--- _id: '10416' abstract: - lang: eng text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks.' acknowledgement: "The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n" article_number: '30' article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Bhavya full_name: Choudhary, Bhavya last_name: Choudhary - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158118 apa: 'Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158118' chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118. ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017. ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30. mla: Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118. short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017). conference: end_date: 2018-01-13 location: Los Angeles, CA, United States name: 'POPL: Programming Languages' start_date: 2018-01-07 date_created: 2021-12-05T23:01:48Z date_published: 2017-12-27T00:00:00Z date_updated: 2023-02-23T12:27:13Z day: '27' ddc: - '000' department: - _id: KrCh doi: 10.1145/3158118 ec_funded: 1 external_id: arxiv: - '1910.00241' file: - access_level: open_access checksum: faa3f7b3fe8aab84b50ed805c26a0ee5 content_type: application/pdf creator: cchlebak date_created: 2021-12-07T08:06:28Z date_updated: 2021-12-07T08:06:28Z file_id: '10421' file_name: 2017_ACMProgLang_Chatterjee.pdf file_size: 460188 relation: main_file success: 1 file_date_updated: 2021-12-07T08:06:28Z has_accepted_license: '1' intvolume: ' 2' issue: POPL language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '12' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the ACM on Programming Languages publication_identifier: eissn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '5455' relation: earlier_version status: public scopus_import: '1' status: public title: Optimal Dyck reachability for data-dependence and Alias analysis 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 2 year: '2017' ... --- _id: '5455' abstract: - lang: eng text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks.' alternative_title: - IST Austria Technical Report article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Bhavya full_name: Choudhary, Bhavya last_name: Choudhary - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1 apa: Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1 chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1. ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017. ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p. mla: Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1. short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017. date_created: 2018-12-12T11:39:26Z date_published: 2017-10-23T00:00:00Z date_updated: 2023-02-21T15:54:10Z day: '23' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2017-870-v1-1 file: - access_level: open_access checksum: 177a84a46e3ac17e87b31534ad16a4c9 content_type: application/pdf creator: system date_created: 2018-12-12T11:54:02Z date_updated: 2020-07-14T12:46:59Z file_id: '5524' file_name: IST-2017-870-v1+1_main.pdf file_size: 960491 relation: main_file file_date_updated: 2020-07-14T12:46:59Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '37' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '870' related_material: record: - id: '10416' relation: later_version status: public status: public title: Optimal Dyck reachability for data-dependence and alias analysis type: technical_report user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2017' ... --- _id: '10417' abstract: - lang: eng text: "We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence." acknowledgement: "The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061." article_number: '31' article_processing_charge: No article_type: original author: - first_name: Marek full_name: Chalupa, Marek last_name: Chalupa - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Nishant full_name: Sinha, Nishant last_name: Sinha - first_name: Kapil full_name: Vaidya, Kapil last_name: Vaidya citation: ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119 apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119' chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119. ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017. ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31. mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119. short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017). conference: end_date: 2018-01-13 location: Los Angeles, CA, United States name: 'POPL: Programming Languages' start_date: 2018-01-07 date_created: 2021-12-05T23:01:49Z date_published: 2017-12-27T00:00:00Z date_updated: 2023-02-23T12:27:16Z day: '27' department: - _id: KrCh doi: 10.1145/3158119 ec_funded: 1 external_id: arxiv: - '1610.01188' intvolume: ' 2' issue: POPL language: - iso: eng main_file_link: - open_access: '1' url: https://dl.acm.org/doi/10.1145/3158119 month: '12' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _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: Proceedings of the ACM on Programming Languages publication_identifier: eissn: - 2475-1421 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: record: - id: '5448' relation: earlier_version status: public - id: '5456' relation: earlier_version status: public scopus_import: '1' status: public title: Data-centric dynamic partial order reduction type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 2 year: '2017' ... --- _id: '5456' abstract: - lang: eng text: "We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes." alternative_title: - IST Austria Technical Report author: - first_name: Marek full_name: Chalupa, Marek last_name: Chalupa - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Nishant full_name: Sinha, Nishant last_name: Sinha - first_name: Kapil full_name: Vaidya, Kapil last_name: Vaidya citation: ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1 apa: Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1 chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1. ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric dynamic partial order reduction. IST Austria, 2017. ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p. mla: Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1. short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017. date_created: 2018-12-12T11:39:26Z date_published: 2017-10-23T00:00:00Z date_updated: 2023-02-23T12:26:54Z day: '23' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2017-872-v1-1 file: - access_level: open_access checksum: d2635c4cf013000f0a1b09e80f9e4ab7 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:26Z date_updated: 2020-07-14T12:46:59Z file_id: '5487' file_name: IST-2017-872-v1+1_main.pdf file_size: 910347 relation: main_file file_date_updated: 2020-07-14T12:46:59Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '36' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '872' related_material: record: - id: '10417' relation: later_version status: public - id: '5448' relation: earlier_version status: public status: public title: Data-centric dynamic partial order reduction type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '551' abstract: - lang: eng text: 'Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. ' alternative_title: - LIPIcs article_number: '61' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: 'Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61' apa: 'Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61' chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61. ieee: K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83. ista: 'Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 61.' mla: Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” Leibniz International Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61. short: K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-25 location: Aalborg, Denmark name: 'MFCS: Mathematical Foundations of Computer Science (SG)' start_date: 2017-08-21 date_created: 2018-12-11T11:47:08Z date_published: 2017-11-01T00:00:00Z date_updated: 2021-01-12T08:02:34Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.MFCS.2017.61 file: - access_level: open_access checksum: 2eed5224c0e4e259484a1d71acb8ba6a content_type: application/pdf creator: system date_created: 2018-12-12T10:18:04Z date_updated: 2020-07-14T12:47:00Z file_id: '5322' file_name: IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf file_size: 535077 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 83' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Leibniz International Proceedings in Informatics publication_identifier: isbn: - 978-395977046-0 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7263' pubrep_id: '924' quality_controlled: '1' scopus_import: 1 status: public title: Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2017' ... --- _id: '552' abstract: - lang: eng text: 'Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective).' alternative_title: - LIPIcs article_number: '39' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Svozil, Alexander last_name: Svozil citation: ama: 'Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39' apa: 'Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms for mean-payoff parity games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.39' chicago: Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39. ieee: K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff parity games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83. ista: 'Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.' mla: Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.” Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39. short: K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-25 location: Aalborg, Denmark name: 'MFCS: Mathematical Foundations of Computer Science (SG)' start_date: 2017-08-21 date_created: 2018-12-11T11:47:08Z date_published: 2017-11-01T00:00:00Z date_updated: 2023-02-14T10:06:46Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.MFCS.2017.39 ec_funded: 1 file: - access_level: open_access checksum: c67f4866ddbfd555afef1f63ae9a8fc7 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:57Z date_updated: 2020-07-14T12:47:00Z file_id: '5248' file_name: IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf file_size: 610339 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 83' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '11' oa: 1 oa_version: Published Version project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Leibniz International Proceedings in Informatics publication_identifier: isbn: - 978-395977046-0 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7262' pubrep_id: '923' quality_controlled: '1' scopus_import: '1' status: public title: Faster algorithms for mean-payoff parity games 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2017' ... --- _id: '553' abstract: - lang: eng text: 'We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. ' alternative_title: - LIPIcs article_number: '55' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Kristofer full_name: Hansen, Kristofer last_name: Hansen - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 citation: ama: 'Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55' apa: 'Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.55' chicago: Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55. ieee: K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83. ista: 'Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.' mla: Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55. short: K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-25 location: Aalborg, Denmark name: 'MFCS: Mathematical Foundations of Computer Science (SG)' start_date: 2017-08-21 date_created: 2018-12-11T11:47:08Z date_published: 2017-11-01T00:00:00Z date_updated: 2021-01-12T08:02:35Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPIcs.MFCS.2017.55 file: - access_level: open_access checksum: 7101facb56ade363205c695d72dbd173 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:29Z date_updated: 2020-07-14T12:47:00Z file_id: '4753' file_name: IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf file_size: 549967 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 83' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1506.02434 month: '11' oa: 1 oa_version: Published Version publication: Leibniz International Proceedings in Informatics publication_identifier: isbn: - 978-395977046-0 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7261' pubrep_id: '922' quality_controlled: '1' scopus_import: 1 status: public title: Strategy complexity of concurrent safety games 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2017' ... --- _id: '560' abstract: - lang: eng text: In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions. article_number: '0104' author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: Arnulf full_name: Jentzen, Arnulf last_name: Jentzen - first_name: Diyora full_name: Salimova, Diyora last_name: Salimova citation: ama: 'Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104' apa: 'Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104' chicago: 'Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.' ieee: 'M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.' ista: 'Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.' mla: 'Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.' short: 'M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017).' date_created: 2018-12-11T11:47:11Z date_published: 2017-11-01T00:00:00Z date_updated: 2021-01-12T08:03:04Z day: '01' department: - _id: JaMa doi: 10.1098/rspa.2017.0104 ec_funded: 1 intvolume: ' 473' issue: '2207' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.03229 month: '11' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences' publication_identifier: issn: - '13645021' publication_status: published publisher: Royal Society of London publist_id: '7256' quality_controlled: '1' scopus_import: 1 status: public title: On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 473 year: '2017' ... --- _id: '567' abstract: - lang: eng text: "This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n" alternative_title: - Courant Lecture Notes article_processing_charge: No author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Horng full_name: Yau, Horng last_name: Yau citation: ama: Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28. American Mathematical Society; 2017. doi:10.1090/cln/028 apa: Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory (Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028 chicago: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. https://doi.org/10.1090/cln/028. ieee: L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory, vol. 28. American Mathematical Society, 2017. ista: Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p. mla: Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028. short: L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017. date_created: 2018-12-11T11:47:13Z date_published: 2017-01-01T00:00:00Z date_updated: 2022-05-24T06:57:28Z day: '01' department: - _id: LaEr doi: 10.1090/cln/028 ec_funded: 1 intvolume: ' 28' language: - iso: eng month: '01' oa_version: None page: '226' project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication_identifier: eisbn: - 978-1-4704-4194-4 isbn: - 9-781-4704-3648-3 publication_status: published publisher: American Mathematical Society publist_id: '7247' quality_controlled: '1' series_title: Courant Lecture Notes status: public title: A Dynamical Approach to Random Matrix Theory type: book user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2017' ... --- _id: '568' abstract: - lang: eng text: 'We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).' author: - first_name: Peter full_name: Franek, Peter id: 473294AE-F248-11E8-B48F-1D18A9856A87 last_name: Franek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál citation: ama: Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications. 