type":"application/pdf","file_size":8439566,"creator":"system","relation":"main_file","file_id":"5371","checksum":"b1bc43f96d1df3313c03032c2a46388d","date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:18:49Z"}],"pubrep_id":"903","type":"journal_article","issue":"MAR","abstract":[{"lang":"eng","text":"With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors "waiting" to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics."}]},{"abstract":[{"text":"Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"system","file_size":9523746,"content_type":"application/pdf","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:21Z","date_updated":"2020-07-14T12:47:34Z","checksum":"dae30190291c3630e8102d8714a8d23e","file_id":"5072","relation":"main_file"}],"pubrep_id":"902","intvolume":" 8","ddc":["570"],"status":"public","title":"FMNL formins boost lamellipodial force generation","_id":"659","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"No","day":"22","scopus_import":1,"date_published":"2017-03-22T00:00:00Z","citation":{"mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832.","short":"F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017).","chicago":"Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14832.","ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832","ista":"Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832.","apa":"Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832","ieee":"F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017."},"publication":"Nature Communications","publist_id":"7075","file_date_updated":"2020-07-14T12:47:34Z","article_number":"14832","volume":8,"date_updated":"2021-01-12T08:08:06Z","date_created":"2018-12-11T11:47:46Z","author":[{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"full_name":"Winterhoff, Moritz","first_name":"Moritz","last_name":"Winterhoff"},{"full_name":"Dimchev, Vanessa","first_name":"Vanessa","last_name":"Dimchev"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","last_name":"Müller","first_name":"Jan","full_name":"Müller, Jan"},{"first_name":"Tobias","last_name":"Thalheim","full_name":"Thalheim, Tobias"},{"last_name":"Freise","first_name":"Anika","full_name":"Freise, Anika"},{"last_name":"Brühmann","first_name":"Stefan","full_name":"Brühmann, Stefan"},{"first_name":"Jana","last_name":"Kollasser","full_name":"Kollasser, Jana"},{"last_name":"Block","first_name":"Jennifer","full_name":"Block, Jennifer"},{"last_name":"Dimchev","first_name":"Georgi A","full_name":"Dimchev, Georgi A"},{"last_name":"Geyer","first_name":"Matthias","full_name":"Geyer, Matthias"},{"full_name":"Schnittler, Hams","last_name":"Schnittler","first_name":"Hams"},{"first_name":"Cord","last_name":"Brakebusch","full_name":"Brakebusch, Cord"},{"last_name":"Stradal","first_name":"Theresia","full_name":"Stradal, Theresia"},{"last_name":"Carlier","first_name":"Marie","full_name":"Carlier, Marie"},{"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":"Käs, Josef","first_name":"Josef","last_name":"Käs"},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"}],"department":[{"_id":"MiSi"}],"publisher":"Nature Publishing Group","publication_status":"published","year":"2017","publication_identifier":{"issn":["20411723"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1038/ncomms14832","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"}},{"abstract":[{"lang":"eng","text":"Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth."}],"issue":"13","type":"journal_article","oa_version":"Submitted Version","_id":"660","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","intvolume":" 114","day":"28","scopus_import":1,"date_published":"2017-03-28T00:00:00Z","publication":"PNAS","citation":{"chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1620274114.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114.","apa":"Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., & Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1620274114","ieee":"J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” PNAS, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.","ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432.","ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 2017;114(13):3427-3432. doi:10.1073/pnas.1620274114"},"page":"3427 - 3432","publist_id":"7073","author":[{"first_name":"Jamie","last_name":"Rickman","full_name":"Rickman, Jamie"},{"full_name":"Düllberg, Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748","first_name":"Christian F","last_name":"Düllberg"},{"full_name":"Cade, Nicholas","first_name":"Nicholas","last_name":"Cade"},{"full_name":"Griffin, Lewis","first_name":"Lewis","last_name":"Griffin"},{"first_name":"Thomas","last_name":"Surrey","full_name":"Surrey, Thomas"}],"date_created":"2018-12-11T11:47:46Z","date_updated":"2021-01-12T08:08:09Z","volume":114,"year":"2017","acknowledgement":"We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.).","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"MaLo"}],"month":"03","publication_identifier":{"issn":["00278424"]},"doi":"10.1073/pnas.1620274114","language":[{"iso":"eng"}],"external_id":{"pmid":["28280102"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/","open_access":"1"}],"quality_controlled":"1"},{"date_published":"2017-04-01T00:00:00Z","publication":"Physics of Fluids","citation":{"chicago":"Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute of Physics, 2017. https://doi.org/10.1063/1.4981525.","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).","mla":"Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:10.1063/1.4981525.","ieee":"L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American Institute of Physics, 2017.","apa":"Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4981525","ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","ama":"Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525"},"day":"01","scopus_import":1,"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"662","status":"public","title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","intvolume":" 29","abstract":[{"text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays.","lang":"eng"}],"issue":"4","type":"journal_article","doi":"10.1063/1.4981525","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1703.01714","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"name":"Astrophysical instability of currents and turbulences","_id":"2511D90C-B435-11E9-9278-68D0E5697425","grant_number":"SFB 963 TP A8"}],"month":"04","publication_identifier":{"issn":["10706631"]},"author":[{"full_name":"Shi, Liang","first_name":"Liang","last_name":"Shi"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof"},{"full_name":"Rampp, Markus","last_name":"Rampp","first_name":"Markus"},{"full_name":"Avila, Marc","first_name":"Marc","last_name":"Avila"}],"date_updated":"2021-01-12T08:08:15Z","date_created":"2018-12-11T11:47:47Z","volume":29,"year":"2017","publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"BjHo"}],"publist_id":"7072","article_number":"044107"},{"scopus_import":1,"day":"01","has_accepted_license":"1","publication":"Proceedings of the 20th International Conference on Hybrid Systems","citation":{"chicago":"Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems, 163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814.","short":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.","mla":"Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814.","ieee":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United