[{"quality_controlled":"1","department":[{"_id":"PeJo"}],"publisher":"Hindawi Publishing Corporation","publication_status":"published","volume":2016,"type":"journal_article","oa_version":"Published Version","date_created":"2018-12-11T11:52:00Z","scopus_import":1,"status":"public","date_published":"2016-01-01T00:00:00Z","publication":"Neural Plasticity","publist_id":"5762","abstract":[{"lang":"eng","text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states."}],"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"},"intvolume":"      2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","doi":"10.1155/2016/1207393","date_updated":"2021-01-12T06:50:43Z","day":"01","year":"2016","has_accepted_license":"1","oa":1,"article_number":"1207393","file_date_updated":"2020-07-14T12:44:54Z","month":"01","file":[{"content_type":"application/pdf","relation":"main_file","file_name":"IST-2016-580-v1+1_1207393.pdf","creator":"system","checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","file_size":1395180,"file_id":"4740","access_level":"open_access","date_created":"2018-12-12T10:09:17Z","date_updated":"2020-07-14T12:44:54Z"}],"author":[{"first_name":"José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"last_name":"Gerevich","first_name":"Zoltan","full_name":"Gerevich, Zoltan"}],"citation":{"chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>. Hindawi Publishing Corporation, 2016. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>.","ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” <i>Neural Plasticity</i>, vol. 2016. Hindawi Publishing Corporation, 2016.","short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>.","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. 2016;2016. doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>","ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393.","apa":"Guzmán, J., &#38; Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. Hindawi Publishing Corporation. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>"},"ddc":["570"],"language":[{"iso":"eng"}],"_id":"1435","pubrep_id":"580"},{"department":[{"_id":"RoSe"}],"project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_status":"published","publisher":"Elsevier","volume":105,"type":"journal_article","oa_version":"Published Version","scopus_import":1,"date_created":"2018-12-11T11:52:00Z","abstract":[{"lang":"eng","text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system."}],"status":"public","date_published":"2016-01-01T00:00:00Z","publication":"Journal de Mathématiques Pures et Appliquées","publist_id":"5763","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","intvolume":"       105","title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","doi":"10.1016/j.matpur.2015.09.003","day":"01","date_updated":"2021-01-12T06:50:43Z","has_accepted_license":"1","ec_funded":1,"year":"2016","oa":1,"month":"01","file_date_updated":"2020-07-14T12:44:54Z","file":[{"checksum":"c5afe1f6935bc7f2b546adbde1d31a35","creator":"system","relation":"main_file","file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:54Z","date_created":"2018-12-12T10:10:36Z","access_level":"open_access","file_id":"4825","file_size":658491}],"author":[{"full_name":"Bach, Volker","first_name":"Volker","last_name":"Bach"},{"full_name":"Breteaux, Sébastien","first_name":"Sébastien","last_name":"Breteaux"},{"first_name":"Sören P","last_name":"Petrat","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P"},{"full_name":"Pickl, Peter","first_name":"Peter","last_name":"Pickl"},{"first_name":"Tim","last_name":"Tzaneteas","full_name":"Tzaneteas, Tim"}],"citation":{"ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>.","mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>.","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30.","ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. 2016;105(1):1-30. doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., &#38; Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>","ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30."},"ddc":["510","530"],"page":"1 - 30","issue":"1","pubrep_id":"581","_id":"1436","language":[{"iso":"eng"}]},{"publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"quality_controlled":"1","volume":"20-22","type":"conference","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.07565"}],"alternative_title":["POPL"],"scopus_import":1,"date_created":"2018-12-11T11:52:01Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks."