[{"language":[{"iso":"eng"}],"conference":{"name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2018-07-19","location":"Stockholm, Sweden","start_date":"2018-07-13"},"doi":"10.24963/ijcai.2018/662","isi":1,"quality_controlled":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.24963/ijcai.2018/662","open_access":"1"}],"external_id":{"isi":["000764175404127"]},"month":"07","date_created":"2018-12-11T11:44:13Z","date_updated":"2023-09-19T14:44:59Z","volume":"2018-July","author":[{"last_name":"Horák","first_name":"Karel","full_name":"Horák, Karel"},{"last_name":"Bošanský","first_name":"Branislav","full_name":"Bošanský, Branislav"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"publication_status":"published","publisher":"IJCAI","department":[{"_id":"KrCh"}],"year":"2018","acknowledgement":"∗This work has been supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games). This research was sponsored by the Army Research Laboratory and was accomplished under Cooperative Agreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). ","ec_funded":1,"publist_id":"8030","date_published":"2018-07-01T00:00:00Z","page":"4764 - 4770","publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence","citation":{"apa":"Horák, K., Bošanský, B., & Chatterjee, K. (2018). Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence (Vol. 2018–July, pp. 4764–4770). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/662","ieee":"K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value iteration for goal-POMDPs,” in Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018–July, pp. 4764–4770.","ista":"Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018–July, 4764–4770.","ama":"Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. Vol 2018-July. IJCAI; 2018:4764-4770. doi:10.24963/ijcai.2018/662","chicago":"Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018–July:4764–70. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/662.","short":"K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.","mla":"Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:10.24963/ijcai.2018/662."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","status":"public","title":"Goal-HSVI: Heuristic search value iteration for goal-POMDPs","_id":"25","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Partially observable Markov decision processes (POMDPs) are the standard models for planning under uncertainty with both finite and infinite horizon. Besides the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs) is another classical objective for POMDPs. In this case, given a set of target states and a positive cost for each transition, the optimization objective is to minimize the expected total cost until a target state is reached. In the literature, RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees, and HSVI may even fail to terminate its trials. We give the following contributions: (1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they prevent the original HSVI from converging. (2) We present a novel algorithm inspired by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees. (3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples."}],"type":"conference"},{"oa_version":"Preprint","intvolume":" 2018","status":"public","title":"Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"24","abstract":[{"lang":"eng","text":"Partially-observable Markov decision processes (POMDPs) with discounted-sum payoff are a standard framework to model a wide range of problems related to decision making under uncertainty. Traditionally, the goal has been to obtain policies that optimize the expectation of the discounted-sum payoff. A key drawback of the expectation measure is that even low probability events with extreme payoff can significantly affect the expectation, and thus the obtained policies are not necessarily risk-averse. An alternate approach is to optimize the probability that the payoff is above a certain threshold, which allows obtaining risk-averse policies, but ignores optimization of the expectation. We consider the expectation optimization with probabilistic guarantee (EOPG) problem, where the goal is to optimize the expectation ensuring that the payoff is above a given threshold with at least a specified probability. We present several results on the EOPG problem, including the first algorithm to solve it."}],"type":"conference","date_published":"2018-07-01T00:00:00Z","page":"4692 - 4699","citation":{"apa":"Chatterjee, K., Elgyütt, A., Novotný, P., & Rouillé, O. (2018). Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives (Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/652","ieee":"K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4692–4699.","ista":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.","ama":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018. IJCAI; 2018:4692-4699. doi:10.24963/ijcai.2018/652","chicago":"Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé. “Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives,” 2018:4692–99. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/652.","short":"K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp. 4692–4699.","mla":"Chatterjee, Krishnendu, et al. Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives. Vol. 2018, IJCAI, 2018, pp. 4692–99, doi:10.24963/ijcai.2018/652."},"article_processing_charge":"No","day":"01","scopus_import":"1","volume":2018,"date_created":"2018-12-11T11:44:13Z","date_updated":"2023-09-19T14:45:48Z","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"first_name":"Adrian","last_name":"Elgyütt","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","full_name":"Elgyütt, Adrian"},{"full_name":"Novotny, Petr","first_name":"Petr","last_name":"Novotny","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rouillé, Owen","first_name":"Owen","last_name":"Rouillé"}],"publisher":"IJCAI","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2018","acknowledgement":"This research was supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and an ERC Start Grant (279307:Graph Games).\r\n","ec_funded":1,"publist_id":"8031","language":[{"iso":"eng"}],"doi":"10.24963/ijcai.2018/652","conference":{"end_date":"2018-07-19","start_date":"2018-07-13","location":"Stockholm, Sweden","name":"IJCAI: International Joint Conference on Artificial Intelligence"},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000764175404117"],"arxiv":["1804.10601"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10601"}],"month":"07"},{"language":[{"iso":"eng"}],"conference":{"end_date":"2018-06-29","location":"Delft, Netherlands","start_date":"2018-06-24","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"isi":1,"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/1710.00675","open_access":"1"}],"external_id":{"isi":["000492986200006"],"arxiv":["1710.00675"]},"oa":1,"month":"06","date_created":"2018-12-11T11:44:16Z","date_updated":"2023-09-19T14:44:14Z","volume":2018,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Chemlík","first_name":"Martin","full_name":"Chemlík, Martin"},{"full_name":"Topcu, Ufuk","first_name":"Ufuk","last_name":"Topcu"}],"publication_status":"published","publisher":"AAAI Press","department":[{"_id":"KrCh"}],"year":"2018","ec_funded":1,"publist_id":"8021","date_published":"2018-06-01T00:00:00Z","page":"47 - 55","citation":{"apa":"Chatterjee, K., Chemlík, M., & Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands: AAAI Press.","ieee":"K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.","ista":"Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. ICAPS: International Conference on Automated Planning and Scheduling, ICAPS, vol. 2018, 47–55.","ama":"Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: Vol 2018. AAAI Press; 2018:47-55.","chicago":"Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018.","short":"K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55.","mla":"Chatterjee, Krishnendu, et al. Sensor Synthesis for POMDPs with Reachability Objectives. Vol. 2018, AAAI Press, 2018, pp. 47–55."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Sensor synthesis for POMDPs with reachability objectives","status":"public","intvolume":" 2018","_id":"34","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies."}],"alternative_title":["ICAPS"],"type":"conference"},{"date_published":"2018-10-01T00:00:00Z","publication":"Ars Combinatoria","citation":{"chicago":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” Ars Combinatoria. Charles Babbage Research Centre, 2018.","mla":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” Ars Combinatoria, vol. 141, no. 10, Charles Babbage Research Centre, 2018, pp. 269–304.","short":"V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304.","ista":"Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria. 141(10), 269–304.","apa":"Kolmogorov, V., & Rolinek, M. (2018). Superconcentrators of density 25.3. Ars Combinatoria. Charles Babbage Research Centre.","ieee":"V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” Ars Combinatoria, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304, 2018.","ama":"Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. Ars Combinatoria. 2018;141(10):269-304."},"page":"269 - 304","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"18","title":"Superconcentrators of density 25.3","status":"public","intvolume":" 141","abstract":[{"lang":"eng","text":"An N-superconcentrator is a directed, acyclic graph with N input nodes and N output nodes such that every subset of the inputs and every subset of the outputs of same cardinality can be connected by node-disjoint paths. It is known that linear-size and bounded-degree superconcentrators exist. We prove the existence of such superconcentrators with asymptotic density 25.3 (where the density is the number of edges divided by N). The previously best known densities were 28 [12] and 27.4136 [17]."}],"issue":"10","type":"journal_article","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1405.7828","open_access":"1"}],"external_id":{"isi":["000446809500022"],"arxiv":["1405.7828"]},"oa":1,"isi":1,"quality_controlled":"1","month":"10","publication_identifier":{"issn":["0381-7032"]},"author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"}],"date_created":"2018-12-11T11:44:11Z","date_updated":"2023-09-19T14:46:18Z","volume":141,"year":"2018","publication_status":"published","publisher":"Charles Babbage Research Centre","department":[{"_id":"VlKo"}],"publist_id":"8037"},{"file":[{"file_id":"6356","relation":"main_file","checksum":"5a71b24ba712a3eb2e46165a38fbc30a","date_updated":"2020-07-14T12:47:28Z","date_created":"2019-04-30T06:14:58Z","access_level":"open_access","file_name":"2018_ForumMahtematics_Akopyan.pdf","creator":"dernst","file_size":249246,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6355","intvolume":" 6","ddc":["510"],"status":"public","title":"Any cyclic quadrilateral can be inscribed in any closed convex smooth curve","abstract":[{"text":"We prove that any cyclic quadrilateral can be inscribed in any closed convex C1-curve. The smoothness condition is not required if the quadrilateral is a rectangle.","lang":"eng"}],"type":"journal_article","date_published":"2018-05-31T00:00:00Z","citation":{"ista":"Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7.","apa":"Akopyan, A., & Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2018.7","ieee":"A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in any closed convex smooth curve,” Forum of Mathematics, Sigma, vol. 6. Cambridge University Press, 2018.","ama":"Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 2018;6. doi:10.1017/fms.2018.7","chicago":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma. Cambridge University Press, 2018. https://doi.org/10.1017/fms.2018.7.","mla":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma, vol. 6, e7, Cambridge University Press, 2018, doi:10.1017/fms.2018.7.","short":"A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018)."},"publication":"Forum of Mathematics, Sigma","article_processing_charge":"No","has_accepted_license":"1","day":"31","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8156"}]},"author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","first_name":"Arseniy"},{"last_name":"Avvakumov","first_name":"Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey"}],"volume":6,"date_updated":"2023-09-19T14:50:12Z","date_created":"2019-04-30T06:09:57Z","year":"2018","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"JaMa"}],"publisher":"Cambridge University Press","publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:28Z","article_number":"e7","doi":"10.1017/fms.2018.7","language":[{"iso":"eng"}],"external_id":{"isi":["000433915500001"],"arxiv":["1712.10205"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["2050-5094"]},"month":"05"},{"scopus_import":"1","month":"09","day":"10","publication_identifier":{"isbn":["9781538630815"]},"article_processing_charge":"No","citation":{"ista":"Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains. ICRA: International Conference on Robotics and Automation, 8461106.","ieee":"M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled as kinematic chains,” presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia, 2018.","apa":"Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock, O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots modeled as kinematic chains. Presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106","ama":"Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106","chicago":"Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106.","mla":"Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106.","short":"M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock, D. Prattichizzo, in:, IEEE, 2018."},"external_id":{"isi":["000446394503031"]},"quality_controlled":"1","isi":1,"conference":{"name":"ICRA: International Conference on Robotics and Automation","start_date":"2018-05-21","location":"Brisbane, Australia","end_date":"2018-05-25"},"date_published":"2018-09-10T00:00:00Z","doi":"10.1109/icra.2018.8461106","language":[{"iso":"eng"}],"article_number":"8461106","type":"conference","abstract":[{"lang":"eng","text":"In the context of robotic manipulation and grasping, the shift from a view that is static (force closure of a single posture) and contact-deprived (only contact for force closure is allowed, everything else is obstacle) towards a view that is dynamic and contact-rich (soft manipulation) has led to an increased interest in soft hands. These hands can easily exploit environmental constraints and object surfaces without risk, and safely interact with humans, but present also some challenges. Designing them is difficult, as well as predicting, modelling, and “programming” their interactions with the objects and the environment. This paper tackles the problem of simulating them in a fast and effective way, leveraging on novel and existing simulation technologies. We present a triple-layered simulation framework where dynamic properties such as stiffness are determined from slow but accurate FEM simulation data once, and then condensed into a lumped parameter model that can be used to fast simulate soft fingers and soft hands. We apply our approach to the simulation of soft pneumatic fingers."}],"year":"2018","_id":"6195","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication_status":"published","title":"Efficient FEM-based simulation of soft robots modeled as kinematic chains","publisher":"IEEE","department":[{"_id":"BeBi"}],"author":[{"full_name":"Pozzi, Maria","last_name":"Pozzi","first_name":"Maria"},{"full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba","first_name":"Eder"},{"last_name":"Deimel","first_name":"Raphael","full_name":"Deimel, Raphael"},{"first_name":"Monica","last_name":"Malvezzi","full_name":"Malvezzi, Monica"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"},{"last_name":"Brock","first_name":"Oliver","full_name":"Brock, Oliver"},{"last_name":"Prattichizzo","first_name":"Domenico","full_name":"Prattichizzo, Domenico"}],"date_updated":"2023-09-19T14:49:03Z","date_created":"2019-04-04T09:50:38Z","oa_version":"None"},{"isi":1,"quality_controlled":"1","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"external_id":{"isi":["000540656400026"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2015/528"}],"language":[{"iso":"eng"}],"conference":{"name":"FC: Financial Cryptography and Data Security","end_date":"2018-03-02","location":"Nieuwpoort, Curacao","start_date":"2018-02-26"},"doi":"10.1007/978-3-662-58387-6_26","month":"12","publication_identifier":{"issn":["0302-9743"],"isbn":["9783662583869","9783662583876"],"eissn":["1611-3349"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"KrPi"}],"year":"2018","date_updated":"2023-09-19T15:02:13Z","date_created":"2019-10-14T06:35:38Z","volume":10957,"author":[{"last_name":"Park","first_name":"Sunoo","full_name":"Park, Sunoo"},{"full_name":"Kwon, Albert","first_name":"Albert","last_name":"Kwon"},{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"first_name":"Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter"},{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F","full_name":"Alwen, Joel F"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"ec_funded":1,"page":"480-499","publication":"22nd International Conference on Financial Cryptography and Data Security","citation":{"chicago":"Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen, and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” In 22nd International Conference on Financial Cryptography and Data Security, 10957:480–99. Springer Nature, 2018. https://doi.org/10.1007/978-3-662-58387-6_26.","short":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:, 22nd International Conference on Financial Cryptography and Data Security, Springer Nature, 2018, pp. 480–499.","mla":"Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” 22nd International Conference on Financial Cryptography and Data Security, vol. 10957, Springer Nature, 2018, pp. 480–99, doi:10.1007/978-3-662-58387-6_26.","apa":"Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., & Pietrzak, K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In 22nd International Conference on Financial Cryptography and Data Security (Vol. 10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. https://doi.org/10.1007/978-3-662-58387-6_26","ieee":"S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak, “SpaceMint: A cryptocurrency based on proofs of space,” in 22nd International Conference on Financial Cryptography and Data Security, Nieuwpoort, Curacao, 2018, vol. 10957, pp. 480–499.","ista":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint: A cryptocurrency based on proofs of space. 