[{"conference":{"start_date":"2015-04-14","end_date":"2015-04-16","name":"HSCC: Hybrid Systems - Computation and Control","location":"Seattle, WA, United States"},"publist_id":"5454","ec_funded":1,"status":"public","year":"2015","doi":"10.1145/2728606.2728630","day":"14","page":"128 - 133","acknowledgement":"The material presented in this paper is based upon work sup-ported by the Air Force Research Laboratory’s Information Directorate (AFRL/RI) through the Visiting Faculty Research Program (VFRP) under contract number FA8750-13-2-0115 and the Air Force Office of Scientific Research (AFOSR). Any opinions,findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the AFRL/RI or AFOSR. This work was also partly supported in part by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR14 AVACS, http://www.avacs.org/), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","_id":"1690","type":"conference","date_created":"2018-12-11T11:53:29Z","title":"HYST: A source transformation and translation tool for hybrid automaton models","publisher":"Springer","language":[{"iso":"eng"}],"date_published":"2015-04-14T00:00:00Z","publication_status":"published","month":"04","abstract":[{"text":"A number of powerful and scalable hybrid systems model checkers have recently emerged. Although all of them honor roughly the same hybrid systems semantics, they have drastically different model description languages. This situation (a) makes it difficult to quickly evaluate a specific hybrid automaton model using the different tools, (b) obstructs comparisons of reachability approaches, and (c) impedes the widespread application of research results that perform model modification and could benefit many of the tools. In this paper, we present Hyst, a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently taking input in the SpaceEx model format, and translating to the formats of HyCreate, Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation passes that serve to both ease the translation and potentially improve reachability results for the supported tools. Although these model transformation passes could be implemented within each tool, the Hyst approach provides a single place for model modification, generating modified input sources for the unmodified target tools. Our evaluation demonstrates Hyst is capable of automatically translating benchmarks in several classes (including affine and nonlinear hybrid automata) to the input formats of several tools. Additionally, we illustrate a general model transformation pass based on pseudo-invariants implemented in Hyst that illustrates the reachability improvement.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bak, Stanley","first_name":"Stanley","last_name":"Bak"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365"},{"first_name":"Taylor","last_name":"Johnson","full_name":"Johnson, Taylor"}],"citation":{"ieee":"S. Bak, S. Bogomolov, and T. Johnson, “HYST: A source transformation and translation tool for hybrid automaton models,” presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States, 2015, pp. 128–133.","ista":"Bak S, Bogomolov S, Johnson T. 2015. HYST: A source transformation and translation tool for hybrid automaton models. HSCC: Hybrid Systems - Computation and Control, 128–133.","ama":"Bak S, Bogomolov S, Johnson T. HYST: A source transformation and translation tool for hybrid automaton models. In: Springer; 2015:128-133. doi:<a href=\"https://doi.org/10.1145/2728606.2728630\">10.1145/2728606.2728630</a>","chicago":"Bak, Stanley, Sergiy Bogomolov, and Taylor Johnson. “HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models,” 128–33. Springer, 2015. <a href=\"https://doi.org/10.1145/2728606.2728630\">https://doi.org/10.1145/2728606.2728630</a>.","apa":"Bak, S., Bogomolov, S., &#38; Johnson, T. (2015). HYST: A source transformation and translation tool for hybrid automaton models (pp. 128–133). Presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States: Springer. <a href=\"https://doi.org/10.1145/2728606.2728630\">https://doi.org/10.1145/2728606.2728630</a>","mla":"Bak, Stanley, et al. <i>HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models</i>. Springer, 2015, pp. 128–33, doi:<a href=\"https://doi.org/10.1145/2728606.2728630\">10.1145/2728606.2728630</a>.","short":"S. Bak, S. Bogomolov, T. Johnson, in:, Springer, 2015, pp. 128–133."},"oa_version":"None","department":[{"_id":"ToHe"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"date_updated":"2021-01-12T06:52:33Z"},{"title":"Temporal logic motion planning using POMDPs with parity objectives: Case study paper","date_published":"2015-04-14T00:00:00Z","publisher":"ACM","language":[{"iso":"eng"}],"publication_status":"published","month":"04","abstract":[{"text":"We consider a case study of the problem of deploying an autonomous air vehicle in a partially observable, dynamic, indoor environment from a specification given as a linear temporal logic (LTL) formula over regions of interest. We model the motion and sensing capabilities of the vehicle as a partially observable Markov decision process (POMDP). We adapt recent results for solving POMDPs with parity objectives to generate a control policy. We also extend the existing framework with a policy minimization technique to obtain a better implementable policy, while preserving its correctness. The proposed techniques are illustrated in an experimental setup involving an autonomous quadrotor performing surveillance in a dynamic environment.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Svoreňová, Mária","last_name":"Svoreňová","first_name":"Mária"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin"},{"first_name":"Kevin","last_name":"Leahy","full_name":"Leahy, Kevin"},{"last_name":"Eniser","first_name":"Hasan","full_name":"Eniser, Hasan"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Cěrná, Ivana","first_name":"Ivana","last_name":"Cěrná"},{"full_name":"Belta, Cǎlin","last_name":"Belta","first_name":"Cǎlin"}],"oa_version":"None","citation":{"ieee":"M. Svoreňová <i>et al.</i>, “Temporal logic motion planning using POMDPs with parity objectives: Case study paper,” in <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i>, Seattle, WA, United States, 2015, pp. 233–238.","apa":"Svoreňová, M., Chmelik, M., Leahy, K., Eniser, H., Chatterjee, K., Cěrná, I., &#38; Belta, C. (2015). Temporal logic motion planning using POMDPs with parity objectives: Case study paper. In <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i> (pp. 233–238). Seattle, WA, United States: ACM. <a href=\"https://doi.org/10.1145/2728606.2728617\">https://doi.org/10.1145/2728606.2728617</a>","ama":"Svoreňová M, Chmelik M, Leahy K, et al. Temporal logic motion planning using POMDPs with parity objectives: Case study paper. In: <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i>. ACM; 2015:233-238. doi:<a href=\"https://doi.org/10.1145/2728606.2728617\">10.1145/2728606.2728617</a>","ista":"Svoreňová M, Chmelik M, Leahy K, Eniser H, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic motion planning using POMDPs with parity objectives: Case study paper. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 233–238.","chicago":"Svoreňová, Mária, Martin Chmelik, Kevin Leahy, Hasan Eniser, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Motion Planning Using POMDPs with Parity Objectives: Case Study Paper.” In <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i>, 233–38. ACM, 2015. <a href=\"https://doi.org/10.1145/2728606.2728617\">https://doi.org/10.1145/2728606.2728617</a>.","short":"M. Svoreňová, M. Chmelik, K. Leahy, H. Eniser, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 233–238.","mla":"Svoreňová, Mária, et al. “Temporal Logic Motion Planning Using POMDPs with Parity Objectives: Case Study Paper.” <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i>, ACM, 2015, pp. 233–38, doi:<a href=\"https://doi.org/10.1145/2728606.2728617\">10.1145/2728606.2728617</a>."