}],"date_published":"2016-01-11T00:00:00Z","status":"public","publist_id":"5761","day":"11","date_updated":"2024-03-25T23:30:18Z","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","doi":"10.1145/2837614.2837624","external_id":{"arxiv":["1510.07565"]},"oa":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5441"},{"relation":"earlier_version","id":"5442","status":"public"},{"id":"821","relation":"dissertation_contains","status":"public"},{"relation":"later_version","id":"6009","status":"public"},{"relation":"dissertation_contains","id":"8934","status":"public"}]},"conference":{"location":"St. Petersburg, FL, USA","name":"POPL: Principles of Programming Languages","start_date":"2016-01-20","end_date":"2016-01-22"},"ec_funded":1,"year":"2016","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>"},"arxiv":1,"month":"01","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Amir","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"_id":"1437","language":[{"iso":"eng"}],"page":"733 - 747"},{"arxiv":1,"citation":{"short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.","mla":"Chatterjee, Krishnendu, et al. <i>Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs</i>. Vol. 20–22, ACM, 2016, pp. 327–42, doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>.","ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 327–342.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>.","apa":"Chatterjee, K., Fu, H., Novotný, P., &#38; Hasheminezhad, R. (2016). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342.","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. In: Vol 20-22. ACM; 2016:327-342. doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>"},"month":"01","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr"},{"first_name":"Rouzbeh","last_name":"Hasheminezhad","full_name":"Hasheminezhad, Rouzbeh"}],"acknowledgement":"Supported by the Natural Science Foundation of China (NSFC) under Grant No. 61532019 ","language":[{"iso":"eng"}],"_id":"1438","page":"327 - 342","day":"11","date_updated":"2023-09-19T14:38:41Z","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","doi":"10.1145/2837614.2837639","external_id":{"arxiv":["1510.08517"]},"oa":1,"related_material":{"record":[{"status":"public","id":"5993","relation":"later_version"}]},"conference":{"start_date":"2016-01-20","end_date":"2016-01-22","location":"St. Petersburg, FL, USA","name":"POPL: Principles of Programming Languages"},"year":"2016","ec_funded":1,"alternative_title":["POPL"],"scopus_import":1,"date_created":"2018-12-11T11:52:01Z","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism.","lang":"eng"}],"status":"public","date_published":"2016-01-11T00:00:00Z","publist_id":"5760","publication_status":"published","publisher":"ACM","department":[{"_id":"KrCh"}],"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"quality_controlled":"1","volume":"20-22","type":"conference","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08517"}]},{"type":"conference","volume":"20-22","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01251199/"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"ToHe"}],"quality_controlled":"1","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification.","lang":"eng"}],"publist_id":"5759","status":"public","date_published":"2016-01-11T00:00:00Z","scopus_import":1,"alternative_title":["ACM SIGPLAN Notices"],"date_created":"2018-12-11T11:52:01Z","oa_version":"Preprint","oa":1,"conference":{"location":"St. Petersburg, FL, USA","name":"POPL: Principles of Programming Languages","start_date":"2016-01-20","end_date":"2016-01-22"},"year":"2016","ec_funded":1,"day":"11","date_updated":"2021-01-12T06:50:45Z","doi":"10.1145/2837614.2837650","title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","language":[{"iso":"eng"}],"_id":"1439","acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","page":"400 - 415","citation":{"ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.","apa":"Dragoi, C., Henzinger, T. A., &#38; Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","mla":"Dragoi, Cezara, et al. <i>PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms</i>. Vol. 20–22, ACM, 2016, pp. 400–15, doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>.","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415."