States, 2017, pp. 163–172.","apa":"Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In Proceedings of the 20th International Conference on Hybrid Systems (pp. 163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814","ista":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.","ama":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: Proceedings of the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814"},"page":"163 - 172","date_published":"2017-04-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. "}],"_id":"663","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Safety verification of nonlinear hybrid systems based on invariant clusters","ddc":["000"],"status":"public","pubrep_id":"817","file":[{"creator":"system","file_size":1650530,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-817-v1+1_p163-kong.pdf","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63","date_updated":"2020-07-14T12:47:34Z","date_created":"2018-12-12T10:11:20Z","file_id":"4873","relation":"main_file"}],"oa_version":"Submitted Version","month":"04","publication_identifier":{"isbn":["978-145034590-3"]},"oa":1,"quality_controlled":"1","conference":{"end_date":"2017-04-20","location":"Pittsburgh, PA, United States","start_date":"2017-04-18","name":"HSCC: Hybrid Systems Computation and Control "},"doi":"10.1145/3049797.3049814","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:34Z","publist_id":"7067","year":"2017","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"ACM","author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","first_name":"Hui","last_name":"Kong","full_name":"Kong, Hui"},{"orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"},{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"date_created":"2018-12-11T11:47:47Z","date_updated":"2021-01-12T08:08:17Z"},{"year":"2017","_id":"667","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","intvolume":" 9","title":"The antisocial side of antibiotics","publication_status":"published","status":"public","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia"}],"volume":9,"oa_version":"None","date_created":"2018-12-11T11:47:48Z","date_updated":"2021-01-12T08:08:30Z","type":"journal_article","article_number":"2786","publist_id":"7060","issue":"387","abstract":[{"text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes.","lang":"eng"}],"citation":{"ama":"Novarino G. The antisocial side of antibiotics. Science Translational Medicine. 2017;9(387). doi:10.1126/scitranslmed.aan2786","apa":"Novarino, G. (2017). The antisocial side of antibiotics. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786","ieee":"G. Novarino, “The antisocial side of antibiotics,” Science Translational Medicine, vol. 9, no. 387. American Association for the Advancement of Science, 2017.","ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786.","short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine, vol. 9, no. 387, 2786, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan2786.","chicago":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786."},"publication":"Science Translational Medicine","quality_controlled":"1","doi":"10.1126/scitranslmed.aan2786","date_published":"2017-04-26T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"publication_identifier":{"issn":["19466234"]},"day":"26","month":"04"},{"scopus_import":1,"day":"28","has_accepted_license":"1","publication":"Journal of Biological Chemistry","citation":{"chicago":"Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther, Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2017. https://doi.org/10.1074/jbc.M116.766923.","mla":"Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry, vol. 292, no. 17, American Society for Biochemistry and Molecular Biology, 2017, pp. 7258–73, doi:10.1074/jbc.M116.766923.","short":"M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R. Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological Chemistry 292 (2017) 7258–7273.","ista":"Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 292(17), 7258–7273.","apa":"Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.766923","ieee":"M. Horsthemke et al., “Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” Journal of Biological Chemistry, vol. 292, no. 17. American Society for Biochemistry and Molecular Biology, pp. 7258–7273, 2017.","ama":"Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 2017;292(17):7258-7273. doi:10.1074/jbc.M116.766923"},"article_type":"original","page":"7258 - 7273","date_published":"2017-04-28T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading."}],"issue":"17","_id":"668","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","status":"public","ddc":["570"],"intvolume":" 292","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":5647880,"file_name":"2017_JBC_Horsthemke.pdf","access_level":"open_access","date_created":"2019-10-24T15:25:42Z","date_updated":"2020-07-14T12:47:37Z","checksum":"d488162874326a4bb056065fa549dc4a","file_id":"6971","relation":"main_file"}],"month":"04","publication_identifier":{"issn":["00219258"]},"oa":1,"quality_controlled":"1","doi":"10.1074/jbc.M116.766923","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:37Z","publist_id":"7059","year":"2017","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"American Society for Biochemistry and Molecular Biology","author":[{"full_name":"Horsthemke, Markus","last_name":"Horsthemke","first_name":"Markus"},{"full_name":"Bachg, Anne","last_name":"Bachg","first_name":"Anne"},{"full_name":"Groll, Katharina","last_name":"Groll","first_name":"Katharina"},{"full_name":"Moyzio, Sven","first_name":"Sven","last_name":"Moyzio"},{"last_name":"Müther","first_name":"Barbara","full_name":"Müther, Barbara"},{"full_name":"Hemkemeyer, Sandra","first_name":"Sandra","last_name":"Hemkemeyer"},{"first_name":"Roland","last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Tacke, Sebastian","first_name":"Sebastian","last_name":"Tacke"},{"full_name":"Bähler, Martin","last_name":"Bähler","first_name":"Martin"},{"first_name":"Peter","last_name":"Hanley","full_name":"Hanley, Peter"}],"date_updated":"2021-01-12T08:08:34Z","date_created":"2018-12-11T11:47:49Z","volume":292},{"type":"journal_article","abstract":[{"text":"The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. ","lang":"eng"}],"issue":"1","status":"public","ddc":["580"],"title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","intvolume":" 174","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"669","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"7041","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-11-18T16:16:18Z","checksum":"97155acc6aa5f0d0a78e0589a932fe02","file_name":"2017_PlantPhysio_Synek.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2176903,"creator":"dernst"}],"scopus_import":1,"day":"01","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","page":"223 - 240","publication":"Plant Physiology","citation":{"ama":"Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 2017;174(1):223-240. doi:10.1104/pp.16.01282","apa":"Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych, M., & Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01282","ieee":"L. Synek et al., “EXO70C2 is a key regulatory factor for optimal tip growth of pollen,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 223–240, 2017.","ista":"Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 174(1), 223–240.","short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240.","mla":"Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 223–40, doi:10.1104/pp.16.01282.","chicago":"Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová, Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01282."