2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16 apa: Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16 chicago: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16. ieee: P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017. ista: Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342. mla: Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16. short: P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342. date_created: 2018-12-11T11:47:14Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:03:12Z day: '01' department: - _id: UlWa - _id: HeEd doi: 10.4310/HHA.2017.v19.n2.a16 ec_funded: 1 intvolume: ' 19' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.04310 month: '01' oa: 1 oa_version: Submitted Version page: 313 - 342 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2590DB08-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '701309' name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020) publication: Homology, Homotopy and Applications publication_identifier: issn: - '15320073' publication_status: published publisher: International Press publist_id: '7246' quality_controlled: '1' scopus_import: 1 status: public title: Persistence of zero sets type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2017' ... --- _id: '570' abstract: - lang: eng text: 'Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. ' article_number: e28921 author: - first_name: Mato full_name: Lagator, Mato id: 345D25EC-F248-11E8-B48F-1D18A9856A87 last_name: Lagator - first_name: Srdjan full_name: Sarikas, Srdjan id: 35F0286E-F248-11E8-B48F-1D18A9856A87 last_name: Sarikas - first_name: Hande full_name: Acar, Hande id: 2DDF136A-F248-11E8-B48F-1D18A9856A87 last_name: Acar orcid: 0000-0003-1986-9753 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921 apa: Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921 chicago: Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921. ieee: M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921. mla: Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921. short: M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017). date_created: 2018-12-11T11:47:14Z date_published: 2017-11-13T00:00:00Z date_updated: 2021-01-12T08:03:15Z day: '13' ddc: - '576' department: - _id: CaGu - _id: JoBo - _id: NiBa doi: 10.7554/eLife.28921 ec_funded: 1 file: - access_level: open_access checksum: 273ab17f33305e4eaafd911ff88e7c5b content_type: application/pdf creator: system date_created: 2018-12-12T10:14:42Z date_updated: 2020-07-14T12:47:10Z file_id: '5096' file_name: IST-2017-918-v1+1_elife-28921-figures-v3.pdf file_size: 8453470 relation: main_file - access_level: open_access checksum: b433f90576c7be597cd43367946f8e7f content_type: application/pdf creator: system date_created: 2018-12-12T10:14:43Z date_updated: 2020-07-14T12:47:10Z file_id: '5097' file_name: IST-2017-918-v1+2_elife-28921-v3.pdf file_size: 1953221 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '7244' pubrep_id: '918' quality_controlled: '1' scopus_import: 1 status: public title: Regulatory network structure determines patterns of intermolecular epistasis 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: '2017' ... --- _id: '569' abstract: - lang: eng text: The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings. article_number: e30867 author: - first_name: Felix full_name: Spira, Felix last_name: Spira - first_name: Sara full_name: Cuylen Haering, Sara last_name: Cuylen Haering - first_name: Shalin full_name: Mehta, Shalin last_name: Mehta - first_name: Matthias full_name: Samwer, Matthias last_name: Samwer - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Amitabh full_name: Verma, Amitabh last_name: Verma - first_name: Rudolf full_name: Oldenbourg, Rudolf last_name: Oldenbourg - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Daniel full_name: Gerlich, Daniel last_name: Gerlich citation: ama: Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867 apa: Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.30867 chicago: Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.30867. ieee: F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867. mla: Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867. short: F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017). date_created: 2018-12-11T11:47:14Z date_published: 2017-11-06T00:00:00Z date_updated: 2023-02-23T12:30:29Z day: '06' ddc: - '570' department: - _id: MiSi doi: 10.7554/eLife.30867 file: - access_level: open_access checksum: ba09c1451153d39e4f4b7cee013e314c content_type: application/pdf creator: system date_created: 2018-12-12T10:10:40Z date_updated: 2020-07-14T12:47:10Z file_id: '4829' file_name: IST-2017-919-v1+1_elife-30867-figures-v1.pdf file_size: 9666973 relation: main_file - access_level: open_access checksum: 01eb51f1d6ad679947415a51c988e137 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:41Z date_updated: 2020-07-14T12:47:10Z file_id: '4830' file_name: IST-2017-919-v1+2_elife-30867-v1.pdf file_size: 5951246 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '7245' pubrep_id: '919' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments 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: '2017' ... --- _id: '571' abstract: - lang: eng text: Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface. author: - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Zerkah full_name: Ahmad, Zerkah last_name: Ahmad - first_name: Gerhild full_name: Rosenberger, Gerhild last_name: Rosenberger - first_name: Shuxia full_name: Fan, Shuxia last_name: Fan - first_name: Leo full_name: Nicolai, Leo last_name: Nicolai - first_name: Benjamin full_name: Busch, Benjamin last_name: Busch - first_name: Gökce full_name: Yavuz, Gökce last_name: Yavuz - first_name: Manja full_name: Luckner, Manja last_name: Luckner - first_name: Hellen full_name: Ishikawa Ankerhold, Hellen last_name: Ishikawa Ankerhold - first_name: Roman full_name: Hennel, Roman last_name: Hennel - first_name: Alexandre full_name: Benechet, Alexandre last_name: Benechet - first_name: Michael full_name: Lorenz, Michael last_name: Lorenz - first_name: Sue full_name: Chandraratne, Sue last_name: Chandraratne - first_name: Irene full_name: Schubert, Irene last_name: Schubert - first_name: Sebastian full_name: Helmer, Sebastian last_name: Helmer - first_name: Bianca full_name: Striednig, Bianca last_name: Striednig - first_name: Konstantin full_name: Stark, Konstantin last_name: Stark - first_name: Marek full_name: Janko, Marek last_name: Janko - first_name: Ralph full_name: Böttcher, Ralph last_name: Böttcher - first_name: Admar full_name: Verschoor, Admar last_name: Verschoor - first_name: Catherine full_name: Leon, Catherine last_name: Leon - first_name: Christian full_name: Gachet, Christian last_name: Gachet - first_name: Thomas full_name: Gudermann, Thomas last_name: Gudermann - first_name: Michael full_name: Mederos Y Schnitzler, Michael last_name: Mederos Y Schnitzler - first_name: Zachary full_name: Pincus, Zachary last_name: Pincus - first_name: Matteo full_name: Iannacone, Matteo last_name: Iannacone - first_name: Rainer full_name: Haas, Rainer last_name: Haas - first_name: Gerhard full_name: Wanner, Gerhard last_name: Wanner - first_name: Kirsten full_name: Lauber, Kirsten last_name: Lauber - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg citation: ama: Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 2017;171(6):1368-1382. doi:10.1016/j.cell.2017.11.001 apa: Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B., … Massberg, S. (2017). Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. Cell Press. https://doi.org/10.1016/j.cell.2017.11.001 chicago: Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.11.001. ieee: F. R. Gärtner et al., “Migrating platelets are mechano scavengers that collect and bundle bacteria,” Cell Press, vol. 171, no. 6. Cell Press, pp. 1368–1382, 2017. ista: Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 171(6), 1368–1382. mla: Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press, vol. 171, no. 6, Cell Press, 2017, pp. 1368–82, doi:10.1016/j.cell.2017.11.001. short: F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G. Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S. Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher, A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus, M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press 171 (2017) 1368–1382. date_created: 2018-12-11T11:47:15Z date_published: 2017-11-30T00:00:00Z date_updated: 2021-01-12T08:03:15Z day: '30' department: - _id: MiSi doi: 10.1016/j.cell.2017.11.001 ec_funded: 1 intvolume: ' 171' issue: '6' language: - iso: eng month: '11' oa_version: None page: 1368 - 1382 project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Cell Press publication_identifier: issn: - '00928674' publication_status: published publisher: Cell Press publist_id: '7243' quality_controlled: '1' scopus_import: 1 status: public title: Migrating platelets are mechano scavengers that collect and bundle bacteria type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 171 year: '2017' ... --- _id: '572' abstract: - lang: eng text: In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture. article_number: '2587' article_processing_charge: No author: - first_name: Damilola full_name: Olatunji, Damilola last_name: Olatunji - first_name: Danny full_name: Geelen, Danny last_name: Geelen - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 citation: ama: Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 2017;18(12). doi:10.3390/ijms18122587 apa: Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms18122587 chicago: Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587. ieee: D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” International Journal of Molecular Sciences, vol. 18, no. 12. MDPI, 2017. ista: Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587. mla: Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences, vol. 18, no. 12, 2587, MDPI, 2017, doi:10.3390/ijms18122587. short: D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017). date_created: 2018-12-11T11:47:15Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:03:16Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.3390/ijms18122587 file: - access_level: open_access checksum: 82d51f11e493f7eec02976d9a9a9805e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:55Z date_updated: 2020-07-14T12:47:10Z file_id: '4718' file_name: IST-2017-917-v1+1_ijms-18-02587.pdf file_size: 920962 relation: main_file file_date_updated: 2020-07-14T12:47:10Z has_accepted_license: '1' intvolume: ' 18' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: International Journal of Molecular Sciences publication_status: published publisher: MDPI publist_id: '7242' pubrep_id: '917' quality_controlled: '1' scopus_import: '1' status: public title: Control of endogenous auxin levels in plant root development 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2017' ... --- _id: '5803' abstract: - lang: eng text: Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept. alternative_title: - LNCS article_processing_charge: No author: - first_name: Ranita full_name: Biswas, Ranita id: 3C2B033E-F248-11E8-B48F-1D18A9856A87 last_name: Biswas orcid: 0000-0002-5372-7890 - first_name: Partha full_name: Bhowmick, Partha last_name: Bhowmick citation: ama: 'Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial Image Analysis. Vol 10256. Cham: Springer Nature; 2017:93-104. doi:10.1007/978-3-319-59108-7_8' apa: 'Biswas, R., & Bhowmick, P. (2017). Construction of persistent Voronoi diagram on 3D digital plane. In Combinatorial image analysis (Vol. 10256, pp. 93–104). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-59108-7_8' chicago: 'Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” In Combinatorial Image Analysis, 10256:93–104. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59108-7_8.' ieee: 'R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on 3D digital plane,” in Combinatorial image analysis, vol. 10256, Cham: Springer Nature, 2017, pp. 93–104.' ista: 'Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.' mla: Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” Combinatorial Image Analysis, vol. 10256, Springer Nature, 2017, pp. 93–104, doi:10.1007/978-3-319-59108-7_8. short: R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104. conference: end_date: 2017-06-21 location: Plovdiv, Bulgaria name: 'IWCIA: International Workshop on Combinatorial Image Analysis' start_date: 2017-06-19 date_created: 2019-01-08T20:42:56Z date_published: 2017-05-17T00:00:00Z date_updated: 2022-01-28T07:48:24Z day: '17' department: - _id: HeEd doi: 10.1007/978-3-319-59108-7_8 extern: '1' intvolume: ' 10256' language: - iso: eng month: '05' oa_version: None page: 93-104 place: Cham publication: Combinatorial image analysis publication_identifier: isbn: - 978-3-319-59107-0 - 978-3-319-59108-7 issn: - 0302-9743 - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Construction of persistent Voronoi diagram on 3D digital plane type: book_chapter user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 10256 year: '2017' ... --- _id: '313' abstract: - lang: eng text: 'Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron.' alternative_title: - 'Journal of Physics: Conference Series' article_number: '012004' author: - first_name: Nicolas full_name: Camus, Nicolas last_name: Camus - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Lutz full_name: Fechner, Lutz last_name: Fechner - first_name: Michael full_name: Klaiber, Michael last_name: Klaiber - first_name: Martin full_name: Laux, Martin last_name: Laux - first_name: Yonghao full_name: Mi, Yonghao last_name: Mi - first_name: Karen full_name: Hatsagortsyan, Karen last_name: Hatsagortsyan - first_name: Thomas full_name: Pfeifer, Thomas last_name: Pfeifer - first_name: Cristoph full_name: Keitel, Cristoph last_name: Keitel - first_name: Robert full_name: Moshammer, Robert last_name: Moshammer citation: ama: 'Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:10.1088/1742-6596/999/1/012004' apa: 'Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. https://doi.org/10.1088/1742-6596/999/1/012004' chicago: Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. https://doi.org/10.1088/1742-6596/999/1/012004. ieee: N. Camus et al., “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1. ista: 'Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.' mla: Camus, Nicolas, et al. Experimental Evidence for Wigner’s Tunneling Time. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:10.1088/1742-6596/999/1/012004. short: N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017. conference: end_date: 2017-08-21 location: Kazan, Russian Federation name: Annual International Laser Physics Workshop LPHYS start_date: 2017-08-17 date_created: 2018-12-11T11:45:46Z date_published: 2017-07-14T00:00:00Z date_updated: 2023-02-23T12:36:07Z day: '14' ddc: - '530' department: - _id: MiLe doi: 10.1088/1742-6596/999/1/012004 external_id: arxiv: - '1611.03701' file: - access_level: open_access checksum: 6e70b525a84f6d5fb175c48e9f5cb59a content_type: application/pdf creator: dernst date_created: 2019-01-22T08:34:10Z date_updated: 2020-07-14T12:46:00Z file_id: '5871' file_name: 2017_Physics_Camus.pdf file_size: 949321 relation: main_file file_date_updated: 2020-07-14T12:46:00Z has_accepted_license: '1' intvolume: ' 999' issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication_identifier: issn: - '17426588' publication_status: published publisher: American Physical Society publist_id: '7552' quality_controlled: '1' related_material: record: - id: '6013' relation: later_version status: public scopus_import: 1 status: public title: Experimental evidence for Wigner's tunneling time 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 999 year: '2017' ... --- _id: '6013' abstract: - lang: eng text: The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.” article_number: '023201' author: - first_name: Nicolas full_name: Camus, Nicolas last_name: Camus - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Lutz full_name: Fechner, Lutz last_name: Fechner - first_name: Michael full_name: Klaiber, Michael last_name: Klaiber - first_name: Martin full_name: Laux, Martin last_name: Laux - first_name: Yonghao full_name: Mi, Yonghao last_name: Mi - first_name: Karen Z. full_name: Hatsagortsyan, Karen Z. last_name: Hatsagortsyan - first_name: Thomas full_name: Pfeifer, Thomas last_name: Pfeifer - first_name: Christoph H. full_name: Keitel, Christoph H. last_name: Keitel - first_name: Robert full_name: Moshammer, Robert last_name: Moshammer citation: ama: Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for quantum tunneling time. Physical Review Letters. 2017;119(2). doi:10.1103/PhysRevLett.119.023201 apa: Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for quantum tunneling time. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.023201 chicago: Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Z. Hatsagortsyan, Thomas Pfeifer, Christoph H. Keitel, and Robert Moshammer. “Experimental Evidence for Quantum Tunneling Time.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.023201. ieee: N. Camus et al., “Experimental evidence for quantum tunneling time,” Physical Review Letters, vol. 119, no. 2. American Physical Society, 2017. ista: Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan KZ, Pfeifer T, Keitel CH, Moshammer R. 2017. Experimental evidence for quantum tunneling time. Physical Review Letters. 119(2), 023201. mla: Camus, Nicolas, et al. “Experimental Evidence for Quantum Tunneling Time.” Physical Review Letters, vol. 119, no. 2, 023201, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.023201. short: N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K.Z. Hatsagortsyan, T. Pfeifer, C.H. Keitel, R. Moshammer, Physical Review Letters 119 (2017). date_created: 2019-02-14T15:24:13Z date_published: 2017-07-14T00:00:00Z date_updated: 2023-02-23T11:13:36Z day: '14' department: - _id: MiLe doi: 10.1103/PhysRevLett.119.023201 external_id: arxiv: - '1611.03701' intvolume: ' 119' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1611.03701 month: '07' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '313' relation: earlier_version status: public scopus_import: 1 status: public title: Experimental evidence for quantum tunneling time type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 119 year: '2017' ... --- _id: '605' abstract: - lang: eng text: 'Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes.' alternative_title: - LNCS author: - first_name: Joshua full_name: Brody, Joshua last_name: Brody - first_name: Stefan full_name: Dziembowski, Stefan last_name: Dziembowski - first_name: Sebastian full_name: Faust, Sebastian last_name: Faust - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Brody J, Dziembowski S, Faust S, Pietrzak KZ. Position based cryptography and multiparty communication complexity. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:56-81. doi:10.1007/978-3-319-70500-2_3' apa: 'Brody, J., Dziembowski, S., Faust, S., & Pietrzak, K. Z. (2017). Position based cryptography and multiparty communication complexity. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677, pp. 56–81). Presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_3' chicago: Brody, Joshua, Stefan Dziembowski, Sebastian Faust, and Krzysztof Z Pietrzak. “Position Based Cryptography and Multiparty Communication Complexity.” edited by Yael Kalai and Leonid Reyzin, 10677:56–81. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_3. ieee: 'J. Brody, S. Dziembowski, S. Faust, and K. Z. Pietrzak, “Position based cryptography and multiparty communication complexity,” presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States, 2017, vol. 10677, pp. 56–81.' ista: 'Brody J, Dziembowski S, Faust S, Pietrzak KZ. 2017. Position based cryptography and multiparty communication complexity. TCC: Theory of Cryptography Conference, LNCS, vol. 10677, 56–81.' mla: Brody, Joshua, et al. Position Based Cryptography and Multiparty Communication Complexity. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 56–81, doi:10.1007/978-3-319-70500-2_3. short: J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 56–81. conference: end_date: 2017-11-15 location: Baltimore, MD, United States name: 'TCC: Theory of Cryptography Conference' start_date: 2017-11-12 date_created: 2018-12-11T11:47:27Z date_published: 2017-11-05T00:00:00Z date_updated: 2021-01-12T08:05:53Z day: '05' department: - _id: KrPi doi: 10.1007/978-3-319-70500-2_3 ec_funded: 1 editor: - first_name: Yael full_name: Kalai, Yael last_name: Kalai - first_name: Leonid full_name: Reyzin, Leonid last_name: Reyzin intvolume: ' 10677' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/536 month: '11' oa: 1 oa_version: Submitted Version page: 56 - 81 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331970499-9 publication_status: published publisher: Springer publist_id: '7200' quality_controlled: '1' scopus_import: 1 status: public title: Position based cryptography and multiparty communication complexity type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10677 year: '2017' ... --- _id: '604' abstract: - lang: eng text: In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies. alternative_title: - Theoretical and Computational Chemistry Series author: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Richard full_name: Schmidt, Richard last_name: Schmidt citation: ama: 'Lemeshko M, Schmidt R. Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Dulieu O, Osterwalder A, eds. Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Vol 11. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry; 2017:444-495. doi:10.1039/9781782626800-00444' apa: 'Lemeshko, M., & Schmidt, R. (2017). Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In O. Dulieu & A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero (Vol. 11, pp. 444–495). The Royal Society of Chemistry. https://doi.org/10.1039/9781782626800-00444' chicago: 'Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” In Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , edited by Oliver Dulieu and Andreas Osterwalder, 11:444–95. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781782626800-00444.' ieee: 'M. Lemeshko and R. Schmidt, “Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets,” in Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , vol. 11, O. Dulieu and A. Osterwalder, Eds. The Royal Society of Chemistry, 2017, pp. 444–495.' ista: 'Lemeshko M, Schmidt R. 2017.Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Theoretical and Computational Chemistry Series, vol. 11, 444–495.' mla: 'Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , edited by Oliver Dulieu and Andreas Osterwalder, vol. 11, The Royal Society of Chemistry, 2017, pp. 444–95, doi:10.1039/9781782626800-00444.' short: 'M. Lemeshko, R. Schmidt, in:, O. Dulieu, A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , The Royal Society of Chemistry, 2017, pp. 444–495.' date_created: 2018-12-11T11:47:27Z date_published: 2017-12-14T00:00:00Z date_updated: 2021-01-12T08:05:50Z day: '14' department: - _id: MiLe doi: 10.1039/9781782626800-00444 editor: - first_name: Oliver full_name: Dulieu, Oliver last_name: Dulieu - first_name: Andreas full_name: Osterwalder, Andreas last_name: Osterwalder intvolume: ' 11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.06753 month: '12' oa: 1 oa_version: Submitted Version page: 444 - 495 publication: 'Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ' publication_identifier: issn: - '20413181' publication_status: published publisher: The Royal Society of Chemistry publist_id: '7201' quality_controlled: '1' scopus_import: 1 series_title: Theoretical and Computational Chemistry Series status: public title: 'Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets' type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2017' ... --- _id: '609' abstract: - lang: eng text: Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover. alternative_title: - LNCS author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Björn full_name: Tackmann, Björn last_name: Tackmann citation: ama: 'Alwen JF, Tackmann B. Moderately hard functions: Definition, instantiations, and applications. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:493-526. doi:10.1007/978-3-319-70500-2_17' apa: 'Alwen, J. F., & Tackmann, B. (2017). Moderately hard functions: Definition, instantiations, and applications. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677, pp. 493–526). Presented at the TCC: Theory of Cryptography, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_17' chicago: 'Alwen, Joel F, and Björn Tackmann. “Moderately Hard Functions: Definition, Instantiations, and Applications.” edited by Yael Kalai and Leonid Reyzin, 10677:493–526. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_17.' ieee: 'J. F. Alwen and B. Tackmann, “Moderately hard functions: Definition, instantiations, and applications,” presented at the TCC: Theory of Cryptography, Baltimore, MD, United States, 2017, vol. 10677, pp. 493–526.' ista: 'Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations, and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 493–526.' mla: 'Alwen, Joel F., and Björn Tackmann. Moderately Hard Functions: Definition, Instantiations, and Applications. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 493–526, doi:10.1007/978-3-319-70500-2_17.' short: J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 493–526. conference: end_date: 2017-11-15 location: Baltimore, MD, United States name: 'TCC: Theory of Cryptography' start_date: 2017-11-12 date_created: 2018-12-11T11:47:28Z date_published: 2017-11-05T00:00:00Z date_updated: 2021-01-12T08:06:04Z day: '05' department: - _id: KrPi doi: 10.1007/978-3-319-70500-2_17 editor: - first_name: Yael full_name: Kalai, Yael last_name: Kalai - first_name: Leonid full_name: Reyzin, Leonid last_name: Reyzin intvolume: ' 10677' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/945 month: '11' oa: 1 oa_version: Submitted Version page: 493 - 526 publication_identifier: isbn: - 978-331970499-9 publication_status: published publisher: Springer publist_id: '7196' quality_controlled: '1' scopus_import: 1 status: public title: 'Moderately hard functions: Definition, instantiations, and applications' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10677 year: '2017' ... --- _id: '610' abstract: - lang: eng text: 'The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.' acknowledgement: The work by Z. P. was partially supported by the Israel Science Foundation grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria, supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58). author: - first_name: Xavier full_name: Goaoc, Xavier last_name: Goaoc - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: Pavel full_name: Paták, Pavel last_name: Paták - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 2017;222(2):841-866. doi:10.1007/s11856-017-1607-7' apa: 'Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-017-1607-7' chicago: 'Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics. Springer, 2017. https://doi.org/10.1007/s11856-017-1607-7.' ieee: 'X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result,” Israel Journal of Mathematics, vol. 222, no. 2. Springer, pp. 841–866, 2017.' ista: 'Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 222(2), 841–866.' mla: 'Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics, vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:10.1007/s11856-017-1607-7.' short: X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866. date_created: 2018-12-11T11:47:29Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-02-23T10:02:13Z day: '01' department: - _id: UlWa doi: 10.1007/s11856-017-1607-7 ec_funded: 1 intvolume: ' 222' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.09063 month: '10' oa: 1 oa_version: Preprint page: 841 - 866 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Israel Journal of Mathematics publication_status: published publisher: Springer publist_id: '7194' quality_controlled: '1' related_material: record: - id: '1511' relation: earlier_version status: public scopus_import: 1 status: public title: 'On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 222 year: '2017' ... --- _id: '611' abstract: - lang: eng text: Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity. author: - first_name: Desmond full_name: Bradley, Desmond last_name: Bradley - first_name: Ping full_name: Xu, Ping last_name: Xu - first_name: Irina full_name: Mohorianu, Irina last_name: Mohorianu - first_name: Annabel full_name: Whibley, Annabel last_name: Whibley - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Hugo full_name: Tavares, Hugo last_name: Tavares - first_name: Matthew full_name: Couchman, Matthew last_name: Couchman - first_name: Lucy full_name: Copsey, Lucy last_name: Copsey - first_name: Rosemary full_name: Carpenter, Rosemary last_name: Carpenter - first_name: Miaomiao full_name: Li, Miaomiao last_name: Li - first_name: Qun full_name: Li, Qun last_name: Li - first_name: Yongbiao full_name: Xue, Yongbiao last_name: Xue - first_name: Tamas full_name: Dalmay, Tamas last_name: Dalmay - first_name: Enrico full_name: Coen, Enrico last_name: Coen citation: ama: Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 2017;358(6365):925-928. doi:10.1126/science.aao3526 apa: Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao3526 chicago: Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aao3526. ieee: D. Bradley et al., “Evolution of flower color pattern through selection on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017. ista: Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928. mla: Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:10.1126/science.aao3526. short: D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928. date_created: 2018-12-11T11:47:29Z date_published: 2017-11-17T00:00:00Z date_updated: 2021-01-12T08:06:10Z day: '17' department: - _id: NiBa doi: 10.1126/science.aao3526 intvolume: ' 358' issue: '6365' language: - iso: eng month: '11' oa_version: None page: 925 - 928 publication: Science publication_identifier: issn: - '00368075' publication_status: published publisher: American Association for the Advancement of Science publist_id: '7193' quality_controlled: '1' scopus_import: 1 status: public title: Evolution of flower color pattern through selection on regulatory small RNAs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 358 year: '2017' ... --- _id: '613' abstract: - lang: eng text: 'Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.' acknowledgement: We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG). article_number: '1535' article_processing_charge: Yes (in subscription journal) author: - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1 apa: Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., & Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01683-1 chicago: Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01683-1. ieee: R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535. mla: Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1. short: R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017). date_created: 2018-12-11T11:47:30Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:06:15Z day: '01' ddc: - '576' - '579' department: - _id: CaGu - _id: GaTk doi: 10.1038/s41467-017-01683-1 ec_funded: 1 file: - access_level: open_access checksum: 44bb5d0229926c23a9955d9fe0f9723f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:05Z date_updated: 2020-07-14T12:47:20Z file_id: '5190' file_name: IST-2017-911-v1+1_s41467-017-01683-1.pdf file_size: 1951699 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7191' pubrep_id: '911' quality_controlled: '1' scopus_import: 1 status: public title: Shaping bacterial population behavior through computer interfaced control of individual cells 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '615' abstract: - lang: eng text: We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law. author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Erdös L, Schnelli K. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2017;53(4):1606-1656. doi:10.1214/16-AIHP765 apa: Erdös, L., & Schnelli, K. (2017). Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AIHP765 chicago: Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AIHP765. ieee: L. Erdös and K. Schnelli, “Universality for random matrix flows with time dependent density,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656, 2017. ista: Erdös L, Schnelli K. 2017. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 53(4), 1606–1656. mla: Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4, Institute of Mathematical Statistics, 2017, pp. 1606–56, doi:10.1214/16-AIHP765. short: L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability and Statistics 53 (2017) 1606–1656. date_created: 2018-12-11T11:47:30Z date_published: 2017-11-01T00:00:00Z date_updated: 2021-01-12T08:06:22Z day: '01' department: - _id: LaEr doi: 10.1214/16-AIHP765 ec_funded: 1 intvolume: ' 53' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.00650 month: '11' oa: 1 oa_version: Submitted Version page: 1606 - 1656 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Annales de l'institut Henri Poincare (B) Probability and Statistics publication_identifier: issn: - '02460203' publication_status: published publisher: Institute of Mathematical Statistics publist_id: '7189' quality_controlled: '1' scopus_import: 1 status: public title: Universality for random matrix flows with time dependent density type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2017' ... --- _id: '623' abstract: - lang: eng text: Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology. alternative_title: - ADVSANAT author: - first_name: Elisa full_name: Hill Yardin, Elisa last_name: Hill Yardin - first_name: Sonja full_name: Mckeown, Sonja last_name: Mckeown - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Andreas full_name: Grabrucker, Andreas last_name: Grabrucker citation: ama: 'Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. Extracerebral dysfunction in animal models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. Translational Anatomy and Cell Biology of Autism Spectrum Disorder. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:159-187. doi:10.1007/978-3-319-52498-6_9' apa: Hill Yardin, E., Mckeown, S., Novarino, G., & Grabrucker, A. (2017). Extracerebral dysfunction in animal models of autism spectrum disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 159–187). Springer. https://doi.org/10.1007/978-3-319-52498-6_9 chicago: Hill Yardin, Elisa, Sonja Mckeown, Gaia Novarino, and Andreas Grabrucker. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” In Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, 224:159–87. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_9. ieee: E. Hill Yardin, S. Mckeown, G. Novarino, and A. Grabrucker, “Extracerebral dysfunction in animal models of autism spectrum disorder,” in Translational Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 159–187. ista: 'Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. 2017.Extracerebral dysfunction in animal models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 159–187.' mla: Hill Yardin, Elisa, et al. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 159–87, doi:10.1007/978-3-319-52498-6_9. short: E. Hill Yardin, S. Mckeown, G. Novarino, A. Grabrucker, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 159–187. date_created: 2018-12-11T11:47:33Z date_published: 2017-05-28T00:00:00Z date_updated: 2021-01-12T08:06:46Z day: '28' department: - _id: GaNo doi: 10.1007/978-3-319-52498-6_9 editor: - first_name: Michael full_name: Schmeisser, Michael last_name: Schmeisser - first_name: Tobias full_name: Boekers, Tobias last_name: Boekers intvolume: ' 224' language: - iso: eng month: '05' oa_version: None page: 159 - 187 publication: Translational Anatomy and Cell Biology of Autism Spectrum Disorder publication_identifier: isbn: - 978-3-319-52496-2 issn: - '03015556' publication_status: published publisher: Springer publist_id: '7177' quality_controlled: '1' scopus_import: 1 series_title: Advances in Anatomy Embryology and Cell Biology status: public title: Extracerebral dysfunction in animal models of autism spectrum disorder type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 224 year: '2017' ... --- _id: '626' abstract: - lang: eng text: 'Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.' author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - first_name: Amandine full_name: Véber, Amandine last_name: Véber citation: ama: 'Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001' apa: 'Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001' chicago: 'Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology. Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.' ieee: 'N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” Theoretical Population Biology, vol. 118. Academic Press, pp. 50–73, 2017.' ista: 'Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.' mla: 'Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology, vol. 118, Academic Press, 2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.' short: N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73. date_created: 2018-12-11T11:47:34Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:06:50Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1016/j.tpb.2017.06.001 ec_funded: 1 file: - access_level: open_access checksum: 7dd02bfcfe8f244f4a6c19091aedf2c8 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:45Z date_updated: 2020-07-14T12:47:25Z file_id: '4964' file_name: IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf file_size: 1133924 relation: main_file file_date_updated: 2020-07-14T12:47:25Z has_accepted_license: '1' intvolume: ' 118' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 50 - 73 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_identifier: issn: - '00405809' publication_status: published publisher: Academic Press publist_id: '7169' pubrep_id: '908' quality_controlled: '1' scopus_import: 1 status: public title: 'The infinitesimal model: Definition derivation and implications' 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: 118 year: '2017' ... --- _id: '625' abstract: - lang: eng text: In the analysis of reactive systems a quantitative objective assigns a real value to every trace of the system. The value decision problem for a quantitative objective requires a trace whose value is at least a given threshold, and the exact value decision problem requires a trace whose value is exactly the threshold. We compare the computational complexity of the value and exact value decision problems for classical quantitative objectives, such as sum, discounted sum, energy, and mean-payoff for two standard models of reactive systems, namely, graphs and graph games. acknowledgement: 'This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 and S11407-N23 (RiSE/SHiNE), and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Doyen L, Henzinger TA. The cost of exactness in quantitative reachability. In: Aceto L, Bacci G, Ingólfsdóttir A, Legay A, Mardare R, eds. Models, Algorithms, Logics and Tools. Vol 10460. Theoretical Computer Science and General Issues. Springer; 2017:367-381. doi:10.1007/978-3-319-63121-9_18' apa: Chatterjee, K., Doyen, L., & Henzinger, T. A. (2017). The cost of exactness in quantitative reachability. In L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, & R. Mardare (Eds.), Models, Algorithms, Logics and Tools (Vol. 10460, pp. 367–381). Springer. https://doi.org/10.1007/978-3-319-63121-9_18 chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “The Cost of Exactness in Quantitative Reachability.” In Models, Algorithms, Logics and Tools, edited by Luca Aceto, Giorgio Bacci, Anna Ingólfsdóttir, Axel Legay, and Radu Mardare, 10460:367–81. Theoretical Computer Science and General Issues. Springer, 2017. https://doi.org/10.1007/978-3-319-63121-9_18. ieee: K. Chatterjee, L. Doyen, and T. A. Henzinger, “The cost of exactness in quantitative reachability,” in Models, Algorithms, Logics and Tools, vol. 10460, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, and R. Mardare, Eds. Springer, 2017, pp. 367–381. ista: 'Chatterjee K, Doyen L, Henzinger TA. 2017.The cost of exactness in quantitative reachability. In: Models, Algorithms, Logics and Tools. LNCS, vol. 10460, 367–381.' mla: Chatterjee, Krishnendu, et al. “The Cost of Exactness in Quantitative Reachability.” Models, Algorithms, Logics and Tools, edited by Luca Aceto et al., vol. 10460, Springer, 2017, pp. 367–81, doi:10.1007/978-3-319-63121-9_18. short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, R. Mardare (Eds.), Models, Algorithms, Logics and Tools, Springer, 2017, pp. 367–381. date_created: 2018-12-11T11:47:34Z date_published: 2017-07-25T00:00:00Z date_updated: 2022-05-23T08:54:02Z day: '25' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-63121-9_18 ec_funded: 1 editor: - first_name: Luca full_name: Aceto, Luca last_name: Aceto - first_name: Giorgio full_name: Bacci, Giorgio last_name: Bacci - first_name: Anna full_name: Ingólfsdóttir, Anna last_name: Ingólfsdóttir - first_name: Axel full_name: Legay, Axel last_name: Legay - first_name: Radu full_name: Mardare, Radu last_name: Mardare file: - access_level: open_access checksum: b2402766ec02c79801aac634bd8f9f6c content_type: application/pdf creator: dernst date_created: 2019-11-19T08:06:50Z date_updated: 2020-07-14T12:47:25Z file_id: '7048' file_name: 2017_ModelsAlgorithms_Chatterjee.pdf file_size: 192826 relation: main_file file_date_updated: 2020-07-14T12:47:25Z has_accepted_license: '1' intvolume: ' 10460' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 367 - 381 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: Models, Algorithms, Logics and Tools publication_identifier: isbn: - 978-3-319-63120-2 issn: - 0302-9743 publication_status: published publisher: Springer publist_id: '7170' quality_controlled: '1' scopus_import: '1' series_title: Theoretical Computer Science and General Issues status: public title: The cost of exactness in quantitative reachability type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10460 year: '2017' ... --- _id: '624' abstract: - lang: eng text: Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein. acknowledgement: 'Austrian Science Fund (FWF): M1697, P22249; Swiss National Science Foundation (SNF): 145706; European Commission;FWF Special Research Program: RNA-REG F43' article_number: '3830' author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Zrinka full_name: Didara, Zrinka last_name: Didara - first_name: Isabella full_name: Moll, Isabella last_name: Moll citation: ama: Nikolic N, Didara Z, Moll I. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017;2017(9). doi:10.7717/peerj.3830 apa: Nikolic, N., Didara, Z., & Moll, I. (2017). MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. PeerJ. https://doi.org/10.7717/peerj.3830 chicago: Nikolic, Nela, Zrinka Didara, and Isabella Moll. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ. PeerJ, 2017. https://doi.org/10.7717/peerj.3830. ieee: N. Nikolic, Z. Didara, and I. Moll, “MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations,” PeerJ, vol. 2017, no. 9. PeerJ, 2017. ista: Nikolic N, Didara Z, Moll I. 2017. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017(9), 3830. mla: Nikolic, Nela, et al. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ, vol. 2017, no. 9, 3830, PeerJ, 2017, doi:10.7717/peerj.3830. short: N. Nikolic, Z. Didara, I. Moll, PeerJ 2017 (2017). date_created: 2018-12-11T11:47:33Z date_published: 2017-09-21T00:00:00Z date_updated: 2021-01-12T08:06:48Z day: '21' ddc: - '579' department: - _id: CaGu doi: 10.7717/peerj.3830 file: - access_level: open_access checksum: 3d79ae6b6eabc90b0eaaed82ff3493b0 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:51Z date_updated: 2020-07-14T12:47:24Z file_id: '4908' file_name: IST-2017-909-v1+1_peerj-3830.pdf file_size: 682064 relation: main_file file_date_updated: 2020-07-14T12:47:24Z has_accepted_license: '1' intvolume: ' 2017' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: PeerJ publication_identifier: issn: - '21678359' publication_status: published publisher: PeerJ publist_id: '7172' pubrep_id: '909' quality_controlled: '1' scopus_import: 1 status: public title: MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations 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: 2017 year: '2017' ... --- _id: '628' abstract: - lang: eng text: We consider the problem of developing automated techniques for solving recurrence relations to aid the expected-runtime analysis of programs. The motivation is that several classical textbook algorithms have quite efficient expected-runtime complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., Quick-Sort), or completely ineffective (e.g., Coupon-Collector). Since the main focus of expected-runtime analysis is to obtain efficient bounds, we consider bounds that are either logarithmic, linear or almost-linear (O(log n), O(n), O(n · log n), respectively, where n represents the input size). Our main contribution is an efficient (simple linear-time algorithm) sound approach for deriving such expected-runtime bounds for the analysis of recurrence relations induced by randomized algorithms. The experimental results show that our approach can efficiently derive asymptotically optimal expected-runtime bounds for recurrences of classical randomized algorithms, including Randomized-Search, Quick-Sort, Quick-Select, Coupon-Collector, where the worst-case bounds are either inefficient (such as linear as compared to logarithmic expected-runtime complexity, or quadratic as compared to linear or almost-linear expected-runtime complexity), or ineffective. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei last_name: Fu - first_name: Aniket full_name: Murhekar, Aniket last_name: Murhekar citation: ama: 'Chatterjee K, Fu H, Murhekar A. Automated recurrence analysis for almost linear expected runtime bounds. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:118-139. doi:10.1007/978-3-319-63387-9_6' apa: 'Chatterjee, K., Fu, H., & Murhekar, A. (2017). Automated recurrence analysis for almost linear expected runtime bounds. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 118–139). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_6' chicago: Chatterjee, Krishnendu, Hongfei Fu, and Aniket Murhekar. “Automated Recurrence Analysis for Almost Linear Expected Runtime Bounds.” edited by Rupak Majumdar and Viktor Kunčak, 10426:118–39. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_6. ieee: 'K. Chatterjee, H. Fu, and A. Murhekar, “Automated recurrence analysis for almost linear expected runtime bounds,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 118–139.' ista: 'Chatterjee K, Fu H, Murhekar A. 2017. Automated recurrence analysis for almost linear expected runtime bounds. CAV: Computer Aided Verification, LNCS, vol. 10426, 118–139.' mla: Chatterjee, Krishnendu, et al. Automated Recurrence Analysis for Almost Linear Expected Runtime Bounds. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 118–39, doi:10.1007/978-3-319-63387-9_6. short: K. Chatterjee, H. Fu, A. Murhekar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 118–139. conference: end_date: 2017-07-28 location: Heidelberg, Germany name: 'CAV: Computer Aided Verification' start_date: 2017-07-24 date_created: 2018-12-11T11:47:35Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:06:55Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-319-63387-9_6 ec_funded: 1 editor: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Viktor full_name: Kunčak, Viktor last_name: Kunčak intvolume: ' 10426' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.00314 month: '01' oa: 1 oa_version: Submitted Version page: 118 - 139 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_identifier: isbn: - 978-331963386-2 publication_status: published publisher: Springer publist_id: '7166' quality_controlled: '1' scopus_import: 1 status: public title: Automated recurrence analysis for almost linear expected runtime bounds type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10426 year: '2017' ... --- _id: '629' abstract: - lang: eng text: Even simple cells like bacteria have precisely regulated cellular anatomies, which allow them to grow, divide and to respond to internal or external cues with high fidelity. How spatial and temporal intracellular organization in prokaryotic cells is achieved and maintained on the basis of locally interacting proteins still remains largely a mystery. Bulk biochemical assays with purified components and in vivo experiments help us to approach key cellular processes from two opposite ends, in terms of minimal and maximal complexity. However, to understand how cellular phenomena emerge, that are more than the sum of their parts, we have to assemble cellular subsystems step by step from the bottom up. Here, we review recent in vitro reconstitution experiments with proteins of the bacterial cell division machinery and illustrate how they help to shed light on fundamental cellular mechanisms that constitute spatiotemporal order and regulate cell division. author: - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Katja full_name: Zieske, Katja last_name: Zieske - first_name: Petra full_name: Schwille, Petra last_name: Schwille citation: ama: 'Loose M, Zieske K, Schwille P. Reconstitution of protein dynamics involved in bacterial cell division. In: Prokaryotic Cytoskeletons. Vol 84. Sub-Cellular Biochemistry. Springer; 2017:419-444. doi:10.1007/978-3-319-53047-5_15' apa: Loose, M., Zieske, K., & Schwille, P. (2017). Reconstitution of protein dynamics involved in bacterial cell division. In Prokaryotic Cytoskeletons (Vol. 84, pp. 419–444). Springer. https://doi.org/10.1007/978-3-319-53047-5_15 chicago: Loose, Martin, Katja Zieske, and Petra Schwille. “Reconstitution of Protein Dynamics Involved in Bacterial Cell Division.” In Prokaryotic Cytoskeletons, 84:419–44. Sub-Cellular Biochemistry. Springer, 2017. https://doi.org/10.1007/978-3-319-53047-5_15. ieee: M. Loose, K. Zieske, and P. Schwille, “Reconstitution of protein dynamics involved in bacterial cell division,” in Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp. 419–444. ista: 'Loose M, Zieske K, Schwille P. 2017.Reconstitution of protein dynamics involved in bacterial cell division. In: Prokaryotic Cytoskeletons. vol. 84, 419–444.' mla: Loose, Martin, et al. “Reconstitution of Protein Dynamics Involved in Bacterial Cell Division.” Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp. 419–44, doi:10.1007/978-3-319-53047-5_15. short: M. Loose, K. Zieske, P. Schwille, in:, Prokaryotic Cytoskeletons, Springer, 2017, pp. 419–444. date_created: 2018-12-11T11:47:35Z date_published: 2017-05-13T00:00:00Z date_updated: 2021-01-12T08:06:57Z day: '13' department: - _id: MaLo doi: 10.1007/978-3-319-53047-5_15 external_id: pmid: - '28500535' intvolume: ' 84' language: - iso: eng month: '05' oa_version: None page: 419 - 444 pmid: 1 publication: Prokaryotic Cytoskeletons publication_identifier: eisbn: - 978-3-319-53047-5 publication_status: published publisher: Springer publist_id: '7165' quality_controlled: '1' scopus_import: 1 series_title: Sub-Cellular Biochemistry status: public title: Reconstitution of protein dynamics involved in bacterial cell division type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 84 year: '2017' ... --- _id: '630' abstract: - lang: eng text: 'Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years.' alternative_title: - Studies in Health Technology and Informatics author: - first_name: Stefan full_name: Sauermann, Stefan last_name: Sauermann - first_name: Veronika full_name: David, Veronika last_name: David - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Reinhard full_name: Egelkraut, Reinhard last_name: Egelkraut - first_name: Matthias full_name: Frohner, Matthias last_name: Frohner - first_name: Birgit full_name: Pohn, Birgit last_name: Pohn - first_name: Philipp full_name: Urbauer, Philipp last_name: Urbauer - first_name: Alexander full_name: Mense, Alexander last_name: Mense citation: ama: 'Sauermann S, David V, Schlögl A, et al. Biosignals standards and FHIR: The way to go. In: Vol 236. IOS Press; 2017:356-362. doi:10.3233/978-1-61499-759-7-356' apa: 'Sauermann, S., David, V., Schlögl, A., Egelkraut, R., Frohner, M., Pohn, B., … Mense, A. (2017). Biosignals standards and FHIR: The way to go (Vol. 236, pp. 356–362). Presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria: IOS Press. https://doi.org/10.3233/978-1-61499-759-7-356' chicago: 'Sauermann, Stefan, Veronika David, Alois Schlögl, Reinhard Egelkraut, Matthias Frohner, Birgit Pohn, Philipp Urbauer, and Alexander Mense. “Biosignals Standards and FHIR: The Way to Go,” 236:356–62. IOS Press, 2017. https://doi.org/10.3233/978-1-61499-759-7-356.' ieee: 'S. Sauermann et al., “Biosignals standards and FHIR: The way to go,” presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria, 2017, vol. 236, pp. 356–362.' ista: 'Sauermann S, David V, Schlögl A, Egelkraut R, Frohner M, Pohn B, Urbauer P, Mense A. 2017. Biosignals standards and FHIR: The way to go. eHealth: Health Informatics Meets eHealth, Studies in Health Technology and Informatics, vol. 236, 356–362.' mla: 'Sauermann, Stefan, et al. Biosignals Standards and FHIR: The Way to Go. Vol. 236, IOS Press, 2017, pp. 356–62, doi:10.3233/978-1-61499-759-7-356.' short: S. Sauermann, V. David, A. Schlögl, R. Egelkraut, M. Frohner, B. Pohn, P. Urbauer, A. Mense, in:, IOS Press, 2017, pp. 356–362. conference: end_date: 2017-05-24 location: Vienna, Austria name: 'eHealth: Health Informatics Meets eHealth' start_date: 2017-05-23 date_created: 2018-12-11T11:47:36Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:06:59Z day: '01' ddc: - '005' department: - _id: ScienComp - _id: PeJo doi: 10.3233/978-1-61499-759-7-356 file: - access_level: open_access checksum: 1254dcc5b04a996d97fad9a726b42727 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:56Z date_updated: 2020-07-14T12:47:27Z file_id: '4913' file_name: IST-2017-906-v1+1_SHTI236-0356.pdf file_size: 443635 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' intvolume: ' 236' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 356 - 362 publication_identifier: isbn: - 978-161499758-0 publication_status: published publisher: IOS Press publist_id: '7164' pubrep_id: '906' quality_controlled: '1' scopus_import: 1 status: public title: 'Biosignals standards and FHIR: The way to go' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 236 year: '2017' ... --- _id: '632' abstract: - lang: eng text: 'We consider a 2D quantum system of N bosons in a trapping potential |x|s, interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all 0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of the many-body system is described in the large N limit by the corresponding cubic nonlinear Schrödinger energy functional. Our result covers the focusing case (w < 0) where even the stability of the many-body system is not obvious. This answers an open question mentioned by X. Chen and J. Holmer for harmonic traps (s = 2). Together with the BBGKY hierarchy approach used by these authors, our result implies the convergence of the many-body quantum dynamics to the focusing NLS equation with harmonic trap for all 0 < β < 3/4. ' author: - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam - first_name: Nicolas full_name: Rougerie, Nicolas last_name: Rougerie citation: ama: Lewin M, Nam P, Rougerie N. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 2017;145(6):2441-2454. doi:10.1090/proc/13468 apa: Lewin, M., Nam, P., & Rougerie, N. (2017). A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13468 chicago: Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/proc/13468. ieee: M. Lewin, P. Nam, and N. Rougerie, “A note on 2D focusing many boson systems,” Proceedings of the American Mathematical Society, vol. 145, no. 6. American Mathematical Society, pp. 2441–2454, 2017. ista: Lewin M, Nam P, Rougerie N. 2017. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 145(6), 2441–2454. mla: Lewin, Mathieu, et al. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society, vol. 145, no. 6, American Mathematical Society, 2017, pp. 2441–54, doi:10.1090/proc/13468. short: M. Lewin, P. Nam, N. Rougerie, Proceedings of the American Mathematical Society 145 (2017) 2441–2454. date_created: 2018-12-11T11:47:36Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:07:03Z day: '01' department: - _id: RoSe doi: 10.1090/proc/13468 ec_funded: 1 intvolume: ' 145' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1509.09045 month: '01' oa: 1 oa_version: Submitted Version page: 2441 - 2454 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Proceedings of the American Mathematical Society publication_status: published publisher: American Mathematical Society publist_id: '7160' quality_controlled: '1' scopus_import: 1 status: public title: A note on 2D focusing many boson systems type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 145 year: '2017' ... --- _id: '634' abstract: - lang: eng text: As autism spectrum disorder (ASD) is largely regarded as a neurodevelopmental condition, long-time consensus was that its hallmark features are irreversible. However, several studies from recent years using defined mouse models of ASD have provided clear evidence that in mice neurobiological and behavioural alterations can be ameliorated or even reversed by genetic restoration or pharmacological treatment either before or after symptom onset. Here, we review findings on genetic and pharmacological reversibility of phenotypes in mouse models of ASD. Our review should give a comprehensive overview on both aspects and encourage future studies to better understand the underlying molecular mechanisms that might be translatable from animals to humans. alternative_title: - ADVSANAT author: - first_name: Jan full_name: Schroeder, Jan last_name: Schroeder - first_name: Elena full_name: Deliu, Elena id: 37A40D7E-F248-11E8-B48F-1D18A9856A87 last_name: Deliu orcid: 0000-0002-7370-5293 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Michael full_name: Schmeisser, Michael last_name: Schmeisser citation: ama: 'Schroeder J, Deliu E, Novarino G, Schmeisser M. Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. Translational Anatomy and Cell Biology of Autism Spectrum Disorder. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:189-211. doi:10.1007/978-3-319-52498-6_10' apa: Schroeder, J., Deliu, E., Novarino, G., & Schmeisser, M. (2017). Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 189–211). Springer. https://doi.org/10.1007/978-3-319-52498-6_10 chicago: Schroeder, Jan, Elena Deliu, Gaia Novarino, and Michael Schmeisser. “Genetic and Pharmacological Reversibility of Phenotypes in Mouse Models of Autism Spectrum Disorder.” In Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, 224:189–211. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_10. ieee: J. Schroeder, E. Deliu, G. Novarino, and M. Schmeisser, “Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder,” in Translational Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 189–211. ista: 'Schroeder J, Deliu E, Novarino G, Schmeisser M. 2017.Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 189–211.' mla: Schroeder, Jan, et al. “Genetic and Pharmacological Reversibility of Phenotypes in Mouse Models of Autism Spectrum Disorder.” Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 189–211, doi:10.1007/978-3-319-52498-6_10. short: J. Schroeder, E. Deliu, G. Novarino, M. Schmeisser, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 189–211. date_created: 2018-12-11T11:47:37Z date_published: 2017-05-28T00:00:00Z date_updated: 2021-01-12T08:07:08Z day: '28' department: - _id: GaNo doi: 10.1007/978-3-319-52498-6_10 editor: - first_name: Michael full_name: Schmeisser, Michael last_name: Schmeisser - first_name: Tobias full_name: Boekers, Tobias last_name: Boekers intvolume: ' 224' language: - iso: eng month: '05' oa_version: None page: 189 - 211 project: - _id: 25473368-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F03523 name: Transmembrane Transporters in Health and Disease publication: Translational Anatomy and Cell Biology of Autism Spectrum Disorder publication_identifier: eisbn: - 978-3-319-52498-6 publication_status: published publisher: Springer publist_id: '7156' quality_controlled: '1' scopus_import: 1 series_title: Advances in Anatomy Embryology and Cell Biology status: public title: Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 224 year: '2017' ... --- _id: '633' abstract: - lang: eng text: A Rapidly-exploring Random Tree (RRT) is an algorithm which can search a non-convex region of space by incrementally building a space-filling tree. The tree is constructed from random points drawn from system’s state space and is biased to grow towards large unexplored areas in the system. RRT can provide better coverage of a system’s possible behaviors compared with random simulations, but is more lightweight than full reachability analysis. In this paper, we explore some of the design decisions encountered while implementing a hybrid extension of the RRT algorithm, which have not been elaborated on before. In particular, we focus on handling non-determinism, which arises due to discrete transitions. We introduce the notion of important points to account for this phenomena. We showcase our ideas using heater and navigation benchmarks. alternative_title: - LNCS author: - first_name: Stanley full_name: Bak, Stanley last_name: Bak - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - 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: Aviral full_name: Kumar, Aviral last_name: Kumar citation: ama: 'Bak S, Bogomolov S, Henzinger TA, Kumar A. Challenges and tool implementation of hybrid rapidly exploring random trees. In: Abate A, Bodo S, eds. Vol 10381. Springer; 2017:83-89. doi:10.1007/978-3-319-63501-9_6' apa: 'Bak, S., Bogomolov, S., Henzinger, T. A., & Kumar, A. (2017). Challenges and tool implementation of hybrid rapidly exploring random trees. In A. Abate & S. Bodo (Eds.) (Vol. 10381, pp. 83–89). Presented at the NSV: Numerical Software Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63501-9_6' chicago: Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, and Aviral Kumar. “Challenges and Tool Implementation of Hybrid Rapidly Exploring Random Trees.” edited by Alessandro Abate and Sylvie Bodo, 10381:83–89. Springer, 2017. https://doi.org/10.1007/978-3-319-63501-9_6. ieee: 'S. Bak, S. Bogomolov, T. A. Henzinger, and A. Kumar, “Challenges and tool implementation of hybrid rapidly exploring random trees,” presented at the NSV: Numerical Software Verification, Heidelberg, Germany, 2017, vol. 10381, pp. 83–89.' ista: 'Bak S, Bogomolov S, Henzinger TA, Kumar A. 2017. Challenges and tool implementation of hybrid rapidly exploring random trees. NSV: Numerical Software Verification, LNCS, vol. 10381, 83–89.' mla: Bak, Stanley, et al. Challenges and Tool Implementation of Hybrid Rapidly Exploring Random Trees. Edited by Alessandro Abate and Sylvie Bodo, vol. 10381, Springer, 2017, pp. 83–89, doi:10.1007/978-3-319-63501-9_6. short: S. Bak, S. Bogomolov, T.A. Henzinger, A. Kumar, in:, A. Abate, S. Bodo (Eds.), Springer, 2017, pp. 83–89. conference: end_date: 2017-07-23 location: Heidelberg, Germany name: 'NSV: Numerical Software Verification' start_date: 2017-07-22 date_created: 2018-12-11T11:47:37Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:07:06Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-319-63501-9_6 editor: - first_name: Alessandro full_name: Abate, Alessandro last_name: Abate - first_name: Sylvie full_name: Bodo, Sylvie last_name: Bodo intvolume: ' 10381' language: - iso: eng month: '01' oa_version: None page: 83 - 89 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-331963500-2 publication_status: published publisher: Springer publist_id: '7159' quality_controlled: '1' scopus_import: 1 status: public title: Challenges and tool implementation of hybrid rapidly exploring random trees type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10381 year: '2017' ... --- _id: '635' abstract: - lang: eng text: Memory-hard functions (MHFs) are hash algorithms whose evaluation cost is dominated by memory cost. As memory, unlike computation, costs about the same across different platforms, MHFs cannot be evaluated at significantly lower cost on dedicated hardware like ASICs. MHFs have found widespread applications including password hashing, key derivation, and proofs-of-work. This paper focuses on scrypt, a simple candidate MHF designed by Percival, and described in RFC 7914. It has been used within a number of cryptocurrencies (e.g., Litecoin and Dogecoin) and has been an inspiration for Argon2d, one of the winners of the recent password-hashing competition. Despite its popularity, no rigorous lower bounds on its memory complexity are known. We prove that scrypt is optimally memory-hard, i.e., its cumulative memory complexity (cmc) in the parallel random oracle model is Ω(n2w), where w and n are the output length and number of invocations of the underlying hash function, respectively. High cmc is a strong security target for MHFs introduced by Alwen and Serbinenko (STOC’15) which implies high memory cost even for adversaries who can amortize the cost over many evaluations and evaluate the underlying hash functions many times in parallel. Our proof is the first showing optimal memory-hardness for any MHF. Our result improves both quantitatively and qualitatively upon the recent work by Alwen et al. (EUROCRYPT’16) who proved a weaker lower bound of Ω(n2w/ log2 n) for a restricted class of adversaries. alternative_title: - LNCS author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Binchi full_name: Chen, Binchi last_name: Chen - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Leonid full_name: Reyzin, Leonid last_name: Reyzin - first_name: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: 'Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. Scrypt is maximally memory hard. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:33-62. doi:10.1007/978-3-319-56617-7_2' apa: 'Alwen, J. F., Chen, B., Pietrzak, K. Z., Reyzin, L., & Tessaro, S. (2017). Scrypt is maximally memory hard. In J.-S. Coron & J. Buus Nielsen (Eds.) (Vol. 10212, pp. 33–62). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_2' chicago: Alwen, Joel F, Binchi Chen, Krzysztof Z Pietrzak, Leonid Reyzin, and Stefano Tessaro. “Scrypt Is Maximally Memory Hard.” edited by Jean-Sébastien Coron and Jesper Buus Nielsen, 10212:33–62. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_2. ieee: 'J. F. Alwen, B. Chen, K. Z. Pietrzak, L. Reyzin, and S. Tessaro, “Scrypt is maximally memory hard,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 33–62.' ista: 'Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. 2017. Scrypt is maximally memory hard. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 10212, 33–62.' mla: Alwen, Joel F., et al. Scrypt Is Maximally Memory Hard. Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 33–62, doi:10.1007/978-3-319-56617-7_2. short: J.F. Alwen, B. Chen, K.Z. Pietrzak, L. Reyzin, S. Tessaro, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 33–62. conference: end_date: 2017-05-04 location: Paris, France name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2017-04-30 date_created: 2018-12-11T11:47:37Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:07:10Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-56617-7_2 ec_funded: 1 editor: - first_name: Jean-Sébastien full_name: Coron, Jean-Sébastien last_name: Coron - first_name: Jesper full_name: Buus Nielsen, Jesper last_name: Buus Nielsen intvolume: ' 10212' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/989 month: '01' oa: 1 oa_version: Submitted Version page: 33 - 62 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331956616-0 publication_status: published publisher: Springer publist_id: '7154' quality_controlled: '1' scopus_import: 1 status: public title: Scrypt is maximally memory hard type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 10212 year: '2017' ... --- _id: '636' abstract: - lang: eng text: Signal regular expressions can specify sequential properties of real-valued signals based on threshold conditions, regular operations, and duration constraints. In this paper we endow them with a quantitative semantics which indicates how robustly a signal matches or does not match a given expression. First, we show that this semantics is a safe approximation of a distance between the signal and the language defined by the expression. Then, we consider the robust matching problem, that is, computing the quantitative semantics of every segment of a given signal relative to an expression. We present an algorithm that solves this problem for piecewise-constant and piecewise-linear signals and show that for such signals the robustness map is a piecewise-linear function. The availability of an indicator describing how robustly a signal segment matches some regular pattern provides a general framework for quantitative monitoring of cyber-physical systems. alternative_title: - LNCS author: - first_name: Alexey full_name: Bakhirkin, Alexey last_name: Bakhirkin - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dogan full_name: Ulus, Dogan last_name: Ulus citation: ama: 'Bakhirkin A, Ferrere T, Maler O, Ulus D. On the quantitative semantics of regular expressions over real-valued signals. In: Abate A, Geeraerts G, eds. Vol 10419. Springer; 2017:189-206. doi:10.1007/978-3-319-65765-3_11' apa: 'Bakhirkin, A., Ferrere, T., Maler, O., & Ulus, D. (2017). On the quantitative semantics of regular expressions over real-valued signals. In A. Abate & G. Geeraerts (Eds.) (Vol. 10419, pp. 189–206). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_11' chicago: Bakhirkin, Alexey, Thomas Ferrere, Oded Maler, and Dogan Ulus. “On the Quantitative Semantics of Regular Expressions over Real-Valued Signals.” edited by Alessandro Abate and Gilles Geeraerts, 10419:189–206. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_11. ieee: 'A. Bakhirkin, T. Ferrere, O. Maler, and D. Ulus, “On the quantitative semantics of regular expressions over real-valued signals,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 189–206.' ista: 'Bakhirkin A, Ferrere T, Maler O, Ulus D. 2017. On the quantitative semantics of regular expressions over real-valued signals. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 189–206.' mla: Bakhirkin, Alexey, et al. On the Quantitative Semantics of Regular Expressions over Real-Valued Signals. Edited by Alessandro Abate and Gilles Geeraerts, vol. 10419, Springer, 2017, pp. 189–206, doi:10.1007/978-3-319-65765-3_11. short: A. Bakhirkin, T. Ferrere, O. Maler, D. Ulus, in:, A. Abate, G. Geeraerts (Eds.), Springer, 2017, pp. 189–206. conference: end_date: 2017-09-07 location: Berlin, Germany name: 'FORMATS: Formal Modelling and Analysis of Timed Systems' start_date: 2017-09-05 date_created: 2018-12-11T11:47:38Z date_published: 2017-08-03T00:00:00Z date_updated: 2021-01-12T08:07:14Z day: '03' department: - _id: ToHe doi: 10.1007/978-3-319-65765-3_11 editor: - first_name: Alessandro full_name: Abate, Alessandro last_name: Abate - first_name: Gilles full_name: Geeraerts, Gilles last_name: Geeraerts intvolume: ' 10419' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01552132 month: '08' oa: 1 oa_version: Submitted Version page: 189 - 206 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-331965764-6 publication_status: published publisher: Springer publist_id: '7152' quality_controlled: '1' scopus_import: 1 status: public title: On the quantitative semantics of regular expressions over real-valued signals type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10419 year: '2017' ... --- _id: '638' abstract: - lang: eng text: "This book constitutes the refereed proceedings of the 9th InternationalWorkshop on Numerical Software Verification, NSV 2016, held in Toronto, ON, Canada in July 2011 - colocated with CAV 2016, the 28th International Conference on Computer Aided Verification.