},"department":[{"_id":"KrCh"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"date_updated":"2021-01-12T06:52:33Z","publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","publist_id":"5453","conference":{"end_date":"2015-04-16","start_date":"2015-04-14","location":"Seattle, WA, United States","name":"HSCC: Hybrid Systems - Computation and Control"},"ec_funded":1,"scopus_import":1,"day":"14","year":"2015","page":"233 - 238","status":"public","doi":"10.1145/2728606.2728617","_id":"1691","type":"conference","date_created":"2018-12-11T11:53:29Z"},{"year":"2015","status":"public","day":"14","page":"149 - 158","doi":"10.1145/2728606.2728622","publication_identifier":{"isbn":["978-1-4503-3433-4"]},"date_created":"2018-12-11T11:53:30Z","_id":"1692","type":"conference","ec_funded":1,"publist_id":"5452","conference":{"start_date":"2015-04-14","end_date":"2015-04-16","location":"Seattle, WA, United States","name":"HSCC: Hybrid Systems - Computation and Control"},"publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","scopus_import":1,"author":[{"first_name":"Goran","last_name":"Frehse","full_name":"Frehse, Goran"},{"last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy"},{"first_name":"Marius","last_name":"Greitschus","full_name":"Greitschus, Marius"},{"full_name":"Strump, Thomas","first_name":"Thomas","last_name":"Strump"},{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:52:33Z","department":[{"_id":"ToHe"}],"quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"None","citation":{"mla":"Frehse, Goran, et al. “Eliminating Spurious Transitions in Reachability with Support Functions.” <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i>, ACM, 2015, pp. 149–58, doi:<a href=\"https://doi.org/10.1145/2728606.2728622\">10.1145/2728606.2728622</a>.","short":"G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, A. Podelski, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–158.","ieee":"G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, and A. Podelski, “Eliminating spurious transitions in reachability with support functions,” in <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i>, Seattle, WA, United States, 2015, pp. 149–158.","apa":"Frehse, G., Bogomolov, S., Greitschus, M., Strump, T., &#38; Podelski, A. (2015). Eliminating spurious transitions in reachability with support functions. In <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i> (pp. 149–158). Seattle, WA, United States: ACM. <a href=\"https://doi.org/10.1145/2728606.2728622\">https://doi.org/10.1145/2728606.2728622</a>","ista":"Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. 2015. Eliminating spurious transitions in reachability with support functions. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 149–158.","ama":"Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. Eliminating spurious transitions in reachability with support functions. In: <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i>. ACM; 2015:149-158. doi:<a href=\"https://doi.org/10.1145/2728606.2728622\">10.1145/2728606.2728622</a>","chicago":"Frehse, Goran, Sergiy Bogomolov, Marius Greitschus, Thomas Strump, and Andreas Podelski. “Eliminating Spurious Transitions in Reachability with Support Functions.” In <i>Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control</i>, 149–58. ACM, 2015. <a href=\"https://doi.org/10.1145/2728606.2728622\">https://doi.org/10.1145/2728606.2728622</a>."},"publisher":"ACM","language":[{"iso":"eng"}],"date_published":"2015-04-14T00:00:00Z","title":"Eliminating spurious transitions in reachability with support functions","abstract":[{"text":"Computing an approximation of the reachable states of a hybrid system is a challenge, mainly because overapproximating the solutions of ODEs with a finite number of sets does not scale well. Using template polyhedra can greatly reduce the computational complexity, since it replaces complex operations on sets with a small number of optimization problems. However, the use of templates may make the over-approximation too conservative. Spurious transitions, which are falsely considered reachable, are particularly detrimental to performance and accuracy, and may exacerbate the state explosion problem. In this paper, we examine how spurious transitions can be avoided with minimal computational effort. To this end, detecting spurious transitions is reduced to the well-known problem of showing that two convex sets are disjoint by finding a hyperplane that separates them. We generalize this to owpipes by considering hyperplanes that evolve with time in correspondence to the dynamics of the system. The approach is implemented in the model checker SpaceEx and demonstrated on examples.","lang":"eng"}],"month":"04","publication_status":"published"},{"citation":{"apa":"Amaro, P., Franke, B., Krauth, J., Diepold, M., Fratini, F., Safari, L., … Santos, J. (2015). Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.92.022514\">https://doi.org/10.1103/PhysRevA.92.022514</a>","ama":"Amaro P, Franke B, Krauth J, et al. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. <i>Physical Review A</i>. 2015;92(2). doi:<a href=\"https://doi.org/10.1103/PhysRevA.92.022514\">10.1103/PhysRevA.92.022514</a>","ista":"Amaro P, Franke B, Krauth J, Diepold M, Fratini F, Safari L, Machado J, Antognini A, Kottmann F, Indelicato P, Pohl R, Santos J. 2015. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 92(2), 022514.","chicago":"Amaro, Pedro, Beatrice Franke, Julian Krauth, Marc Diepold, Filippo Fratini, Laleh Safari, Jorge Machado, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” <i>Physical Review A</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevA.92.022514\">https://doi.org/10.1103/PhysRevA.92.022514</a>.","ieee":"P. Amaro <i>et al.</i>, “Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3,” <i>Physical Review A</i>, vol. 92, no. 2. American Physical Society, 2015.","short":"P. Amaro, B. Franke, J. Krauth, M. Diepold, F. Fratini, L. Safari, J. Machado, A. Antognini, F. Kottmann, P. Indelicato, R. Pohl, J. Santos, Physical Review A 92 (2015).","mla":"Amaro, Pedro, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” <i>Physical Review A</i>, vol. 92, no. 2, 022514, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevA.92.022514\">10.1103/PhysRevA.92.022514</a>."},"date_updated":"2021-01-12T06:52:34Z","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Quantum interference between energetically close states is theoretically investigated, with the state structure being observed via laser spectroscopy. In this work, we focus on hyperfine states of selected hydrogenic muonic isotopes, and on how quantum interference affects the measured Lamb shift. The process of photon excitation and subsequent photon decay is implemented within the framework of nonrelativistic second-order perturbation theory. Due to its experimental interest, calculations are performed for muonic hydrogen, deuterium, and helium-3. We restrict our analysis to the case of photon scattering by incident linear polarized photons and the polarization of the scattered photons not being observed. We conclude that while quantum interference effects can be safely neglected in muonic hydrogen and helium-3, in the case of muonic deuterium there are resonances with close proximity, where quantum interference effects can induce shifts up to a few percent of the linewidth, assuming a pointlike detector. However, by taking into account the geometry of the setup used by the CREMA collaboration, this effect is reduced to less than 0.2% of the linewidth in all possible cases, which makes it irrelevant at the present level of accuracy. © 2015 American Physical Society."