--- _id: '5442' 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 properties that arise in program analysis.\r\nWe consider that each component of the concurrent system is a graph with constant treewidth, and it is known that the controlflow graphs of most programs have constant treewidth. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis problems (e.g., alias analysis). The study of multiple queries allows us to consider the tradeoff between the resource usage of the \\emph{one-time} preprocessing and for \\emph{each individual} query. The traditional approaches construct the product graph of all components and apply the best-known graph algorithm on the product. In the traditional approach, even the answer to a single query requires the transitive closure computation (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\n\r\nOur 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, \r\neach 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 that show that the worst-case running times of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (such as improving \r\nthe worst-case bounds for the shortest path problem in general graphs whose current best-known bound has not been improved in five decades). Finally, we provide a prototype implementation of our algorithms which significantly outperforms the existing algorithmic methods on several benchmarks." alternative_title: - IST Austria Technical Report author: - first_name: '1' full_name: Anonymous, 1 last_name: Anonymous - first_name: '2' full_name: Anonymous, 2 last_name: Anonymous - first_name: '3' full_name: Anonymous, 3 last_name: Anonymous - first_name: '4' full_name: Anonymous, 4 last_name: Anonymous citation: ama: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015. apa: Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria. chicago: Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015. ieee: 1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015. ista: Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 22p. mla: Anonymous, 1, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015. short: 1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015. date_created: 2018-12-12T11:39:21Z date_published: 2015-07-14T00:00:00Z date_updated: 2023-09-19T14:36:19Z day: '14' ddc: - '000' file: - access_level: open_access checksum: 98fd936102f3e057fc321ef6d316001d content_type: application/pdf creator: system date_created: 2018-12-12T11:53:37Z date_updated: 2020-07-14T12:46:57Z file_id: '5498' file_name: IST-2015-343-v2+1_main.pdf file_size: 658747 relation: main_file - access_level: closed checksum: b31d09b1241b59c75e1f42dadf09d258 content_type: text/plain creator: dernst date_created: 2019-04-16T12:36:08Z date_updated: 2020-07-14T12:46:57Z file_id: '6316' file_name: IST-2015-343-v2+2_anonymous.txt file_size: 139 relation: main_file file_date_updated: 2020-07-14T12:46:57Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '22' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '344' related_material: record: - id: '1437' relation: later_version status: public - id: '5441' relation: later_version status: public - id: '6009' relation: later_version status: public scopus_import: 1 status: public title: Algorithms for algebraic path properties in concurrent systems of constant treewidth components type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1689' abstract: - lang: eng text: We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. We demonstrate our approach on an illustrative case study. author: - first_name: Mária full_name: Svoreňová, Mária last_name: Svoreňová - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ivana full_name: Cěrná, Ivana last_name: Cěrná - first_name: Cǎlin full_name: Belta, Cǎlin last_name: Belta citation: ama: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:259-268. doi:10.1145/2728606.2728608' apa: 'Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2015). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 259–268). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728608' chicago: 'Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 259–68. ACM, 2015. https://doi.org/10.1145/2728606.2728608.' ieee: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 259–268.' ista: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 259–268.' mla: 'Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–68, doi:10.1145/2728606.2728608.' short: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–268.' conference: end_date: 2015-04-16 location: Seattle, WA, United States name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2015-04-14 date_created: 2018-12-11T11:53:29Z date_published: 2015-04-14T00:00:00Z date_updated: 2023-09-20T09:43:09Z day: '14' department: - _id: ToHe - _id: KrCh doi: 10.1145/2728606.2728608 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.5387 month: '04' oa: 1 oa_version: Preprint page: 259 - 268 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: 'Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control' publication_status: published publisher: ACM publist_id: '5456' related_material: record: - id: '1407' relation: later_version status: public scopus_import: 1 status: public title: Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1729' abstract: - lang: eng text: We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions. alternative_title: - LNCS author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Edmund full_name: Clarke, Edmund last_name: Clarke - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Leonid full_name: Ryzhyk, Leonid last_name: Ryzhyk - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta - first_name: Thorsten full_name: Tarrach, Thorsten id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87 last_name: Tarrach orcid: 0000-0003-4409-8487 citation: ama: Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. 