22nd International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 10957, 480–499.","ama":"Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A cryptocurrency based on proofs of space. In: 22nd International Conference on Financial Cryptography and Data Security. Vol 10957. Springer Nature; 2018:480-499. doi:10.1007/978-3-662-58387-6_26"},"date_published":"2018-12-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"No","status":"public","title":"SpaceMint: A cryptocurrency based on proofs of space","intvolume":" 10957","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6941","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Bitcoin has become the most successful cryptocurrency ever deployed, and its most distinctive feature is that it is decentralized. Its underlying protocol (Nakamoto consensus) achieves this by using proof of work, which has the drawback that it causes the consumption of vast amounts of energy to maintain the ledger. Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather than computation. We argue that SpaceMint’s design solves or alleviates several of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also rewards smaller miners fairly according to their contribution to the network, thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof of space to enable its use in cryptocurrency, studies the attacks that can arise against a Bitcoin-like blockchain that uses proof of space, and proposes a new blockchain format and transaction types to address these attacks. Our prototype shows that initializing 1 TB for mining takes about a day (a one-off setup cost), and miners spend on average just a fraction of a second per block mined. Finally, we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the canonical game-theoretic notion for games that take place over time) and show that this stylized game satisfies a strong equilibrium notion, thereby arguing for SpaceMint ’s stability and consensus.","lang":"eng"}]},{"citation":{"mla":"Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:10.1084/jem.20170896.","short":"F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890.","chicago":"Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20170896.","ama":"Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2018;2015(7):1869–1890. doi:10.1084/jem.20170896","ista":"Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890.","apa":"Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20170896","ieee":"F. Moalli et al., “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” The Journal of Experimental Medicine, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018."},"publication":"The Journal of Experimental Medicine","page":"1869–1890","date_published":"2018-06-06T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"06","_id":"6497","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 2015","ddc":["570"],"title":"The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells","status":"public","file":[{"file_name":"2018_rupress_Moalli.pdf","access_level":"open_access","creator":"kschuh","file_size":3841660,"content_type":"application/pdf","file_id":"6498","relation":"main_file","date_updated":"2020-07-14T12:47:32Z","date_created":"2019-05-28T12:40:05Z","checksum":"86ae5331f9bfced9a6358a790a04bef4"}],"oa_version":"Published Version","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations."}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"external_id":{"isi":["000440822900011"]},"quality_controlled":"1","isi":1,"doi":"10.1084/jem.20170896","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1540-9538"],"issn":["0022-1007"]},"month":"06","year":"2018","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"}],"publication_status":"published","author":[{"full_name":"Moalli, Federica","last_name":"Moalli","first_name":"Federica"},{"first_name":"Xenia","last_name":"Ficht","full_name":"Ficht, Xenia"},{"first_name":"Philipp","last_name":"Germann","full_name":"Germann, Philipp"},{"full_name":"Vladymyrov, Mykhailo","last_name":"Vladymyrov","first_name":"Mykhailo"},{"first_name":"Bettina","last_name":"Stolp","full_name":"Stolp, Bettina"},{"full_name":"de Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"de Vries","first_name":"Ingrid"},{"first_name":"Ruth","last_name":"Lyck","full_name":"Lyck, Ruth"},{"full_name":"Balmer, Jasmin","last_name":"Balmer","first_name":"Jasmin"},{"full_name":"Fiocchi, Amleto","first_name":"Amleto","last_name":"Fiocchi"},{"first_name":"Mario","last_name":"Kreutzfeldt","full_name":"Kreutzfeldt, Mario"},{"first_name":"Doron","last_name":"Merkler","full_name":"Merkler, Doron"},{"last_name":"Iannacone","first_name":"Matteo","full_name":"Iannacone, Matteo"},{"first_name":"Akitaka","last_name":"Ariga","full_name":"Ariga, Akitaka"},{"full_name":"Stoffel, Michael H.","last_name":"Stoffel","first_name":"Michael H."},{"last_name":"Sharpe","first_name":"James","full_name":"Sharpe, James"},{"full_name":"Bähler, Martin","first_name":"Martin","last_name":"Bähler"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Alba","last_name":"Diz-Muñoz","full_name":"Diz-Muñoz, Alba"},{"last_name":"Stein","first_name":"Jens V.","full_name":"Stein, Jens V."}],"volume":2015,"date_created":"2019-05-28T12:36:47Z","date_updated":"2023-09-19T14:52:08Z","file_date_updated":"2020-07-14T12:47:32Z"},{"day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2018-09-01T00:00:00Z","publication":"EMBO reports","citation":{"chicago":"Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports. EMBO, 2018. https://doi.org/10.15252/embr.201845836.","mla":"Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports, vol. 19, no. 9, e45836, EMBO, 2018, doi:10.15252/embr.201845836.","short":"S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018).","ista":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836.","ieee":"S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” EMBO reports, vol. 19, no. 9. EMBO, 2018.","apa":"Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., & Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO Reports. EMBO. https://doi.org/10.15252/embr.201845836","ama":"Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 2018;19(9). doi:10.15252/embr.201845836"},"abstract":[{"lang":"eng","text":"Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge."}],"issue":"9","type":"journal_article","oa_version":"Published Version","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":2005572,"file_name":"2018_embo_Truckenbrodt.pdf","access_level":"open_access","date_created":"2019-05-28T13:17:19Z","date_updated":"2020-07-14T12:47:32Z","checksum":"6ec90abc637f09cca3a7b6424d7e7a26","file_id":"6500","relation":"main_file"}],"status":"public","title":"X10 expansion microscopy enables 25‐nm resolution on conventional microscopes","ddc":["580"],"intvolume":" 19","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6499","month":"09","publication_identifier":{"issn":["1469-221X"],"eissn":["1469-3178"]},"language":[{"iso":"eng"}],"doi":"10.15252/embr.201845836","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000443682200009"]},"oa":1,"file_date_updated":"2020-07-14T12:47:32Z","article_number":"e45836","date_updated":"2023-09-19T14:52:32Z","date_created":"2019-05-28T13:16:08Z","volume":19,"author":[{"full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87","first_name":"Sven M","last_name":"Truckenbrodt"},{"full_name":"Maidorn, Manuel","last_name":"Maidorn","first_name":"Manuel"},{"last_name":"Crzan","first_name":"Dagmar","full_name":"Crzan, Dagmar"},{"full_name":"Wildhagen, Hanna","first_name":"Hanna","last_name":"Wildhagen"},{"full_name":"Kabatas, Selda","last_name":"Kabatas","first_name":"Selda"},{"first_name":"Silvio O","last_name":"Rizzoli","full_name":"Rizzoli, Silvio O"}],"publication_status":"published","department":[{"_id":"JoDa"}],"publisher":"EMBO","year":"2018"},{"date_published":"2018-01-30T00:00:00Z","doi":"10.1137/1.9781611975031.144","conference":{"end_date":"2018-01-10","start_date":"2018-01-07","location":"New Orleans, LA, United States","name":"SODA: Symposium on Discrete Algorithms"},"language":[{"iso":"eng"}],"citation":{"short":"D.-A. Alistarh, J. Aspnes, R. Gelashvili, in:, Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–2239.","mla":"Alistarh, Dan-Adrian, et al. “Space-Optimal Majority in Population Protocols.” Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, ACM, 2018, pp. 2221–39, doi:10.1137/1.9781611975031.144.","chicago":"Alistarh, Dan-Adrian, James Aspnes, and Rati Gelashvili. “Space-Optimal Majority in Population Protocols.” In Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, 2221–39. ACM, 2018. https://doi.org/10.1137/1.9781611975031.144.","ama":"Alistarh D-A, Aspnes J, Gelashvili R. Space-optimal majority in population protocols. In: Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms. ACM; 2018:2221-2239. doi:10.1137/1.9781611975031.144","ieee":"D.-A. Alistarh, J. Aspnes, and R. Gelashvili, “Space-optimal majority in population protocols,” in Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, United States, 2018, pp. 2221–2239.","apa":"Alistarh, D.-A., Aspnes, J., & Gelashvili, R. (2018). Space-optimal majority in population protocols. In Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 2221–2239). New Orleans, LA, United States: ACM. https://doi.org/10.1137/1.9781611975031.144","ista":"Alistarh D-A, Aspnes J, Gelashvili R. 2018. Space-optimal majority in population protocols. Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 2221–2239."},"external_id":{"arxiv":["1704.04947"],"isi":["000483921200145"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.04947"}],"publication":"Proceedings of the 29th Annual ACM-SIAM Symposium on Discrete Algorithms","page":"2221-2239","quality_controlled":"1","isi":1,"article_processing_charge":"No","publication_identifier":{"isbn":["9781611975031"]},"day":"30","month":"01","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Aspnes, James","first_name":"James","last_name":"Aspnes"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"}],"oa_version":"Preprint","date_created":"2019-11-26T15:10:55Z","date_updated":"2023-09-19T15:03:16Z","year":"2018","_id":"7123","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"DaAl"}],"publisher":"ACM","publication_status":"published","status":"public","title":"Space-optimal majority in population protocols","abstract":[{"lang":"eng","text":"Population protocols are a popular model of distributed computing, in which n agents with limited local state interact randomly, and cooperate to collectively compute global predicates. Inspired by recent developments in DNA programming, an extensive series of papers, across different communities, has examined the computability and complexity characteristics of this model. Majority, or consensus, is a central task in this model, in which agents need to collectively reach a decision as to which one of two states A or B had a higher initial count. Two metrics are important: the time that a protocol requires to stabilize to an output decision, and the state space size that each agent requires to do so. It is known that majority requires Ω(log log n) states per agent to allow for fast (poly-logarithmic time) stabilization, and that O(log2 n) states are sufficient. Thus, there is an exponential gap between the space upper and lower bounds for this problem. This paper addresses this question.\r\n\r\nOn the negative side, we provide a new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c) expected time, for any constant c > 0. This result is conditional on monotonicity and output assumptions, satisfied by all known protocols. Technically, it represents a departure from previous lower bounds, in that it does not rely on the existence of dense configurations. Instead, we introduce a new generalized surgery technique to prove the existence of incorrect executions for any algorithm which would contradict the lower bound. Subsequently, our lower bound also applies to general initial configurations, including ones with a leader. On the positive side, we give a new algorithm for majority which uses O(log n) states, and stabilizes in O(log2 n) expected time. Central to the algorithm is a new leaderless phase clock technique, which allows agents to synchronize in phases of Θ(n log n) consecutive interactions using O(log n) states per agent, exploiting a new connection between population protocols and power-of-two-choices load balancing mechanisms. We also employ our phase clock to build a leader election algorithm with a state space of size O(log n), which stabilizes in O(log2 n) expected time."}],"type":"conference"},{"file_date_updated":"2021-08-16T07:48:03Z","acknowledgement":"We are very grateful to people who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot and Irena Senčić. We would also like to thank Magnus Alm Rosenblad and Mats Töpel for their contribution to assembling the Littorina saxatilis genome, Carl André, Pasi Rastas, and Romain Villoutreix for discussion, and two anonymous reviewers for their helpful comments on the manuscript. We are grateful to RapidGenomics for library preparation and sequencing. We thank the Natural Environment Research Council, the European Research Council and the Swedish Research Councils VR and Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology and Tage Erlander Guest Professorship) for funding. P.C. was funded by the University of Sheffield Vice-chancellor's India scholarship. R.F. is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 706376. M. Raf. was supported by the Adlerbert Research Foundation.","year":"2018","pmid":1,"publication_status":"published","publisher":"Wiley","department":[{"_id":"BeVi"}],"author":[{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"full_name":"Blomberg, Anders","first_name":"Anders","last_name":"Blomberg"},{"last_name":"Mehlig","first_name":"Bernhard","full_name":"Mehlig, Bernhard"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"related_material":{"record":[{"id":"9930","relation":"research_data","status":"public"}]},"date_updated":"2023-09-19T15:08:25Z","date_created":"2021-08-16T07:45:38Z","volume":2,"month":"08","publication_identifier":{"issn":["2056-3744"],"eissn":["2056-3744"]},"external_id":{"pmid":["30283683"],"isi":["000446774400004"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1002/evl3.74","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems."}],"issue":"4","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9917","ddc":["570"],"status":"public","title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow","intvolume":" 2","file":[{"success":1,"checksum":"8524e72507d521416be3f8ccfcd5e3f5","date_created":"2021-08-16T07:48:03Z","date_updated":"2021-08-16T07:48:03Z","file_id":"9918","relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_size":764299,"access_level":"open_access","file_name":"2018_EvolutionLetters_Westram.pdf"}],"oa_version":"Published Version","day":"20","article_processing_charge":"Yes","has_accepted_license":"1","publication":"Evolution Letters","citation":{"ama":"Westram AM, Rafajlović M, Chaube P, et al. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2018;2(4):297-309. doi:10.1002/evl3.74","ieee":"A. M. Westram et al., “Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow,” Evolution Letters, vol. 2, no. 4. Wiley, pp. 297–309, 2018.","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.74","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2(4), 297–309.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, Evolution Letters 2 (2018) 297–309.","mla":"Westram, Anja M., et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Evolution Letters, vol. 2, no. 4, Wiley, 2018, pp. 297–309, doi:10.1002/evl3.74.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Evolution Letters. Wiley, 2018. https://doi.org/10.1002/evl3.74."},"article_type":"letter_note","page":"297-309","date_published":"2018-08-20T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"Yes","day":"13","citation":{"ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2(6), 557–566.","ieee":"J. Hollander et al., “Are assortative mating and genital divergence driven by reinforcement?,” Evolution Letters, vol. 2, no. 6. Wiley, pp. 557–566, 2018.","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. Wiley. https://doi.org/10.1002/evl3.85","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2018;2(6):557-566. doi:10.1002/evl3.85","chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Evolution Letters. Wiley, 2018. https://doi.org/10.1002/evl3.85.","mla":"Hollander, Johan, et al. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Evolution Letters, vol. 2, no. 6, Wiley, 2018, pp. 557–66, doi:10.1002/evl3.85.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, Evolution Letters 2 (2018) 557–566."},"publication":"Evolution Letters","page":"557-566","article_type":"letter_note","date_published":"2018-12-13T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9915","intvolume":" 2","status":"public","ddc":["570"],"title":"Are assortative mating and genital divergence driven by reinforcement?","file":[{"date_updated":"2021-08-16T07:37:28Z","date_created":"2021-08-16T07:37:28Z","success":1,"checksum":"997a78ac41c809975ca69cbdea441f88","file_id":"9916","relation":"main_file","creator":"asandaue","content_type":"application/pdf","file_size":584606,"file_name":"2018_EvolutionLetters_Hollander.pdf","access_level":"open_access"}],"oa_version":"Published Version","publication_identifier":{"issn":[" 2056-3744"],"eissn":["2056-3744"]},"month":"12","external_id":{"pmid":["30564439"],"isi":["000452990000002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1002/evl3.85","language":[{"iso":"eng"}],"file_date_updated":"2021-08-16T07:37:28Z","pmid":1,"acknowledgement":"The authors express a special thanks to Dr Richard Willan at the Museum and Art Gallery of the Northern Territory for guidance and support in the field, and to Carole Smadja for reading and commenting on the manuscript. The authors thank the Government of Western Australia Department of Parks and Wildlife (license no. 009254) and Fishery Research Division (exemption no. 2262) for assistance with permits. Khalid Belkhir modified the coalescent sampler msnsam for the specific needs of this project and Martin Hirsch helped to set up the ABC pipeline and to modify the summary statistic calculator mscalc. The authors are grateful to the Crafoord Foundation for supporting this project. R.K.B., A.M.W., and L.D. were supported by grants from the Natural Environment Research Council, R.K.B. and A.M.W. were also supported by the European Research Council and R.K.B. and L.D. by the Leverhulme Trust. M.M.R. was supported by Consejo Nacional de Ciencia y Tecnología and Secretaría de Educación Pública, Mexico. G.B. was supported by the Centre for Animal Movement Research (CAnMove) financed by a Linnaeus grant (No. 349-2007-8690) from the Swedish Research Council and Lund University.","year":"2018","publisher":"Wiley","department":[{"_id":"BeVi"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"research_data","id":"9929"}]},"author":[{"last_name":"Hollander","first_name":"Johan","full_name":"Hollander, Johan"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"first_name":"Giuseppe","last_name":"Bianco","full_name":"Bianco, Giuseppe"},{"full_name":"Yang, Xi","first_name":"Xi","last_name":"Yang"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"full_name":"Duvaux, Ludovic","first_name":"Ludovic","last_name":"Duvaux"},{"full_name":"Reid, David G.","first_name":"David G.","last_name":"Reid"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"volume":2,"date_created":"2021-08-16T07:30:00Z","date_updated":"2023-09-19T15:08:53Z"},{"type":"journal_article","abstract":[{"lang":"eng","text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting."}],"status":"public","ddc":["570"],"title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","intvolume":" 8","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8618","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8619","date_created":"2020-10-06T16:35:16Z","date_updated":"2020-10-06T16:35:16Z","checksum":"e642080fcbde9584c63544f587c74f03","success":1,"file_name":"2018_ScientificReports_Gregor.pdf","access_level":"open_access","file_size":2818077,"content_type":"application/pdf","creator":"dernst"}],"keyword":["Multidisciplinary"],"day":"09","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Scientific Reports","citation":{"mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” Scientific Reports, vol. 8, 2724, Springer Nature, 2018, doi:10.1038/s41598-018-19947-1.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” Scientific Reports. Springer Nature, 2018. https://doi.org/10.1038/s41598-018-19947-1.","ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 2018;8. doi:10.1038/s41598-018-19947-1","ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” Scientific Reports, vol. 8. Springer Nature, 2018.","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., & Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-018-19947-1"},"date_published":"2018-02-09T00:00:00Z","article_number":"2724","file_date_updated":"2020-10-06T16:35:16Z","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JoDa"}],"year":"2018","pmid":1,"date_created":"2020-10-06T16:33:37Z","date_updated":"2023-09-19T15:04:49Z","volume":8,"author":[{"full_name":"Gregor, Carola","last_name":"Gregor","first_name":"Carola"},{"full_name":"Sidenstein, Sven C.","last_name":"Sidenstein","first_name":"Sven C."},{"full_name":"Andresen, Martin","last_name":"Andresen","first_name":"Martin"},{"first_name":"Steffen J.","last_name":"Sahl","full_name":"Sahl, Steffen J."},{"first_name":"Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Hell, Stefan W.","first_name":"Stefan W.","last_name":"Hell"}],"month":"02","publication_identifier":{"issn":["2045-2322"]},"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000424630400037"],"pmid":["29426833"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41598-018-19947-1"},{"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","external_id":{"pmid":["29538714"],"isi":["000430727000016"]},"language":[{"iso":"eng"}],"doi":"10.1093/jxb/ery097","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"month":"04","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","year":"2018","volume":69,"date_created":"2022-03-18T12:43:22Z","date_updated":"2023-09-19T15:10:43Z","author":[{"full_name":"Moturu, Taraka Ramji","first_name":"Taraka Ramji","last_name":"Moturu"},{"full_name":"Thula, Sravankumar","last_name":"Thula","first_name":"Sravankumar"},{"full_name":"Singh, Ravi Kumar","last_name":"Singh","first_name":"Ravi Kumar"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Vařeková, Radka Svobodová","last_name":"Vařeková","first_name":"Radka Svobodová"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"first_name":"Sibu","last_name":"Simon","full_name":"Simon, Sibu"}],"ec_funded":1,"page":"2367-2378","article_type":"original","citation":{"ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","ieee":"T. R. Moturu et al., “Molecular evolution and diversification of the SMXL gene family,” Journal of Experimental Botany, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., & Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery097","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 2018;69(9):2367-2378. doi:10.1093/jxb/ery097","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery097.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” Journal of Experimental Botany, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:10.1093/jxb/ery097.","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378."},"publication":"Journal of Experimental Botany","date_published":"2018-04-13T00:00:00Z","keyword":["Plant Science","Physiology"],"scopus_import":"1","article_processing_charge":"No","day":"13","intvolume":" 69","status":"public","title":"Molecular evolution and diversification of the SMXL gene family","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10881","oa_version":"None","type":"journal_article","issue":"9","abstract":[{"text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants.","lang":"eng"}]},{"year":"2018","acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","pmid":1,"publication_status":"published","department":[{"_id":"CaHe"}],"publisher":"Oxford University Press","author":[{"full_name":"Yuuta, Moriyama","last_name":"Yuuta","first_name":"Moriyama","orcid":"0000-0002-2853-8051","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Koshiba-Takeuchi, Kazuko","last_name":"Koshiba-Takeuchi","first_name":"Kazuko"}],"date_created":"2022-03-18T12:40:35Z","date_updated":"2023-09-19T15:11:22Z","volume":17,"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bfgp/ely007"}],"external_id":{"isi":["000456054400004"],"pmid":["29579140"]},"quality_controlled":"1","isi":1,"doi":"10.1093/bfgp/ely007","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["2041-2657"],"issn":["2041-2649"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10880","title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","status":"public","intvolume":" 17","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation."}],"issue":"5","publication":"Briefings in Functional Genomics","citation":{"mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:10.1093/bfgp/ely007.","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics. Oxford University Press, 2018. https://doi.org/10.1093/bfgp/ely007.","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 2018;17(5):329-338. doi:10.1093/bfgp/ely007","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338.","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” Briefings in Functional Genomics, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.","apa":"Yuuta, M., & Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. Oxford University Press. https://doi.org/10.1093/bfgp/ely007"},"article_type":"original","page":"329-338","date_published":"2018-09-01T00:00:00Z","scopus_import":"1","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"day":"01","article_processing_charge":"No"},{"abstract":[{"lang":"eng","text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems."}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-09-19T15:08:24Z","date_created":"2021-08-17T08:58:47Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9917"}]},"author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Tomas","last_name":"Larsson","full_name":"Larsson, Tomas"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"full_name":"Blomberg, Anders","first_name":"Anders","last_name":"Blomberg"},{"full_name":"Mehlig, Bernhard","first_name":"Bernhard","last_name":"Mehlig"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"department":[{"_id":"BeVi"}],"publisher":"Dryad","status":"public","title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","_id":"9930","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","article_processing_charge":"No","month":"07","day":"23","doi":"10.5061/dryad.bp25b65","date_published":"2018-07-23T00:00:00Z","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.bp25b65","open_access":"1"}],"citation":{"ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow, Dryad, 10.5061/dryad.bp25b65.","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. Dryad. https://doi.org/10.5061/dryad.bp25b65","ieee":"A. M. Westram et al., “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.","ama":"Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. 2018. doi:10.5061/dryad.bp25b65","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018. https://doi.org/10.5061/dryad.bp25b65.","mla":"Westram, Anja M., et al. Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow. Dryad, 2018, doi:10.5061/dryad.bp25b65.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018)."}},{"day":"17","month":"10","article_processing_charge":"No","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51sd2p5"}],"citation":{"ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative mating and genital divergence driven by reinforcement? 2018. doi:10.5061/dryad.51sd2p5","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Data from: Are assortative mating and genital divergence driven by reinforcement?, Dryad, 10.5061/dryad.51sd2p5.","ieee":"J. Hollander et al., “Data from: Are assortative mating and genital divergence driven by reinforcement?” Dryad, 2018.","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Data from: Are assortative mating and genital divergence driven by reinforcement? Dryad. https://doi.org/10.5061/dryad.51sd2p5","mla":"Hollander, Johan, et al. Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement? Dryad, 2018, doi:10.5061/dryad.51sd2p5.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, (2018).","chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Dryad, 2018. https://doi.org/10.5061/dryad.51sd2p5."},"doi":"10.5061/dryad.51sd2p5","date_published":"2018-10-17T00:00:00Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favour reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence."}],"status":"public","title":"Data from: Are assortative mating and genital divergence driven by reinforcement?","department":[{"_id":"BeVi"}],"publisher":"Dryad","year":"2018","_id":"9929","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-19T15:08:53Z","date_created":"2021-08-17T08:51:06Z","oa_version":"Published Version","author":[{"full_name":"Hollander, Johan","first_name":"Johan","last_name":"Hollander"},{"last_name":"Montaño-Rendón","first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio"},{"full_name":"Bianco, Giuseppe","last_name":"Bianco","first_name":"Giuseppe"},{"last_name":"Yang","first_name":"Xi","full_name":"Yang, Xi"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"full_name":"Duvaux, Ludovic","last_name":"Duvaux","first_name":"Ludovic"},{"last_name":"Reid","first_name":"David G.","full_name":"Reid, David G."},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9915"}]}},{"month":"12","publication_identifier":{"eissn":["2575-7075"],"isbn":["9781538664209"]},"external_id":{"arxiv":["1712.08087"],"isi":["000457843609036"]},"oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"quality_controlled":"1","isi":1,"conference":{"name":"CVF: Conference on Computer Vision and Pattern Recognition","location":"Salt Lake City, UT, United States","start_date":"2018-06-18","end_date":"2018-06-23"},"doi":"10.1109/cvpr.2018.00956","language":[{"iso":"eng"}],"year":"2018","publication_status":"published","publisher":"IEEE","department":[{"_id":"ChLa"}],"author":[{"first_name":"Jasper","last_name":"Uijlings","full_name":"Uijlings, Jasper"},{"full_name":"Konyushkova, Ksenia","first_name":"Ksenia","last_name":"Konyushkova"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"full_name":"Ferrari, Vittorio","last_name":"Ferrari","first_name":"Vittorio"}],"date_updated":"2023-09-19T15:11:49Z","date_created":"2022-03-18T12:45:09Z","scopus_import":"1","day":"17","article_processing_charge":"No","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","citation":{"ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:9175-9184. doi:10.1109/cvpr.2018.00956","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, United States, 2018, pp. 9175–9184.","apa":"Uijlings, J., Konyushkova, K., Lampert, C., & Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. https://doi.org/10.1109/cvpr.2018.00956","ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–84, doi:10.1109/cvpr.2018.00956.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 9175–84. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00956."},"page":"9175-9184","date_published":"2018-12-17T00:00:00Z","type":"conference","abstract":[{"text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger.","lang":"eng"}],"_id":"10882","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Learning intelligent dialogs for bounding box annotation","oa_version":"Preprint"},{"conference":{"end_date":"2018-12-08","location":"Montreal, Canada","start_date":"2018-12-02","name":"NeurIPS: Conference on Neural Information Processing Systems"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["1803.08917"],"isi":["000461823304061"]},"main_file_link":[{"url":"https://arxiv.org/abs/1803.08917","open_access":"1"}],"oa":1,"isi":1,"quality_controlled":"1","month":"12","author":[{"full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh"},{"first_name":"Zeyuan","last_name":"Allen-Zhu","full_name":"Allen-Zhu, Zeyuan"},{"full_name":"Li, Jerry","first_name":"Jerry","last_name":"Li"}],"date_created":"2019-06-13T08:22:37Z","date_updated":"2023-09-19T15:12:45Z","volume":2018,"year":"2018","publication_status":"published","publisher":"Neural Information Processing Systems Foundation","department":[{"_id":"DaAl"}],"date_published":"2018-12-01T00:00:00Z","publication":"Advances in Neural Information Processing Systems","citation":{"ama":"Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In: Advances in Neural Information Processing Systems. Vol 2018. Neural Information Processing Systems Foundation; 2018:4613-4623.","ieee":"D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,” in Advances in Neural Information Processing Systems, Montreal, Canada, 2018, vol. 2018, pp. 4613–4623.","apa":"Alistarh, D.-A., Allen-Zhu, Z., & Li, J. (2018). Byzantine stochastic gradient descent. In Advances in Neural Information Processing Systems (Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems Foundation.","ista":"Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent. Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural Information Processing Systems vol. 2018, 4613–4623.","short":"D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018, pp. 4613–4623.","mla":"Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” Advances in Neural Information Processing Systems, vol. 2018, Neural Information Processing Systems Foundation, 2018, pp. 4613–23.","chicago":"Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic Gradient Descent.” In Advances in Neural Information Processing Systems, 2018:4613–23. Neural Information Processing Systems Foundation, 2018."},"page":"4613-4623","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6558","title":"Byzantine stochastic gradient descent","status":"public","intvolume":" 2018","abstract":[{"lang":"eng","text":"This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of m machines which allegedly compute stochastic gradients every iteration, an α-fraction are Byzantine, and may behave adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations. In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sample complexity and time complexity."}],"type":"conference"},{"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"ACM Transactions on Algorithms","citation":{"chicago":"Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms. ACM, 2018. https://doi.org/10.1145/3230649.","short":"A. Kazda, V. Kolmogorov, M. Rolinek, ACM Transactions on Algorithms 15 (2018).","mla":"Kazda, Alexandr, et al. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms, vol. 15, no. 2, 22, ACM, 2018, doi:10.1145/3230649.","apa":"Kazda, A., Kolmogorov, V., & Rolinek, M. (2018). Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3230649","ieee":"A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar boolean CSPs,” ACM Transactions on Algorithms, vol. 15, no. 2. ACM, 2018.","ista":"Kazda A, Kolmogorov V, Rolinek M. 2018. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 15(2), 22.","ama":"Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar boolean CSPs. ACM Transactions on Algorithms. 2018;15(2). doi:10.1145/3230649"},"article_type":"original","date_published":"2018-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then extend the tractability result to larger classes of Δ-matroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, co-independent, compact, local, linear, and binary, with the following caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δ-matroids."}],"issue":"2","_id":"6032","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Even delta-matroids and the complexity of planar boolean CSPs","status":"public","intvolume":" 15","oa_version":"Preprint","month":"12","oa":1,"external_id":{"isi":["000468036500007"],"arxiv":["1602.03124"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.03124"}],"isi":1,"quality_controlled":"1","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"doi":"10.1145/3230649","language":[{"iso":"eng"}],"article_number":"22","ec_funded":1,"year":"2018","publication_status":"published","publisher":"ACM","department":[{"_id":"VlKo"}],"author":[{"full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","last_name":"Kazda","first_name":"Alexandr"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","last_name":"Rolinek","first_name":"Michal","full_name":"Rolinek, Michal"}],"related_material":{"record":[{"id":"1192","status":"public","relation":"earlier_version"}]},"date_updated":"2023-09-20T11:20:26Z","date_created":"2019-02-17T22:59:25Z","volume":15},{"article_processing_charge":"No","has_accepted_license":"1","day":"21","page":"146","citation":{"ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963."},"date_published":"2018-02-21T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm."}],"ddc":["576"],"title":"Inferring recent demography from spatial genetic structure","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"200","file":[{"file_size":5792935,"content_type":"application/pdf","creator":"system","file_name":"IST-2018-963-v1+1_thesis.