}],"publication_status":"published","title":"Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3","publisher":"American Physical Society","date_published":"2015-08-28T00:00:00Z","oa":1,"day":"28","year":"2015","doi":"10.1103/PhysRevA.92.022514","scopus_import":1,"publication":"Physical Review A","intvolume":"        92","publist_id":"5451","oa_version":"Preprint","quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"author":[{"full_name":"Amaro, Pedro","last_name":"Amaro","first_name":"Pedro"},{"full_name":"Franke, Beatrice","last_name":"Franke","first_name":"Beatrice"},{"full_name":"Krauth, Julian","last_name":"Krauth","first_name":"Julian"},{"last_name":"Diepold","first_name":"Marc","full_name":"Diepold, Marc"},{"full_name":"Fratini, Filippo","first_name":"Filippo","last_name":"Fratini"},{"full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","last_name":"Safari"},{"first_name":"Jorge","last_name":"Machado","full_name":"Machado, Jorge"},{"last_name":"Antognini","first_name":"Aldo","full_name":"Antognini, Aldo"},{"full_name":"Kottmann, Franz","first_name":"Franz","last_name":"Kottmann"},{"full_name":"Indelicato, Paul","last_name":"Indelicato","first_name":"Paul"},{"last_name":"Pohl","first_name":"Randolf","full_name":"Pohl, Randolf"},{"full_name":"Santos, José","first_name":"José","last_name":"Santos"}],"issue":"2","article_number":"022514","month":"08","volume":92,"language":[{"iso":"eng"}],"type":"journal_article","_id":"1693","date_created":"2018-12-11T11:53:30Z","main_file_link":[{"url":"http://arxiv.org/abs/1506.02734","open_access":"1"}],"status":"public","ec_funded":1},{"title":"Quantitative temporal simulation and refinement distances for timed systems","volume":60,"language":[{"iso":"eng"}],"publisher":"IEEE","date_published":"2015-02-24T00:00:00Z","issue":"9","publication_status":"published","month":"02","abstract":[{"text":"\r\nWe introduce quantitative timed refinement and timed simulation (directed) metrics, incorporating zenoness checks, for timed systems. These metrics assign positive real numbers which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximal timing mismatch that can arise, (2) the “steady-state” maximal timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation distances to within any desired degree of accuracy. In order to compute the values of the quantitative simulation distances, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite-state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives in graph games, and then use these algorithms to compute the values of the timed simulation distances over timed automata.\r\n","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Prabhu","first_name":"Vinayak","full_name":"Prabhu, Vinayak"}],"citation":{"ista":"Chatterjee K, Prabhu V. 2015. Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. 60(9), 2291–2306.","ama":"Chatterjee K, Prabhu V. Quantitative temporal simulation and refinement distances for timed systems. <i>IEEE Transactions on Automatic Control</i>. 2015;60(9):2291-2306. doi:<a href=\"https://doi.org/10.1109/TAC.2015.2404612\">10.1109/TAC.2015.2404612</a>","chicago":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation and Refinement Distances for Timed Systems.” <i>IEEE Transactions on Automatic Control</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TAC.2015.2404612\">https://doi.org/10.1109/TAC.2015.2404612</a>.","apa":"Chatterjee, K., &#38; Prabhu, V. (2015). Quantitative temporal simulation and refinement distances for timed systems. <i>IEEE Transactions on Automatic Control</i>. IEEE. <a href=\"https://doi.org/10.1109/TAC.2015.2404612\">https://doi.org/10.1109/TAC.2015.2404612</a>","ieee":"K. Chatterjee and V. Prabhu, “Quantitative temporal simulation and refinement distances for timed systems,” <i>IEEE Transactions on Automatic Control</i>, vol. 60, no. 9. IEEE, pp. 2291–2306, 2015.","short":"K. Chatterjee, V. Prabhu, IEEE Transactions on Automatic Control 60 (2015) 2291–2306.","mla":"Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation and Refinement Distances for Timed Systems.” <i>IEEE Transactions on Automatic Control</i>, vol. 60, no. 9, IEEE, 2015, pp. 2291–306, doi:<a href=\"https://doi.org/10.1109/TAC.2015.2404612\">10.1109/TAC.2015.2404612</a>."},"oa_version":"None","department":[{"_id":"KrCh"}],"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"date_updated":"2021-01-12T06:52:34Z","publication":"IEEE Transactions on Automatic Control","publist_id":"5450","ec_funded":1,"intvolume":"        60","scopus_import":1,"page":"2291 - 2306","doi":"10.1109/TAC.2015.2404612","year":"2015","status":"public","day":"24","type":"journal_article","_id":"1694","date_created":"2018-12-11T11:53:30Z"},{"oa":1,"year":"2015","page":"2059 - 2071","doi":"10.1002/pssb.201552082","day":"01","scopus_import":1,"publist_id":"5449","intvolume":"       252","publication":"Physica Status Solidi (B): Basic Solid State Physics","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:52:34Z","citation":{"short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physica Status Solidi (B): Basic Solid State Physics 252 (2015) 2059–2071.","mla":"Kaczmarczyk, Jan, et al. “Evaluation Techniques for Gutzwiller Wave Functions in Finite Dimensions.” <i>Physica Status Solidi (B): Basic Solid State Physics</i>, vol. 252, no. 9, Wiley, 2015, pp. 2059–71, doi:<a href=\"https://doi.org/10.1002/pssb.201552082\">10.1002/pssb.201552082</a>.","ieee":"J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Evaluation techniques for Gutzwiller wave functions in finite dimensions,” <i>Physica Status Solidi (B): Basic Solid State Physics</i>, vol. 252, no. 9. Wiley, pp. 2059–2071, 2015.","apa":"Kaczmarczyk, J., Schickling, T., &#38; Bünemann, J. (2015). Evaluation techniques for Gutzwiller wave functions in finite dimensions. <i>Physica Status Solidi (B): Basic Solid State Physics</i>. Wiley. <a href=\"https://doi.org/10.1002/pssb.201552082\">https://doi.org/10.1002/pssb.201552082</a>","ista":"Kaczmarczyk J, Schickling T, Bünemann J. 2015. Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. 252(9), 2059–2071.","chicago":"Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Evaluation Techniques for Gutzwiller Wave Functions in Finite Dimensions.” <i>Physica Status Solidi (B): Basic Solid State Physics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/pssb.201552082\">https://doi.org/10.1002/pssb.201552082</a>.","ama":"Kaczmarczyk J, Schickling T, Bünemann J. Evaluation techniques for Gutzwiller wave functions in finite dimensions. <i>Physica Status Solidi (B): Basic Solid State Physics</i>. 2015;252(9):2059-2071. doi:<a href=\"https://doi.org/10.1002/pssb.201552082\">10.1002/pssb.201552082</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"We give a comprehensive introduction into a diagrammatic method that allows for the evaluation of Gutzwiller wave functions in finite spatial dimensions. We discuss in detail some numerical schemes that turned out to be useful in the real-space evaluation of the diagrams. The method is applied to the problem of d-wave superconductivity in a two-dimensional single-band Hubbard model. Here, we discuss in particular the role of long-range contributions in our diagrammatic expansion. We further reconsider our previous analysis on the kinetic energy gain in the superconducting state.","lang":"eng"}],"publisher":"Wiley","date_published":"2015-09-01T00:00:00Z","title":"Evaluation techniques for Gutzwiller wave functions in finite dimensions","date_created":"2018-12-11T11:53:31Z","type":"journal_article","_id":"1695","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1503.03738"}],"ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"orcid":"0000-0002-1629-3675","last_name":"Kaczmarczyk","first_name":"Jan","full_name":"Kaczmarczyk, Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schickling, Tobias","first_name":"Tobias","last_name":"Schickling"},{"full_name":"Bünemann, Jörg","last_name":"Bünemann","first_name":"Jörg"}],"month":"09","issue":"9","language":[{"iso":"eng"}],"volume":252},{"publication_status":"published","abstract":[{"lang":"eng","text":"The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller wave function (GWF) is applied to the Anderson lattice model. This approach allows for a systematic evaluation of the expectation values with full Gutzwiller wave function in finite-dimensional systems. It introduces results extending in an essential manner those obtained by means of the standard Gutzwiller approximation (GA), which is variationally exact only in infinite dimensions. Within the DE-GWF approach we discuss the principal paramagnetic properties and their relevance to heavy-fermion systems. We demonstrate the formation of an effective, narrow f band originating from atomic f-electron states and subsequently interpret this behavior as a direct itineracy of f electrons; it represents a combined effect of both the hybridization and the correlations induced by the Coulomb repulsive interaction. Such a feature is absent on the level of GA, which is equivalent to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent narrow f band rationalizes the common assumption of such dispersion of f levels in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it is shown that the emerging f-electron direct itineracy leads in a natural manner to three physically distinct regimes within a single model that are frequently discussed for 4f- or 5f-electron compounds as separate model situations. We identify these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging correlated quantum liquid state are stressed."