},"author":[{"full_name":"Dragoi, Cezara","last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","first_name":"Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"month":"01"},{"page":"213 - 215","date_published":"2016-02-02T00:00:00Z","status":"public","publication":"Structure","issue":"2","publist_id":"5756","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The author thanks Banerjee et al. (2016) for providing coordinates prior to public release and apologizes to colleagues whose work was not cited or discussed due to the limited space available. The author is supported by grants from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232).","_id":"1440","language":[{"iso":"eng"}],"intvolume":"        24","month":"02","author":[{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","scopus_import":1,"citation":{"mla":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>.","short":"H.L. Janovjak, Structure 24 (2016) 213–215.","ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” <i>Structure</i>, vol. 24, no. 2. Cell Press, pp. 213–215, 2016.","chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>.","apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>","ista":"Janovjak HL. 2016. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 24(2), 213–215.","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. 2016;24(2):213-215. doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>"},"date_created":"2018-12-11T11:52:02Z","year":"2016","ec_funded":1,"volume":24,"type":"journal_article","title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","department":[{"_id":"HaJa"}],"doi":"10.1016/j.str.2016.01.002","project":[{"grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","name":"Microbial Ion Channels for Synthetic Neurobiology","grant_number":"303564"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"quality_controlled":"1","publication_status":"published","day":"02","publisher":"Cell Press","date_updated":"2021-01-12T06:50:46Z"},{"abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1."}],"date_published":"2016-05-17T00:00:00Z","status":"public","publication":"Angewandte Chemie - International Edition","publist_id":"5755","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        55","oa_version":"Submitted Version","scopus_import":1,"date_created":"2018-12-11T11:52:02Z","volume":55,"type":"journal_article","department":[{"_id":"HaJa"}],"project":[{"grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"quality_controlled":"1","publication_status":"published","publisher":"Wiley","page":"6339 - 6342","issue":"21","acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","_id":"1441","pubrep_id":"840","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:55Z","month":"05","file":[{"date_created":"2018-12-12T10:17:03Z","date_updated":"2020-07-14T12:44:55Z","access_level":"open_access","file_id":"5255","file_size":1268662,"checksum":"26da07960e57ac4750b54179197ce57f","creator":"system","relation":"main_file","file_name":"IST-2017-840-v1+1_reichhart.pdf","content_type":"application/pdf"}],"author":[{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","first_name":"Eva","last_name":"Gschaider-Reichhart","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto","first_name":"Álvaro"},{"full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tichy","first_name":"Alexandra-Madelaine"},{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"citation":{"ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. 2016;55(21):6339-6342. doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. 55(21), 6339–6342.","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &#38; Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>","chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>.","ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016.","short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>."},"ddc":["571","576"],"related_material":{"record":[{"status":"public","id":"418","relation":"dissertation_contains"}]},"has_accepted_license":"1","year":"2016","ec_funded":1,"oa":1,"title":"A phytochrome sensory domain permits receptor activation by red light","doi":"10.1002/anie.201601736","day":"17","date_updated":"2023-09-07T12:49:08Z"},{"publisher":"Springer","publication_status":"published","quality_controlled":"1","department":[{"_id":"BeBi"}],"type":"journal_article","volume":107,"date_created":"2018-12-11T11:52:04Z","scopus_import":"1","oa_version":"Published Version","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"},"intvolume":"       107","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"5750","publication":"Scientometrics","status":"public","date_published":"2016-04-01T00:00:00Z","abstract":[{"lang":"eng","text":"The accuracy of interdisciplinarity measurements is directly related to the quality of the underlying bibliographic data. Existing indicators of interdisciplinarity are not capable of reflecting the inaccuracies introduced by incorrect and incomplete records because correct and complete bibliographic data can rarely be obtained. This is the case for the Rao–Stirling index, which cannot handle references that are not categorized into disciplinary fields. We introduce a method that addresses this problem. It extends the Rao–Stirling index to acknowledge missing data by calculating its interval of uncertainty using computational optimization. The evaluation of our method indicates that the uncertainty interval is not only useful for estimating the inaccuracy of interdisciplinarity measurements, but it also delivers slightly more accurate aggregated interdisciplinarity measurements than the Rao–Stirling index."