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:23Z","date_created":"2018-12-12T10:14:55Z","checksum":"8cc534d2b528ae017acf80874cce48c9","relation":"main_file","file_id":"5111"},{"file_id":"6224","relation":"source_file","date_created":"2019-04-05T09:30:12Z","date_updated":"2020-07-14T12:45:23Z","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","file_name":"2018_thesis_ringbauer_source.zip","access_level":"closed","creator":"dernst","file_size":113365,"content_type":"application/zip"}],"oa_version":"Published Version","pubrep_id":"963","publication_identifier":{"issn":["2663-337X"]},"month":"02","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_963","publist_id":"7713","file_date_updated":"2020-07-14T12:45:23Z","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","date_updated":"2023-09-20T12:00:56Z","date_created":"2018-12-11T11:45:10Z","related_material":{"record":[{"id":"563","status":"public","relation":"part_of_dissertation"},{"id":"1074","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald"}]},{"issue":"4","abstract":[{"lang":"eng","text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2018_DiscreteComp_Akopyan.pdf","creator":"dernst","file_size":482518,"content_type":"application/pdf","file_id":"5844","relation":"main_file","success":1,"date_created":"2019-01-18T09:27:36Z","date_updated":"2019-01-18T09:27:36Z"}],"oa_version":"Published Version","_id":"1064","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 59","title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","ddc":["516","000"],"status":"public","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2018-06-01T00:00:00Z","citation":{"ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","apa":"Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9883-x","ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009. doi:10.1007/s00454-017-9883-x","chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x.","short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry 59 (2018) 1001–1009."},"publication":"Discrete & Computational Geometry","page":"1001-1009","article_type":"original","publist_id":"6324","ec_funded":1,"file_date_updated":"2019-01-18T09:27:36Z","author":[{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"full_name":"Balitskiy, Alexey","last_name":"Balitskiy","first_name":"Alexey"},{"full_name":"Grigorev, Mikhail","last_name":"Grigorev","first_name":"Mikhail"}],"volume":59,"date_created":"2018-12-11T11:49:57Z","date_updated":"2023-09-20T12:08:51Z","year":"2018","publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","publication_identifier":{"issn":["01795376"],"eissn":["14320444"]},"month":"06","doi":"10.1007/s00454-017-9883-x","language":[{"iso":"eng"}],"external_id":{"isi":["000432205500011"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"doi":"10.15479/AT:ISTA:th_913","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"01","date_created":"2018-12-11T11:46:22Z","date_updated":"2023-09-22T09:20:10Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1441"},{"relation":"part_of_dissertation","status":"public","id":"1678"},{"status":"public","relation":"part_of_dissertation","id":"2084"},{"relation":"part_of_dissertation","status":"public","id":"1028"}]},"author":[{"orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva"}],"department":[{"_id":"HaJa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","publist_id":"7405","file_date_updated":"2020-07-14T12:46:24Z","date_published":"2018-01-08T00:00:00Z","page":"107","citation":{"chicago":"Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation and Survival .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_913.","mla":"Gschaider-Reichhart, Eva. Optical and Optogenetic Control of Proliferation and Survival . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_913.","short":"E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation and Survival , Institute of Science and Technology Austria, 2018.","ista":"Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria.","ieee":"E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation and survival ,” Institute of Science and Technology Austria, 2018.","apa":"Gschaider-Reichhart, E. (2018). Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_913","ama":"Gschaider-Reichhart E. Optical and optogenetic control of proliferation and survival . 2018. doi:10.15479/AT:ISTA:th_913"},"article_processing_charge":"No","has_accepted_license":"1","day":"08","file":[{"date_created":"2019-04-05T09:28:03Z","date_updated":"2020-07-14T12:46:24Z","checksum":"697fa72ca36fb1b8ceabc133d58a73e5","file_id":"6222","relation":"source_file","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":7012495,"file_name":"2018_THESIS_Gschaider-Reichhart_source.docx","access_level":"closed"},{"file_id":"6223","relation":"main_file","checksum":"58d7d1e9e58aeb7f061ab686b1d8a48c","date_created":"2019-04-05T09:28:03Z","date_updated":"2020-07-14T12:46:24Z","access_level":"open_access","file_name":"2018_THESIS_Gschaider-Reichhart.pdf","creator":"dernst","file_size":6355280,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"913","ddc":["571","570"],"status":"public","title":"Optical and optogenetic control of proliferation and survival ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"418","abstract":[{"text":"The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown.\r\nSummarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"abstract":[{"text":"We prove a new central limit theorem (CLT) for the difference of linear eigenvalue statistics of a Wigner random matrix H and its minor H and find that the fluctuation is much smaller than the fluctuations of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of H and H. In particular, our theorem identifies the fluctuation of Kerov's rectangular Young diagrams, defined by the interlacing eigenvalues ofH and H, around their asymptotic shape, the Vershik'Kerov'Logan'Shepp curve. Young diagrams equipped with the Plancherel measure follow the same limiting shape. For this, algebraically motivated, ensemble a CLT has been obtained in Ivanov and Olshanski [20] which is structurally similar to our result but the variance is different, indicating that the analogy between the two models has its limitations. Moreover, our theorem shows that Borodin's result [7] on the convergence of the spectral distribution of Wigner matrices to a Gaussian free field also holds in derivative sense.","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Preprint","title":"Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues","status":"public","intvolume":" 2018","_id":"1012","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"18","article_processing_charge":"No","scopus_import":"1","date_published":"2018-05-18T00:00:00Z","page":"3255-3298","publication":"International Mathematics Research Notices","citation":{"ama":"Erdös L, Schröder DJ. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018;2018(10):3255-3298. doi:10.1093/imrn/rnw330","ista":"Erdös L, Schröder DJ. 2018. Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. 2018(10), 3255–3298.","ieee":"L. Erdös and D. J. Schröder, “Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues,” International Mathematics Research Notices, vol. 2018, no. 10. Oxford University Press, pp. 3255–3298, 2018.","apa":"Erdös, L., & Schröder, D. J. (2018). Fluctuations of rectangular young diagrams of interlacing wigner eigenvalues. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnw330","mla":"Erdös, László, and Dominik J. Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research Notices, vol. 2018, no. 10, Oxford University Press, 2018, pp. 3255–98, doi:10.1093/imrn/rnw330.","short":"L. Erdös, D.J. Schröder, International Mathematics Research Notices 2018 (2018) 3255–3298.","chicago":"Erdös, László, and Dominik J Schröder. “Fluctuations of Rectangular Young Diagrams of Interlacing Wigner Eigenvalues.” International Mathematics Research Notices. Oxford University Press, 2018. https://doi.org/10.1093/imrn/rnw330."},"publist_id":"6383","ec_funded":1,"date_updated":"2023-09-22T09:44:21Z","date_created":"2018-12-11T11:49:41Z","volume":2018,"author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"Erdös, László"},{"orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","last_name":"Schröder","first_name":"Dominik J","full_name":"Schröder, Dominik J"}],"related_material":{"record":[{"id":"6179","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"LaEr"}],"year":"2018","month":"05","publication_identifier":{"issn":["10737928"]},"language":[{"iso":"eng"}],"doi":"10.1093/imrn/rnw330","quality_controlled":"1","isi":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.05163"}],"oa":1,"external_id":{"arxiv":["1608.05163"],"isi":["000441668300009"]}},{"language":[{"iso":"eng"}],"doi":"10.3390/g9030039","project":[{"grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"issn":["2073-4336"]},"month":"09","volume":9,"date_updated":"2023-09-22T09:48:59Z","date_created":"2019-02-14T14:17:54Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1003"}]},"author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"full_name":"Guha, Shibashis","first_name":"Shibashis","last_name":"Guha"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"publisher":"MDPI AG","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2018","file_date_updated":"2020-07-14T12:47:16Z","article_number":"39","date_published":"2018-09-01T00:00:00Z","citation":{"ama":"Avni G, Guha S, Kupferman O. An abstraction-refinement methodology for reasoning about network games. Games. 2018;9(3). doi:10.3390/g9030039","ista":"Avni G, Guha S, Kupferman O. 2018. An abstraction-refinement methodology for reasoning about network games. Games. 9(3), 39.","ieee":"G. Avni, S. Guha, and O. Kupferman, “An abstraction-refinement methodology for reasoning about network games,” Games, vol. 9, no. 3. MDPI AG, 2018.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). An abstraction-refinement methodology for reasoning about network games. Games. MDPI AG. https://doi.org/10.3390/g9030039","mla":"Avni, Guy, et al. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” Games, vol. 9, no. 3, 39, MDPI AG, 2018, doi:10.3390/g9030039.","short":"G. Avni, S. Guha, O. Kupferman, Games 9 (2018).","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “An Abstraction-Refinement Methodology for Reasoning about Network Games.” Games. MDPI AG, 2018. https://doi.org/10.3390/g9030039."},"publication":"Games","has_accepted_license":"1","day":"01","scopus_import":1,"oa_version":"Published Version","file":[{"file_size":505155,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2018_MDPI_Avni.pdf","checksum":"749d65ca4ce74256a029d9644a1b1cb0","date_created":"2019-02-14T14:20:31Z","date_updated":"2020-07-14T12:47:16Z","relation":"main_file","file_id":"6008"}],"intvolume":" 9","ddc":["004"],"status":"public","title":"An abstraction-refinement methodology for reasoning about network games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6006","issue":"3","abstract":[{"text":"Network games (NGs) are played on directed graphs and are extensively used in network design and analysis. Search problems for NGs include finding special strategy profiles such as a Nash equilibrium and a globally-optimal solution. The networks modeled by NGs may be huge. In formal verification, abstraction has proven to be an extremely effective technique for reasoning about systems with big and even infinite state spaces. We describe an abstraction-refinement methodology for reasoning about NGs. Our methodology is based on an abstraction function that maps the state space of an NG to a much smaller state space. We search for a global optimum and a Nash equilibrium by reasoning on an under- and an over-approximation defined on top of this smaller state space. When the approximations are too coarse to find such profiles, we refine the abstraction function. We extend the abstraction-refinement methodology to labeled networks, where the objectives of the players are regular languages. Our experimental results demonstrate the effectiveness of the methodology. ","lang":"eng"}],"type":"journal_article"},{"_id":"35","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Algorithms and conditional lower bounds for planning problems","oa_version":"None","type":"conference","abstract":[{"lang":"eng","text":"We consider planning problems for graphs, Markov decision processes (MDPs), and games on graphs. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems where there are k different target sets, and the problems are as follows: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) objective-separation results showing that for MDPs the coverage problem is harder than the sequential target problem."}],"citation":{"ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. In: 28th International Conference on Automated Planning and Scheduling . AAAI Press; 2018.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2018). Algorithms and conditional lower bounds for planning problems. In 28th International Conference on Automated Planning and Scheduling . Delft, Netherlands: AAAI Press.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” in 28th International Conference on Automated Planning and Scheduling , Delft, Netherlands, 2018.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2018. Algorithms and conditional lower bounds for planning problems. 28th International Conference on Automated Planning and Scheduling . ICAPS: International Conference on Automated Planning and Scheduling.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In 28th International Conference on Automated Planning and Scheduling . AAAI Press, 2018."},"publication":"28th International Conference on Automated Planning and Scheduling ","date_published":"2018-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","year":"2018","department":[{"_id":"KrCh"}],"publisher":"AAAI Press","publication_status":"published","related_material":{"record":[{"id":"9293","status":"public","relation":"later_version"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Wolfgang","last_name":"Dvorák","full_name":"Dvorák, Wolfgang"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Svozil","first_name":"Alexander","full_name":"Svozil, Alexander"}],"date_created":"2018-12-11T11:44:17Z","date_updated":"2023-09-26T10:41:41Z","publist_id":"8020","ec_funded":1,"oa":1,"external_id":{"isi":["000492986200007"],"arxiv":["1804.07031"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07031"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"isi":1,"quality_controlled":"1","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","start_date":"2018-06-24","location":"Delft, Netherlands","end_date":"2018-06-29"},"language":[{"iso":"eng"}],"month":"06"},{"issue":"1","abstract":[{"text":"This paper is devoted to automatic competitive analysis of real-time scheduling algorithms for firm-deadline tasksets, where only completed tasks con- tribute some utility to the system. Given such a taskset T , the competitive ratio of an on-line scheduling algorithm A for T is the worst-case utility ratio of A over the utility achieved by a clairvoyant algorithm. We leverage the theory of quantitative graph games to address the competitive analysis and competitive synthesis problems. For the competitive analysis case, given any taskset T and any finite-memory on- line scheduling algorithm A , we show that the competitive ratio of A in T can be computed in polynomial time in the size of the state space of A . Our approach is flexible as it also provides ways to model meaningful constraints on the released task sequences that determine the competitive ratio. We provide an experimental study of many well-known on-line scheduling algorithms, which demonstrates the feasibility of our competitive analysis approach that effectively replaces human ingenuity (required Preliminary versions of this paper have appeared in Chatterjee et al. ( 2013 , 2014 ). B Andreas Pavlogiannis pavlogiannis@ist.ac.at Krishnendu Chatterjee krish.chat@ist.ac.at Alexander Kößler koe@ecs.tuwien.ac.at Ulrich Schmid s@ecs.tuwien.ac.at 1 IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400 Klosterneuburg, Austria 2 Embedded Computing Systems Group, Vienna University of Technology, Treitlstrasse 3, 1040 Vienna, Austria 123 Real-Time Syst for finding worst-case scenarios) by computing power. For the competitive synthesis case, we are just given a taskset T , and the goal is to automatically synthesize an opti- mal on-line scheduling algorithm A , i.e., one that guarantees the largest competitive ratio possible for T . We show how the competitive synthesis problem can be reduced to a two-player graph game with partial information, and establish that the compu- tational complexity of solving this game is Np -complete. The competitive synthesis problem is hence in Np in the size of the state space of the non-deterministic labeled transition system encoding the taskset. Overall, the proposed framework assists in the selection of suitable scheduling algorithms for a given taskset, which is in fact the most common situation in real-time systems design. ","lang":"eng"}],"type":"journal_article","pubrep_id":"960","file":[{"file_id":"5267","relation":"main_file","date_updated":"2020-07-14T12:47:56Z","date_created":"2018-12-12T10:17:14Z","checksum":"c2590ef160709d8054cf29ee173f1454","file_name":"IST-2018-960-v1+1_2017_Chatterjee_Automated_competetive.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1163507}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"738","intvolume":" 54","status":"public","ddc":["000"],"title":"Automated competitive analysis of real time scheduling with graph games","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-01-01T00:00:00Z","citation":{"ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2018. Automated competitive analysis of real time scheduling with graph games. Real-Time Systems. 54(1), 166–207.","ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “Automated competitive analysis of real time scheduling with graph games,” Real-Time Systems, vol. 54, no. 1. Springer, pp. 166–207, 2018.","apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., & Schmid, U. (2018). Automated competitive analysis of real time scheduling with graph games. Real-Time Systems. Springer. https://doi.org/10.1007/s11241-017-9293-4","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. Automated competitive analysis of real time scheduling with graph games. Real-Time Systems. 2018;54(1):166-207. doi:10.1007/s11241-017-9293-4","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “Automated Competitive Analysis of Real Time Scheduling with Graph Games.” Real-Time Systems. Springer, 2018. https://doi.org/10.1007/s11241-017-9293-4.","mla":"Chatterjee, Krishnendu, et al. “Automated Competitive Analysis of Real Time Scheduling with Graph Games.” Real-Time Systems, vol. 54, no. 1, Springer, 2018, pp. 166–207, doi:10.1007/s11241-017-9293-4.","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, Real-Time Systems 54 (2018) 166–207."