},"date_published":"2017-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:37Z","publist_id":"7058","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"American Society of Plant Biologists","year":"2017","pmid":1,"date_updated":"2021-01-12T08:08:35Z","date_created":"2018-12-11T11:47:49Z","volume":174,"author":[{"full_name":"Synek, Lukáš","first_name":"Lukáš","last_name":"Synek"},{"first_name":"Nemanja","last_name":"Vukašinović","full_name":"Vukašinović, Nemanja"},{"full_name":"Kulich, Ivan","last_name":"Kulich","first_name":"Ivan"},{"last_name":"Hála","first_name":"Michal","full_name":"Hála, Michal"},{"full_name":"Aldorfová, Klára","last_name":"Aldorfová","first_name":"Klára"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych"},{"first_name":"Viktor","last_name":"Žárský","full_name":"Žárský, Viktor"}],"month":"05","publication_identifier":{"issn":["00320889"]},"quality_controlled":"1","oa":1,"external_id":{"pmid":["28356503"]},"language":[{"iso":"eng"}],"doi":"10.1104/pp.16.01282"},{"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","author":[{"full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian"},{"full_name":"Martinez, Vaquero","last_name":"Martinez","first_name":"Vaquero"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"date_updated":"2021-01-12T08:08:37Z","date_created":"2018-12-11T11:47:50Z","volume":114,"ec_funded":1,"publist_id":"7053","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/"}],"external_id":{"pmid":["28420786"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"doi":"10.1073/pnas.1621239114","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["00278424"]},"_id":"671","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Memory-n strategies of direct reciprocity","status":"public","intvolume":" 114","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation.","lang":"eng"}],"issue":"18","publication":"PNAS","citation":{"chicago":"Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621239114.","mla":"Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” PNAS, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:10.1073/pnas.1621239114.","short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720.","apa":"Hilbe, C., Martinez, V., Chatterjee, K., & Nowak, M. (2017). Memory-n strategies of direct reciprocity. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1621239114","ieee":"C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” PNAS, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017.","ama":"Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. PNAS. 2017;114(18):4715-4720. doi:10.1073/pnas.1621239114"},"page":"4715 - 4720","date_published":"2017-05-02T00:00:00Z","scopus_import":1,"day":"02","article_processing_charge":"Yes (in subscription journal)"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf"}],"quality_controlled":"1","project":[{"grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"doi":"10.1111/cgf.13110","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["01677055"]},"year":"2017","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Wiley","author":[{"full_name":"Schreck, Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille","last_name":"Schreck"},{"last_name":"Rohmer","first_name":"Damien","full_name":"Rohmer, Damien"},{"first_name":"Stefanie","last_name":"Hahmann","full_name":"Hahmann, Stefanie"}],"date_created":"2018-12-11T11:47:49Z","date_updated":"2021-01-12T08:08:37Z","volume":36,"publist_id":"7056","publication":"Computer Graphics Forum","citation":{"mla":"Schreck, Camille, et al. “Interactive Paper Tearing.” Computer Graphics Forum, vol. 36, no. 2, Wiley, 2017, pp. 95–106, doi:10.1111/cgf.13110.","short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106.","chicago":"Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” Computer Graphics Forum. Wiley, 2017. https://doi.org/10.1111/cgf.13110.","ama":"Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. Computer Graphics Forum. 2017;36(2):95-106. doi:10.1111/cgf.13110","ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106.","ieee":"C. Schreck, D. Rohmer, and S. Hahmann, “Interactive paper tearing,” Computer Graphics Forum, vol. 36, no. 2. Wiley, pp. 95–106, 2017.","apa":"Schreck, C., Rohmer, D., & Hahmann, S. (2017). Interactive paper tearing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13110"},"article_type":"original","page":"95 - 106","date_published":"2017-05-01T00:00:00Z","scopus_import":1,"day":"01","article_processing_charge":"No","_id":"670","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Interactive paper tearing","status":"public","ddc":["000"],"intvolume":" 36","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears.","lang":"eng"}],"issue":"2"},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"},{"call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"oa":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"},"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2017.04.027","month":"05","publication_identifier":{"issn":["22111247"]},"publication_status":"published","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publisher":"Cell Press","year":"2017","date_updated":"2023-02-23T12:50:09Z","date_created":"2018-12-11T11:47:50Z","volume":19,"author":[{"last_name":"Vaahtomeri","first_name":"Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","full_name":"Vaahtomeri, Kari"},{"full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Markus"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"full_name":"Leithner, Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F"},{"first_name":"Matthias","last_name":"Mehling","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8599-1226","full_name":"Mehling, Matthias"},{"full_name":"Kaufmann, Walter","last_name":"Kaufmann","first_name":"Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"file_date_updated":"2020-07-14T12:47:38Z","ec_funded":1,"publist_id":"7052","page":"902 - 909","publication":"Cell Reports","citation":{"chicago":"Vaahtomeri, Kari, Markus Brown, Robert Hauschild, Ingrid de Vries, Alexander F Leithner, Matthias Mehling, Walter Kaufmann, and Michael K Sixt. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.027.","short":"K. Vaahtomeri, M. Brown, R. Hauschild, I. de Vries, A.F. Leithner, M. Mehling, W. Kaufmann, M.K. Sixt, Cell Reports 19 (2017) 902–909.","mla":"Vaahtomeri, Kari, et al. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports, vol. 19, no. 5, Cell Press, 2017, pp. 902–09, doi:10.1016/j.celrep.2017.04.027.","ieee":"K. Vaahtomeri et al., “Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia,” Cell Reports, vol. 19, no. 5. Cell Press, pp. 902–909, 2017.","apa":"Vaahtomeri, K., Brown, M., Hauschild, R., de Vries, I., Leithner, A. F., Mehling, M., … Sixt, M. K. (2017). Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.027","ista":"Vaahtomeri K, Brown M, Hauschild R, de Vries I, Leithner AF, Mehling M, Kaufmann W, Sixt MK. 2017. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 19(5), 902–909.","ama":"Vaahtomeri K, Brown M, Hauschild R, et al. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 2017;19(5):902-909. doi:10.1016/j.celrep.2017.04.027"},"date_published":"2017-05-02T00:00:00Z","scopus_import":1,"day":"02","article_processing_charge":"Yes","has_accepted_license":"1","status":"public","title":"Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia","ddc":["570"],"intvolume":" 19","_id":"672","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","content_type":"application/pdf","file_size":2248814,"file_name":"IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:38Z","date_created":"2018-12-12T10:14:54Z","checksum":"8fdddaab1f1d76a6ec9ca94dcb6b07a2","file_id":"5109","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"900","type":"journal_article","abstract":[{"lang":"eng","text":"Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration."}],"issue":"5"},{"oa_version":"None","_id":"674","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6","intvolume":" 27","abstract":[{"lang":"eng","text":"Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo."}],"issue":"9","type":"journal_article","date_published":"2017-05-09T00:00:00Z","publication":"Current Biology","citation":{"ama":"Schwarz J, Bierbaum V, Vaahtomeri K, et al. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 2017;27(9):1314-1325. doi:10.1016/j.cub.2017.04.004","ieee":"J. Schwarz et al., “Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6,” Current Biology, vol. 27, no. 9. Cell Press, pp. 1314–1325, 2017.","apa":"Schwarz, J., Bierbaum, V., Vaahtomeri, K., Hauschild, R., Brown, M., de Vries, I., … Sixt, M. K. (2017). Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.04.004","ista":"Schwarz J, Bierbaum V, Vaahtomeri K, Hauschild R, Brown M, de Vries I, Leithner AF, Reversat A, Merrin J, Tarrant T, Bollenbach MT, Sixt MK. 2017. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 27(9), 1314–1325.","short":"J. Schwarz, V. Bierbaum, K. Vaahtomeri, R. Hauschild, M. Brown, I. de Vries, A.F. Leithner, A. Reversat, J. Merrin, T. Tarrant, M.T. Bollenbach, M.K. Sixt, Current Biology 27 (2017) 1314–1325.","mla":"Schwarz, Jan, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology, vol. 27, no. 9, Cell Press, 2017, pp. 1314–25, doi:10.1016/j.cub.2017.04.004.","chicago":"Schwarz, Jan, Veronika Bierbaum, Kari Vaahtomeri, Robert Hauschild, Markus Brown, Ingrid de Vries, Alexander F Leithner, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.04.004."},"page":"1314 - 1325","day":"09","scopus_import":1,"author":[{"full_name":"Schwarz, Jan","last_name":"Schwarz","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Veronika","last_name":"Bierbaum","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","full_name":"Bierbaum, Veronika"},{"last_name":"Vaahtomeri","first_name":"Kari","orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","full_name":"Vaahtomeri, Kari"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"first_name":"Markus","last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","last_name":"Leithner","first_name":"Alexander F","full_name":"Leithner, Alexander F"},{"full_name":"Reversat, Anne","orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"full_name":"Tarrant, Teresa","first_name":"Teresa","last_name":"Tarrant"},{"last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"}],"date_updated":"2023-02-23T12:50:44Z","date_created":"2018-12-11T11:47:51Z","volume":27,"year":"2017","publication_status":"published","publisher":"Cell Press","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"ec_funded":1,"publist_id":"7050","doi":"10.1016/j.cub.2017.04.004","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"month":"05","publication_identifier":{"issn":["09609822"]}},{"file":[{"file_id":"5171","relation":"main_file","date_created":"2018-12-12T10:15:48Z","date_updated":"2020-07-14T12:47:40Z","checksum":"efc7287d9c6354983cb151880e9ad72a","file_name":"IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf","access_level":"open_access","creator":"system","file_size":3005610,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"899","intvolume":" 19","ddc":["570"],"status":"public","title":"The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination","_id":"677","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7","abstract":[{"text":"The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR.","lang":"eng"}],"type":"journal_article","date_published":"2017-05-16T00:00:00Z","page":"1294 - 1303","citation":{"ama":"Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 2017;19(7):1294-1303. doi:10.1016/j.celrep.2017.04.051","ieee":"C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” Cell Reports, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017.","apa":"Lademann, C., Renkawitz, J., Pfander, B., & Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.051","ista":"Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303.","short":"C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303.","mla":"Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:10.1016/j.celrep.2017.04.051.","chicago":"Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.051."},"publication":"Cell Reports","has_accepted_license":"1","day":"16","scopus_import":1,"volume":19,"date_updated":"2021-01-12T08:08:57Z","date_created":"2018-12-11T11:47:52Z","author":[{"full_name":"Lademann, Claudio","last_name":"Lademann","first_name":"Claudio"},{"first_name":"Jörg","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg"},{"last_name":"Pfander","first_name":"Boris","full_name":"Pfander, Boris"},{"full_name":"Jentsch, Stefan","last_name":"Jentsch","first_name":"Stefan"}],"department":[{"_id":"MiSi"}],"publisher":"Cell Press","publication_status":"published","year":"2017","publist_id":"7046","file_date_updated":"2020-07-14T12:47:40Z","language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2017.04.051","quality_controlled":"1","oa":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"},"publication_identifier":{"issn":["22111247"]},"month":"05"},{"abstract":[{"lang":"eng","text":"The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development."}],"publist_id":"7040","issue":"6","type":"journal_article","date_updated":"2021-01-12T08:08:59Z","date_created":"2018-12-11T11:47:53Z","oa_version":"None","volume":19,"author":[{"last_name":"Petridou","first_name":"Nicoletta","orcid":"0000-0002-8451-1195","id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","full_name":"Petridou, Nicoletta"},{"full_name":"Spiro, Zoltan P","last_name":"Spiro","first_name":"Zoltan P","id":"426AD026-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"status":"public","publication_status":"published","title":"Multiscale force sensing in development","publisher":"Nature Publishing Group","intvolume":" 19","department":[{"_id":"CaHe"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"678","year":"2017","day":"31","month":"05","publication_identifier":{"issn":["14657392"]},"scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2017-05-31T00:00:00Z","doi":"10.1038/ncb3524","quality_controlled":"1","project":[{"name":"The generation and function of anisotropic tissue tension in zebrafish epiboly (EMBO Fellowship)","_id":"25236028-B435-11E9-9278-68D0E5697425","grant_number":"ALTF534-2016"}],"page":"581 - 588","publication":"Nature Cell Biology","citation":{"chicago":"Petridou, Nicoletta, Zoltan P Spiro, and Carl-Philipp J Heisenberg. “Multiscale Force Sensing in Development.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3524.","short":"N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588.","mla":"Petridou, Nicoletta, et al. “Multiscale Force Sensing in Development.” Nature Cell Biology, vol. 19, no. 6, Nature Publishing Group, 2017, pp. 581–88, doi:10.1038/ncb3524.","apa":"Petridou, N., Spiro, Z. P., & Heisenberg, C.