}],"date_updated":"2021-11-16T08:29:11Z","day":"01","doi":"10.1007/s11192-016-1842-4","title":"On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data","article_processing_charge":"No","oa":1,"year":"2016","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s11192-016-1902-9"}]},"has_accepted_license":"1","ddc":["000"],"citation":{"ieee":"M. Calatrava Moreno, T. Auzinger, and H. Werthner, “On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data,” <i>Scientometrics</i>, vol. 107, no. 1. Springer, pp. 213–232, 2016.","chicago":"Calatrava Moreno, Maria, Thomas Auzinger, and Hannes Werthner. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” <i>Scientometrics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11192-016-1842-4\">https://doi.org/10.1007/s11192-016-1842-4</a>.","short":"M. Calatrava Moreno, T. Auzinger, H. Werthner, Scientometrics 107 (2016) 213–232.","mla":"Calatrava Moreno, Maria, et al. “On the Uncertainty of Interdisciplinarity Measurements Due to Incomplete Bibliographic Data.” <i>Scientometrics</i>, vol. 107, no. 1, Springer, 2016, pp. 213–32, doi:<a href=\"https://doi.org/10.1007/s11192-016-1842-4\">10.1007/s11192-016-1842-4</a>.","ama":"Calatrava Moreno M, Auzinger T, Werthner H. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. <i>Scientometrics</i>. 2016;107(1):213-232. doi:<a href=\"https://doi.org/10.1007/s11192-016-1842-4\">10.1007/s11192-016-1842-4</a>","apa":"Calatrava Moreno, M., Auzinger, T., &#38; Werthner, H. (2016). On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. <i>Scientometrics</i>. Springer. <a href=\"https://doi.org/10.1007/s11192-016-1842-4\">https://doi.org/10.1007/s11192-016-1842-4</a>","ista":"Calatrava Moreno M, Auzinger T, Werthner H. 2016. On the uncertainty of interdisciplinarity measurements due to incomplete bibliographic data. Scientometrics. 107(1), 213–232."},"author":[{"full_name":"Calatrava Moreno, Maria","last_name":"Calatrava Moreno","first_name":"Maria"},{"first_name":"Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265"},{"full_name":"Werthner, Hannes","last_name":"Werthner","first_name":"Hannes"}],"file":[{"content_type":"application/pdf","file_name":"IST-2016-530-v1+1_s11192-016-1842-4.pdf","relation":"main_file","checksum":"32d46268588b87d9b686492018e6a2b2","creator":"system","file_size":806035,"file_id":"4848","access_level":"open_access","date_created":"2018-12-12T10:10:56Z","date_updated":"2020-07-14T12:44:55Z"}],"month":"04","file_date_updated":"2020-07-14T12:44:55Z","pubrep_id":"530","_id":"1446","language":[{"iso":"eng"}],"issue":"1","page":"213 - 232"},{"page":"1774 - 1806","issue":"3","_id":"1448","language":[{"iso":"eng"}],"acknowledgement":"Supported by the German Research Foundation through the Collaborative Research Center 1060\r\nThe Mathematics of Emergent Effects and the Hausdorff Center for Mathematics. Part of this work has been done while M. Fathi visited J. Maas at the University of Bonn in July 2014.We would like to thank the referees for their careful reading of the manuscript. ","author":[{"last_name":"Fathi","first_name":"Max","full_name":"Fathi, Max"},{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"month":"06","citation":{"chicago":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2016. <a href=\"https://doi.org/10.1214/15-AAP1133\">https://doi.org/10.1214/15-AAP1133</a>.","ieee":"M. Fathi and J. Maas, “Entropic Ricci curvature bounds for discrete interacting systems,” <i>The Annals of Applied Probability</i>, vol. 26, no. 3. Institute of Mathematical Statistics, pp. 1774–1806, 2016.","mla":"Fathi, Max, and Jan Maas. “Entropic Ricci Curvature Bounds for Discrete Interacting Systems.” <i>The Annals of Applied Probability</i>, vol. 26, no. 3, Institute of Mathematical Statistics, 2016, pp. 1774–806, doi:<a href=\"https://doi.org/10.1214/15-AAP1133\">10.1214/15-AAP1133</a>.","short":"M. Fathi, J. Maas, The Annals of Applied Probability 26 (2016) 1774–1806.","ama":"Fathi M, Maas J. Entropic Ricci curvature bounds for discrete interacting systems. <i>The Annals of Applied Probability</i>. 2016;26(3):1774-1806. doi:<a href=\"https://doi.org/10.1214/15-AAP1133\">10.1214/15-AAP1133</a>","ista":"Fathi M, Maas J. 2016. Entropic Ricci curvature bounds for discrete interacting systems. The Annals of Applied Probability. 