},"publication":"Real-Time Systems","page":"166 - 207","ec_funded":1,"publist_id":"6929","file_date_updated":"2020-07-14T12:47:56Z","related_material":{"record":[{"id":"2820","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"full_name":"Kößler, Alexander","first_name":"Alexander","last_name":"Kößler"},{"full_name":"Schmid, Ulrich","first_name":"Ulrich","last_name":"Schmid"}],"volume":54,"date_updated":"2023-09-27T12:52:38Z","date_created":"2018-12-11T11:48:14Z","year":"2018","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","month":"01","doi":"10.1007/s11241-017-9293-4","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000419955500006"]},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1},{"citation":{"mla":"Moser, Thomas. Point Interactions in Systems of Fermions. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1043.","short":"T. Moser, Point Interactions in Systems of Fermions, Institute of Science and Technology Austria, 2018.","chicago":"Moser, Thomas. “Point Interactions in Systems of Fermions.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1043.","ama":"Moser T. Point interactions in systems of fermions. 2018. doi:10.15479/AT:ISTA:th_1043","ista":"Moser T. 2018. Point interactions in systems of fermions. Institute of Science and Technology Austria.","apa":"Moser, T. (2018). Point interactions in systems of fermions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1043","ieee":"T. Moser, “Point interactions in systems of fermions,” Institute of Science and Technology Austria, 2018."},"page":"115","date_published":"2018-09-04T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"04","_id":"52","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["515","530","519"],"status":"public","title":"Point interactions in systems of fermions","pubrep_id":"1043","file":[{"access_level":"open_access","file_name":"2018_Thesis_Moser.pdf","file_size":851164,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6256","checksum":"fbd8c747d148b468a21213b7cf175225","date_updated":"2020-07-14T12:46:37Z","date_created":"2019-04-09T07:45:38Z"},{"creator":"dernst","content_type":"application/zip","file_size":1531516,"access_level":"closed","file_name":"2018_Thesis_Moser_Source.zip","checksum":"c28e16ecfc1126d3ce324ec96493c01e","date_updated":"2020-07-14T12:46:37Z","date_created":"2019-04-09T07:45:38Z","file_id":"6257","relation":"source_file"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"In this thesis we will discuss systems of point interacting fermions, their stability and other spectral properties. Whereas for bosons a point interacting system is always unstable this ques- tion is more subtle for a gas of two species of fermions. In particular the answer depends on the mass ratio between these two species. Most of this work will be focused on the N + M model which consists of two species of fermions with N, M particles respectively which interact via point interactions. We will introduce this model using a formal limit and discuss the N + 1 system in more detail. In particular, we will show that for mass ratios above a critical one, which does not depend on the particle number, the N + 1 system is stable. In the context of this model we will prove rigorous versions of Tan relations which relate various quantities of the point-interacting model. By restricting the N + 1 system to a box we define a finite density model with point in- teractions. In the context of this system we will discuss the energy change when introducing a point-interacting impurity into a system of non-interacting fermions. We will see that this change in energy is bounded independently of the particle number and in particular the bound only depends on the density and the scattering length. As another special case of the N + M model we will show stability of the 2 + 2 model for mass ratios in an interval around one. Further we will investigate a different model of point interactions which was discussed before in the literature and which is, contrary to the N + M model, not given by a limiting procedure but is based on a Dirichlet form. We will show that this system behaves trivially in the thermodynamic limit, i.e. the free energy per particle is the same as the one of the non-interacting system.","lang":"eng"}],"oa":1,"project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"doi":"10.15479/AT:ISTA:th_1043","language":[{"iso":"eng"}],"supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"09","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"RoSe"}],"publication_status":"published","related_material":{"record":[{"id":"5856","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"154"},{"status":"public","relation":"part_of_dissertation","id":"1198"},{"status":"public","relation":"part_of_dissertation","id":"741"}]},"author":[{"full_name":"Moser, Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Moser"}],"date_created":"2018-12-11T11:44:22Z","date_updated":"2023-09-27T12:34:14Z","publist_id":"8002","file_date_updated":"2020-07-14T12:46:37Z"},{"date_published":"2018-01-29T00:00:00Z","citation":{"apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., & Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.204198","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” Journal of Cell Science, vol. 131, no. 2. Company of Biologists, 2018.","ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.","ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 2018;131(2). doi:10.1242/jcs.204198","chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.204198.","short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018).","mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” Journal of Cell Science, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:10.1242/jcs.204198."},"publication":"Journal of Cell Science","has_accepted_license":"1","article_processing_charge":"No","day":"29","scopus_import":"1","pubrep_id":"988","file":[{"file_id":"6299","relation":"main_file","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-12T08:46:32Z","checksum":"bf156c20a4f117b4b932370d54cbac8c","file_name":"2017_adamowski_PATELLINS_are.pdf","access_level":"open_access","creator":"dernst","file_size":14925985,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"913","intvolume":" 131","status":"public","title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","ddc":["581"],"issue":"2","abstract":[{"text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis.","lang":"eng"}],"type":"journal_article","doi":"10.1242/jcs.204198","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000424842400019"]},"project":[{"name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["00219533"]},"month":"01","author":[{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Cecilia","last_name":"Rodríguez Furlán","full_name":"Rodríguez Furlán, Cecilia"},{"first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"last_name":"Norambuena","first_name":"Lorena","full_name":"Norambuena, Lorena"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"volume":131,"date_created":"2018-12-11T11:49:10Z","date_updated":"2023-09-26T15:47:50Z","year":"2018","department":[{"_id":"JiFr"}],"publisher":"Company of Biologists","publication_status":"published","ec_funded":1,"publist_id":"6530","file_date_updated":"2020-07-14T12:48:15Z","article_number":"jcs.204198"},{"year":"2018","department":[{"_id":"GeKa"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","related_material":{"record":[{"id":"23","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"840"}]},"author":[{"first_name":"Lada","last_name":"Vukušić","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","full_name":"Vukušić, Lada"}],"date_created":"2018-12-11T11:44:28Z","date_updated":"2023-09-26T15:50:22Z","publist_id":"7985","file_date_updated":"2020-07-14T12:47:44Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"doi":"10.15479/AT:ISTA:TH_1047","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios"}],"publication_identifier":{"issn":["2663-337X"]},"month":"09","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"69","status":"public","ddc":["530","600"],"title":"Charge sensing and spin relaxation times of holes in Ge hut wires","pubrep_id":"1047","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":28452385,"access_level":"open_access","file_name":"2018_Thesis_Vukusic.pdf","checksum":"c570b656e30749cd65b1c7e13a9ce0a8","date_created":"2019-04-09T07:00:40Z","date_updated":"2020-07-14T12:47:44Z","file_id":"6247","relation":"main_file"},{"creator":"dernst","content_type":"application/zip","file_size":53058704,"file_name":"2018_Thesis_Vukusic_source.zip","access_level":"closed","date_updated":"2020-07-14T12:47:44Z","date_created":"2019-04-09T07:00:40Z","checksum":"7856771d9cd401fe0b311191076db6e1","file_id":"6248","relation":"source_file"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"A qubit, a unit of quantum information, is essentially any quantum mechanical two-level system which can be coherently controlled. Still, to be used for computation, it has to fulfill criteria. Qubits, regardless of the system in which they are realized, suffer from decoherence. This leads to loss of the information stored in the qubit. The upper bound of the time scale on which decoherence happens is set by the spin relaxation time. In this thesis I studied a two-level system consisting of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire. Such Ge hut wires have emerged as a promising material system for the realization of spin qubits, due to the combination of two significant properties: long spin coherence time as expected for group IV semiconductors due to the low hyperfine interaction and a strong valence band spin-orbit coupling. Here, I present how to fabricate quantum dot devices suitable for electrical transport measurements. Coupled quantum dot devices allowed the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot. By integrating the charge sensor into a radio-frequency reflectometry setup, I performed for the first time single-shot readout measurements of hole spins and extracted the hole spin relaxation times in Ge hut wires."}],"citation":{"chicago":"Vukušić, Lada. “Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1047.","mla":"Vukušić, Lada. Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1047.","short":"L. Vukušić, Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires, Institute of Science and Technology Austria, 2018.","ista":"Vukušić L. 2018. Charge sensing and spin relaxation times of holes in Ge hut wires. Institute of Science and Technology Austria.","apa":"Vukušić, L. (2018). Charge sensing and spin relaxation times of holes in Ge hut wires. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1047","ieee":"L. Vukušić, “Charge sensing and spin relaxation times of holes in Ge hut wires,” Institute of Science and Technology Austria, 2018.","ama":"Vukušić L. Charge sensing and spin relaxation times of holes in Ge hut wires. 2018. doi:10.15479/AT:ISTA:TH_1047"},"page":"103","date_published":"2018-09-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"PeJo"}],"publication_status":"published","related_material":{"record":[{"id":"1117","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"749"}]},"author":[{"full_name":"Chen, Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chong"}],"date_created":"2018-12-11T11:45:49Z","date_updated":"2023-09-27T12:26:03Z","publist_id":"7541","file_date_updated":"2020-07-14T12:46:04Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/AT:ISTA:th_997","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"03","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"324","title":"Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release","status":"public","ddc":["571"],"pubrep_id":"997","file":[{"file_name":"IST-2018-997-v1+1_Thesis_chong_a.pdf","access_level":"open_access","creator":"system","file_size":8719458,"content_type":"application/pdf","file_id":"5046","relation":"main_file","date_updated":"2020-07-14T12:46:04Z","date_created":"2018-12-12T10:13:58Z","checksum":"8e163ae9e927401b9fa7c1b3e6a3631a"},{"date_updated":"2020-07-14T12:46:04Z","date_created":"2019-04-05T09:25:26Z","checksum":"f7d7260029a5fbb5c982db61328ade52","file_id":"6221","relation":"source_file","creator":"dernst","file_size":47841940,"content_type":"application/octet-stream","file_name":"2018_Thesis_chong_source.pages","access_level":"closed"}],"oa_version":"Published Version","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Neuronal networks in the brain consist of two main types of neuron, glutamatergic principal neurons and GABAergic interneurons. Although these interneurons only represent 10–20% of the whole population, they mediate feedback and feedforward inhibition and are involved in the generation of high-frequency network oscillations. A hallmark functional property of GABAergic interneurons, especially of the parvalbumin‑expressing (PV+) subtypes, is the speed of signaling at their output synapse across species and brain regions. Several molecular and subcellular factors may underlie the submillisecond signaling at GABAergic synapses. Such as the selective use of P/Q type Ca2+ channels and the tight coupling between Ca2+ channels and Ca2+ sensors of exocytosis. However, whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Besides, these interneurons are mainly show depression in response to train of stimuli. How could they keep sufficient release to control the activity of postsynaptic principal neurons during high network activity, is largely elusive. For my Ph.D. work, we firstly examined the Ca2+ sensor of exocytosis at the GABAergic basket cell (BC) to Purkinje cell (PC) synapse in the cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ~10% compared to the wild-type control, identifying Syt2 as the major Ca2+ sensor at BC‑PC synapses. Differential adenovirus-mediated rescue revealed Syt2 triggered release with shorter latency and higher temporal precision, and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as the release sensor at BC–PC synapse ensures fast feedforward inhibition in cerebellar microcircuits. Additionally, we tested the function of another synaptotagmin member, Syt7, for inhibitory synaptic transmission at the BC–PC synapse. Syt7 is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, it is strongly expressed in fast-spiking, PV+ GABAergic interneurons and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. How could Syt7, a facilitation sensor, contribute to the depressed inhibitory synaptic transmission needs to be further investigated and understood. Our results indicated that at the BC–PC synapse, Syt7 contributes to asynchronous release, pool replenishment and facilitation. In combination, these three effects ensure efficient transmitter release during high‑frequency activity and guarantee frequency independence of inhibition. Taken together, our results confirmed that Syt2, which has the fastest kinetic properties among all synaptotagmin members, is mainly used by the inhibitory BC‑PC synapse for synaptic transmission, contributing to the speed and temporal precision of transmitter release. Furthermore, we showed that Syt7, another highly expressed synaptotagmin member in the output synapses of cerebellar BCs, is used for ensuring efficient inhibitor synaptic transmission during high activity.","lang":"eng"}],"citation":{"short":"C. Chen, Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release, Institute of Science and Technology Austria, 2018.","mla":"Chen, Chong. Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_997.","chicago":"Chen, Chong. “Synaptotagmins Ensure Speed and Efficiency of Inhibitory Neurotransmitter Release.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_997.","ama":"Chen C. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. 2018. doi:10.15479/AT:ISTA:th_997","ieee":"C. Chen, “Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release,” Institute of Science and Technology Austria, 2018.","apa":"Chen, C. (2018). Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_997","ista":"Chen C. 2018. Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release. Institute of Science and Technology Austria."},"page":"110","date_published":"2018-03-01T00:00:00Z","article_processing_charge":"No","has_accepted_license":"1","day":"01"},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","citation":{"chicago":"Dotterrer, Dominic, Tali Kaufman, and Uli Wagner. “On Expansion and Topological Overlap.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0291-4.","mla":"Dotterrer, Dominic, et al. “On Expansion and Topological Overlap.” Geometriae Dedicata, vol. 195, no. 1, Springer, 2018, pp. 307–317, doi:10.1007/s10711-017-0291-4.","short":"D. Dotterrer, T. Kaufman, U. Wagner, Geometriae Dedicata 195 (2018) 307–317.","ista":"Dotterrer D, Kaufman T, Wagner U. 2018. On expansion and topological overlap. Geometriae Dedicata. 195(1), 307–317.","ieee":"D. Dotterrer, T. Kaufman, and U. Wagner, “On expansion and topological overlap,” Geometriae Dedicata, vol. 195, no. 1. Springer, pp. 307–317, 2018.","apa":"Dotterrer, D., Kaufman, T., & Wagner, U. (2018). On expansion and topological overlap. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0291-4","ama":"Dotterrer D, Kaufman T, Wagner U. On expansion and topological overlap. Geometriae Dedicata. 2018;195(1):307–317. doi:10.1007/s10711-017-0291-4"},"publication":"Geometriae Dedicata","page":"307–317","date_published":"2018-08-01T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"We give a detailed and easily accessible proof of Gromov’s Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higher-dimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map (Formula presented.) there exists a point (Formula presented.) that is contained in the images of a positive fraction (Formula presented.) of the d-cells of X. More generally, the conclusion holds if (Formula presented.) is replaced by any d-dimensional piecewise-linear manifold M, with a constant (Formula presented.) that depends only on d and on the expansion properties of X, but not on M."