-P. J. (2017). Multiscale force sensing in development. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3524","ieee":"N. Petridou, Z. P. Spiro, and C.-P. J. Heisenberg, “Multiscale force sensing in development,” Nature Cell Biology, vol. 19, no. 6. Nature Publishing Group, pp. 581–588, 2017.","ista":"Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588.","ama":"Petridou N, Spiro ZP, Heisenberg C-PJ. Multiscale force sensing in development. Nature Cell Biology. 2017;19(6):581-588. doi:10.1038/ncb3524"}},{"abstract":[{"lang":"eng","text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information. In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile where all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players' objective, then the objective of every player is violated. We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games. We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games."}],"type":"journal_article","oa_version":"Submitted Version","_id":"681","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Doomsday equilibria for omega-regular games","intvolume":" 254","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2017-06-01T00:00:00Z","publication":"Information and Computation","citation":{"ama":"Chatterjee K, Doyen L, Filiot E, Raskin J. Doomsday equilibria for omega-regular games. Information and Computation. 2017;254:296-315. doi:10.1016/j.ic.2016.10.012","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J. Raskin, “Doomsday equilibria for omega-regular games,” Information and Computation, vol. 254. Elsevier, pp. 296–315, 2017.","apa":"Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J. (2017). Doomsday equilibria for omega-regular games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.012","ista":"Chatterjee K, Doyen L, Filiot E, Raskin J. 2017. Doomsday equilibria for omega-regular games. Information and Computation. 254, 296–315.","short":"K. Chatterjee, L. Doyen, E. Filiot, J. Raskin, Information and Computation 254 (2017) 296–315.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation, vol. 254, Elsevier, 2017, pp. 296–315, doi:10.1016/j.ic.2016.10.012.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean Raskin. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.012."},"article_type":"original","page":"296 - 315","ec_funded":1,"publist_id":"7036","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"first_name":"Emmanuel","last_name":"Filiot","full_name":"Filiot, Emmanuel"},{"first_name":"Jean","last_name":"Raskin","full_name":"Raskin, Jean"}],"related_material":{"record":[{"id":"10885","relation":"earlier_version","status":"public"}]},"date_updated":"2023-02-21T16:06:02Z","date_created":"2018-12-11T11:47:53Z","volume":254,"year":"2017","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"month":"06","publication_identifier":{"issn":["08905401"]},"doi":"10.1016/j.ic.2016.10.012","language":[{"iso":"eng"}],"external_id":{"arxiv":["1311.3238"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1311.3238","open_access":"1"}],"quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}]},{"_id":"6841","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","department":[{"_id":"ChLa"}],"publisher":"International Conference on Learning Representations","title":"Extrapolation and learning equations","publication_status":"published","status":"public","author":[{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"oa_version":"Preprint","date_created":"2019-09-01T22:01:00Z","date_updated":"2021-01-12T08:09:17Z","type":"conference","ec_funded":1,"abstract":[{"lang":"eng","text":"In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified."}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.02995"}],"citation":{"chicago":"Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations, 2017.","mla":"Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","ista":"Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations.","ieee":"G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, Toulon, France, 2017.","apa":"Martius, G. S., & Lampert, C. (2017). Extrapolation and learning equations. In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. Toulon, France: International Conference on Learning Representations.","ama":"Martius GS, Lampert C. Extrapolation and learning equations. In: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations; 2017."},"external_id":{"arxiv":["1610.02995"]},"publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"quality_controlled":"1","date_published":"2017-02-21T00:00:00Z","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2017-04-26","location":"Toulon, France","start_date":"2017-04-24"},"language":[{"iso":"eng"}],"scopus_import":1,"day":"21","month":"02"},{"language":[{"iso":"eng"}],"doi":"10.1017/jsl.2016.71","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1206.5174"}],"publication_identifier":{"issn":["0022-4812"],"eissn":["1943-5886"]},"month":"06","volume":82,"date_created":"2018-12-11T11:47:54Z","date_updated":"2021-04-16T12:10:53Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Piterman, Nir","first_name":"Nir","last_name":"Piterman"}],"publisher":"Cambridge University Press","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2017","publist_id":"7026","date_published":"2017-06-01T00:00:00Z","page":"420 - 452","citation":{"ama":"Chatterjee K, Piterman N. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 2017;82(2):420-452. doi:10.1017/jsl.2016.71","apa":"Chatterjee, K., & Piterman, N. (2017). Obligation blackwell games and p-automata. Journal of Symbolic Logic. Cambridge University Press. https://doi.org/10.1017/jsl.2016.71","ieee":"K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” Journal of Symbolic Logic, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017.","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452.","short":"K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452.","mla":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:10.1017/jsl.2016.71.","chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic. Cambridge University Press, 2017. https://doi.org/10.1017/jsl.2016.71."},"publication":"Journal of Symbolic Logic","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 82","status":"public","title":"Obligation blackwell games and p-automata","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"684","issue":"2","abstract":[{"text":"We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic.","lang":"eng"}],"type":"journal_article"},{"file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"publist_id":"7025","date_updated":"2021-01-12T08:09:20Z","date_created":"2018-12-11T11:47:55Z","volume":145,"author":[{"full_name":"Briscoe, James","first_name":"James","last_name":"Briscoe"},{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"AnKi"}],"year":"2017","pmid":1,"month":"06","publication_identifier":{"issn":["09254773"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.mod.2017.03.005","quality_controlled":"1","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037"}],"external_id":{"pmid":["28366718"]},"oa":1,"abstract":[{"lang":"eng","text":"By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube."}],"type":"journal_article","oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":652313,"file_name":"2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-04-17T07:58:48Z","checksum":"727043d2e4199fbef6b3704e6d1ac105","file_id":"6335","relation":"main_file"}],"pubrep_id":"985","title":"The physics of development 100 years after D'Arcy Thompson's “on growth and form”","ddc":["571"],"status":"public","intvolume":" 145","_id":"685","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-06-01T00:00:00Z","page":"26 - 31","publication":"Mechanisms of Development","citation":{"ista":"Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31.","ieee":"J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” Mechanisms of Development, vol. 145. Elsevier, pp. 26–31, 2017.","apa":"Briscoe, J., & Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.005","ama":"Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. 2017;145:26-31. doi:10.1016/j.mod.2017.03.005","chicago":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.005.","mla":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 26–31, doi:10.1016/j.mod.2017.03.005.","short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31."}},{"month":"06","publication_identifier":{"issn":["18688969"]},"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,"language":[{"iso":"eng"}],"conference":{"location":"Brisbane, Australia","start_date":"2017-07-04","end_date":"2017-07-07","name":"Symposium on Computational Geometry, SoCG"},"doi":"10.4230/LIPIcs.SoCG.2017.39","file_date_updated":"2020-07-14T12:47:42Z","publist_id":"7021","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"year":"2017","date_updated":"2021-01-12T08:09:26Z","date_created":"2018-12-11T11:47:56Z","volume":77,"author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"day":"01","has_accepted_license":"1","page":"391-3916","citation":{"chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.39.","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916.","mla":"Edelsbrunner, Herbert, and Hubert Wagner. Topological Data Analysis with Bregman Divergences. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:10.4230/LIPIcs.SoCG.2017.39.","ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916.","apa":"Edelsbrunner, H., & Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.39","ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:10.4230/LIPIcs.SoCG.2017.39"},"date_published":"2017-06-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. ","lang":"eng"}],"title":"Topological data analysis with Bregman divergences","ddc":["514","516"],"status":"public","intvolume":" 77","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"688","file":[{"access_level":"open_access","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","creator":"system","file_size":990546,"content_type":"application/pdf","file_id":"4856","relation":"main_file","checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","date_updated":"2020-07-14T12:47:42Z","date_created":"2018-12-12T10:11:03Z"}],"oa_version":"Published Version","pubrep_id":"895"},{"intvolume":" 68","status":"public","title":"The critical CoHA of a quiver with potential","_id":"687","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs."}],"page":"635 - 703","citation":{"short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703.","mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053.","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053.","ama":"Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053","ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703."},"publication":"Quarterly Journal of Mathematics","date_published":"2017-06-01T00:00:00Z","scopus_import":1,"day":"01","department":[{"_id":"TaHa"}],"publisher":"Oxford University Press","publication_status":"published","year":"2017","volume":68,"date_created":"2018-12-11T11:47:55Z","date_updated":"2021-01-12T08:09:24Z","author":[{"full_name":"Davison, Ben","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8944-4390","first_name":"Ben","last_name":"Davison"}],"ec_funded":1,"publist_id":"7022","project":[{"grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","name":"Arithmetic and physics of Higgs moduli spaces","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.7172"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/qmath/haw053","publication_identifier":{"issn":["00335606"]},"month":"06"},{"scopus_import":1,"day":"01","month":"06","publication_identifier":{"issn":["09254773"]},"quality_controlled":"1","page":"32 - 37","publication":"Mechanisms of Development","citation":{"mla":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.","short":"C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37.","chicago":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006.","ama":"Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006","ista":"Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.","apa":"Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006","ieee":"C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017."},"language":[{"iso":"eng"}],"doi":"10.1016/j.mod.2017.03.006","date_published":"2017-06-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology."}],"publist_id":"7024","status":"public","publication_status":"published","title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","department":[{"_id":"CaHe"}],"intvolume":" 145","publisher":"Elsevier","_id":"686","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:09:23Z","date_created":"2018-12-11T11:47:55Z","oa_version":"None","volume":145,"author":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}]},{"scopus_import":1,"month":"06","day":"07","publication_identifier":{"issn":["19466234"]},"publication":"Science Translational Medicine","citation":{"short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan8196.","chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan8196.","ama":"Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan8196","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196."},"quality_controlled":"1","date_published":"2017-06-07T00:00:00Z","doi":"10.1126/scitranslmed.aan8196","language":[{"iso":"eng"}],"article_number":"eaan8196","type":"journal_article","abstract":[{"text":"Rett syndrome modeling in monkey mirrors the human disorder.","lang":"eng"}],"issue":"393","publist_id":"7019","_id":"689","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"Rett syndrome modeling goes simian","publisher":"American Association for the Advancement of Science","intvolume":" 9","department":[{"_id":"GaNo"}],"author":[{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"date_updated":"2021-01-12T08:09:29Z","date_created":"2018-12-11T11:47:56Z","oa_version":"None","volume":9},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1704470114","quality_controlled":"1","external_id":{"pmid":["28607047"]},"oa":1,"publication_identifier":{"issn":["00278424"]},"month":"06","volume":114,"date_updated":"2023-02-23T12:54:57Z","date_created":"2018-12-11T11:47:57Z","author":[{"first_name":"Takafumi","last_name":"Miki","full_name":"Miki, Takafumi"},{"id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","first_name":"Walter","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Gerardo","last_name":"Malagon","full_name":"Malagon, Gerardo"},{"full_name":"Gomez, Laura","last_name":"Gomez","first_name":"Laura"},{"full_name":"Tabuchi, Katsuhiko","first_name":"Katsuhiko","last_name":"Tabuchi"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444"},{"full_name":"Marty, Alain","last_name":"Marty","first_name":"Alain"}],"publisher":"National Academy of Sciences","department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publication_status":"published","pmid":1,"year":"2017","publist_id":"7013","file_date_updated":"2020-07-14T12:47:44Z","date_published":"2017-06-27T00:00:00Z","page":"E5246 - E5255","citation":{"chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114.","ieee":"T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114"},"publication":"PNAS","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"27","scopus_import":1,"oa_version":"Published Version","file":[{"file_name":"2017_PNAS_Miki.