26(3), 1774–1806.","apa":"Fathi, M., &#38; Maas, J. (2016). Entropic Ricci curvature bounds for discrete interacting systems. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/15-AAP1133\">https://doi.org/10.1214/15-AAP1133</a>"},"year":"2016","oa":1,"doi":"10.1214/15-AAP1133","title":"Entropic Ricci curvature bounds for discrete interacting systems","day":"01","date_updated":"2021-01-12T06:50:49Z","abstract":[{"lang":"eng","text":"We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli–Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities."}],"publist_id":"5748","publication":"The Annals of Applied Probability","status":"public","date_published":"2016-06-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"        26","oa_version":"Preprint","scopus_import":1,"date_created":"2018-12-11T11:52:05Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00562"}],"type":"journal_article","volume":26,"department":[{"_id":"JaMa"}],"quality_controlled":"1","publication_status":"published","publisher":"Institute of Mathematical Statistics"},{"quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions"}],"department":[{"_id":"DaSi"}],"publisher":"eLife Sciences Publications","publication_status":"published","type":"journal_article","volume":5,"oa_version":"Published Version","date_created":"2018-12-11T11:52:14Z","scopus_import":1,"publist_id":"5721","publication":"eLife","status":"public","date_published":"2016-02-25T00:00:00Z","abstract":[{"text":"The actin cytoskeleton plays important roles in the formation and internalization of endocytic vesicles. In yeast, endocytic vesicles move towards early endosomes along actin cables, however, the molecular machinery regulating interaction between endocytic vesicles and actin cables is poorly understood. The Eps15-like protein Pan1p plays a key role in actin-mediated endocytosis and is negatively regulated by Ark1 and Prk1 kinases. Here we show that pan1 mutated to prevent phosphorylation at all 18 threonines, pan1-18TA, displayed almost the same endocytic defect as ark1Δ prk1Δ cells, and contained abnormal actin concentrations including several endocytic compartments. Early endosomes were highly localized in the actin concentrations and displayed movement along actin cables. The dephosphorylated form of Pan1p also caused stable associations between endocytic vesicles and actin cables, and between endocytic vesicles and endosomes. Thus Pan1 phosphorylation is part of a novel mechanism that regulates endocytic compartment interactions with each other and with actin cables.","lang":"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"},"intvolume":"         5","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.7554/eLife.10276","title":"Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton","date_updated":"2021-01-12T06:50:59Z","day":"25","ec_funded":1,"year":"2016","has_accepted_license":"1","oa":1,"author":[{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"last_name":"Furuya","first_name":"Eri","full_name":"Furuya, Eri"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"last_name":"Kanno","first_name":"Chisa","full_name":"Kanno, Chisa"},{"full_name":"Sakamoto, Yuta","first_name":"Yuta","last_name":"Sakamoto"},{"last_name":"Ebihara","first_name":"Masashi","full_name":"Ebihara, Masashi"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"file":[{"file_id":"4793","file_size":5198001,"date_created":"2018-12-12T10:10:08Z","date_updated":"2020-07-14T12:44:56Z","access_level":"open_access","content_type":"application/pdf","checksum":"d1cc44870580756ba8badd8e41adfdb5","creator":"system","file_name":"IST-2016-529-v1+1_elife-10276-v1.pdf","relation":"main_file"}],"month":"02","article_number":"e10276","file_date_updated":"2020-07-14T12:44:56Z","ddc":["570"],"citation":{"ama":"Toshima J, Furuya E, Nagano M, et al. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. <i>eLife</i>. 2016;5(February 2016). doi:<a href=\"https://doi.org/10.7554/eLife.10276\">10.7554/eLife.10276</a>","ista":"Toshima J, Furuya E, Nagano M, Kanno C, Sakamoto Y, Ebihara M, Siekhaus DE, Toshima J. 2016. Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. eLife. 5(February 2016), e10276.","apa":"Toshima, J., Furuya, E., Nagano, M., Kanno, C., Sakamoto, Y., Ebihara, M., … Toshima, J. (2016). Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.10276\">https://doi.org/10.7554/eLife.10276</a>","chicago":"Toshima, Junko, Eri Furuya, Makoto Nagano, Chisa Kanno, Yuta Sakamoto, Masashi Ebihara, Daria E Siekhaus, and Jiro Toshima. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.10276\">https://doi.org/10.7554/eLife.10276</a>.","ieee":"J. Toshima <i>et al.</i>, “Yeast Eps15-like endocytic protein Pan1p regulates the interaction between endocytic vesicles, endosomes and the actin cytoskeleton,” <i>eLife</i>, vol. 5, no. February 2016. eLife Sciences Publications, 2016.","mla":"Toshima, Junko, et al. “Yeast Eps15-like Endocytic Protein Pan1p Regulates the Interaction between Endocytic Vesicles, Endosomes and the Actin Cytoskeleton.” <i>ELife</i>, vol. 5, no. February 2016, e10276, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.10276\">10.7554/eLife.10276</a>.","short":"J. Toshima, E. Furuya, M. Nagano, C. Kanno, Y. Sakamoto, M. Ebihara, D.E. Siekhaus, J. Toshima, ELife 5 (2016)."},"issue":"February 2016","_id":"1475","language":[{"iso":"eng"}],"pubrep_id":"529"},{"type":"journal_article","volume":129,"publication_status":"published","publisher":"Company of Biologists","department":[{"_id":"DaSi"}],"quality_controlled":"1","project":[{"grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"       129","abstract":[{"lang":"eng","text":"The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis"}],"publication":"Journal of Cell Science","publist_id":"5720","status":"public","date_published":"2016-01-15T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:52:14Z","oa_version":"Published Version","oa":1,"has_accepted_license":"1","ec_funded":1,"year":"2016","day":"15","date_updated":"2021-01-12T06:51:00Z","doi":"10.1242/jcs.176651","title":"Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis","_id":"1476","language":[{"iso":"eng"}],"pubrep_id":"767","acknowledgement":"We are grateful to Anthony Bretscher (Cornell University, NY) for providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported by the European Union [grant number PCIG12-GA-2012-334077].","page":"367 - 379","issue":"2","ddc":["570","576"],"citation":{"short":"J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto, D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379.","mla":"Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” <i>Journal of Cell Science</i>, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:<a href=\"https://doi.org/10.1242/jcs.176651\">10.1242/jcs.176651</a>.","ieee":"J. Toshima <i>et al.</i>, “Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis,” <i>Journal of Cell Science</i>, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.","chicago":"Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano, Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” <i>Journal of Cell Science</i>. Company of Biologists, 2016. <a href=\"https://doi.org/10.1242/jcs.176651\">https://doi.org/10.1242/jcs.176651</a>.","apa":"Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., … Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.176651\">https://doi.org/10.1242/jcs.176651</a>","ista":"Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W, Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 129(2), 367–379.","ama":"Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. <i>Journal of Cell Science</i>. 2016;129(2):367-379. doi:<a href=\"https://doi.org/10.1242/jcs.176651\">10.1242/jcs.176651</a>"},"author":[{"last_name":"Toshima","first_name":"Junko","full_name":"Toshima, Junko"},{"full_name":"Horikomi, Chika","first_name":"Chika","last_name":"Horikomi"},{"last_name":"Okada","first_name":"Asuka","full_name":"Okada, Asuka"},{"first_name":"Makiko","last_name":"Hatori","full_name":"Hatori, Makiko"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"full_name":"Masuda, Atsushi","last_name":"Masuda","first_name":"Atsushi"},{"last_name":"Yamamoto","first_name":"Wataru","full_name":"Yamamoto, Wataru"},{"first_name":"Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"file":[{"file_id":"4861","file_size":7176912,"date_created":"2018-12-12T10:11:08Z","date_updated":"2020-07-14T12:44:56Z","access_level":"open_access","content_type":"application/pdf","creator":"system","checksum":"2da0a09149a9ed956cdf79a95c17f08a","relation":"main_file","file_name":"IST-2017-767-v1+1_367.full.pdf"}],"month":"01","file_date_updated":"2020-07-14T12:44:56Z"},{"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tracol","first_name":"Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","full_name":"Tracol, Mathieu"}],"month":"08","arxiv":1,"citation":{"ama":"Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with ω-regular objectives. <i>Journal of Computer and System Sciences</i>. 2016;82(5):878-911. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">10.1016/j.jcss.2016.02.009</a>","ista":"Chatterjee K, Chmelik M, Tracol M. 2016. What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. 