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"742","intvolume":" 195","ddc":["514","516"],"title":"On expansion and topological overlap","status":"public","pubrep_id":"912","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"s10711-017-0291-4.pdf","creator":"kschuh","file_size":412486,"content_type":"application/pdf","file_id":"5835","relation":"main_file","checksum":"d2f70fc132156504aa4c626aa378a7ab","date_created":"2019-01-15T13:44:05Z","date_updated":"2020-07-14T12:47:58Z"}],"month":"08","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000437122700017"]},"project":[{"name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics","grant_number":"PP00P2_138948","_id":"25FA3206-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","doi":"10.1007/s10711-017-0291-4","language":[{"iso":"eng"}],"publist_id":"6925","file_date_updated":"2020-07-14T12:47:58Z","year":"2018","publisher":"Springer","department":[{"_id":"UlWa"}],"publication_status":"published","related_material":{"record":[{"id":"1378","status":"public","relation":"earlier_version"}]},"author":[{"first_name":"Dominic","last_name":"Dotterrer","full_name":"Dotterrer, Dominic"},{"full_name":"Kaufman, Tali","last_name":"Kaufman","first_name":"Tali"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"volume":195,"date_updated":"2023-09-27T12:29:57Z","date_created":"2018-12-11T11:48:16Z"},{"month":"10","publication_identifier":{"issn":["1980-0436"]},"doi":"10.30757/ALEA.v15-49","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000460475800022"],"arxiv":["1705.08836"]},"quality_controlled":"1","isi":1,"project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"},{"name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117"}],"file_date_updated":"2020-07-14T12:47:46Z","ec_funded":1,"author":[{"id":"4BF426E2-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Nejjar","full_name":"Nejjar, Peter"}],"date_created":"2018-12-11T11:44:28Z","date_updated":"2023-10-10T13:11:29Z","volume":15,"year":"2018","publication_status":"published","publisher":"Instituto Nacional de Matematica Pura e Aplicada","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-10-01T00:00:00Z","publication":"Latin American Journal of Probability and Mathematical Statistics","citation":{"ama":"Nejjar P. Transition to shocks in TASEP and decoupling of last passage times. Latin American Journal of Probability and Mathematical Statistics. 2018;15(2):1311-1334. doi:10.30757/ALEA.v15-49","ista":"Nejjar P. 2018. Transition to shocks in TASEP and decoupling of last passage times. Latin American Journal of Probability and Mathematical Statistics. 15(2), 1311–1334.","ieee":"P. Nejjar, “Transition to shocks in TASEP and decoupling of last passage times,” Latin American Journal of Probability and Mathematical Statistics, vol. 15, no. 2. Instituto Nacional de Matematica Pura e Aplicada, pp. 1311–1334, 2018.","apa":"Nejjar, P. (2018). Transition to shocks in TASEP and decoupling of last passage times. Latin American Journal of Probability and Mathematical Statistics. Instituto Nacional de Matematica Pura e Aplicada. https://doi.org/10.30757/ALEA.v15-49","mla":"Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage Times.” Latin American Journal of Probability and Mathematical Statistics, vol. 15, no. 2, Instituto Nacional de Matematica Pura e Aplicada, 2018, pp. 1311–34, doi:10.30757/ALEA.v15-49.","short":"P. Nejjar, Latin American Journal of Probability and Mathematical Statistics 15 (2018) 1311–1334.","chicago":"Nejjar, Peter. “Transition to Shocks in TASEP and Decoupling of Last Passage Times.” Latin American Journal of Probability and Mathematical Statistics. Instituto Nacional de Matematica Pura e Aplicada, 2018. https://doi.org/10.30757/ALEA.v15-49."},"article_type":"original","page":"1311-1334","abstract":[{"text":"We consider the totally asymmetric simple exclusion process in a critical scaling parametrized by a≥0, which creates a shock in the particle density of order aT−1/3, T the observation time. When starting from step initial data, we provide bounds on the limiting law which in particular imply that in the double limit lima→∞limT→∞ one recovers the product limit law and the degeneration of the correlation length observed at shocks of order 1. This result is shown to apply to a general last-passage percolation model. We also obtain bounds on the two-point functions of several airy processes.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:46Z","date_created":"2019-02-14T09:44:10Z","checksum":"2ded46aa284a836a8cbb34133a64f1cb","relation":"main_file","file_id":"5981","file_size":394851,"content_type":"application/pdf","creator":"kschuh","file_name":"2018_ALEA_Nejjar.pdf","access_level":"open_access"}],"_id":"70","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Transition to shocks in TASEP and decoupling of last passage times","ddc":["510"],"status":"public","intvolume":" 15"},{"type":"journal_article","issue":"15","abstract":[{"text":"Recent realization of a kinetically constrained chain of Rydberg atoms by Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation of unusual revivals in the many-body quantum dynamics. In our previous work [C. J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to the existence of “quantum scarred” eigenstates in the many-body spectrum of the experimentally realized model. Here, we present a detailed study of the eigenstate properties of the same model. We find that the majority of the eigenstates exhibit anomalous thermalization: the observable expectation values converge to their Gibbs ensemble values, but parametrically slower compared to the predictions of the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum, we identify nonergodic eigenstates that strongly violate the ETH, whose number grows polynomially with system size. Previously, the same eigenstates were identified via large overlaps with certain product states, and were used to explain the revivals observed in experiment. Here, we find that these eigenstates, in addition to highly atypical expectation values of local observables, also exhibit subthermal entanglement entropy that scales logarithmically with the system size. Moreover, we identify an additional class of quantum scarred eigenstates, and discuss their manifestations in the dynamics starting from initial product states. We use forward scattering approximation to describe the structure and physical properties of quantum scarred eigenstates. Finally, we discuss the stability of quantum scars to various perturbations. We observe that quantum scars remain robust when the introduced perturbation is compatible with the forward scattering approximation. In contrast, the perturbations which most efficiently destroy quantum scars also lead to the restoration of “canonical” thermalization.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"44","intvolume":" 98","title":"Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations","status":"public","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"22","citation":{"ama":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 2018;98(15). doi:10.1103/PhysRevB.98.155134","ieee":"C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations,” Physical Review B, vol. 98, no. 15. American Physical Society, 2018.","apa":"Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., & Papić, Z. (2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.155134","ista":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 98(15), 155134.","short":"C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review B 98 (2018).","mla":"Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” Physical Review B, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:10.1103/PhysRevB.98.155134.","chicago":"Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.155134."},"publication":"Physical Review B","date_published":"2018-10-22T00:00:00Z","article_number":"155134","publist_id":"8010","year":"2018","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","publication_status":"published","author":[{"full_name":"Turner, C J","last_name":"Turner","first_name":"C J"},{"first_name":"Alexios","last_name":"Michailidis","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios"},{"full_name":"Abanin, D A","last_name":"Abanin","first_name":"D A"},{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Serbyn, Maksym"},{"first_name":"Z","last_name":"Papić","full_name":"Papić, Z"}],"volume":98,"date_updated":"2023-10-10T13:28:49Z","date_created":"2018-12-11T11:44:19Z","month":"10","external_id":{"isi":["000447919100001"],"arxiv":["1806.10933"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10933"}],"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1103/PhysRevB.98.155134","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}]},{"type":"journal_article","issue":"12","abstract":[{"text":"The drag of turbulent flows can be drastically decreased by adding small amounts of high molecular weight polymers. While drag reduction initially increases with polymer concentration, it eventually saturates to what is known as the maximum drag reduction (MDR) asymptote; this asymptote is generally attributed to the dynamics being reduced to a marginal yet persistent state of subdued turbulent motion. Contrary to this accepted view, we show that, for an appropriate choice of parameters, polymers can reduce the drag beyond the suggested asymptotic limit, eliminating turbulence and giving way to laminar flow. At higher polymer concentrations, however, the laminar state becomes unstable, resulting in a fluctuating flow with the characteristic drag of the MDR asymptote. Our findings indicate that the asymptotic state is hence dynamically disconnected from ordinary turbulence. © 2018 American Physical Society.","lang":"eng"}],"intvolume":" 120","title":"Exceeding the asymptotic limit of polymer drag reduction","status":"public","_id":"328","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"19","citation":{"ama":"Choueiri GH, Lopez Alonso JM, Hof B. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 2018;120(12). doi:10.1103/PhysRevLett.120.124501","ieee":"G. H. Choueiri, J. M. Lopez Alonso, and B. Hof, “Exceeding the asymptotic limit of polymer drag reduction,” Physical Review Letters, vol. 120, no. 12. American Physical Society, 2018.","apa":"Choueiri, G. H., Lopez Alonso, J. M., & Hof, B. (2018). Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.124501","ista":"Choueiri GH, Lopez Alonso JM, Hof B. 2018. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 120(12), 124501.","short":"G.H. Choueiri, J.M. Lopez Alonso, B. Hof, Physical Review Letters 120 (2018).","mla":"Choueiri, George H., et al. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” Physical Review Letters, vol. 120, no. 12, 124501, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.124501.","chicago":"Choueiri, George H, Jose M Lopez Alonso, and Björn Hof. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.124501."},"publication":"Physical Review Letters","date_published":"2018-03-19T00:00:00Z","article_number":"124501","ec_funded":1,"publist_id":"7537","publisher":"American Physical Society","department":[{"_id":"BjHo"}],"publication_status":"published","acknowledgement":"The authors thank Philipp Maier and the IST Austria workshop for their dedicated technical support.","year":"2018","volume":120,"date_created":"2018-12-11T11:45:51Z","date_updated":"2023-10-10T13:27:44Z","author":[{"last_name":"Choueiri","first_name":"George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","full_name":"Choueiri, George H"},{"full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","first_name":"Jose M"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"month":"03","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.06271","open_access":"1"}],"external_id":{"isi":["000427804000005"]},"oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1103/PhysRevLett.120.124501"},{"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.98.023105","quality_controlled":"1","isi":1,"external_id":{"isi":["000441466800010"],"arxiv":["1808.02088"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1808.02088","open_access":"1"}],"month":"08","volume":98,"date_updated":"2023-10-10T13:29:10Z","date_created":"2018-12-11T11:44:49Z","author":[{"full_name":"Suri, Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87","last_name":"Suri","first_name":"Balachandra"},{"full_name":"Tithof, Jeffrey","first_name":"Jeffrey","last_name":"Tithof"},{"full_name":"Grigoriev, Roman","last_name":"Grigoriev","first_name":"Roman"},{"last_name":"Schatz","first_name":"Michael","full_name":"Schatz, Michael"}],"publisher":"American Physical Society","department":[{"_id":"BjHo"}],"publication_status":"published","year":"2018","date_published":"2018-08-13T00:00:00Z","citation":{"ieee":"B. Suri, J. Tithof, R. Grigoriev, and M. Schatz, “Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow,” Physical Review E, vol. 98, no. 2. American Physical Society, 2018.","apa":"Suri, B., Tithof, J., Grigoriev, R., & Schatz, M. (2018). Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.023105","ista":"Suri B, Tithof J, Grigoriev R, Schatz M. 2018. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 98(2).","ama":"Suri B, Tithof J, Grigoriev R, Schatz M. Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow. Physical Review E. 2018;98(2). doi:10.1103/PhysRevE.98.023105","chicago":"Suri, Balachandra, Jeffrey Tithof, Roman Grigoriev, and Michael Schatz. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.023105.","short":"B. Suri, J. Tithof, R. Grigoriev, M. Schatz, Physical Review E 98 (2018).","mla":"Suri, Balachandra, et al. “Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow.” Physical Review E, vol. 98, no. 2, American Physical Society, 2018, doi:10.1103/PhysRevE.98.023105."},"publication":"Physical Review E","article_processing_charge":"No","day":"13","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 98","title":"Unstable equilibria and invariant manifolds in quasi-two-dimensional Kolmogorov-like flow","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"136","issue":"2","abstract":[{"lang":"eng","text":"Recent studies suggest that unstable, nonchaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space."}],"type":"journal_article"},{"intvolume":" 55","title":"A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"691","oa_version":"Submitted Version","type":"journal_article","issue":"1","abstract":[{"text":"Background: Transport protein particle (TRAPP) is a multisubunit complex that regulates membrane trafficking through the Golgi apparatus. The clinical phenotype associated with mutations in various TRAPP subunits has allowed elucidation of their functions in specific tissues. The role of some subunits in human disease, however, has not been fully established, and their functions remain uncertain.\r\n\r\nObjective: We aimed to expand the range of neurodevelopmental disorders associated with mutations in TRAPP subunits by exome sequencing of consanguineous families.\r\n\r\nMethods: Linkage and homozygosity mapping and candidate gene analysis were used to identify homozygous mutations in families. Patient fibroblasts were used to study splicing defect and zebrafish to model the disease.\r\n\r\nResults: We identified six individuals from three unrelated families with a founder homozygous splice mutation in TRAPPC6B, encoding a core subunit of the complex TRAPP I. Patients manifested a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features, and showed splicing defect. Zebrafish trappc6b morphants replicated the human phenotype, displaying decreased head size and neuronal hyperexcitability, leading to a lower seizure threshold.\r\n\r\nConclusion: This study provides clinical and functional evidence of the role of TRAPPC6B in brain development and function.","lang":"eng"}],"page":"48 - 54","article_type":"original","citation":{"short":"I. Marin Valencia, G. Novarino, A. Johansen, B. Rosti, M. Issa, D. Musaev, G. Bhat, E. Scott, J. Silhavy, V. Stanley, R. Rosti, J. Gleeson, F. Imam, M. Zaki, J. Gleeson, Journal of Medical Genetics 55 (2018) 48–54.","mla":"Marin Valencia, Isaac, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” Journal of Medical Genetics, vol. 55, no. 1, BMJ Publishing Group, 2018, pp. 48–54, doi:10.1136/jmedgenet-2017-104627.","chicago":"Marin Valencia, Isaac, Gaia Novarino, Anide Johansen, Başak Rosti, Mahmoud Issa, Damir Musaev, Gifty Bhat, et al. “A Homozygous Founder Mutation in TRAPPC6B Associates with a Neurodevelopmental Disorder Characterised by Microcephaly Epilepsy and Autistic Features.” Journal of Medical Genetics. BMJ Publishing Group, 2018. https://doi.org/10.1136/jmedgenet-2017-104627.","ama":"Marin Valencia I, Novarino G, Johansen A, et al. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 2018;55(1):48-54. doi:10.1136/jmedgenet-2017-104627","apa":"Marin Valencia, I., Novarino, G., Johansen, A., Rosti, B., Issa, M., Musaev, D., … Gleeson, J. (2018). A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. BMJ Publishing Group. https://doi.org/10.1136/jmedgenet-2017-104627","ieee":"I. Marin Valencia et al., “A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features,” Journal of Medical Genetics, vol. 55, no. 1. BMJ Publishing Group, pp. 48–54, 2018.","ista":"Marin Valencia I, Novarino G, Johansen A, Rosti B, Issa M, Musaev D, Bhat G, Scott E, Silhavy J, Stanley V, Rosti R, Gleeson J, Imam F, Zaki M, Gleeson J. 2018. A homozygous founder mutation in TRAPPC6B associates with a neurodevelopmental disorder characterised by microcephaly epilepsy and autistic features. Journal of Medical Genetics. 55(1), 48–54."},"publication":"Journal of Medical Genetics","date_published":"2018-01-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","department":[{"_id":"GaNo"}],"publisher":"BMJ Publishing Group","publication_status":"published","pmid":1,"year":"2018","volume":55,"date_updated":"2023-10-16T09:55:43Z","date_created":"2018-12-11T11:47:57Z","author":[{"last_name":"Marin Valencia","first_name":"Isaac","full_name":"Marin Valencia, Isaac"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"last_name":"Johansen","first_name":"Anide","full_name":"Johansen, Anide"},{"first_name":"Başak","last_name":"Rosti","full_name":"Rosti, Başak"},{"full_name":"Issa, Mahmoud","last_name":"Issa","first_name":"Mahmoud"},{"first_name":"Damir","last_name":"Musaev","full_name":"Musaev, Damir"},{"first_name":"Gifty","last_name":"Bhat","full_name":"Bhat, Gifty"},{"full_name":"Scott, Eric","last_name":"Scott","first_name":"Eric"},{"full_name":"Silhavy, Jennifer","last_name":"Silhavy","first_name":"Jennifer"},{"full_name":"Stanley, Valentina","first_name":"Valentina","last_name":"Stanley"},{"full_name":"Rosti, Rasim","first_name":"Rasim","last_name":"Rosti"},{"full_name":"Gleeson, Jeremy","last_name":"Gleeson","first_name":"Jeremy"},{"full_name":"Imam, Farhad","last_name":"Imam","first_name":"Farhad"},{"full_name":"Zaki, Maha","first_name":"Maha","last_name":"Zaki"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"}],"publist_id":"7016","project":[{"name":"Probing development and reversibility of autism spectrum disorders","grant_number":"401299","_id":"254BA948-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6056005/","open_access":"1"}],"external_id":{"pmid":["28626029"],"isi":["000418199800007"]},"language":[{"iso":"eng"}],"doi":"10.1136/jmedgenet-2017-104627","publication_identifier":{"issn":["0022-2593"]},"month":"01"},{"publication_identifier":{"eissn":["2064-8316"],"issn":["0001-6969"]},"month":"06","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.03305","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1802.03305"]},"language":[{"iso":"eng"}],"doi":"10.14232/actasm-018-753-y","ec_funded":1,"publist_id":"7615","department":[{"_id":"LaEr"}],"publisher":"Springer Nature","publication_status":"published","year":"2018","acknowledgement":"The author was supported by the ISTFELLOW program of the Institute of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported by the Hungarian National Research, Development and Innovation Office, NKFIH (grant no. K124152).","volume":84,"date_created":"2018-12-11T11:45:36Z","date_updated":"2023-10-16T10:29:22Z","author":[{"full_name":"Virosztek, Daniel","first_name":"Daniel","last_name":"Virosztek","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511"}],"scopus_import":"1","article_processing_charge":"No","day":"04","page":"65 - 80","article_type":"original","citation":{"ista":"Virosztek D. 2018. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.","ieee":"D. Virosztek, “Maps on probability measures preserving certain distances - a survey and some new results,” Acta Scientiarum Mathematicarum, vol. 84, no. 1–2. Springer Nature, pp. 65–80, 2018.","apa":"Virosztek, D. (2018). Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. Springer Nature. https://doi.org/10.14232/actasm-018-753-y","ama":"Virosztek D. Maps on probability measures preserving certain distances - a survey and some new results. Acta Scientiarum Mathematicarum. 2018;84(1-2):65-80. doi:10.14232/actasm-018-753-y","chicago":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” Acta Scientiarum Mathematicarum. Springer Nature, 2018. https://doi.org/10.14232/actasm-018-753-y.","mla":"Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances - a Survey and Some New Results.” Acta Scientiarum Mathematicarum, vol. 84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:10.14232/actasm-018-753-y.","short":"D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80."},"publication":"Acta Scientiarum Mathematicarum","date_published":"2018-06-04T00:00:00Z","type":"journal_article","issue":"1-2","abstract":[{"lang":"eng","text":"Borel probability measures living on metric spaces are fundamental\r\nmathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p >= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere."}],"intvolume":" 84","status":"public","title":"Maps on probability measures preserving certain distances - a survey and some new results","_id":"284","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"date_published":"2018-07-01T00:00:00Z","page":"79 - 116","article_type":"original","citation":{"mla":"Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5, Ecole Polytechnique, 2018, pp. 79–116, doi:10.5802/jep.64.","short":"M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques 5 (2018) 79–116.","chicago":"Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics of the Uniform Electron Gas.” Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique, 2018. https://doi.org/10.5802/jep.64.","ama":"Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 2018;5:79-116. doi:10.5802/jep.64","ista":"Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.","ieee":"M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform electron gas,” Journal de l’Ecole Polytechnique - Mathematiques, vol. 5. Ecole Polytechnique, pp. 79–116, 2018.","apa":"Lewi, M., Lieb, É., & Seiringer, R. (2018). Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. Ecole Polytechnique. https://doi.org/10.5802/jep.64"},"publication":"Journal de l'Ecole Polytechnique - Mathematiques","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"access_level":"open_access","file_name":"2018_JournaldeLecoleMath_Lewi.pdf","file_size":843938,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"5726","checksum":"1ba7cccdf3900f42c4f715ae75d6813c","date_updated":"2020-07-14T12:45:16Z","date_created":"2018-12-17T16:38:18Z"}],"oa_version":"Published Version","intvolume":" 5","title":"Statistical mechanics of the uniform electron gas","status":"public","ddc":["510"],"_id":"180","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.5802/jep.64","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020"},{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"quality_controlled":"1","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"external_id":{"arxiv":["1705.10676"]},"oa":1,"publication_identifier":{"eissn":["2270-518X"],"issn":["2429-7100"]},"month":"07","volume":5,"date_created":"2018-12-11T11:45:03Z","date_updated":"2023-10-17T08:05:28Z","author":[{"full_name":"Lewi, Mathieu","first_name":"Mathieu","last_name":"Lewi"},{"last_name":"Lieb","first_name":"Élliott","full_name":"Lieb, Élliott"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"department":[{"_id":"RoSe"}],"publisher":"Ecole Polytechnique","publication_status":"published","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged.","year":"2018","license":"https://creativecommons.org/licenses/by-nd/4.0/","publist_id":"7741","ec_funded":1,"file_date_updated":"2020-07-14T12:45:16Z"},{"isi":1,"quality_controlled":"1","external_id":{"isi":["000452277700005"],"pmid":["29969056"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1369/0022155418786698"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1369/0022155418786698","publication_identifier":{"issn":["0022-1554"]},"month":"12","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"publisher":"SAGE Publications","publication_status":"published","pmid":1,"year":"2018","volume":66,"date_updated":"2023-10-17T08:42:24Z","date_created":"2018-12-11T11:44:57Z","author":[{"first_name":"Siegfried","last_name":"Reipert","full_name":"Reipert, Siegfried"},{"first_name":"Helmuth","last_name":"Goldammer","full_name":"Goldammer, Helmuth"},{"full_name":"Richardson, Christine","first_name":"Christine","last_name":"Richardson"},{"first_name":"Martin","last_name":"Goldberg","full_name":"Goldberg, Martin"},{"full_name":"Hawkins, Timothy","first_name":"Timothy","last_name":"Hawkins"},{"full_name":"Hollergschwandtner, Elena","last_name":"Hollergschwandtner","first_name":"Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"full_name":"Antreich, Sebastian","first_name":"Sebastian","last_name":"Antreich"},{"full_name":"Stierhof, York","last_name":"Stierhof","first_name":"York"}],"page":"903-921","article_type":"original","citation":{"ieee":"S. Reipert et al., “Agitation modules: Flexible means to accelerate automated freeze substitution,” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. SAGE Publications. https://doi.org/10.1369/0022155418786698","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 2018;66(12):903-921. doi:10.1369/0022155418786698","chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry. SAGE Publications, 2018. https://doi.org/10.1369/0022155418786698.","short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” Journal of Histochemistry and Cytochemistry, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:10.1369/0022155418786698."},"publication":"Journal of Histochemistry and Cytochemistry","date_published":"2018-12-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 66","title":"Agitation modules: Flexible means to accelerate automated freeze substitution","status":"public","_id":"163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches.","lang":"eng"}]},{"month":"02","oa":1,"external_id":{"isi":["000683379204058"],"arxiv":["1806.07259"]},"main_file_link":[{"url":"https://arxiv.org/abs/1806.07259","open_access":"1"}],"isi":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"conference":{"location":"Stockholm, Sweden","start_date":"2018-07-10","end_date":"2018-07-15","name":"ICML: International Conference on Machine Learning"},"language":[{"iso":"eng"}],"ec_funded":1,"year":"2018","publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"ML Research Press","author":[{"first_name":"Subham","last_name":"Sahoo","full_name":"Sahoo, Subham"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","last_name":"Martius","first_name":"Georg S","full_name":"Martius, Georg S"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/first-machine-learning-method-capable-of-accurate-extrapolation/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2019-02-14T15:21:07Z","date_updated":"2023-10-17T09:50:53Z","volume":80,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Proceedings of the 35th International Conference on Machine Learning","citation":{"mla":"Sahoo, Subham, et al. “Learning Equations for Extrapolation and Control.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 4442–50.","short":"S. Sahoo, C. Lampert, G.S. Martius, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 4442–4450.","chicago":"Sahoo, Subham, Christoph Lampert, and Georg S Martius. “Learning Equations for Extrapolation and Control.” In Proceedings of the 35th International Conference on Machine Learning, 80:4442–50. ML Research Press, 2018.","ama":"Sahoo S, Lampert C, Martius GS. Learning equations for extrapolation and control. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:4442-4450.","ista":"Sahoo S, Lampert C, Martius GS. 2018. Learning equations for extrapolation and control. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 4442–4450.","apa":"Sahoo, S., Lampert, C., & Martius, G. S. (2018). Learning equations for extrapolation and control. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 4442–4450). Stockholm, Sweden: ML Research Press.","ieee":"S. Sahoo, C. Lampert, and G. S. Martius, “Learning equations for extrapolation and control,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 4442–4450."},"page":"4442-4450","date_published":"2018-02-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary black-box regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging real-world data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swing-up task."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6012","status":"public","title":"Learning equations for extrapolation and control","intvolume":" 80","oa_version":"Preprint"},{"abstract":[{"lang":"eng","text":"We establish a data-dependent notion of algorithmic stability for Stochastic Gradient Descent (SGD), and employ it to develop novel generalization bounds. This is in contrast to previous distribution-free algorithmic stability results for SGD which depend on the worst-case constants. By virtue of the data-dependent argument, our bounds provide new insights into learning with SGD on convex and non-convex problems. In the convex case, we show that the bound on the generalization error depends on the risk at the initialization point. In the non-convex case, we prove that the expected curvature of the objective function around the initialization point has crucial influence on the generalization error. In both cases, our results suggest a simple data-driven strategy to stabilize SGD by pre-screening its initialization. As a corollary, our results allow us to show optimistic generalization bounds that exhibit fast convergence rates for SGD subject to a vanishing empirical risk and low noise of stochastic gradient. "}],"type":"conference","oa_version":"Preprint","intvolume":" 80","status":"public","title":"Data-dependent stability of stochastic gradient descent","_id":"6011","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-02-01T00:00:00Z","page":"2815-2824","citation":{"chicago":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” In Proceedings of the 35 Th International Conference on Machine Learning, 80:2815–24. ML Research Press, 2018.","mla":"Kuzborskij, Ilja, and Christoph Lampert. “Data-Dependent Stability of Stochastic Gradient Descent.” Proceedings of the 35 Th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 2815–24.","short":"I. Kuzborskij, C. Lampert, in:, Proceedings of the 35 Th International Conference on Machine Learning, ML Research Press, 2018, pp. 2815–2824.","ista":"Kuzborskij I, Lampert C. 2018. Data-dependent stability of stochastic gradient descent. Proceedings of the 35 th International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 80, 2815–2824.","ieee":"I. Kuzborskij and C. Lampert, “Data-dependent stability of stochastic gradient descent,” in Proceedings of the 35 th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 2815–2824.","apa":"Kuzborskij, I., & Lampert, C. (2018). Data-dependent stability of stochastic gradient descent. In Proceedings of the 35 th International Conference on Machine Learning (Vol. 80, pp. 2815–2824). Stockholm, Sweden: ML Research Press.","ama":"Kuzborskij I, Lampert C. Data-dependent stability of stochastic gradient descent. In: Proceedings of the 35 Th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:2815-2824."},"publication":"Proceedings of the 35 th International Conference on Machine Learning","ec_funded":1,"volume":80,"date_created":"2019-02-14T14:51:57Z","date_updated":"2023-10-17T09:51:13Z","author":[{"full_name":"Kuzborskij, Ilja","last_name":"Kuzborskij","first_name":"Ilja"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"department":[{"_id":"ChLa"}],"publisher":"ML Research Press","publication_status":"published","year":"2018","month":"02","language":[{"iso":"eng"}],"conference":{"name":"ICML: International Conference on Machine Learning","location":"Stockholm, Sweden","start_date":"2018-07-10","end_date":"2018-07-15"},"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1703.01678"],"isi":["000683379202095"]},"main_file_link":[{"url":"https://arxiv.org/abs/1703.01678","open_access":"1"}],"oa":1},{"_id":"5686","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2018","department":[{"_id":"E-Lib"}],"title":"An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors","ddc":["020"],"status":"public","publication_status":"published","related_material":{"record":[{"id":"6657","relation":"later_version","status":"public"}]},"author":[{"last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick"}],"file":[{"creator":"dernst","content_type":"application/pdf","file_size":202798,"access_level":"open_access","file_name":"2018_WorkingPaper_Danowski.pdf","checksum":"6cb95f8772491d155ce77c6160655fff","date_created":"2019-01-22T09:06:51Z","date_updated":"2020-07-14T12:47:10Z","file_id":"5872","relation":"main_file"}],"oa_version":"Published Version","date_created":"2018-12-17T10:28:26Z","date_updated":"2023-10-17T11:33:57Z","type":"working_paper","file_date_updated":"2020-07-14T12:47:10Z","citation":{"mla":"Danowski, Patrick. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors. 2018, doi:10.5281/zenodo.1244154.","short":"P. Danowski, An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018.","chicago":"Danowski, Patrick. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors, 2018. https://doi.org/10.5281/zenodo.1244154.","ama":"Danowski P. An Austrian Proposal for the Classification of Open Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.; 2018. doi:10.5281/zenodo.1244154","ista":"Danowski P. 2018. An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors, 5p.","apa":"Danowski, P. (2018). An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. https://doi.org/10.5281/zenodo.1244154","ieee":"P. Danowski, An Austrian proposal for the Classification of Open Access Tuples (COAT) - Distinguish different Open Access types beyond colors. 2018."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"page":"5","date_published":"2018-05-09T00:00:00Z","doi":"10.5281/zenodo.1244154","language":[{"iso":"eng"}],"scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"09","month":"05"},{"type":"conference","abstract":[{"lang":"eng","text":"Distributed training of massive machine learning models, in particular deep neural networks, via Stochastic Gradient Descent (SGD) is becoming commonplace. Several families of communication-reduction methods, such as quantization, large-batch methods, and gradient sparsification, have been proposed. To date, gradient sparsification methods--where each node sorts gradients by magnitude, and only communicates a subset of the components, accumulating the rest locally--are known to yield some of the largest practical gains. Such methods can reduce the amount of communication per step by up to \\emph{three orders of magnitude}, while preserving model accuracy. Yet, this family of methods currently has no theoretical justification. This is the question we address in this paper. We prove that, under analytic assumptions, sparsifying gradients by magnitude with local error correction provides convergence guarantees, for both convex and non-convex smooth objectives, for data-parallel SGD. The main insight is that sparsification methods implicitly maintain bounds on the maximum impact of stale updates, thanks to selection by magnitude. Our analysis and empirical validation also reveal that these methods do require analytical conditions to converge well, justifying existing heuristics."}],"title":"The convergence of sparsified gradient methods","status":"public","_id":"6589","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","page":"5973-5983","publication":"Advances in Neural Information Processing Systems 31","citation":{"ista":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. 2018. The convergence of sparsified gradient methods. Advances in Neural Information Processing Systems 31. NeurIPS: Conference on Neural Information Processing Systems vol. Volume 2018, 5973–5983.","apa":"Alistarh, D.-A., Hoefler, T., Johansson, M., Konstantinov, N. H., Khirirat, S., & Renggli, C. (2018). The convergence of sparsified gradient methods. In Advances in Neural Information Processing Systems 31 (Vol. Volume 2018, pp. 5973–5983). Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"D.-A. Alistarh, T. Hoefler, M. Johansson, N. H. Konstantinov, S. Khirirat, and C. Renggli, “The convergence of sparsified gradient methods,” in Advances in Neural Information Processing Systems 31, Montreal, Canada, 2018, vol. Volume 2018, pp. 5973–5983.","ama":"Alistarh D-A, Hoefler T, Johansson M, Konstantinov NH, Khirirat S, Renggli C. The convergence of sparsified gradient methods. In: Advances in Neural Information Processing Systems 31. Vol Volume 2018. Neural Information Processing Systems Foundation; 2018:5973-5983.","chicago":"Alistarh, Dan-Adrian, Torsten Hoefler, Mikael Johansson, Nikola H Konstantinov, Sarit Khirirat, and Cedric Renggli. “The Convergence of Sparsified Gradient Methods.” In Advances in Neural Information Processing Systems 31, Volume 2018:5973–83. Neural Information Processing Systems Foundation, 2018.","mla":"Alistarh, Dan-Adrian, et al. “The Convergence of Sparsified Gradient Methods.” Advances in Neural Information Processing Systems 31, vol. Volume 2018, Neural Information Processing Systems Foundation, 2018, pp. 5973–83.","short":"D.-A. Alistarh, T. Hoefler, M. Johansson, N.H. Konstantinov, S. Khirirat, C. Renggli, in:, Advances in Neural Information Processing Systems 31, Neural Information Processing Systems Foundation, 2018, pp. 5973–5983."