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":2721544,"file_id":"7223","relation":"main_file","date_created":"2020-01-03T13:27:29Z","date_updated":"2020-07-14T12:47:44Z","checksum":"2ab75d554f3df4a34d20fa8040589b7e"}],"intvolume":" 114","ddc":["570"],"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"693","issue":"26","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"type":"journal_article"},{"volume":130,"date_updated":"2021-01-12T08:09:41Z","date_created":"2018-12-11T11:47:58Z","author":[{"first_name":"Astrid","last_name":"Veß","full_name":"Veß, Astrid"},{"full_name":"Blache, Ulrich","first_name":"Ulrich","last_name":"Blache"},{"last_name":"Leitner","first_name":"Laura","full_name":"Leitner, Laura"},{"first_name":"Angela","last_name":"Kurz","full_name":"Kurz, Angela"},{"last_name":"Ehrenpfordt","first_name":"Anja","full_name":"Ehrenpfordt, Anja"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"last_name":"Posern","first_name":"Guido","full_name":"Posern, Guido"}],"publisher":"Company of Biologists","department":[{"_id":"MiSi"}],"publication_status":"published","pmid":1,"year":"2017","publist_id":"7008","file_date_updated":"2020-07-14T12:47:45Z","language":[{"iso":"eng"}],"doi":"10.1242/jcs.200899","quality_controlled":"1","external_id":{"pmid":["28515231"]},"oa":1,"publication_identifier":{"issn":["00219533"]},"month":"07","oa_version":"Published Version","file":[{"file_name":"2017_CellScience_Vess.pdf","access_level":"open_access","content_type":"application/pdf","file_size":10847596,"creator":"dernst","relation":"main_file","file_id":"6966","date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-24T09:43:56Z","checksum":"42c81a0a4fc3128883b391c3af3f74bc"}],"intvolume":" 130","status":"public","ddc":["570"],"title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","_id":"694","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"13","abstract":[{"lang":"eng","text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells."}],"type":"journal_article","date_published":"2017-07-01T00:00:00Z","page":"2172 - 2184","article_type":"original","citation":{"short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:10.1242/jcs.200899.","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.200899.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 2017;130(13):2172-2184. doi:10.1242/jcs.200899","ieee":"A. Veß et al., “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” Journal of Cell Science, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., & Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.200899","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184."},"publication":"Journal of Cell Science","has_accepted_license":"1","day":"01","scopus_import":1},{"scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. Non Uniform Attacks against Pseudoentropy. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.ICALP.2017.39.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ICALP.2017.39.","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.ICALP.2017.39","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","apa":"Pietrzak, K. Z., & Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2017.39","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39."},"date_published":"2017-07-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. "}],"status":"public","title":"Non uniform attacks against pseudoentropy","ddc":["005"],"intvolume":" 80","_id":"697","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","access_level":"open_access","creator":"system","file_size":601004,"content_type":"application/pdf","file_id":"4701","relation":"main_file","date_updated":"2020-07-14T12:47:46Z","date_created":"2018-12-12T10:08:40Z","checksum":"e95618a001692f1af2d68f5fde43bc1f"}],"oa_version":"Published Version","pubrep_id":"893","month":"07","publication_identifier":{"issn":["18688969"]},"quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"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,"language":[{"iso":"eng"}],"conference":{"name":"ICALP: International Colloquium on Automata, Languages, and Programming","start_date":"2017-07-10","location":"Warsaw, Poland","end_date":"2017-07-14"},"doi":"10.4230/LIPIcs.ICALP.2017.39","article_number":"39","file_date_updated":"2020-07-14T12:47:46Z","publist_id":"7003","ec_funded":1,"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2017","date_created":"2018-12-11T11:47:59Z","date_updated":"2021-01-12T08:11:15Z","volume":80,"author":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","first_name":"Maciej","full_name":"Skórski, Maciej"}]},{"pubrep_id":"892","oa_version":"Published Version","file":[{"creator":"system","file_size":1086097,"content_type":"application/pdf","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","access_level":"open_access","date_created":"2018-12-12T10:10:53Z","date_updated":"2020-07-14T12:47:46Z","checksum":"de01dac9e30970cfa6ae902480a4e04d","file_id":"4844","relation":"main_file"}],"_id":"698","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 28","title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","ddc":["519"],"status":"public","issue":"14","abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"type":"journal_article","date_published":"2017-07-07T00:00:00Z","citation":{"ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” Molecular Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","apa":"Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell. American Society for Cell Biology, 2017. https://doi.org/10.1091/mbc.E16-12-0825.","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825."},"publication":"Molecular Biology of the Cell","page":"1997 - 2009","has_accepted_license":"1","day":"07","scopus_import":1,"author":[{"last_name":"Wang","first_name":"Yejun","full_name":"Wang, Yejun"},{"full_name":"Nagarajan, Mallika","first_name":"Mallika","last_name":"Nagarajan"},{"first_name":"Caroline","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline"},{"last_name":"Shivashankar","first_name":"Gv","full_name":"Shivashankar, Gv"}],"volume":28,"date_created":"2018-12-11T11:47:59Z","date_updated":"2021-01-12T08:11:17Z","year":"2017","department":[{"_id":"CaUh"}],"publisher":"American Society for Cell Biology","publication_status":"published","publist_id":"7001","file_date_updated":"2020-07-14T12:47:46Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","doi":"10.1091/mbc.E16-12-0825","language":[{"iso":"eng"}],"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,"project":[{"_id":"2530CA10-B435-11E9-9278-68D0E5697425","grant_number":"Y 903-N35","call_identifier":"FWF","name":"Gaussian Graphical Models: Theory and Applications"}],"quality_controlled":"1","publication_identifier":{"issn":["10591524"]},"month":"07"},{"publist_id":"7002","year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","author":[{"full_name":"Veller, Carl","first_name":"Carl","last_name":"Veller"},{"full_name":"Hayward, Laura","last_name":"Hayward","first_name":"Laura"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T08:11:21Z","date_created":"2018-12-11T11:48:00Z","volume":114,"month":"07","publication_identifier":{"issn":["00278424"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"external_id":{"pmid":["28630336"]},"oa":1,"quality_controlled":"1","doi":"10.1073/pnas.1702020114","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. "}],"issue":"27","_id":"699","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The red queen and king in finite populations","intvolume":" 114","oa_version":"Submitted Version","scopus_import":1,"day":"03","publication":"PNAS","citation":{"chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114.","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","apa":"Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114"},"page":"E5396 - E5405","date_published":"2017-07-03T00:00:00Z"},{"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"700","intvolume":" 96","title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","status":"public","oa_version":"Submitted Version","scopus_import":1,"day":"12","citation":{"chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.012404.","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.012404.