82(5), 878–911.","apa":"Chatterjee, K., Chmelik, M., &#38; Tracol, M. (2016). What is decidable about partially observable Markov decision processes with ω-regular objectives. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">https://doi.org/10.1016/j.jcss.2016.02.009</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">https://doi.org/10.1016/j.jcss.2016.02.009</a>.","ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with ω-regular objectives,” <i>Journal of Computer and System Sciences</i>, vol. 82, no. 5. Elsevier, pp. 878–911, 2016.","mla":"Chatterjee, Krishnendu, et al. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” <i>Journal of Computer and System Sciences</i>, vol. 82, no. 5, Elsevier, 2016, pp. 878–911, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">10.1016/j.jcss.2016.02.009</a>.","short":"K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences 82 (2016) 878–911."},"issue":"5","page":"878 - 911","_id":"1477","language":[{"iso":"eng"}],"external_id":{"arxiv":["1309.2802"]},"doi":"10.1016/j.jcss.2016.02.009","title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","date_updated":"2023-02-23T12:24:38Z","day":"01","year":"2016","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2295"},{"relation":"earlier_version","id":"5400","status":"public"}]},"oa":1,"oa_version":"Preprint","date_created":"2018-12-11T11:52:15Z","scopus_import":1,"publist_id":"5718","publication":"Journal of Computer and System Sciences","status":"public","date_published":"2016-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples."}],"intvolume":"        82","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"department":[{"_id":"KrCh"}],"publisher":"Elsevier","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2802"}],"type":"journal_article","volume":82},{"title":"Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas","doi":"10.1088/1367-2630/18/3/035002","day":"29","date_updated":"2021-01-12T06:51:01Z","has_accepted_license":"1","year":"2016","oa":1,"month":"02","article_number":"035002","file_date_updated":"2020-07-14T12:44:56Z","author":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer"},{"first_name":"Simone","last_name":"Warzel","full_name":"Warzel, Simone"}],"file":[{"file_size":965607,"file_id":"5276","access_level":"open_access","date_updated":"2020-07-14T12:44:56Z","date_created":"2018-12-12T10:17:22Z","content_type":"application/pdf","file_name":"IST-2016-579-v1+1_njp_18_3_035002.pdf","relation":"main_file","checksum":"4f959eabc19d2a2f518318a450a4d424","creator":"system"}],"citation":{"ama":"Seiringer R, Warzel S. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. <i>New Journal of Physics</i>. 2016;18(3). doi:<a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">10.1088/1367-2630/18/3/035002</a>","ista":"Seiringer R, Warzel S. 2016. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 18(3), 035002.","apa":"Seiringer, R., &#38; Warzel, S. (2016). Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">https://doi.org/10.1088/1367-2630/18/3/035002</a>","chicago":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">https://doi.org/10.1088/1367-2630/18/3/035002</a>.","ieee":"R. Seiringer and S. Warzel, “Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas,” <i>New Journal of Physics</i>, vol. 18, no. 3. IOP Publishing Ltd., 2016.","short":"R. Seiringer, S. Warzel, New Journal of Physics 18 (2016).","mla":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” <i>New Journal of Physics</i>, vol. 18, no. 3, 035002, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">10.1088/1367-2630/18/3/035002</a>."},"ddc":["510","530"],"issue":"3","_id":"1478","pubrep_id":"579","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"project":[{"call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"quality_controlled":"1","publication_status":"published","publisher":"IOP Publishing Ltd.","volume":18,"type":"journal_article","oa_version":"Published Version","scopus_import":1,"date_created":"2018-12-11T11:52:15Z","abstract":[{"text":"We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature.","lang":"eng"}],"status":"public","date_published":"2016-02-29T00:00:00Z","publication":"New Journal of Physics","publist_id":"5716","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":"        18","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"}},{"year":"2016","related_material":{"record":[{"id":"1604","relation":"later_version","status":"public"}]},"has_accepted_license":"1","oa":1,"type":"technical_report","doi":"10.15479/AT:IST-2016-523-v1-1","department":[{"_id":"KrCh"}],"title":"Quantitative interprocedural