\r\nThe NSV workshop is dedicated to the development of logical and mathematical techniques for the reasoning about programmability and reliability." article_processing_charge: No citation: ama: Bogomolov S, Martel M, Prabhakar P, eds. Numerical Software Verification. Vol 10152. Springer; 2017. doi:10.1007/978-3-319-54292-8 apa: 'Bogomolov, S., Martel, M., & Prabhakar, P. (Eds.). (2017). Numerical Software Verification (Vol. 10152). Presented at the NSV: Numerical Software Verification, Toronto, ON, Canada: Springer. https://doi.org/10.1007/978-3-319-54292-8' chicago: Bogomolov, Sergiy, Matthieu Martel, and Pavithra Prabhakar, eds. Numerical Software Verification. Vol. 10152. LNCS. Springer, 2017. https://doi.org/10.1007/978-3-319-54292-8. ieee: S. Bogomolov, M. Martel, and P. Prabhakar, Eds., Numerical Software Verification, vol. 10152. Springer, 2017. ista: Bogomolov S, Martel M, Prabhakar P eds. 2017. Numerical Software Verification, Springer,p. mla: Bogomolov, Sergiy, et al., editors. Numerical Software Verification. Vol. 10152, Springer, 2017, doi:10.1007/978-3-319-54292-8. short: S. Bogomolov, M. Martel, P. Prabhakar, eds., Numerical Software Verification, Springer, 2017. conference: end_date: 2016-07-18 location: Toronto, ON, Canada name: 'NSV: Numerical Software Verification' start_date: 2016-07-17 date_created: 2018-12-11T11:47:38Z date_published: 2017-01-01T00:00:00Z date_updated: 2022-05-24T07:09:52Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-319-54292-8 editor: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Matthieu full_name: Martel, Matthieu last_name: Martel - first_name: Pavithra full_name: Prabhakar, Pavithra last_name: Prabhakar intvolume: ' 10152' language: - iso: eng month: '01' oa_version: None publication_identifier: eisbn: - 978-3-319-54292-8 issn: - 0302-9743 publication_status: published publisher: Springer publist_id: '7150' quality_controlled: '1' series_title: LNCS status: public title: Numerical Software Verification type: conference_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10152 year: '2017' ... --- _id: '640' abstract: - lang: eng text: 'Data-independent Memory Hard Functions (iMHFS) are finding a growing number of applications in security; especially in the domain of password hashing. An important property of a concrete iMHF is specified by fixing a directed acyclic graph (DAG) Gn on n nodes. The quality of that iMHF is then captured by the following two pebbling complexities of Gn: – The parallel cumulative pebbling complexity Π∥cc(Gn) must be as high as possible (to ensure that the amortized cost of computing the function on dedicated hardware is dominated by the cost of memory). – The sequential space-time pebbling complexity Πst(Gn) should be as close as possible to Π∥cc(Gn) (to ensure that using many cores in parallel and amortizing over many instances does not give much of an advantage). In this paper we construct a family of DAGs with best possible parameters in an asymptotic sense, i.e., where Π∥cc(Gn) = Ω(n2/ log(n)) (which matches a known upper bound) and Πst(Gn) is within a constant factor of Π∥cc(Gn). Our analysis relies on a new connection between the pebbling complexity of a DAG and its depth-robustness (DR) – a well studied combinatorial property. We show that high DR is sufficient for high Π∥cc. Alwen and Blocki (CRYPTO’16) showed that high DR is necessary and so, together, these results fully characterize DAGs with high Π∥cc in terms of DR. Complementing these results, we provide new upper and lower bounds on the Π∥cc of several important candidate iMHFs from the literature. We give the first lower bounds on the memory hardness of the Catena and Balloon Hashing functions in a parallel model of computation and we give the first lower bounds of any kind for (a version) of Argon2i. Finally we describe a new class of pebbling attacks improving on those of Alwen and Blocki (CRYPTO’16). By instantiating these attacks we upperbound the Π∥cc of the Password Hashing Competition winner Argon2i and one of the Balloon Hashing functions by O (n1.71). We also show an upper bound of O(n1.625) for the Catena functions and the two remaining Balloon Hashing functions.' alternative_title: - LNCS author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Jeremiah full_name: Blocki, Jeremiah last_name: Blocki - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Alwen JF, Blocki J, Pietrzak KZ. Depth-robust graphs and their cumulative memory complexity. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:3-32. doi:10.1007/978-3-319-56617-7_1' apa: 'Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2017). Depth-robust graphs and their cumulative memory complexity. In J.-S. Coron & J. Buus Nielsen (Eds.) (Vol. 10212, pp. 3–32). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_1' chicago: Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Depth-Robust Graphs and Their Cumulative Memory Complexity.” edited by Jean-Sébastien Coron and Jesper Buus Nielsen, 10212:3–32. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_1. ieee: 'J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Depth-robust graphs and their cumulative memory complexity,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 3–32.' ista: 'Alwen JF, Blocki J, Pietrzak KZ. 2017. Depth-robust graphs and their cumulative memory complexity. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 10212, 3–32.' mla: Alwen, Joel F., et al. Depth-Robust Graphs and Their Cumulative Memory Complexity. Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 3–32, doi:10.1007/978-3-319-56617-7_1. short: J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 3–32. conference: end_date: 2017-05-04 location: Paris, France name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' start_date: 2017-04-30 date_created: 2018-12-11T11:47:39Z date_published: 2017-04-01T00:00:00Z date_updated: 2021-01-12T08:07:22Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-56617-7_1 ec_funded: 1 editor: - first_name: Jean-Sébastien full_name: Coron, Jean-Sébastien last_name: Coron - first_name: Jesper full_name: Buus Nielsen, Jesper last_name: Buus Nielsen intvolume: ' 10212' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/875 month: '04' oa: 1 oa_version: Submitted Version page: 3 - 32 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331956616-0 publication_status: published publisher: Springer publist_id: '7148' quality_controlled: '1' scopus_import: 1 status: public title: Depth-robust graphs and their cumulative memory complexity type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10212 year: '2017' ... --- _id: '641' abstract: - lang: eng text: 'We introduce two novel methods for learning parameters of graphical models for image labelling. The following two tasks underline both methods: (i) perturb model parameters based on given features and ground truth labelings, so as to exactly reproduce these labelings as optima of the local polytope relaxation of the labelling problem; (ii) train a predictor for the perturbed model parameters so that improved model parameters can be applied to the labelling of novel data. Our first method implements task (i) by inverse linear programming and task (ii) using a regressor e.g. a Gaussian process. Our second approach simultaneously solves tasks (i) and (ii) in a joint manner, while being restricted to linearly parameterised predictors. Experiments demonstrate the merits of both approaches.' alternative_title: - LNCS author: - first_name: Vera full_name: Trajkovska, Vera last_name: Trajkovska - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Freddie full_name: Åström, Freddie last_name: Åström - first_name: Stefanie full_name: Petra, Stefanie last_name: Petra citation: ama: 'Trajkovska V, Swoboda P, Åström F, Petra S. Graphical model parameter learning by inverse linear programming. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:323-334. doi:10.1007/978-3-319-58771-4_26' apa: 'Trajkovska, V., Swoboda, P., Åström, F., & Petra, S. (2017). Graphical model parameter learning by inverse linear programming. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 323–334). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_26' chicago: Trajkovska, Vera, Paul Swoboda, Freddie Åström, and Stefanie Petra. “Graphical Model Parameter Learning by Inverse Linear Programming.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:323–34. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_26. ieee: 'V. Trajkovska, P. Swoboda, F. Åström, and S. Petra, “Graphical model parameter learning by inverse linear programming,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 323–334.' ista: 'Trajkovska V, Swoboda P, Åström F, Petra S. 2017. Graphical model parameter learning by inverse linear programming. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 323–334.' mla: Trajkovska, Vera, et al. Graphical Model Parameter Learning by Inverse Linear Programming. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 323–34, doi:10.1007/978-3-319-58771-4_26. short: V. Trajkovska, P. Swoboda, F. Åström, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 323–334. conference: end_date: 2017-06-08 location: Kolding, Denmark name: 'SSVM: Scale Space and Variational Methods in Computer Vision' start_date: 2017-06-04 date_created: 2018-12-11T11:47:39Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:07:23Z day: '01' department: - _id: VlKo doi: 10.1007/978-3-319-58771-4_26 editor: - first_name: François full_name: Lauze, François last_name: Lauze - first_name: Yiqiu full_name: Dong, Yiqiu last_name: Dong - first_name: Anders full_name: Bjorholm Dahl, Anders last_name: Bjorholm Dahl intvolume: ' 10302' language: - iso: eng month: '01' oa_version: None page: 323 - 334 publication_identifier: isbn: - 978-331958770-7 publication_status: published publisher: Springer publist_id: '7147' quality_controlled: '1' scopus_import: 1 status: public title: Graphical model parameter learning by inverse linear programming type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10302 year: '2017' ... --- _id: '6426' abstract: - lang: eng text: Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent asynchronous computation threads. We show that specifications and correctness proofs for asynchronous programs can be structured by introducing the fiction, for proof purposes, that intermediate, non-quiescent states of asynchronous operations can be ignored. Then, the task of specification becomes relatively simple and the task of verification can be naturally decomposed into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure of an asynchronous program, the atomic effect of non-atomic operations and the synchronous effect of asynchronous operations. This structuring of specifications and proofs corresponds to the introduction of multiple layers of stepwise refinement for asynchronous programs. We present the first proof rule, called synchronization, to reduce asynchronous invocations on a lower layer to synchronous invocations on a higher layer. We implemented our proof method in CIVL and evaluated it on a collection of benchmark programs. alternative_title: - IST Austria Technical Report author: - 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: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: ama: Henzinger TA, Kragl B, Qadeer S. Synchronizing the Asynchronous. IST Austria; 2017. doi:10.15479/AT:IST-2018-853-v2-2 apa: Henzinger, T. A., Kragl, B., & Qadeer, S. (2017). Synchronizing the asynchronous. IST Austria. https://doi.org/10.15479/AT:IST-2018-853-v2-2 chicago: Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. Synchronizing the Asynchronous. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2018-853-v2-2. ieee: T. A. Henzinger, B. Kragl, and S. Qadeer, Synchronizing the asynchronous. IST Austria, 2017. ista: Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST Austria, 28p. mla: Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria, 2017, doi:10.15479/AT:IST-2018-853-v2-2. short: T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST Austria, 2017. date_created: 2019-05-13T08:15:55Z date_published: 2017-08-04T00:00:00Z date_updated: 2023-02-21T16:59:21Z day: '04' ddc: - '000' department: - _id: ToHe doi: 10.15479/AT:IST-2018-853-v2-2 file: - access_level: open_access checksum: b48d42725182d7ca10107a118815f4cf content_type: application/pdf creator: dernst date_created: 2019-05-13T08:14:44Z date_updated: 2020-07-14T12:47:30Z file_id: '6431' file_name: main(1).pdf file_size: 971347 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '28' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria related_material: record: - id: '133' relation: later_version status: public status: public title: Synchronizing the asynchronous type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '643' abstract: - lang: eng text: It has been reported that nicotinamide-overload induces oxidative stress associated with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT) were also carried out in adult Sprague-Dawley rats treated with or without cumulative doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration significantly increased the plasma H2O2 levels associated with high insulin levels. Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration of nicotinic acid, another form of Vitamin B3, also significantly increased plasma insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic acid or nicotinamide impaired glucose metabolism. This study suggested that excess Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance. article_processing_charge: No article_type: original author: - first_name: Wuping full_name: Sun, Wuping last_name: Sun - first_name: Ming-Zhu full_name: Zhai, Ming-Zhu id: 34009CFA-F248-11E8-B48F-1D18A9856A87 last_name: Zhai - first_name: Qian full_name: Zhou, Qian last_name: Zhou - first_name: Chengrui full_name: Qian, Chengrui last_name: Qian - first_name: Changyu full_name: Jiang, Changyu last_name: Jiang citation: ama: Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469 apa: Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469 chicago: Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469. ieee: W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp. 207–214, 2017. ista: Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 60(4), 207–214. mla: Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology, vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:10.4077/CJP.2017.BAF469. short: W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology 60 (2017) 207–214. date_created: 2018-12-11T11:47:40Z date_published: 2017-08-31T00:00:00Z date_updated: 2021-01-12T08:07:28Z day: '31' ddc: - '570' department: - _id: RySh doi: 10.4077/CJP.2017.BAF469 external_id: pmid: - '28847140' intvolume: ' 60' issue: '4' language: - iso: eng month: '08' oa_version: Published Version page: 207 - 214 pmid: 1 publication: Chinese Journal of Physiology publication_identifier: issn: - '03044920' publication_status: published publisher: Chinese Physiological Society publist_id: '7142' quality_controlled: '1' scopus_import: 1 status: public title: Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2017' ... --- _id: '642' abstract: - lang: eng text: Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable. author: - first_name: Mate full_name: Gerencser, Mate id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87 last_name: Gerencser - first_name: István full_name: Gyöngy, István last_name: Gyöngy citation: ama: Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397. doi:10.1090/mcom/3201 apa: Gerencser, M., & Gyöngy, I. (2017). Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. American Mathematical Society. https://doi.org/10.1090/mcom/3201 chicago: Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation. American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201. ieee: M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial differential equations in the whole space,” Mathematics of Computation, vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017. ista: Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 86(307), 2373–2397. mla: Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation, vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201. short: M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397. date_created: 2018-12-11T11:47:40Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:07:26Z day: '01' department: - _id: JaMa doi: 10.1090/mcom/3201 intvolume: ' 86' issue: '307' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.05535 month: '01' oa: 1 oa_version: Submitted Version page: 2373 - 2397 publication: Mathematics of Computation publication_identifier: issn: - '00255718' publication_status: published publisher: American Mathematical Society publist_id: '7144' quality_controlled: '1' scopus_import: 1 status: public title: Localization errors in solving stochastic partial differential equations in the whole space type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 86 year: '2017' ... --- _id: '645' abstract: - lang: eng text: Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks. alternative_title: - LNCS author: - first_name: Pranav full_name: Ashok, Pranav last_name: Ashok - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Tobias full_name: Meggendorfer, Tobias last_name: Meggendorfer citation: ama: 'Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration for long run average reward in markov decision processes. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:201-221. doi:10.1007/978-3-319-63387-9_10' apa: 'Ashok, P., Chatterjee, K., Daca, P., Kretinsky, J., & Meggendorfer, T. (2017). Value iteration for long run average reward in markov decision processes. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 201–221). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_10' chicago: Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_10. ieee: 'P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, and T. Meggendorfer, “Value iteration for long run average reward in markov decision processes,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 201–221.' ista: 'Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration for long run average reward in markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 10426, 201–221.' mla: Ashok, Pranav, et al. Value Iteration for Long Run Average Reward in Markov Decision Processes. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 201–21, doi:10.1007/978-3-319-63387-9_10. short: P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221. conference: end_date: 2017-07-28 location: Heidelberg, Germany name: 'CAV: Computer Aided Verification' start_date: 2017-07-24 date_created: 2018-12-11T11:47:41Z date_published: 2017-07-13T00:00:00Z date_updated: 2021-01-12T08:07:32Z day: '13' department: - _id: KrCh doi: 10.1007/978-3-319-63387-9_10 ec_funded: 1 editor: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Viktor full_name: Kunčak, Viktor last_name: Kunčak intvolume: ' 10426' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.02326 month: '07' oa: 1 oa_version: Submitted Version page: 201 - 221 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_identifier: isbn: - 978-331963386-2 publication_status: published publisher: Springer publist_id: '7135' quality_controlled: '1' scopus_import: 1 status: public title: Value iteration for long run average reward in markov decision processes type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10426 year: '2017' ... --- _id: '644' abstract: - lang: eng text: An instance of the valued constraint satisfaction problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P 6= NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in f0;1g corresponds to ordinary CSPs, where one deals only with the feasibility issue, and there is no optimization. This case is the subject of the algebraic CSP dichotomy conjecture predicting for which constraint languages CSPs are tractable (i.e., solvable in polynomial time) and for which they are NP-hard. The case when all allowed functions take only finite values corresponds to a finitevalued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Živný. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e., the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs. author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Andrei full_name: Krokhin, Andrei last_name: Krokhin - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. SIAM Journal on Computing. 2017;46(3):1087-1110. doi:10.1137/16M1091836 apa: Kolmogorov, V., Krokhin, A., & Rolinek, M. (2017). The complexity of general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16M1091836 chicago: Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2017. https://doi.org/10.1137/16M1091836. ieee: V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” SIAM Journal on Computing, vol. 46, no. 3. SIAM, pp. 1087–1110, 2017. ista: Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued CSPs. SIAM Journal on Computing. 46(3), 1087–1110. mla: Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:10.1137/16M1091836. short: V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017) 1087–1110. date_created: 2018-12-11T11:47:40Z date_published: 2017-06-29T00:00:00Z date_updated: 2023-02-23T10:07:49Z day: '29' department: - _id: VlKo doi: 10.1137/16M1091836 ec_funded: 1 intvolume: ' 46' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1502.07327 month: '06' oa: 1 oa_version: Preprint page: 1087 - 1110 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: SIAM Journal on Computing publication_status: published publisher: SIAM publist_id: '7138' quality_controlled: '1' related_material: record: - id: '1637' relation: other status: public scopus_import: 1 status: public title: The complexity of general-valued CSPs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 46 year: '2017' ... --- _id: '646' abstract: - lang: eng text: We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations. alternative_title: - LNCS author: - first_name: Jan full_name: Kuske, Jan last_name: Kuske - first_name: Paul full_name: Swoboda, Paul id: 446560C6-F248-11E8-B48F-1D18A9856A87 last_name: Swoboda - first_name: Stefanie full_name: Petra, Stefanie last_name: Petra citation: ama: 'Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246. doi:10.1007/978-3-319-58771-4_19' apa: 'Kuske, J., Swoboda, P., & Petra, S. (2017). A novel convex relaxation for non binary discrete tomography. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_19' chicago: Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_19. ieee: 'J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary discrete tomography,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246.' ista: 'Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 235–246.' mla: Kuske, Jan, et al. A Novel Convex Relaxation for Non Binary Discrete Tomography. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:10.1007/978-3-319-58771-4_19. short: J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 235–246. conference: end_date: 2017-06-08 location: Kolding, Denmark name: 'SSVM: Scale Space and Variational Methods in Computer Vision' start_date: 2017-06-04 date_created: 2018-12-11T11:47:41Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:07:34Z day: '01' department: - _id: VlKo doi: 10.1007/978-3-319-58771-4_19 ec_funded: 1 editor: - first_name: François full_name: Lauze, François last_name: Lauze - first_name: Yiqiu full_name: Dong, Yiqiu last_name: Dong - first_name: Anders full_name: Bjorholm Dahl, Anders last_name: Bjorholm Dahl intvolume: ' 10302' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.03769 month: '06' oa: 1 oa_version: Submitted Version page: 235 - 246 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: isbn: - 978-331958770-7 publication_status: published publisher: Springer publist_id: '7132' quality_controlled: '1' scopus_import: 1 status: public title: A novel convex relaxation for non binary discrete tomography type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10302 year: '2017' ... --- _id: '648' abstract: - lang: eng text: 'Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) differs from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method.' alternative_title: - LNCS author: - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:600-613. doi:10.1007/978-3-319-55911-7_43' apa: 'Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_43' chicago: Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_43. ieee: 'M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 600–613.' ista: 'Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 600–613.' mla: Skórski, Maciej. On the Complexity of Breaking Pseudoentropy. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:10.1007/978-3-319-55911-7_43. short: M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613. conference: end_date: 2017-04-22 location: Bern, Switzerland name: 'TAMC: Theory and Applications of Models of Computation' start_date: 2017-04-20 date_created: 2018-12-11T11:47:42Z date_published: 2017-04-01T00:00:00Z date_updated: 2021-01-12T08:07:39Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-55911-7_43 editor: - first_name: Gerhard full_name: Jäger, Gerhard last_name: Jäger - first_name: Silvia full_name: Steila, Silvia last_name: Steila intvolume: ' 10185' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/1186.pdf month: '04' oa: 1 oa_version: Submitted Version page: 600 - 613 publication_identifier: isbn: - 978-331955910-0 publication_status: published publisher: Springer publist_id: '7125' quality_controlled: '1' scopus_import: 1 status: public title: On the complexity of breaking pseudoentropy type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10185 year: '2017' ... --- _id: '649' abstract: - lang: eng text: We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani. article_processing_charge: No author: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: 'Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. Modern Approaches to Discrete Curvature. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:10.1007/978-3-319-58002-9_5' apa: Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman & P. Romon (Eds.), Modern Approaches to Discrete Curvature (Vol. 2184, pp. 159–174). Springer. https://doi.org/10.1007/978-3-319-58002-9_5 chicago: Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. https://doi.org/10.1007/978-3-319-58002-9_5. ieee: J. Maas, “Entropic Ricci curvature for discrete spaces,” in Modern Approaches to Discrete Curvature, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174. ista: 'Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.' mla: Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:10.1007/978-3-319-58002-9_5. short: J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174. date_created: 2018-12-11T11:47:42Z date_published: 2017-10-05T00:00:00Z date_updated: 2022-05-24T07:01:33Z day: '05' department: - _id: JaMa doi: 10.1007/978-3-319-58002-9_5 editor: - first_name: Laurent full_name: Najman, Laurent last_name: Najman - first_name: Pascal full_name: Romon, Pascal last_name: Romon intvolume: ' 2184' language: - iso: eng month: '10' oa_version: None page: 159 - 174 publication: Modern Approaches to Discrete Curvature publication_identifier: eissn: - 978-3-319-58002-9 isbn: - 978-3-319-58001-2 publication_status: published publisher: Springer publist_id: '7123' quality_controlled: '1' scopus_import: '1' series_title: Lecture Notes in Mathematics status: public title: Entropic Ricci curvature for discrete spaces type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2184 year: '2017' ... --- _id: '650' abstract: - lang: eng text: 'In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy.' alternative_title: - LNCS author: - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Skórski M. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:586-599. doi:10.1007/978-3-319-55911-7_42' apa: 'Skórski, M. (2017). A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 586–599). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_42' chicago: 'Skórski, Maciej. “A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds.” edited by Gerhard Jäger and Silvia Steila, 10185:586–99. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_42.' ieee: 'M. Skórski, “A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 586–599.' ista: 'Skórski M. 2017. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 586–599.' mla: 'Skórski, Maciej. A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 586–99, doi:10.1007/978-3-319-55911-7_42.' short: M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599. conference: end_date: 2017-04-22 location: Bern, Switzerland name: 'TAMC: Theory and Applications of Models of Computation' start_date: 2017-04-20 date_created: 2018-12-11T11:47:42Z date_published: 2017-01-01T00:00:00Z date_updated: 2021-01-12T08:07:46Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-55911-7_42 editor: - first_name: Gerhard full_name: Jäger, Gerhard last_name: Jäger - first_name: Silvia full_name: Steila, Silvia last_name: Steila intvolume: ' 10185' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/965.pdf month: '01' oa: 1 oa_version: Submitted Version page: 586 - 599 publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '7119' quality_controlled: '1' scopus_import: 1 status: public title: 'A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10185 year: '2017' ... --- _id: '6519' abstract: - lang: eng text: 'Graph games with omega-regular winning conditions provide a mathematical framework to analyze a wide range of problems in the analysis of reactive systems and programs (such as the synthesis of reactive systems, program repair, and the verification of branching time properties). Parity conditions are canonical forms to specify omega-regular winning conditions. Graph games with parity conditions are equivalent to mu-calculus model checking, and thus a very important algorithmic problem. Symbolic algorithms are of great significance because they provide scalable algorithms for the analysis of large finite-state systems, as well as algorithms for the analysis of infinite-state systems with finite quotient. A set-based symbolic algorithm uses the basic set operations and the one-step predecessor operators. We consider graph games with n vertices and parity conditions with c priorities (equivalently, a mu-calculus formula with c alternations of least and greatest fixed points). While many explicit algorithms exist for graph games with parity conditions, for set-based symbolic algorithms there are only two algorithms (notice that we use space to refer to the number of sets stored by a symbolic algorithm): (a) the basic algorithm that requires O(n^c) symbolic operations and linear space; and (b) an improved algorithm that requires O(n^{c/2+1}) symbolic operations but also O(n^{c/2+1}) space (i.e., exponential space). In this work we present two set-based symbolic algorithms for parity games: (a) our first algorithm requires O(n^{c/2+1}) symbolic operations and only requires linear space; and (b) developing on our first algorithm, we present an algorithm that requires O(n^{c/3+1}) symbolic operations and only linear space. We also present the first linear space set-based symbolic algorithm for parity games that requires at most a sub-exponential number of symbolic operations. ' article_number: '18' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Wolfgang full_name: Dvorák, Wolfgang last_name: Dvorák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Improved set-based symbolic algorithms for parity games. In: Vol 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik; 2017. doi:10.4230/LIPICS.CSL.2017.18' apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved set-based symbolic algorithms for parity games (Vol. 82). Presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden: Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik. https://doi.org/10.4230/LIPICS.CSL.2017.18' chicago: Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Set-Based Symbolic Algorithms for Parity Games,” Vol. 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017. https://doi.org/10.4230/LIPICS.CSL.2017.18. ieee: 'K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Improved set-based symbolic algorithms for parity games,” presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden, 2017, vol. 82.' ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2017. Improved set-based symbolic algorithms for parity games. CSL: Conference on Computer Science Logic vol. 82, 18.' mla: Chatterjee, Krishnendu, et al. Improved Set-Based Symbolic Algorithms for Parity Games. Vol. 82, 18, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017, doi:10.4230/LIPICS.CSL.2017.18. short: K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017. conference: end_date: 2017-08-24 location: Stockholm, Sweden name: 'CSL: Conference on Computer Science Logic' start_date: 2017-08-20 date_created: 2019-06-04T12:42:43Z date_published: 2017-08-01T00:00:00Z date_updated: 2023-02-14T10:08:25Z day: '01' ddc: - '004' department: - _id: KrCh doi: 10.4230/LIPICS.CSL.2017.18 ec_funded: 1 file: - access_level: open_access checksum: 7c2c9d09970af79026d7e37d9b632ef8 content_type: application/pdf creator: kschuh date_created: 2019-06-04T12:56:52Z date_updated: 2020-07-14T12:47:33Z file_id: '6520' file_name: 2017_LIPIcs-Chatterjee.pdf file_size: 710185 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 82' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _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' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_status: published publisher: Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik quality_controlled: '1' scopus_import: '1' status: public title: Improved set-based symbolic algorithms for parity games 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2017' ... --- _id: '6517' abstract: - lang: eng text: A (possibly degenerate) drawing of a graph G in the plane is approximable by an embedding if it can be turned into an embedding by an arbitrarily small perturbation. We show that testing, whether a drawing of a planar graph G in the plane is approximable by an embedding, can be carried out in polynomial time, if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation system (or equivalently the faces) of the embedding of G and the choice of outer face are fixed. In other words, we show that c-planarity with embedded pipes is tractable for graphs with fixed embeddings. To the best of our knowledge an analogous result was previously known essentially only when G is a cycle. article_number: '34' author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 citation: ama: 'Fulek R. Embedding graphs into embedded graphs. In: Vol 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ISAAC.2017.34' apa: 'Fulek, R. (2017). Embedding graphs into embedded graphs (Vol. 92). Presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ISAAC.2017.34' chicago: Fulek, Radoslav. “Embedding Graphs into Embedded Graphs,” Vol. 