2015;9207:180-197. doi:10.1007/978-3-319-21668-3_11 apa: 'Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., & Tarrach, T. (2015). From non-preemptive to preemptive scheduling using synchronization synthesis. Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21668-3_11' chicago: Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-21668-3_11. ieee: P. Cerny et al., “From non-preemptive to preemptive scheduling using synchronization synthesis,” vol. 9207. Springer, pp. 180–197, 2015. ista: Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2015. From non-preemptive to preemptive scheduling using synchronization synthesis. 9207, 180–197. mla: Cerny, Pavol, et al. From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis. Vol. 9207, Springer, 2015, pp. 180–97, doi:10.1007/978-3-319-21668-3_11. short: P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, 9207 (2015) 180–197. conference: end_date: 2015-07-24 location: San Francisco, CA, United States name: 'CAV: Computer Aided Verification' start_date: 2015-07-18 date_created: 2018-12-11T11:53:42Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-09-20T11:13:50Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-21668-3_11 ec_funded: 1 file: - access_level: local checksum: 6ff58ac220e2f20cb001ba35d4924495 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:53Z date_updated: 2020-07-14T12:45:13Z file_id: '4715' file_name: IST-2015-336-v1+1_long_version.pdf file_size: 481922 relation: main_file file_date_updated: 2020-07-14T12:45:13Z has_accepted_license: '1' intvolume: ' 9207' language: - iso: eng month: '07' oa_version: Submitted Version page: 180 - 197 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5398' pubrep_id: '336' quality_controlled: '1' related_material: record: - id: '1130' relation: dissertation_contains status: public - id: '1338' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: From non-preemptive to preemptive scheduling using synchronization synthesis type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9207 year: '2015' ... --- _id: '1835' abstract: - lang: eng text: The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights. acknowledgement: "SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n" alternative_title: - LNCS author: - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47 apa: 'Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47' chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47. ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015. ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483. mla: Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47. short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483. conference: end_date: 2015-04-18 location: London, United Kingdom name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2015-04-11 date_created: 2018-12-11T11:54:16Z date_published: 2015-04-01T00:00:00Z date_updated: 2023-09-20T11:06:03Z day: '01' department: - _id: ToHe - _id: CaGu - _id: NiBa doi: 10.1007/978-3-662-46681-0_47 ec_funded: 1 intvolume: ' 9035' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.7704 month: '04' oa: 1 oa_version: Preprint page: 469 - 483 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5267' quality_controlled: '1' related_material: record: - id: '1351' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Model checking gene regulatory networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9035 year: '2015' ... --- _id: '1509' abstract: - lang: eng text: The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1. acknowledgement: "This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554" article_processing_charge: No author: - first_name: Jaroslav full_name: Michalko, Jaroslav id: 483727CA-F248-11E8-B48F-1D18A9856A87 last_name: Michalko - first_name: Marta full_name: Dravecka, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Dravecka orcid: 0000-0002-2519-8004 - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 2015;4. doi:10.12688/f1000research.7143.1 apa: Michalko, J., Lukacisinova, M., Bollenbach, M. T., & Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7143.1 chicago: Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research . F1000 Research, 2015. https://doi.org/10.12688/f1000research.7143.1. ieee: J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” F1000 Research , vol. 4. F1000 Research, 2015. ista: Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4. mla: Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research , vol. 4, F1000 