}],"publisher":"American Physical Society","date_published":"2015-09-18T00:00:00Z","title":"Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:52:35Z","citation":{"ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states,” <i>Physical Review B</i>, vol. 92, no. 12. American Physical Society, 2015.","apa":"Wysokiński, M., Kaczmarczyk, J., &#38; Spałek, J. (2015). Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.92.125135\">https://doi.org/10.1103/PhysRevB.92.125135</a>","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. <i>Physical Review B</i>. 2015;92(12). doi:<a href=\"https://doi.org/10.1103/PhysRevB.92.125135\">10.1103/PhysRevB.92.125135</a>","chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” <i>Physical Review B</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevB.92.125135\">https://doi.org/10.1103/PhysRevB.92.125135</a>.","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2015. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 92(12), 125135.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B 92 (2015).","mla":"Wysokiński, Marcin, et al. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” <i>Physical Review B</i>, vol. 92, no. 12, 125135, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevB.92.125135\">10.1103/PhysRevB.92.125135</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publist_id":"5448","intvolume":"        92","publication":"Physical Review B","oa":1,"acknowledgement":"The work was partly supported by the National Science Centre (NCN) under MAESTRO, Grant No. DEC-2012/04/A/ST3/00342. M.W. acknowledges the hospitality of the Institute of Science and Technology Austria during the final stage of development of the present work, as well as partial financial support from the Society-Environment-Technology project of the Jagiellonian University for that stay. J.K. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. [291734 ].","day":"18","doi":"10.1103/PhysRevB.92.125135","year":"2015","month":"09","article_number":"125135","issue":"12","language":[{"iso":"eng"}],"volume":92,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"last_name":"Wysokiński","first_name":"Marcin","full_name":"Wysokiński, Marcin"},{"first_name":"Jan","last_name":"Kaczmarczyk","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarczyk, Jan"},{"first_name":"Jozef","last_name":"Spałek","full_name":"Spałek, Jozef"}],"ec_funded":1,"date_created":"2018-12-11T11:53:31Z","_id":"1696","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1505.07003","open_access":"1"}],"status":"public"},{"publist_id":"5447","intvolume":"        11","publication":"PLoS Computational Biology","scopus_import":1,"acknowledgement":"This work was supported by grants EY 014196 and EY 017934 to MJB, ANR OPTIMA, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche [LIFESENSES: ANR-10-LABX-65], and by a EC grant from the Human Brain Project (CLAP) to OM, the Austrian Research Foundation FWF P25651 to VBS and GT. VBS is partially supported by contracts MEC, Spain (Grant No. AYA2010- 22111-C03-02, Grant No. AYA2013-48623-C2-2 and FEDER Funds).","year":"2015","doi":"10.1371/journal.pcbi.1004304","day":"01","oa":1,"publisher":"Public Library of Science","date_published":"2015-07-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:12Z","title":"High accuracy decoding of dynamical motion from a large retinal population","publication_status":"published","abstract":[{"text":"Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits.","lang":"eng"}],"ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:52:35Z","citation":{"mla":"Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” <i>PLoS Computational Biology</i>, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004304\">10.1371/journal.pcbi.1004304</a>.","short":"O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015).","chicago":"Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” <i>PLoS Computational Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004304\">https://doi.org/10.1371/journal.pcbi.1004304</a>.","ama":"Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy decoding of dynamical motion from a large retinal population. <i>PLoS Computational Biology</i>. 2015;11(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004304\">10.1371/journal.pcbi.1004304</a>","ista":"Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7), e1004304.","apa":"Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkačik, G., &#38; Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004304\">https://doi.org/10.1371/journal.pcbi.1004304</a>","ieee":"O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” <i>PLoS Computational Biology</i>, vol. 11, no. 7. Public Library of Science, 2015."},"pubrep_id":"455","status":"public","date_created":"2018-12-11T11:53:31Z","_id":"1697","type":"journal_article","language":[{"iso":"eng"}],"volume":11,"has_accepted_license":"1","month":"07","file":[{"creator":"system","checksum":"472b979f3f1cffb37b3e503f085115ca","file_id":"5212","file_size":4673930,"access_level":"open_access","relation":"main_file","file_name":"IST-2016-455-v1+1_journal.pcbi.1004304.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:12Z","date_created":"2018-12-12T10:16:25Z"}],"article_number":"e1004304","issue":"7","author":[{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"id":"421234E8-F248-11E8-B48F-1D18A9856A87","full_name":"Botella Soler, Vicente","last_name":"Botella Soler","first_name":"Vicente","orcid":"0000-0002-8790-1914"},{"first_name":"Kristina","last_name":"Simmons","full_name":"Simmons, Kristina"},{"first_name":"Thierry","last_name":"Mora","full_name":"Mora, Thierry"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Berry","first_name":"Michael","full_name":"Berry, Michael"}],"quality_controlled":"1","project":[{"_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF"}],"oa_version":"Published Version"},{"scopus_import":1,"publist_id":"5443","intvolume":"       241","publication":"Information and Computation","oa":1,"acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 and S11402-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (267989: Quantitative Reactive Modeling), European project Cassting (FP7-601148), ERC Start grant (279499: inVEST).","page":"177 - 196","year":"2015","doi":"10.1016/j.ic.2015.03.001","day":"01","publication_status":"published","abstract":[{"text":"In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Multi-mean-payoff and multi-energy games replace individual weights by tuples, and the limit average (resp., running sum) of each coordinate must be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy games and show inter-reducibility of multi-mean-payoff and multi-energy games for finite-memory strategies. We improve the computational complexity for solving both classes with finite-memory strategies: we prove coNP-completeness improving the previous known EXPSPACE bound. For memoryless strategies, we show that deciding the existence of a winning strategy for the protagonist is NP-complete. We present the first solution of multi-mean-payoff games with infinite-memory strategies: we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf objectives are coNP-complete.","lang":"eng"}],"publisher":"Elsevier","date_published":"2015-04-01T00:00:00Z","title":"The complexity of multi-mean-payoff and multi-energy games","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-01-12T06:52:36Z","citation":{"mla":"Velner, Yaron, et al. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” <i>Information and Computation</i>, vol. 241, no. 4, Elsevier, 2015, pp. 177–96, doi:<a href=\"https://doi.org/10.1016/j.ic.2015.03.001\">10.1016/j.ic.2015.03.001</a>.","short":"Y. Velner, K. Chatterjee, L. Doyen, T.A. Henzinger, A. Rabinovich, J. Raskin, Information and Computation 241 (2015) 177–196.","chicago":"Velner, Yaron, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger, Alexander Rabinovich, and Jean Raskin. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” <i>Information and Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ic.2015.03.001\">https://doi.org/10.1016/j.ic.2015.03.001</a>.","ama":"Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. The complexity of multi-mean-payoff and multi-energy games. <i>Information and Computation</i>. 2015;241(4):177-196. doi:<a href=\"https://doi.org/10.1016/j.ic.2015.03.001\">10.1016/j.ic.2015.03.001</a>","ista":"Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. 2015. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 241(4), 177–196.","apa":"Velner, Y., Chatterjee, K., Doyen, L., Henzinger, T. A., Rabinovich, A., &#38; Raskin, J. (2015). The complexity of multi-mean-payoff and multi-energy games. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2015.03.001\">https://doi.org/10.1016/j.ic.2015.03.001</a>","ieee":"Y. Velner, K. Chatterjee, L. Doyen, T. A. Henzinger, A. Rabinovich, and J. Raskin, “The complexity of multi-mean-payoff and multi-energy games,” <i>Information and Computation</i>, vol. 241, no. 4. Elsevier, pp. 177–196, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"date_created":"2018-12-11T11:53:32Z","type":"journal_article","_id":"1698","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1209.3234"}],"status":"public","month":"04","issue":"4","language":[{"iso":"eng"}],"volume":241,"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Rabinovich, Alexander","first_name":"Alexander","last_name":"Rabinovich"},{"last_name":"Raskin","first_name":"Jean","full_name":"Raskin, Jean"}]},{"acknowledgement":"This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria).","day":"01","year":"2015","page":"1523 - 1580","doi":"10.1007/s00285-014-0802-y","oa":1,"publist_id":"5442","intvolume":"        70","publication":"Journal of Mathematical Biology","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"NiBa"}],"date_updated":"2023-02-23T10:10:36Z","citation":{"chicago":"Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” <i>Journal of Mathematical Biology</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00285-014-0802-y\">https://doi.org/10.1007/s00285-014-0802-y</a>.","ista":"Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580.","ama":"Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. <i>Journal of Mathematical Biology</i>. 2015;70(7):1523-1580. doi:<a href=\"https://doi.org/10.1007/s00285-014-0802-y\">10.1007/s00285-014-0802-y</a>","apa":"Uecker, H., Setter, D., &#38; Hermisson, J. (2015). Adaptive gene introgression after secondary contact. <i>Journal of Mathematical Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s00285-014-0802-y\">https://doi.org/10.1007/s00285-014-0802-y</a>","ieee":"H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” <i>Journal of Mathematical Biology</i>, vol. 70, no. 7. Springer, pp. 1523–1580, 2015.","short":"H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580.","mla":"Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” <i>Journal of Mathematical Biology</i>, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:<a href=\"https://doi.org/10.1007/s00285-014-0802-y\">10.1007/s00285-014-0802-y</a>."},"publisher":"Springer","date_published":"2015-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:12Z","title":"Adaptive gene introgression after secondary contact","publication_status":"published","abstract":[{"text":"By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range.","lang":"eng"}],"ddc":["576"],"status":"public","date_created":"2018-12-11T11:53:32Z","_id":"1699","type":"journal_article","pubrep_id":"458","author":[{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","full_name":"Uecker, Hildegard","last_name":"Uecker","first_name":"Hildegard","orcid":"0000-0001-9435-2813"},{"full_name":"Setter, Derek","first_name":"Derek","last_name":"Setter"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"}],"project":[{"_id":"25B67606-B435-11E9-9278-68D0E5697425","name":"L'OREAL Fellowship"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":70,"has_accepted_license":"1","month":"06","file":[{"relation":"main_file","file_id":"5079","checksum":"00e3a67bda05d4cc165b3a48b41ef9ad","creator":"system","access_level":"open_access","file_size":1321527,"content_type":"application/pdf","date_created":"2018-12-12T10:14:27Z","date_updated":"2020-07-14T12:45:12Z","file_name":"IST-2016-458-v1+1_s00285-014-0802-y.pdf"}],"issue":"7"},{"oa_version":"Preprint","citation":{"mla":"Van Loon, Erik, et al. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” <i>Physical Review B</i>, vol. 92, no. 8, 081106, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevB.92.081106\">10.1103/PhysRevB.92.081106</a>.","short":"E. Van Loon, M. Katsnelson, M. Lemeshko, Physical Review B 92 (2015).","chicago":"Van Loon, Erik, Mikhail Katsnelson, and Mikhail Lemeshko. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” <i>Physical Review B</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevB.92.081106\">https://doi.org/10.1103/PhysRevB.92.081106</a>.","ista":"Van Loon E, Katsnelson M, Lemeshko M. 2015. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 92(8), 081106.","ama":"Van Loon E, Katsnelson M, Lemeshko M. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. <i>Physical Review B</i>. 2015;92(8). doi:<a href=\"https://doi.org/10.1103/PhysRevB.92.081106\">10.1103/PhysRevB.92.081106</a>","apa":"Van Loon, E., Katsnelson, M., &#38; Lemeshko, M. (2015). Ultralong-range order in the Fermi-Hubbard model with long-range interactions. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.92.081106\">https://doi.org/10.1103/PhysRevB.92.081106</a>","ieee":"E. Van Loon, M. Katsnelson, and M. Lemeshko, “Ultralong-range order in the Fermi-Hubbard model with long-range interactions,” <i>Physical Review B</i>, vol. 92, no. 8. American Physical Society, 2015."},"date_updated":"2021-01-12T06:52:37Z","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Van Loon, Erik","last_name":"Van Loon","first_name":"Erik"},{"full_name":"Katsnelson, Mikhail","first_name":"Mikhail","last_name":"Katsnelson"},{"orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"issue":"8","article_number":"081106","abstract":[{"text":"We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an &quot;ultralong-range&quot; order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms.","lang":"eng"}],"publication_status":"published","month":"08","volume":92,"title":"Ultralong-range order in the Fermi-Hubbard model with long-range interactions","publisher":"American Physical Society","date_published":"2015-08-10T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","_id":"1700","date_created":"2018-12-11T11:53:32Z","oa":1,"doi":"10.1103/PhysRevB.92.081106","year":"2015","main_file_link":[{"url":"http://arxiv.org/abs/1506.06007","open_access":"1"}],"status":"public","day":"10","acknowledgement":"The work is supported by European Research Council (ERC) Advanced Grant No. 338957 FEMTO/NANO.","scopus_import":1,"publication":"Physical Review B","intvolume":"        92","publist_id":"5441"},{"intvolume":"       112","publist_id":"5440","publication":"PNAS","scopus_import":1,"acknowledgement":"Research was supported in part by National Science Foundation Grants PHY-1305525, PHY-1451171, and CCF-0939370, by National Institutes of Health Grant R01 EY14196, and by Austrian Science Foundation Grant FWF P25651. Additional support was provided by the\r\nFannie and John Hertz Foundation, by the Swartz Foundation, by the W. M. Keck Foundation, and by the Simons Foundation.","page":"11508 - 11513","doi":"10.1073/pnas.1514188112","year":"2015","day":"15","oa":1,"publisher":"National Academy of Sciences","date_published":"2015-09-15T00:00:00Z","pmid":1,"title":"Thermodynamics and signatures of criticality in a network of neurons","abstract":[{"text":"The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance. ","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26330611"]},"date_updated":"2021-01-12T06:52:37Z","department":[{"_id":"GaTk"}],"citation":{"mla":"Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” <i>PNAS</i>, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:<a href=\"https://doi.org/10.1073/pnas.1514188112\">10.1073/pnas.1514188112</a>.","short":"G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513.","ieee":"G. Tkačik <i>et al.