},"date_published":"2018-12-01T00:00:00Z","ec_funded":1,"publication_status":"published","publisher":"Neural Information Processing Systems Foundation","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"year":"2018","date_created":"2019-06-27T09:32:55Z","date_updated":"2023-10-17T11:47:20Z","volume":"Volume 2018","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Hoefler, Torsten","last_name":"Hoefler","first_name":"Torsten"},{"full_name":"Johansson, Mikael","first_name":"Mikael","last_name":"Johansson"},{"first_name":"Nikola H","last_name":"Konstantinov","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","full_name":"Konstantinov, Nikola H"},{"last_name":"Khirirat","first_name":"Sarit","full_name":"Khirirat, Sarit"},{"first_name":"Cedric","last_name":"Renggli","full_name":"Renggli, Cedric"}],"month":"12","isi":1,"quality_controlled":"1","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"external_id":{"isi":["000461852000047"],"arxiv":["1809.10505"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1809.10505","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"location":"Montreal, Canada","start_date":"2018-12-02","end_date":"2018-12-08","name":"NeurIPS: Conference on Neural Information Processing Systems"}},{"status":"public","title":"Social network plasticity decreases disease transmission in a eusocial insect","intvolume":" 362","_id":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogen-triggered responses. We tested this hypothesis experimentally in the ant Lasius niger using a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmission-inhibitory properties of the colony's contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups."}],"issue":"6417","article_type":"original","page":"941 - 945","publication":"Science","citation":{"chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science. AAAS, 2018. https://doi.org/10.1126/science.aat4793.","mla":"Stroeymeyt, Nathalie, et al. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Science, vol. 362, no. 6417, AAAS, 2018, pp. 941–45, doi:10.1126/science.aat4793.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, Science 362 (2018) 941–945.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect. Science. 362(6417), 941–945.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Science. AAAS. https://doi.org/10.1126/science.aat4793","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect,” Science, vol. 362, no. 6417. AAAS, pp. 941–945, 2018.","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. Science. 2018;362(6417):941-945. doi:10.1126/science.aat4793"},"date_published":"2018-11-23T00:00:00Z","scopus_import":"1","day":"23","article_processing_charge":"No","publication_status":"published","publisher":"AAAS","department":[{"_id":"SyCr"}],"year":"2018","acknowledgement":"This project was funded by two European Research Council Advanced Grants (Social Life, 249375, and resiliANT, 741491) and two Swiss National Science Foundation grants (CR32I3_141063 and 310030_156732) to L.K. and a European Research Council Starting Grant (SocialVaccines, 243071) to S.C.","date_updated":"2023-10-17T11:50:05Z","date_created":"2018-12-11T11:44:07Z","volume":362,"author":[{"full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie","last_name":"Stroeymeyt"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"last_name":"Crespi","first_name":"Alessandro","full_name":"Crespi, Alessandro"},{"full_name":"Mersch, Danielle","last_name":"Mersch","first_name":"Danielle"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"},{"full_name":"Keller, Laurent","first_name":"Laurent","last_name":"Keller"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/for-ants-unity-is-strength-and-health/"}],"record":[{"relation":"research_data","status":"public","id":"13055"}]},"ec_funded":1,"publist_id":"8049","quality_controlled":"1","isi":1,"project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","grant_number":"243071","_id":"25DC711C-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://serval.unil.ch/resource/serval:BIB_E9228C205467.P001/REF.pdf"}],"external_id":{"isi":["000451124500041"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.aat4793","month":"11","publication_identifier":{"issn":["1095-9203"]}},{"type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses."}],"intvolume":" 35","status":"public","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"19","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"28","page":"2669 - 2684","article_type":"original","citation":{"short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:10.1093/molbev/msy163.","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” Molecular Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/molbev/msy163.","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 2018;35(11):2669-2684. doi:10.1093/molbev/msy163","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” Molecular Biology and Evolution, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","apa":"Palmer, A., Chait, R. P., & Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy163","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684."},"publication":"Molecular Biology and Evolution","date_published":"2018-08-28T00:00:00Z","publist_id":"8036","publisher":"Oxford University Press","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publication_status":"published","pmid":1,"year":"2018","volume":35,"date_created":"2018-12-11T11:44:11Z","date_updated":"2023-10-17T11:51:06Z","author":[{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"publication_identifier":{"issn":["0737-4038"]},"month":"08","isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy163"},{"article_processing_charge":"No","day":"08","month":"11","scopus_import":"1","doi":"10.3791/58585","date_published":"2018-11-08T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"isi":["000456469400103"]},"citation":{"mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments, vol. 141, MyJove Corporation, 2018, doi:10.3791/58585.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Journal of Visualized Experiments 141 (2018).","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Characterising Lesions and Locating Electrodes in Small Animal Brains.” Journal of Visualized Experiments. MyJove Corporation, 2018. https://doi.org/10.3791/58585.","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 2018;141. doi:10.3791/58585","ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of visualized experiments. 141.","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for characterising lesions and locating electrodes in small animal brains. Journal of Visualized Experiments. MyJove Corporation. https://doi.org/10.3791/58585","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for characterising lesions and locating electrodes in small animal brains,” Journal of visualized experiments, vol. 141. MyJove Corporation, 2018."},"publication":"Journal of visualized experiments","quality_controlled":"1","isi":1,"publist_id":"8050","abstract":[{"lang":"eng","text":"Lesion and electrode location verification are traditionally done via histological examination of stained brain slices, a time-consuming procedure that requires manual estimation. Here, we describe a simple, straightforward method for quantifying lesions and locating electrodes in the brain that is less laborious and yields more detailed results. Whole brains are stained with osmium tetroxide, embedded in resin, and imaged with a micro-CT scanner. The scans result in 3D digital volumes of the brains with resolutions and virtual section thicknesses dependent on the sample size (12-15 and 5-6 µm per voxel for rat and zebra finch brains, respectively). Surface and deep lesions can be characterized, and single tetrodes, tetrode arrays, electrolytic lesions, and silicon probes can also be localized. Free and proprietary software allows experimenters to examine the sample volume from any plane and segment the volume manually or automatically. Because this method generates whole brain volume, lesions and electrodes can be quantified to a much higher degree than in current methods, which will help standardize comparisons within and across studies."}],"type":"journal_article","author":[{"full_name":"Masís, Javier","last_name":"Masís","first_name":"Javier"},{"last_name":"Mankus","first_name":"David","full_name":"Mankus, David"},{"first_name":"Steffen","last_name":"Wolff","full_name":"Wolff, Steffen"},{"last_name":"Guitchounts","first_name":"Grigori","full_name":"Guitchounts, Grigori"},{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"},{"full_name":"Cox, David","first_name":"David","last_name":"Cox"}],"oa_version":"None","volume":141,"date_updated":"2023-10-17T11:49:25Z","date_created":"2018-12-11T11:44:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6","year":"2018","publisher":"MyJove Corporation","department":[{"_id":"MaJö"}],"intvolume":" 141","status":"public","title":"A micro-CT-based method for characterising lesions and locating electrodes in small animal brains","publication_status":"published"},{"date_created":"2023-05-23T13:24:51Z","date_updated":"2023-10-17T11:50:04Z","oa_version":"Published Version","author":[{"full_name":"Stroeymeyt, Nathalie","first_name":"Nathalie","last_name":"Stroeymeyt"},{"first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"full_name":"Crespi, Alessandro","last_name":"Crespi","first_name":"Alessandro"},{"full_name":"Mersch, Danielle","first_name":"Danielle","last_name":"Mersch"},{"last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"},{"last_name":"Keller","first_name":"Laurent","full_name":"Keller, Laurent"}],"related_material":{"record":[{"id":"7","status":"public","relation":"used_in_publication"}]},"ddc":["570"],"status":"public","title":"Social network plasticity decreases disease transmission in a eusocial insect","publisher":"Zenodo","department":[{"_id":"SyCr"}],"_id":"13055","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","abstract":[{"text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n - correction of URLs within README.txt file\r\n","lang":"eng"}],"type":"research_data_reference","doi":"10.5281/ZENODO.1322669","date_published":"2018-10-23T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.1480665"}],"oa":1,"citation":{"chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.1322669.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","mla":"Stroeymeyt, Nathalie, et al. Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect. Zenodo, 2018, doi:10.5281/ZENODO.1322669.","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., & Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. https://doi.org/10.5281/ZENODO.1322669","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, 10.5281/ZENODO.1322669.","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:10.5281/ZENODO.1322669"},"day":"23","month":"10","article_processing_charge":"No"},{"date_updated":"2023-10-17T12:12:40Z","date_created":"2018-12-11T11:44:12Z","volume":5,"author":[{"full_name":"Botello, Gabriel","last_name":"Botello","first_name":"Gabriel"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","first_name":"Alfredo R","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Abdalmalak, Kerlos","last_name":"Abdalmalak","first_name":"Kerlos"},{"full_name":"Brown, Elliott","first_name":"Elliott","last_name":"Brown"},{"last_name":"Leuchs","first_name":"Gerd","full_name":"Leuchs, Gerd"},{"full_name":"Preu, Sascha","last_name":"Preu","first_name":"Sascha"},{"last_name":"Segovia Vargas","first_name":"Daniel","full_name":"Segovia Vargas, Daniel"},{"last_name":"Strekalov","first_name":"Dmitry","full_name":"Strekalov, Dmitry"},{"full_name":"Munoz, Luis","last_name":"Munoz","first_name":"Luis"},{"full_name":"Schwefel, Harald","first_name":"Harald","last_name":"Schwefel"}],"publication_status":"published","department":[{"_id":"JoFi"}],"year":"2018","publist_id":"8033","language":[{"iso":"eng"}],"doi":"10.1364/OPTICA.5.001210","quality_controlled":"1","isi":1,"main_file_link":[{"url":"www.doi.org/10.1364/OPTICA.5.001210 ","open_access":"1"}],"oa":1,"external_id":{"isi":["000447853100007"]},"month":"10","publication_identifier":{"issn":["23342536"]},"oa_version":"Published Version","status":"public","title":"Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters","intvolume":" 5","_id":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Conventional ultra-high sensitivity detectors in the millimeter-wave range are usually cooled as their own thermal noise at room temperature would mask the weak received radiation. The need for cryogenic systems increases the cost and complexity of the instruments, hindering the development of, among others, airborne and space applications. In this work, the nonlinear parametric upconversion of millimeter-wave radiation to the optical domain inside high-quality (Q) lithium niobate whispering-gallery mode (WGM) resonators is proposed for ultra-low noise detection. We experimentally demonstrate coherent upconversion of millimeter-wave signals to a 1550 nm telecom carrier, with a photon conversion efficiency surpassing the state-of-the-art by 2 orders of magnitude. Moreover, a theoretical model shows that the thermal equilibrium of counterpropagating WGMs is broken by overcoupling the millimeter-wave WGM, effectively cooling the upconverted mode and allowing ultra-low noise detection. By theoretically estimating the sensitivity of a correlation radiometer based on the presented scheme, it is found that room-temperature radiometers with better sensitivity than state-of-the-art high-electron-mobility transistor (HEMT)-based radiometers can be designed. This detection paradigm can be used to develop room-temperature instrumentation for radio astronomy, earth observation, planetary missions, and imaging systems."}],"issue":"10","type":"journal_article","date_published":"2018-10-20T00:00:00Z","article_type":"original","page":"1210 - 1219","publication":"Optica","citation":{"chicago":"Botello, Gabriel, Florian Sedlmeir, Alfredo R Rueda Sanchez, Kerlos Abdalmalak, Elliott Brown, Gerd Leuchs, Sascha Preu, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, 2018. https://doi.org/10.1364/OPTICA.5.001210.","short":"G. Botello, F. Sedlmeir, A.R. Rueda Sanchez, K. Abdalmalak, E. Brown, G. Leuchs, S. Preu, D. Segovia Vargas, D. Strekalov, L. Munoz, H. Schwefel, Optica 5 (2018) 1210–1219.","mla":"Botello, Gabriel, et al. “Sensitivity Limits of Millimeter-Wave Photonic Radiometers Based on Efficient Electro-Optic Upconverters.” Optica, vol. 5, no. 10, 2018, pp. 1210–19, doi:10.1364/OPTICA.5.001210.","ieee":"G. Botello et al., “Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters,” Optica, vol. 5, no. 10. pp. 1210–1219, 2018.","apa":"Botello, G., Sedlmeir, F., Rueda Sanchez, A. R., Abdalmalak, K., Brown, E., Leuchs, G., … Schwefel, H. (2018). Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. https://doi.org/10.1364/OPTICA.5.001210","ista":"Botello G, Sedlmeir F, Rueda Sanchez AR, Abdalmalak K, Brown E, Leuchs G, Preu S, Segovia Vargas D, Strekalov D, Munoz L, Schwefel H. 2018. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 5(10), 1210–1219.","ama":"Botello G, Sedlmeir F, Rueda Sanchez AR, et al. Sensitivity limits of millimeter-wave photonic radiometers based on efficient electro-optic upconverters. Optica. 2018;5(10):1210-1219. doi:10.1364/OPTICA.5.001210"},"day":"20","article_processing_charge":"No","scopus_import":"1"},{"quality_controlled":"1","main_file_link":[{"url":"https://hal.inria.fr/hal-00757488/","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1561/1000000053","month":"05","publication_identifier":{"issn":["1551-3939"]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Now Publishers","year":"2018","date_updated":"2023-10-17T11:53:09Z","date_created":"2018-12-16T22:59:19Z","volume":12,"author":[{"full_name":"Benveniste, Albert","last_name":"Benveniste","first_name":"Albert"},{"first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"},{"full_name":"Caillaud, Benoît","last_name":"Caillaud","first_name":"Benoît"},{"first_name":"Roberto","last_name":"Passerone","full_name":"Passerone, Roberto"},{"last_name":"Raclet","first_name":"Jean Baptiste","full_name":"Raclet, Jean Baptiste"},{"full_name":"Reinkemeier, Philipp","last_name":"Reinkemeier","first_name":"Philipp"},{"first_name":"Alberto","last_name":"Sangiovanni-Vincentelli","full_name":"Sangiovanni-Vincentelli, Alberto"},{"full_name":"Damm, Werner","last_name":"Damm","first_name":"Werner"},{"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":"Larsen, Kim G.","last_name":"Larsen","first_name":"Kim G."}],"article_type":"original","page":"124-400","publication":"Foundations and Trends in Electronic Design Automation","citation":{"chicago":"Benveniste, Albert, Dejan Nickovic, Benoît Caillaud, Roberto Passerone, Jean Baptiste Raclet, Philipp Reinkemeier, Alberto Sangiovanni-Vincentelli, Werner Damm, Thomas A Henzinger, and Kim G. Larsen. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation. Now Publishers, 2018. https://doi.org/10.1561/1000000053.","mla":"Benveniste, Albert, et al. “Contracts for System Design.” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3, Now Publishers, 2018, pp. 124–400, doi:10.1561/1000000053.","short":"A. Benveniste, D. Nickovic, B. Caillaud, R. Passerone, J.B. Raclet, P. Reinkemeier, A. Sangiovanni-Vincentelli, W. Damm, T.A. Henzinger, K.G. Larsen, Foundations and Trends in Electronic Design Automation 12 (2018) 124–400.","ista":"Benveniste A, Nickovic D, Caillaud B, Passerone R, Raclet JB, Reinkemeier P, Sangiovanni-Vincentelli A, Damm W, Henzinger TA, Larsen KG. 2018. Contracts for system design. Foundations and Trends in Electronic Design Automation. 12(2–3), 124–400.","ieee":"A. Benveniste et al., “Contracts for system design,” Foundations and Trends in Electronic Design Automation, vol. 12, no. 2–3. Now Publishers, pp. 124–400, 2018.","apa":"Benveniste, A., Nickovic, D., Caillaud, B., Passerone, R., Raclet, J. B., Reinkemeier, P., … Larsen, K. G. (2018). Contracts for system design. Foundations and Trends in Electronic Design Automation. Now Publishers. https://doi.org/10.1561/1000000053","ama":"Benveniste A, Nickovic D, Caillaud B, et al. Contracts for system design. Foundations and Trends in Electronic Design Automation. 2018;12(2-3):124-400. doi:10.1561/1000000053"},"date_published":"2018-05-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","status":"public","title":"Contracts for system design","intvolume":" 12","_id":"5677","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Recently, contract-based design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contract-based design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contract-based design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “meta-theory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the meta-theory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector.","lang":"eng"}],"issue":"2-3"}]