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., & Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.012404","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.012404"},"publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","date_published":"2017-07-12T00:00:00Z","article_number":"012404","publist_id":"6997","ec_funded":1,"year":"2017","department":[{"_id":"JoFi"}],"publisher":"American Institute of Physics","publication_status":"published","author":[{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423"},{"full_name":"Salari, Vahid","last_name":"Salari","first_name":"Vahid"},{"full_name":"Tuszynski, Jack","first_name":"Jack","last_name":"Tuszynski"},{"first_name":"Michal","last_name":"Cifra","full_name":"Cifra, Michal"},{"last_name":"Simon","first_name":"Christoph","full_name":"Simon, Christoph"}],"volume":96,"date_updated":"2023-02-23T12:56:35Z","date_created":"2018-12-11T11:48:00Z","publication_identifier":{"issn":["24700045"]},"month":"07","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1612.07061.pdf"}],"project":[{"_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","call_identifier":"H2020","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"quality_controlled":"1","doi":"10.1103/PhysRevE.96.012404","language":[{"iso":"eng"}]},{"publication":"The Electronic Journal of Combinatorics","citation":{"mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics, vol. 24, no. 3, International Press, 2017, pp. 1–44.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics. International Press, 2017.","ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 2017;24(3):1-44.","ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44.","ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” The Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, pp. 1–44, 2017.","apa":"Kynčl, J., & Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. International Press."},"page":"1-44","date_published":"2017-07-14T00:00:00Z","day":"14","has_accepted_license":"1","_id":"701","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["500"],"title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","status":"public","intvolume":" 24","pubrep_id":"984","file":[{"access_level":"open_access","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf","file_size":544042,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5077","checksum":"a431e573e31df13bc0f66de3061006ec","date_created":"2018-12-12T10:14:25Z","date_updated":"2020-07-14T12:47:47Z"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2.","lang":"eng"}],"issue":"3","oa":1,"quality_controlled":"1","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"issn":["10778926"]},"year":"2017","publication_status":"published","publisher":"International Press","department":[{"_id":"UlWa"}],"author":[{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"},{"orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","first_name":"Zuzana","full_name":"Patakova, Zuzana"}],"date_created":"2018-12-11T11:48:00Z","date_updated":"2021-01-12T08:11:28Z","volume":24,"file_date_updated":"2020-07-14T12:47:47Z","publist_id":"6996"},{"publication_identifier":{"issn":["19466234"]},"month":"07","day":"19","scopus_import":1,"doi":"10.1126/scitranslmed.aao0972","date_published":"2017-07-19T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 2017;9(399):eaao0972. doi:10.1126/scitranslmed.aao0972","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” Science Translational Medicine, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao0972","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:10.1126/scitranslmed.aao0972.","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao0972."},"publication":"Science Translational Medicine","page":"eaao0972","quality_controlled":"1","publist_id":"6993","issue":"399","abstract":[{"lang":"eng","text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n"}],"type":"journal_article","author":[{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"volume":9,"oa_version":"None","date_created":"2018-12-11T11:48:01Z","date_updated":"2021-01-12T08:11:31Z","_id":"702","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaNo"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","status":"public","title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","publication_status":"published"},{"quality_controlled":"1","page":"715 - 722","publication":"Genes to Cells","citation":{"chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells. Wiley-Blackwell, 2017. https://doi.org/10.1111/gtc.12508.","mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:10.1111/gtc.12508.","short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722.","apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. Wiley-Blackwell. https://doi.org/10.1111/gtc.12508","ieee":"X. Geng et al., “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” Genes to Cells, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 2017;22(8):715-722. doi:10.1111/gtc.12508"},"language":[{"iso":"eng"}],"date_published":"2017-08-01T00:00:00Z","doi":"10.1111/gtc.12508","scopus_import":1,"day":"01","month":"08","publication_identifier":{"issn":["13569597"]},"title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","status":"public","publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Wiley-Blackwell","intvolume":" 22","year":"2017","_id":"706","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:02Z","date_updated":"2021-01-12T08:11:37Z","oa_version":"None","volume":22,"author":[{"first_name":"Xiaoqi","last_name":"Geng","id":"3395256A-F248-11E8-B48F-1D18A9856A87","full_name":"Geng, Xiaoqi"},{"first_name":"Tomohiko","last_name":"Maruo","full_name":"Maruo, Tomohiko"},{"full_name":"Mandai, Kenji","first_name":"Kenji","last_name":"Mandai"},{"full_name":"Supriyanto, Irwan","first_name":"Irwan","last_name":"Supriyanto"},{"last_name":"Miyata","first_name":"Muneaki","full_name":"Miyata, Muneaki"},{"last_name":"Sakakibara","first_name":"Shotaro","full_name":"Sakakibara, Shotaro"},{"first_name":"Akira","last_name":"Mizoguchi","full_name":"Mizoguchi, Akira"},{"full_name":"Takai, Yoshimi","last_name":"Takai","first_name":"Yoshimi"},{"first_name":"Masahiro","last_name":"Mori","full_name":"Mori, Masahiro"}],"type":"journal_article","abstract":[{"lang":"eng","text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse."}],"issue":"8","publist_id":"6987"}]