</i>, “Thermodynamics and signatures of criticality in a network of neurons,” <i>PNAS</i>, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015.","chicago":"Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1514188112\">https://doi.org/10.1073/pnas.1514188112</a>.","ista":"Tkačik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37), 11508–11513.","ama":"Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality in a network of neurons. <i>PNAS</i>. 2015;112(37):11508-11513. doi:<a href=\"https://doi.org/10.1073/pnas.1514188112\">10.1073/pnas.1514188112</a>","apa":"Tkačik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., &#38; Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1514188112\">https://doi.org/10.1073/pnas.1514188112</a>"},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577210/","open_access":"1"}],"status":"public","date_created":"2018-12-11T11:53:33Z","_id":"1701","type":"journal_article","language":[{"iso":"eng"}],"volume":112,"month":"09","issue":"37","author":[{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"full_name":"Amodei, Dario","first_name":"Dario","last_name":"Amodei"},{"last_name":"Palmer","first_name":"Stephanie","full_name":"Palmer, Stephanie"},{"full_name":"Berry Ii, Michael","first_name":"Michael","last_name":"Berry Ii"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"}],"project":[{"call_identifier":"FWF","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes"}],"quality_controlled":"1","oa_version":"Submitted Version"},{"abstract":[{"text":"Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.","lang":"eng"}],"publication_status":"published","month":"05","issue":"5","language":[{"iso":"eng"}],"publisher":"CSIRO","date_published":"2015-05-26T00:00:00Z","volume":63,"title":"An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas","date_updated":"2021-01-12T06:52:38Z","department":[{"_id":"NiBa"}],"quality_controlled":"1","citation":{"chicago":"Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” <i>Australian Journal of Botany</i>. CSIRO, 2015. <a href=\"https://doi.org/10.1071/BT15023\">https://doi.org/10.1071/BT15023</a>.","ista":"Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466.","ama":"Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. <i>Australian Journal of Botany</i>. 2015;63(5):455-466. doi:<a href=\"https://doi.org/10.1071/BT15023\">10.1071/BT15023</a>","apa":"Broadhurst, L., Fifield, G., Vanzella, B., &#38; Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. <i>Australian Journal of Botany</i>. CSIRO. <a href=\"https://doi.org/10.1071/BT15023\">https://doi.org/10.1071/BT15023</a>","ieee":"L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” <i>Australian Journal of Botany</i>, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.","short":"L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466.","mla":"Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” <i>Australian Journal of Botany</i>, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:<a href=\"https://doi.org/10.1071/BT15023\">10.1071/BT15023</a>."},"oa_version":"None","author":[{"first_name":"Linda","last_name":"Broadhurst","full_name":"Broadhurst, Linda"},{"full_name":"Fifield, Graham","last_name":"Fifield","first_name":"Graham"},{"first_name":"Bindi","last_name":"Vanzella","full_name":"Vanzella, Bindi"},{"last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"intvolume":"        63","publist_id":"5434","publication":"Australian Journal of Botany","date_created":"2018-12-11T11:53:34Z","_id":"1703","type":"journal_article","status":"public","year":"2015","page":"455 - 466","day":"26","doi":"10.1071/BT15023"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T06:52:38Z","citation":{"chicago":"Deuchert, Andreas, Christian Hainzl, and Robert Seiringer. “Note on a Family of Monotone Quantum Relative Entropies.” <i>Letters in Mathematical Physics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s11005-015-0787-5\">https://doi.org/10.1007/s11005-015-0787-5</a>.","ista":"Deuchert A, Hainzl C, Seiringer R. 2015. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 105(10), 1449–1466.","ama":"Deuchert A, Hainzl C, Seiringer R. Note on a family of monotone quantum relative entropies. <i>Letters in Mathematical Physics</i>. 2015;105(10):1449-1466. doi:<a href=\"https://doi.org/10.1007/s11005-015-0787-5\">10.1007/s11005-015-0787-5</a>","apa":"Deuchert, A., Hainzl, C., &#38; Seiringer, R. (2015). Note on a family of monotone quantum relative entropies. <i>Letters in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s11005-015-0787-5\">https://doi.org/10.1007/s11005-015-0787-5</a>","ieee":"A. Deuchert, C. Hainzl, and R. Seiringer, “Note on a family of monotone quantum relative entropies,” <i>Letters in Mathematical Physics</i>, vol. 105, no. 10. Springer, pp. 1449–1466, 2015.","mla":"Deuchert, Andreas, et al. “Note on a Family of Monotone Quantum Relative Entropies.” <i>Letters in Mathematical Physics</i>, vol. 105, no. 10, Springer, 2015, pp. 1449–66, doi:<a href=\"https://doi.org/10.1007/s11005-015-0787-5\">10.1007/s11005-015-0787-5</a>.","short":"A. Deuchert, C. Hainzl, R. Seiringer, Letters in Mathematical Physics 105 (2015) 1449–1466."},"publisher":"Springer","date_published":"2015-08-05T00:00:00Z","file_date_updated":"2020-07-14T12:45:13Z","title":"Note on a family of monotone quantum relative entropies","publication_status":"published","abstract":[{"lang":"eng","text":"Given a convex function (Formula presented.) and two hermitian matrices A and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative entropy defined by (Formula presented.). Among other things, they prove that the so-defined quantity is monotone if and only if (Formula presented.) is operator monotone. The monotonicity is then used to properly define (Formula presented.) for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional projections (Formula presented.) with (Formula presented.) strongly, the limit (Formula presented.) is shown to exist and to be independent of the sequence of projections (Formula presented.). The question whether this sequence converges to its &quot;obvious&quot; limit, namely (Formula presented.), has been left open. We answer this question in principle affirmatively and show that (Formula presented.). If the operators A and B are regular enough, that is (A − B), (Formula presented.) and (Formula presented.) are trace-class, the identity (Formula presented.) holds."}],"ddc":["510"],"doi":"10.1007/s11005-015-0787-5","page":"1449 - 1466","year":"2015","day":"05","oa":1,"publist_id":"5432","intvolume":"       105","publication":"Letters in Mathematical Physics","scopus_import":1,"author":[{"orcid":"0000-0003-3146-6746","first_name":"Andreas","last_name":"Deuchert","full_name":"Deuchert, Andreas"},{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}],"quality_controlled":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"volume":105,"month":"08","has_accepted_license":"1","file":[{"relation":"main_file","creator":"dernst","file_id":"5836","checksum":"fd7307282a314cc1fbbaef77b187516b","file_size":484967,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:13Z","date_created":"2019-01-15T14:42:07Z","file_name":"2015_LettersMathPhys_Deuchert.pdf"}],"issue":"10","main_file_link":[{"url":"http://arxiv.org/abs/1502.07205","open_access":"1"}],"status":"public","date_created":"2018-12-11T11:53:34Z","type":"journal_article","_id":"1704"},{"ec_funded":1,"conference":{"end_date":"2015-10-06","start_date":"2015-10-04","location":"Banff, AB, Canada","name":"ALT: Algorithmic Learning Theory"},"status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1602.06531","open_access":"1"}],"date_created":"2018-12-11T11:53:35Z","type":"conference","_id":"1706","language":[{"iso":"eng"}],"volume":9355,"month":"01","author":[{"first_name":"Anastasia","last_name":"Pentina","full_name":"Pentina, Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ben David, Shai","first_name":"Shai","last_name":"Ben David"}],"project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"quality_controlled":"1","oa_version":"Preprint","intvolume":"      9355","publist_id":"5430","scopus_import":1,"doi":"10.1007/978-3-319-24486-0_13","day":"01","year":"2015","page":"194 - 208","oa":1,"date_published":"2015-01-01T00:00:00Z","publisher":"Springer","title":"Multi-task and lifelong learning of kernels","abstract":[{"lang":"eng","text":"We consider a problem of learning kernels for use in SVM classification in the multi-task and lifelong scenarios and provide generalization bounds on the error of a large margin classifier. Our results show that, under mild conditions on the family of kernels used for learning, solving several related tasks simultaneously is beneficial over single task learning. In particular, as the number of observed tasks grows, assuming that in the considered family of kernels there exists one that yields low approximation error on all tasks, the overhead associated with learning such a kernel vanishes and the complexity converges to that of learning when this good kernel is given to the learner."