analysis","date_updated":"2023-02-23T10:06:22Z","publisher":"IST Austria","day":"31","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","status":"public","date_published":"2016-03-31T00:00:00Z","page":"33","abstract":[{"text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. ","lang":"eng"}],"_id":"5445","pubrep_id":"523","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"oa_version":"Published Version","file":[{"checksum":"cef516fa091925b5868813e355268fb4","creator":"system","relation":"main_file","file_name":"IST-2016-523-v1+1_main.pdf","content_type":"application/pdf","date_created":"2018-12-12T11:53:52Z","date_updated":"2020-07-14T12:46:58Z","access_level":"open_access","file_id":"5513","file_size":1012204}],"month":"03","file_date_updated":"2020-07-14T12:46:58Z","ddc":["005"],"date_created":"2018-12-12T11:39:22Z","citation":{"short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>.","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, <i>Quantitative interprocedural analysis</i>. IST Austria, 2016.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Velner, Y. (2016). <i>Quantitative interprocedural analysis</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p.","ama":"Chatterjee K, Pavlogiannis A, Velner Y. <i>Quantitative Interprocedural Analysis</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>"},"alternative_title":["IST Austria Technical Report"]},{"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"512","relation":"later_version"}]},"year":"2016","type":"technical_report","oa":1,"department":[{"_id":"KrCh"}],"title":"Amplification on undirected population structures: Comets beat stars","doi":"10.15479/AT:IST-2016-648-v1-1","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"day":"09","publisher":"IST Austria","date_updated":"2023-02-23T12:22:21Z","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.","lang":"eng"}],"page":"22","status":"public","date_published":"2016-11-09T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"648","_id":"5449","language":[{"iso":"eng"}],"month":"11","file_date_updated":"2020-07-14T12:46:58Z","file":[{"date_created":"2018-12-12T11:54:07Z","date_updated":"2020-07-14T12:46:58Z","access_level":"open_access","file_id":"5529","file_size":1264221,"checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","creator":"system","relation":"main_file","file_name":"IST-2016-648-v1+1_tr.pdf","content_type":"application/pdf"}],"author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"oa_version":"Updated Version","alternative_title":["IST Austria Technical Report"],"date_created":"2018-12-12T11:39:24Z","citation":{"mla":"Pavlogiannis, Andreas, et al. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. 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We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"license":"https://creativecommons.org/publicdomain/zero/1.0/","_id":"5550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:00Z","month":"02","oa_version":"Published Version","author":[{"first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"}],"file":[{"content_type":"application/zip","creator":"system","checksum":"950f85b80427d357bfeff09608ba02e9","relation":"main_file","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","file_id":"5594","file_size":4468543,"date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T13:02:27Z","access_level":"open_access"}],"citation":{"ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>.","mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","short":"T. Ellis, D. Field, (2016).","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>","apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. 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Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>."},"date_created":"2018-12-12T12:31:29Z","ddc":["576"]},{"oa":1,"article_processing_charge":"No","type":"research_data","year":"2016","datarep_id":"35","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"research_paper","id":"1398"}]},"publisher":"Institute of Science and Technology Austria","date_updated":"2024-02-21T13:51:27Z","day":"19","department":[{"_id":"NiBa"}],"title":"Data on pollinator observations and offpsring phenotypes","doi":"10.15479/AT:ISTA:35","_id":"5551","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2016-02-19T00:00:00Z","status":"public","abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}],"citation":{"ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>.","short":"T. Ellis, (2016).","mla":"Ellis, Thomas. <i>Data on Pollinator Observations and Offpsring Phenotypes</i>. 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