Research, 2015, doi:10.12688/f1000research.7143.1. short: J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research 4 (2015). date_created: 2018-12-11T11:52:26Z date_published: 2015-10-01T00:00:00Z date_updated: 2023-10-10T14:10:24Z day: '01' ddc: - '570' department: - _id: JiFr - _id: ToBo doi: 10.12688/f1000research.7143.1 ec_funded: 1 file: - access_level: open_access checksum: 8beae5cbe988e1060265ae7de2ee8306 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:12Z date_updated: 2020-07-14T12:44:59Z file_id: '5198' file_name: IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf file_size: 4414248 relation: main_file file_date_updated: 2020-07-14T12:44:59Z has_accepted_license: '1' intvolume: ' 4' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: 'F1000 Research ' publication_status: published publisher: F1000 Research publist_id: '5668' pubrep_id: '497' quality_controlled: '1' scopus_import: '1' status: public title: Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2015' ... --- _id: '1681' abstract: - lang: eng text: In many social situations, individuals endeavor to find the single best possible partner, but are constrained to evaluate the candidates in sequence. Examples include the search for mates, economic partnerships, or any other long-term ties where the choice to interact involves two parties. Surprisingly, however, previous theoretical work on mutual choice problems focuses on finding equilibrium solutions, while ignoring the evolutionary dynamics of decisions. Empirically, this may be of high importance, as some equilibrium solutions can never be reached unless the population undergoes radical changes and a sufficient number of individuals change their decisions simultaneously. To address this question, we apply a mutual choice sequential search problem in an evolutionary game-theoretical model that allows one to find solutions that are favored by evolution. As an example, we study the influence of sequential search on the evolutionary dynamics of cooperation. For this, we focus on the classic snowdrift game and the prisoner’s dilemma game. article_processing_charge: No article_type: original author: - first_name: Tadeas full_name: Priklopil, Tadeas id: 3C869AA0-F248-11E8-B48F-1D18A9856A87 last_name: Priklopil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: Priklopil T, Chatterjee K. Evolution of decisions in population games with sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413 apa: Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413 chicago: Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games. MDPI, 2015. https://doi.org/10.3390/g6040413. ieee: T. Priklopil and K. Chatterjee, “Evolution of decisions in population games with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp. 413–437, 2015. ista: Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games with sequentially searching individuals. Games. 6(4), 413–437. mla: Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI, 2015, pp. 413–37, doi:10.3390/g6040413. short: T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437. date_created: 2018-12-11T11:53:26Z date_published: 2015-09-29T00:00:00Z date_updated: 2023-10-17T11:42:52Z day: '29' ddc: - '000' department: - _id: NiBa - _id: KrCh doi: 10.3390/g6040413 ec_funded: 1 file: - access_level: open_access checksum: 912e1acbaf201100f447a43e4d5958bd content_type: application/pdf creator: system date_created: 2018-12-12T10:12:41Z date_updated: 2020-07-14T12:45:12Z file_id: '4959' file_name: IST-2016-448-v1+1_games-06-00413.pdf file_size: 518832 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 6' issue: '4' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 413 - 437 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Games publication_identifier: eissn: - 2073-4336 publication_status: published publisher: MDPI publist_id: '5467' pubrep_id: '448' quality_controlled: '1' scopus_import: '1' status: public title: Evolution of decisions in population games with sequentially searching individuals tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '1655' abstract: - lang: eng text: Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration. acknowledgement: This work was supported by the DFG priority program 1527 (Autonomous Learning) and by the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 318723 (MatheMACS) and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. article_processing_charge: No author: - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Eckehard full_name: Olbrich, Eckehard last_name: Olbrich citation: ama: Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266 apa: Martius, G. S., & Olbrich, E. (2015). Quantifying emergent behavior of autonomous robots. Entropy. MDPI. https://doi.org/10.3390/e17107266 chicago: Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy. MDPI, 2015. https://doi.org/10.3390/e17107266. ieee: G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous robots,” Entropy, vol. 17, no. 10. MDPI, pp. 7266–7297, 2015. ista: Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297. mla: Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy, vol. 17, no. 10, MDPI, 2015, pp. 7266–97, doi:10.3390/e17107266. short: G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297. date_created: 2018-12-11T11:53:17Z date_published: 2015-10-23T00:00:00Z date_updated: 2023-10-17T11:42:00Z day: '23' ddc: - '000' department: - _id: ChLa - _id: GaTk doi: 10.3390/e17107266 ec_funded: 1 file: - access_level: open_access checksum: 945d99631a96e0315acb26dc8541dcf9 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:25Z date_updated: 2020-07-14T12:45:08Z file_id: '4943' file_name: IST-2016-464-v1+1_entropy-17-07266.pdf file_size: 6455007 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 17' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 7266 - 7297 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Entropy publication_status: published publisher: MDPI publist_id: '5495' pubrep_id: '464' quality_controlled: '1' scopus_import: '1' status: public title: Quantifying emergent behavior of autonomous robots tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '1834' abstract: - lang: eng text: Huge body of evidences demonstrated that volatile anesthetics affect the hippocampal neurogenesis and neurocognitive functions, and most of them showed impairment at anesthetic dose. Here, we investigated the effect of low dose (1.8%) sevoflurane on hippocampal neurogenesis and dentate gyrus-dependent learning. Neonatal rats at postnatal day 4 to 6 (P4-6) were treated with 1.8% sevoflurane for 6 hours. Neurogenesis was quantified by bromodeoxyuridine labeling and electrophysiology recording. Four and seven weeks after treatment, the Morris water maze and contextual-fear discrimination learning tests were performed to determine the influence on spatial learning and pattern separation. A 6-hour treatment with 1.8% sevoflurane promoted hippocampal neurogenesis and increased the survival of newborn cells and the proportion of immature granular cells in the dentate gyrus of neonatal rats. Sevoflurane-treated rats performed better during the training days of the Morris water maze test and in contextual-fear discrimination learning test. These results suggest that a subanesthetic dose of sevoflurane promotes hippocampal neurogenesis in neonatal rats and facilitates their performance in dentate gyrus-dependent learning tasks. article_processing_charge: No article_type: original author: - first_name: Chong full_name: Chen, Chong id: 3DFD581A-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Xuan full_name: Zhao, Xuan last_name: Zhao - first_name: Tao full_name: Zhou, Tao last_name: Zhou - first_name: Dao full_name: Xu, Dao last_name: Xu - first_name: Zhi full_name: Wang, Zhi last_name: Wang - first_name: Ying full_name: Wang, Ying last_name: Wang citation: ama: Chen C, Wang C, Zhao X, et al. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 2015;7(2). doi:10.1177/1759091415575845 apa: Chen, C., Wang, C., Zhao, X., Zhou, T., Xu, D., Wang, Z., & Wang, Y. (2015). Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. SAGE Publications. https://doi.org/10.1177/1759091415575845 chicago: Chen, Chong, Chao Wang, Xuan Zhao, Tao Zhou, Dao Xu, Zhi Wang, and Ying Wang. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro. SAGE Publications, 2015. https://doi.org/10.1177/1759091415575845. ieee: C. Chen et al., “Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats,” ASN Neuro, vol. 7, no. 2. SAGE Publications, 2015. ista: Chen C, Wang C, Zhao X, Zhou T, Xu D, Wang Z, Wang Y. 2015. Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats. ASN Neuro. 7(2). mla: Chen, Chong, et al. “Low-Dose Sevoflurane Promoteshippocampal Neurogenesis and Facilitates the Development of Dentate Gyrus-Dependent Learning in Neonatal Rats.” ASN Neuro, vol. 7, no. 2, SAGE Publications, 2015, doi:10.1177/1759091415575845. short: C. Chen, C. Wang, X. Zhao, T. Zhou, D. Xu, Z. Wang, Y. Wang, ASN Neuro 7 (2015). date_created: 2018-12-11T11:54:16Z date_published: 2015-04-13T00:00:00Z date_updated: 2023-10-18T06:47:30Z day: '13' ddc: - '570' department: - _id: PeJo doi: 10.1177/1759091415575845 file: - access_level: open_access checksum: 53e16bd3fc2ae2c0d7de9164626c37aa content_type: application/pdf creator: system date_created: 2018-12-12T10:14:08Z date_updated: 2020-07-14T12:45:18Z file_id: '5057' file_name: IST-2016-456-v1+1_ASN_Neuro-2015-Chen-.pdf file_size: 1146814 relation: main_file file_date_updated: 2020-07-14T12:45:18Z has_accepted_license: '1' intvolume: ' 7' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '04' oa: 1 oa_version: Published Version publication: ASN Neuro publication_status: published publisher: SAGE Publications publist_id: '5269' pubrep_id: '456' quality_controlled: '1' scopus_import: '1' status: public title: Low-dose sevoflurane promoteshippocampal neurogenesis and facilitates the development of dentate gyrus-dependent learning in neonatal rats tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2015' ... --- _id: '1635' abstract: - lang: eng text: We calculate a Ricci curvature lower bound for some classical examples of random walks, namely, a chain on a slice of the n-dimensional discrete cube (the so-called Bernoulli-Laplace model) and the random transposition shuffle of the symmetric group of permutations on n letters. article_processing_charge: No article_type: original author: - first_name: Matthias full_name: Erbar, Matthias last_name: Erbar - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Prasad full_name: Tetali, Prasad last_name: Tetali citation: ama: Erbar M, Maas J, Tetali P. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 2015;24(4):781-800. doi:10.5802/afst.1464 apa: Erbar, M., Maas, J., & Tetali, P. (2015). Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse. https://doi.org/10.5802/afst.1464 chicago: Erbar, Matthias, Jan Maas, and Prasad Tetali. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse. Faculté des sciences de Toulouse, 2015. https://doi.org/10.5802/afst.1464. ieee: M. Erbar, J. Maas, and P. Tetali, “Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models,” Annales de la faculté des sciences de Toulouse, vol. 24, no. 4. Faculté des sciences de Toulouse, pp. 781–800, 2015. ista: Erbar M, Maas J, Tetali P. 2015. Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models. Annales de la faculté des sciences de Toulouse. 24(4), 781–800. mla: Erbar, Matthias, et al. “Discrete Ricci Curvature Bounds for Bernoulli-Laplace and Random Transposition Models.” Annales de La Faculté Des Sciences de Toulouse, vol. 24, no. 4, Faculté des sciences de Toulouse, 2015, pp. 781–800, doi:10.5802/afst.1464. short: M. Erbar, J. Maas, P. Tetali, Annales de La Faculté Des Sciences de Toulouse 24 (2015) 781–800. date_created: 2018-12-11T11:53:10Z date_published: 2015-01-01T00:00:00Z date_updated: 2023-10-18T07:48:28Z day: '01' department: - _id: JaMa doi: 10.5802/afst.1464 external_id: arxiv: - '1409.8605' intvolume: ' 24' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1409.8605 month: '01' oa: 1 oa_version: Preprint page: 781 - 800 publication: Annales de la faculté des sciences de Toulouse publication_status: published publisher: Faculté des sciences de Toulouse publist_id: '5520' quality_controlled: '1' status: public title: Discrete Ricci curvature bounds for Bernoulli-Laplace and random transposition models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2015' ... --- _id: '14303' abstract: - lang: eng text: Scaffolded DNA origami enables the fabrication of a variety of complex nanostructures that promise utility in diverse fields of application, ranging from biosensing over advanced therapeutics to metamaterials. The broad applicability of DNA origami as a material beyond the level of proof-of-concept studies critically depends, among other factors, on the availability of large amounts of pure single-stranded scaffold DNA. Here, we present a method for the efficient production of M13 bacteriophage-derived genomic DNA using high-cell-density fermentation of Escherichia coli in stirred-tank bioreactors. We achieve phage titers of up to 1.6 × 1014 plaque-forming units per mL. Downstream processing yields up to 410 mg of high-quality single-stranded DNA per one liter reaction volume, thus upgrading DNA origami-based nanotechnology from the milligram to the gram scale. article_processing_charge: No article_type: letter_note author: - first_name: B full_name: Kick, B last_name: Kick - first_name: Florian M full_name: Praetorius, Florian M id: dfec9381-4341-11ee-8fd8-faa02bba7d62 last_name: Praetorius - first_name: H full_name: Dietz, H last_name: Dietz - first_name: D full_name: Weuster-Botz, D last_name: Weuster-Botz citation: ama: Kick B, Praetorius FM, Dietz H, Weuster-Botz D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 2015;15(7):4672-4676. doi:10.1021/acs.nanolett.5b01461 apa: Kick, B., Praetorius, F. M., Dietz, H., & Weuster-Botz, D. (2015). Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. ACS Publications. https://doi.org/10.1021/acs.nanolett.5b01461 chicago: Kick, B, Florian M Praetorius, H Dietz, and D Weuster-Botz. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters. ACS Publications, 2015. https://doi.org/10.1021/acs.nanolett.5b01461. ieee: B. Kick, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Efficient production of single-stranded phage DNA as scaffolds for DNA origami,” Nano Letters, vol. 15, no. 7. ACS Publications, pp. 4672–4676, 2015. ista: Kick B, Praetorius FM, Dietz H, Weuster-Botz D. 2015. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Letters. 15(7), 4672–4676. mla: Kick, B., et al. “Efficient Production of Single-Stranded Phage DNA as Scaffolds for DNA Origami.” Nano Letters, vol. 15, no. 7, ACS Publications, 2015, pp. 4672–76, doi:10.1021/acs.nanolett.5b01461. short: B. Kick, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Nano Letters 15 (2015) 4672–4676. date_created: 2023-09-06T12:52:47Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-11-07T11:56:32Z day: '01' doi: 10.1021/acs.nanolett.5b01461 extern: '1' external_id: pmid: - '26028443' intvolume: ' 15' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acs.nanolett.5b01461 month: '06' oa: 1 oa_version: Published Version page: 4672-4676 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: ACS Publications quality_controlled: '1' status: public title: Efficient production of single-stranded phage DNA as scaffolds for DNA origami type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2015' ...