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"date_updated":"2021-01-12T06:52:39Z","department":[{"_id":"ChLa"}],"citation":{"apa":"Pentina, A., &#38; Ben David, S. (2015). Multi-task and lifelong learning of kernels (Vol. 9355, pp. 194–208). Presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-24486-0_13\">https://doi.org/10.1007/978-3-319-24486-0_13</a>","chicago":"Pentina, Anastasia, and Shai Ben David. “Multi-Task and Lifelong Learning of Kernels,” 9355:194–208. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-24486-0_13\">https://doi.org/10.1007/978-3-319-24486-0_13</a>.","ama":"Pentina A, Ben David S. Multi-task and lifelong learning of kernels. In: Vol 9355. Springer; 2015:194-208. doi:<a href=\"https://doi.org/10.1007/978-3-319-24486-0_13\">10.1007/978-3-319-24486-0_13</a>","ista":"Pentina A, Ben David S. 2015. Multi-task and lifelong learning of kernels. ALT: Algorithmic Learning Theory, LNCS, vol. 9355, 194–208.","ieee":"A. Pentina and S. Ben David, “Multi-task and lifelong learning of kernels,” presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada, 2015, vol. 9355, pp. 194–208.","mla":"Pentina, Anastasia, and Shai Ben David. <i>Multi-Task and Lifelong Learning of Kernels</i>. Vol. 9355, Springer, 2015, pp. 194–208, doi:<a href=\"https://doi.org/10.1007/978-3-319-24486-0_13\">10.1007/978-3-319-24486-0_13</a>.","short":"A. Pentina, S. Ben David, in:, Springer, 2015, pp. 194–208."}},{"abstract":[{"text":"The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards.","lang":"eng"}],"publication_status":"published","date_published":"2015-07-15T00:00:00Z","publisher":"Royal Society","pmid":1,"title":"Biological auctions with multiple rewards","date_updated":"2023-09-07T11:40:43Z","department":[{"_id":"KrCh"}],"citation":{"mla":"Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1812, Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2015.1041\">10.1098/rspb.2015.1041</a>.","short":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","ieee":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1812. Royal Society, 2015.","apa":"Reiter, J., Kanodia, A., Gupta, R., Nowak, M., &#38; Chatterjee, K. (2015). Biological auctions with multiple rewards. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2015.1041\">https://doi.org/10.1098/rspb.2015.1041</a>","ama":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1812). doi:<a href=\"https://doi.org/10.1098/rspb.2015.1041\">10.1098/rspb.2015.1041</a>","ista":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812).","chicago":"Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2015.1041\">https://doi.org/10.1098/rspb.2015.1041</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["26180069"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1400"}]},"scopus_import":1,"intvolume":"       282","publist_id":"5425","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","oa":1,"acknowledgement":"This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award.","doi":"10.1098/rspb.2015.1041","year":"2015","day":"15","month":"07","issue":"1812","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":282,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa_version":"Submitted Version","author":[{"first_name":"Johannes","last_name":"Reiter","orcid":"0000-0002-0170-7353","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","full_name":"Reiter, Johannes"},{"first_name":"Ayush","last_name":"Kanodia","full_name":"Kanodia, Ayush"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"date_created":"2018-12-11T11:53:35Z","type":"journal_article","_id":"1709","article_type":"original","status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/"}]},{"scopus_import":1,"publication":"Society for Industrial and Applied Mathematics","publist_id":"5423","intvolume":"        47","oa":1,"year":"2015","page":"2754 - 2769","doi":"10.1137/140993843","day":"14","publication_status":"published","abstract":[{"text":"We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) &lt; 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) &lt; 0 for 0 ≤ ξ &lt; 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞.","lang":"eng"}],"title":"Minimal resistance of curves under the single impact assumption","publisher":"SIAM","date_published":"2015-07-14T00:00:00Z","citation":{"short":"A. Akopyan, A. Plakhov, Society for Industrial and Applied Mathematics 47 (2015) 2754–2769.","mla":"Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” <i>Society for Industrial and Applied Mathematics</i>, vol. 47, no. 4, SIAM, 2015, pp. 2754–69, doi:<a href=\"https://doi.org/10.1137/140993843\">10.1137/140993843</a>.","ieee":"A. Akopyan and A. Plakhov, “Minimal resistance of curves under the single impact assumption,” <i>Society for Industrial and Applied Mathematics</i>, vol. 47, no. 4. SIAM, pp. 2754–2769, 2015.","apa":"Akopyan, A., &#38; Plakhov, A. (2015). Minimal resistance of curves under the single impact assumption. <i>Society for Industrial and Applied Mathematics</i>. SIAM. <a href=\"https://doi.org/10.1137/140993843\">https://doi.org/10.1137/140993843</a>","ista":"Akopyan A, Plakhov A. 2015. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 47(4), 2754–2769.","ama":"Akopyan A, Plakhov A. Minimal resistance of curves under the single impact assumption. <i>Society for Industrial and Applied Mathematics</i>. 2015;47(4):2754-2769. doi:<a href=\"https://doi.org/10.1137/140993843\">10.1137/140993843</a>","chicago":"Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” <i>Society for Industrial and Applied Mathematics</i>. SIAM, 2015. <a href=\"https://doi.org/10.1137/140993843\">https://doi.org/10.1137/140993843</a>."},"department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T06:52:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"_id":"1710","type":"journal_article","date_created":"2018-12-11T11:53:36Z","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.3736"}],"issue":"4","month":"07","volume":47,"language":[{"iso":"eng"}],"oa_version":"Preprint","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"author":[{"full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan"},{"last_name":"Plakhov","first_name":"Alexander","full_name":"Plakhov, Alexander"}]},{"oa_version":"Published Version","project":[{"call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077"}],"quality_controlled":"1","author":[{"last_name":"Ratheesh","first_name":"Aparna","full_name":"Ratheesh, Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87"},{"id":"47F080FE-F248-11E8-B48F-1D18A9856A87","full_name":"Belyaeva, Vera","last_name":"Belyaeva","first_name":"Vera"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"issue":"10","file":[{"creator":"system","checksum":"bbb1ee39ca52929aefe4f48752b166ee","file_id":"5098","file_size":1023680,"access_level":"open_access","relation":"main_file","file_name":"IST-2015-346-v1+1_Current_Opinion_Review_Ratheesh_et_al_2015.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:13Z","date_created":"2018-12-12T10:14:44Z"}],"has_accepted_license":"1","month":"10","volume":36,"language":[{"iso":"eng"}],"_id":"1712","type":"journal_article","date_created":"2018-12-11T11:53:36Z","status":"public","pubrep_id":"346","ec_funded":1,"citation":{"apa":"Ratheesh, A., Belyaeva, V., &#38; Siekhaus, D. E. (2015). Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. <i>Current Opinion in Cell Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ceb.2015.07.003\">https://doi.org/10.1016/j.ceb.2015.07.003</a>","chicago":"Ratheesh, Aparna, Vera Belyaeva, and Daria E Siekhaus. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” <i>Current Opinion in Cell Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ceb.2015.07.003\">https://doi.org/10.1016/j.ceb.2015.07.003</a>.","ama":"Ratheesh A, Belyaeva V, Siekhaus DE. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. <i>Current Opinion in Cell Biology</i>. 2015;36(10):71-79. doi:<a href=\"https://doi.org/10.1016/j.ceb.2015.07.003\">10.1016/j.ceb.2015.07.003</a>","ista":"Ratheesh A, Belyaeva V, Siekhaus DE. 2015. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 36(10), 71–79.","ieee":"A. Ratheesh, V. Belyaeva, and D. E. Siekhaus, “Drosophila immune cell migration and adhesion during embryonic development and larval immune responses,” <i>Current Opinion in Cell Biology</i>, vol. 36, no. 10. Elsevier, pp. 71–79, 2015.","mla":"Ratheesh, Aparna, et al. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” <i>Current Opinion in Cell Biology</i>, vol. 36, no. 10, Elsevier, 2015, pp. 71–79, doi:<a href=\"https://doi.org/10.1016/j.ceb.2015.07.003\">10.1016/j.ceb.2015.07.003</a>.","short":"A. Ratheesh, V. Belyaeva, D.E. Siekhaus, Current Opinion in Cell Biology 36 (2015) 71–79."},"date_updated":"2021-01-12T06:52:41Z","department":[{"_id":"DaSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"ddc":["573"],"abstract":[{"text":"The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses.","lang":"eng"}],"publication_status":"published","title":"Drosophila immune cell migration and adhesion during embryonic development and larval immune responses","file_date_updated":"2020-07-14T12:45:13Z","date_published":"2015-10-01T00:00:00Z","publisher":"Elsevier","oa":1,"day":"01","year":"2015","page":"71 - 79","doi":"10.1016/j.ceb.2015.07.003","scopus_import":1,"publication":"Current Opinion in Cell Biology","intvolume":"        36","publist_id":"5421"},{"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kößler, Alexander","first_name":"Alexander","last_name":"Kößler"},{"full_name":"Schmid, Ulrich","first_name":"Ulrich","last_name":"Schmid"}],"quality_controlled":"1","oa_version":"None","language":[{"iso":"eng"}],"volume":2015,"article_processing_charge":"No","month":"01","issue":"January","status":"public","date_created":"2018-12-11T11:53:37Z","type":"conference","_id":"1714","conference":{"start_date":"2014-12-02","end_date":"2014-12-05","location":"Rome, Italy","name":"RTSS: Real-Time Systems Symposium"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"date_updated":"2023-09-07T12:01:59Z","citation":{"ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks,” in <i>Real-Time Systems Symposium</i>, Rome, Italy, 2015, vol. 2015, no. January, pp. 118–127.","ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127.","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In: <i>Real-Time Systems Symposium</i>. Vol 2015. IEEE; 2015:118-127. doi:<a href=\"https://doi.org/10.1109/RTSS.2014.9\">10.1109/RTSS.2014.9</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” In <i>Real-Time Systems Symposium</i>, 2015:118–27. IEEE, 2015. <a href=\"https://doi.org/10.1109/RTSS.2014.9\">https://doi.org/10.1109/RTSS.2014.9</a>.","apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., &#38; Schmid, U. (2015). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In <i>Real-Time Systems Symposium</i> (Vol. 2015, pp. 118–127). Rome, Italy: IEEE. <a href=\"https://doi.org/10.1109/RTSS.2014.9\">https://doi.org/10.1109/RTSS.2014.9</a>","mla":"Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” <i>Real-Time Systems Symposium</i>, vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:<a href=\"https://doi.org/10.1109/RTSS.2014.9\">10.1109/RTSS.2014.9</a>.","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems Symposium, IEEE, 2015, pp. 118–127."},"date_published":"2015-01-15T00:00:00Z","publisher":"IEEE","title":"A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks","publication_status":"published","abstract":[{"text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application.","lang":"eng"}],"year":"2015","day":"15","page":"118 - 127","doi":"10.1109/RTSS.2014.9","publist_id":"5417","intvolume":"      2015","publication":"Real-Time Systems Symposium","scopus_import":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5423"},{"relation":"dissertation_contains","id":"821","status":"public"}]}},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Cohen","first_name":"Michael","full_name":"Cohen, Michael H"},{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Anna Kicheva"},{"full_name":"Ribeiro, Ana C","last_name":"Ribeiro","first_name":"Ana"},{"full_name":"Blassberg, Robert A","first_name":"Robert","last_name":"Blassberg"},{"full_name":"Page, Karen M","first_name":"Karen","last_name":"Page"},{"full_name":"Barnes, Chris P","last_name":"Barnes","first_name":"Chris"},{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"}],"citation":{"short":"M. Cohen, A. Kicheva, A. Ribeiro, R. Blassberg, K. Page, C. Barnes, J. Briscoe, Nature Communications 6 (2015).","mla":"Cohen, Michael, et al. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” <i>Nature Communications</i>, vol. 6, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms7709\">10.1038/ncomms7709</a>.","ieee":"M. Cohen <i>et al.</i>, “Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","apa":"Cohen, M., Kicheva, A., Ribeiro, A., Blassberg, R., Page, K., Barnes, C., &#38; Briscoe, J. (2015). Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms7709\">https://doi.org/10.1038/ncomms7709</a>","ama":"Cohen M, Kicheva A, Ribeiro A, et al. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms7709\">10.1038/ncomms7709</a>","ista":"Cohen M, Kicheva A, Ribeiro A, Blassberg R, Page K, Barnes C, Briscoe J. 2015. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 6.","chicago":"Cohen, Michael, Anna Kicheva, Ana Ribeiro, Robert Blassberg, Karen Page, Chris Barnes, and James Briscoe. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms7709\">https://doi.org/10.1038/ncomms7709</a>."},"date_updated":"2021-01-12T06:52:48Z","extern":1,"quality_controlled":0,"volume":6,"title":"Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms","publisher":"Nature Publishing Group","date_published":"2015-04-02T00:00:00Z","abstract":[{"text":"In the vertebrate neural tube, the morphogen Sonic Hedgehog (Shh) establishes a characteristic pattern of gene expression. Here we quantify the Shh gradient in the developing mouse neural tube and show that while the amplitude of the gradient increases over time, the activity of the pathway transcriptional effectors, Gli proteins, initially increases but later decreases. Computational analysis of the pathway suggests three mechanisms that could contribute to this adaptation: transcriptional upregulation of the inhibitory receptor Ptch1, transcriptional downregulation of Gli and the differential stability of active and inactive Gli isoforms. Consistent with this, Gli2 protein expression is downregulated during neural tube patterning and adaptation continues when the pathway is stimulated downstream of Ptch1. Moreover, the Shh-induced upregulation of Gli2 transcription prevents Gli activity levels from adapting in a different cell type, NIH3T3 fibroblasts, despite the upregulation of Ptch1. Multiple mechanisms therefore contribute to the intracellular dynamics of Shh signalling, resulting in different signalling dynamics in different cell types.","lang":"eng"}],"publication_status":"published","month":"04","doi":"10.1038/ncomms7709","status":"public","year":"2015","day":"02","acknowledgement":"C.P.B. gratefully acknowledges funding from the Wellcome Trust through a Research Career Development Fellowship (097319/Z/11/Z). This work was supported by the Medical Research Council (U117560541) and Wellcome Trust (WT098326MA, WT098325MA).","_id":"1728","type":"journal_article","date_created":"2018-12-11T11:53:42Z","publication":"Nature Communications","intvolume":"         6","publist_id":"5399"}]