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ISAAC.2017.34. ieee: 'R. Fulek, “Embedding graphs into embedded graphs,” presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand, 2017, vol. 92.' ista: 'Fulek R. 2017. Embedding graphs into embedded graphs. ISAAC: International Symposium on Algorithms and Computation vol. 92, 34.' mla: Fulek, Radoslav. Embedding Graphs into Embedded Graphs. Vol. 92, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ISAAC.2017.34. short: R. Fulek, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-12-22 location: Phuket, Thailand name: 'ISAAC: International Symposium on Algorithms and Computation' start_date: 2017-12-09 date_created: 2019-06-04T12:11:52Z date_published: 2017-12-01T00:00:00Z date_updated: 2021-01-12T08:07:51Z day: '01' ddc: - '510' department: - _id: UlWa doi: 10.4230/LIPICS.ISAAC.2017.34 ec_funded: 1 file: - access_level: open_access checksum: fc7a643e29621c8bbe49d36b39081f31 content_type: application/pdf creator: kschuh date_created: 2019-06-04T12:20:35Z date_updated: 2020-07-14T12:47:33Z file_id: '6518' file_name: 2017_LIPIcs-Fulek.pdf file_size: 588982 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 92' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Embedding graphs into embedded graphs 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2017' ... --- _id: '652' abstract: - lang: eng text: 'We present an approach that enables robots to self-organize their sensorimotor behavior from scratch without providing specific information about neither the robot nor its environment. This is achieved by a simple neural control law that increases the consistency between external sensor dynamics and internal neural dynamics of the utterly simple controller. In this way, the embodiment and the agent-environment coupling are the only source of individual development. We show how an anthropomorphic tendon driven arm-shoulder system develops different behaviors depending on that coupling. For instance: Given a bottle half-filled with water, the arm starts to shake it, driven by the physical response of the water. When attaching a brush, the arm can be manipulated into wiping a table, and when connected to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said to discover the affordances of the world. When allowing two (simulated) humanoid robots to interact physically, they engage into a joint behavior development leading to, for instance, spontaneous cooperation. More social effects are observed if the robots can visually perceive each other. Although, as an observer, it is tempting to attribute an apparent intentionality, there is nothing of the kind put in. As a conclusion, we argue that emergent behavior may be much less rooted in explicit intentions, internal motivations, or specific reward systems than is commonly believed.' article_number: '7846789' author: - first_name: Ralf full_name: Der, Ralf last_name: Der - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius citation: ama: 'Der R, Martius GS. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. In: IEEE; 2017. doi:10.1109/DEVLRN.2016.7846789' apa: 'Der, R., & Martius, G. S. (2017). Dynamical self consistency leads to behavioral development and emergent social interactions in robots. Presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France: IEEE. https://doi.org/10.1109/DEVLRN.2016.7846789' chicago: Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots.” IEEE, 2017. https://doi.org/10.1109/DEVLRN.2016.7846789. ieee: 'R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral development and emergent social interactions in robots,” presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France, 2017.' ista: 'Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , 7846789.' mla: Der, Ralf, and Georg S. Martius. Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots. 7846789, IEEE, 2017, doi:10.1109/DEVLRN.2016.7846789. short: R. Der, G.S. Martius, in:, IEEE, 2017. conference: end_date: 2016-09-22 location: Cergy-Pontoise, France name: 'ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics ' start_date: 2016-09-19 date_created: 2018-12-11T11:47:43Z date_published: 2017-02-07T00:00:00Z date_updated: 2021-01-12T08:07:51Z day: '07' department: - _id: ChLa - _id: GaTk doi: 10.1109/DEVLRN.2016.7846789 language: - iso: eng month: '02' oa_version: None publication_identifier: isbn: - 978-150905069-7 publication_status: published publisher: IEEE publist_id: '7100' quality_controlled: '1' scopus_import: 1 status: public title: Dynamical self consistency leads to behavioral development and emergent social interactions in robots type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '651' abstract: - lang: eng text: "Superhydrophobic surfaces reduce the frictional drag between water and solid materials, but this effect is often temporary. The realization of sustained drag reduction has applications for water vehicles and pipeline flows.\r\n\r\n" author: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: 'Hof B. Fluid dynamics: Water flows out of touch. Nature. 2017;541(7636):161-162. doi:10.1038/541161a' apa: 'Hof, B. (2017). Fluid dynamics: Water flows out of touch. Nature. Nature Publishing Group. https://doi.org/10.1038/541161a' chicago: 'Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/541161a.' ieee: 'B. Hof, “Fluid dynamics: Water flows out of touch,” Nature, vol. 541, no. 7636. Nature Publishing Group, pp. 161–162, 2017.' ista: 'Hof B. 2017. Fluid dynamics: Water flows out of touch. Nature. 541(7636), 161–162.' mla: 'Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature, vol. 541, no. 7636, Nature Publishing Group, 2017, pp. 161–62, doi:10.1038/541161a.' short: B. Hof, Nature 541 (2017) 161–162. date_created: 2018-12-11T11:47:43Z date_published: 2017-01-11T00:00:00Z date_updated: 2021-01-12T08:07:49Z day: '11' department: - _id: BjHo doi: 10.1038/541161a intvolume: ' 541' issue: '7636' language: - iso: eng month: '01' oa_version: None page: 161 - 162 publication: Nature publication_identifier: issn: - '00280836' publication_status: published publisher: Nature Publishing Group publist_id: '7116' quality_controlled: '1' scopus_import: 1 status: public title: 'Fluid dynamics: Water flows out of touch' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 541 year: '2017' ... --- _id: '653' abstract: - lang: eng text: The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease. acknowledgement: 'We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).' article_processing_charge: No article_type: original author: - first_name: Alvin full_name: Makohon Moore, Alvin last_name: Makohon Moore - first_name: Ming full_name: Zhang, Ming last_name: Zhang - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Benjamin full_name: Allen, Benjamin last_name: Allen - first_name: Deepanjan full_name: Kundu, Deepanjan id: 1d4c0f4f-e8a3-11ec-a351-e36772758c45 last_name: Kundu - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Fay full_name: Wong, Fay last_name: Wong - first_name: Yuchen full_name: Jiao, Yuchen last_name: Jiao - first_name: Zachary full_name: Kohutek, Zachary last_name: Kohutek - first_name: Jungeui full_name: Hong, Jungeui last_name: Hong - first_name: Marc full_name: Attiyeh, Marc last_name: Attiyeh - first_name: Breanna full_name: Javier, Breanna last_name: Javier - first_name: Laura full_name: Wood, Laura last_name: Wood - first_name: Ralph full_name: Hruban, Ralph last_name: Hruban - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Nickolas full_name: Papadopoulos, Nickolas last_name: Papadopoulos - first_name: Kenneth full_name: Kinzler, Kenneth last_name: Kinzler - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein - first_name: Christine full_name: Iacobuzio Donahue, Christine last_name: Iacobuzio Donahue citation: ama: Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 2017;49(3):358-366. doi:10.1038/ng.3764 apa: Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng.3764 chicago: Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics. Nature Publishing Group, 2017. https://doi.org/10.1038/ng.3764. ieee: A. Makohon Moore et al., “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” Nature Genetics, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017. ista: Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366. mla: Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:10.1038/ng.3764. short: A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366. date_created: 2018-12-11T11:47:43Z date_published: 2017-03-01T00:00:00Z date_updated: 2022-06-10T09:55:08Z day: '01' ddc: - '000' department: - _id: KrCh doi: 10.1038/ng.3764 ec_funded: 1 external_id: pmid: - '28092682' file: - access_level: open_access checksum: e442dc3b7420a36ec805e9bb45cc1a2e content_type: application/pdf creator: dernst date_created: 2019-11-19T08:13:50Z date_updated: 2020-07-14T12:47:33Z file_id: '7050' file_name: 2017_NatureGenetics_Makohon.pdf file_size: 908099 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 49' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 358 - 366 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _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: Nature Genetics publication_identifier: issn: - '10614036' publication_status: published publisher: Nature Publishing Group publist_id: '7092' quality_controlled: '1' scopus_import: '1' status: public title: Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2017' ... --- _id: '6527' abstract: - lang: eng text: "A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called \"depth-robustness\") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.\r\n*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n" author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Jeremiah full_name: Blocki, Jeremiah last_name: Blocki - first_name: Ben full_name: Harsha, Ben last_name: Harsha citation: ama: 'Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant memory-hard functions. In: Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. ACM Press; 2017:1001-1017. doi:10.1145/3133956.3134031' apa: 'Alwen, J. F., Blocki, J., & Harsha, B. (2017). Practical graphs for optimal side-channel resistant memory-hard functions. In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security (pp. 1001–1017). Dallas, TX, USA: ACM Press. https://doi.org/10.1145/3133956.3134031' chicago: Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, 1001–17. ACM Press, 2017. https://doi.org/10.1145/3133956.3134031. ieee: J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel resistant memory-hard functions,” in Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, Dallas, TX, USA, 2017, pp. 1001–1017. ista: 'Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1001–1017.' mla: Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–17, doi:10.1145/3133956.3134031. short: J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017. conference: end_date: 2017-11-03 location: Dallas, TX, USA name: 'CCS: Conference on Computer and Communications Security' start_date: 2017-10-30 date_created: 2019-06-06T13:21:29Z date_published: 2017-10-30T00:00:00Z date_updated: 2021-01-12T08:07:53Z day: '30' department: - _id: KrPi doi: 10.1145/3133956.3134031 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/443 month: '10' oa: 1 oa_version: Submitted Version page: 1001-1017 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security publication_identifier: isbn: - '9781450349468' publication_status: published publisher: ACM Press quality_controlled: '1' scopus_import: 1 status: public title: Practical graphs for optimal side-channel resistant memory-hard functions type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '654' abstract: - lang: eng text: In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations. author: - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Nicolas full_name: Rivron, Nicolas last_name: Rivron citation: ama: Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. Development. 2017;144(5):733-736. doi:10.1242/dev.144915 apa: Kicheva, A., & Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. Development. Company of Biologists. https://doi.org/10.1242/dev.144915 chicago: Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144915. ieee: A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” Development, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017. ista: Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736. mla: Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:10.1242/dev.144915. short: A. Kicheva, N. Rivron, Development 144 (2017) 733–736. date_created: 2018-12-11T11:47:44Z date_published: 2017-03-01T00:00:00Z date_updated: 2021-01-12T08:07:54Z day: '01' ddc: - '571' department: - _id: AnKi doi: 10.1242/dev.144915 ec_funded: 1 file: - access_level: open_access checksum: eef22a0f42a55b232cb2d1188a2322cb content_type: application/pdf creator: system date_created: 2018-12-12T10:15:20Z date_updated: 2020-07-14T12:47:33Z file_id: '5139' file_name: IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf file_size: 228206 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 144' issue: '5' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 733 - 736 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord publication: Development publication_identifier: issn: - '09501991' publication_status: published publisher: Company of Biologists publist_id: '7089' pubrep_id: '987' quality_controlled: '1' scopus_import: 1 status: public title: Creating to understand – developmental biology meets engineering in Paris type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 144 year: '2017' ... --- _id: '6526' abstract: - lang: eng text: 'This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA''15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity.' article_number: '8006529' author: - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Skórski M. On the complexity of estimating Rènyi divergences. In: 2017 IEEE International Symposium on Information Theory (ISIT). IEEE; 2017. doi:10.1109/isit.2017.8006529' apa: 'Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In 2017 IEEE International Symposium on Information Theory (ISIT). Aachen, Germany: IEEE. https://doi.org/10.1109/isit.2017.8006529' chicago: Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In 2017 IEEE International Symposium on Information Theory (ISIT). IEEE, 2017. https://doi.org/10.1109/isit.2017.8006529. ieee: M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017. ista: 'Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017 IEEE International Symposium on Information Theory (ISIT). ISIT: International Symposium on Information Theory, 8006529.' mla: Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” 2017 IEEE International Symposium on Information Theory (ISIT), 8006529, IEEE, 2017, doi:10.1109/isit.2017.8006529. short: M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017. conference: end_date: 2017-06-30 location: Aachen, Germany name: 'ISIT: International Symposium on Information Theory' start_date: 2017-06-25 date_created: 2019-06-06T12:53:09Z date_published: 2017-08-09T00:00:00Z date_updated: 2021-01-12T08:07:53Z day: '09' department: - _id: KrPi doi: 10.1109/isit.2017.8006529 ec_funded: 1 external_id: arxiv: - '1702.01666' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.01666 month: '08' oa: 1 oa_version: Preprint project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 2017 IEEE International Symposium on Information Theory (ISIT) publication_identifier: isbn: - '9781509040964' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: 1 status: public title: On the complexity of estimating Rènyi divergences type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '655' abstract: - lang: eng text: 'The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell.' article_number: e23136 author: - first_name: Thibaud full_name: Renault, Thibaud last_name: Renault - first_name: Anthony full_name: Abraham, Anthony last_name: Abraham - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Guillaume full_name: Paradis, Guillaume last_name: Paradis - first_name: Simon full_name: Rainville, Simon last_name: Rainville - first_name: Emmanuelle full_name: Charpentier, Emmanuelle last_name: Charpentier - 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: Yuhai full_name: Tu, Yuhai last_name: Tu - first_name: Keiichi full_name: Namba, Keiichi last_name: Namba - first_name: James full_name: Keener, James last_name: Keener - first_name: Tohru full_name: Minamino, Tohru last_name: Minamino - first_name: Marc full_name: Erhardt, Marc last_name: Erhardt citation: ama: Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through an injection diffusion mechanism. eLife. 2017;6. doi:10.7554/eLife.23136 apa: Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier, E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.23136 chicago: Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.23136. ieee: T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella grow through an injection diffusion mechanism. eLife. 6, e23136. mla: Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife, vol. 6, e23136, eLife Sciences Publications, 2017, doi:10.7554/eLife.23136. short: T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017). date_created: 2018-12-11T11:47:44Z date_published: 2017-03-06T00:00:00Z date_updated: 2021-01-12T08:07:55Z day: '06' ddc: - '579' department: - _id: CaGu doi: 10.7554/eLife.23136 file: - access_level: open_access checksum: 39e1c3e82ddac83a30422fa72fa1a383 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:53Z date_updated: 2020-07-14T12:47:33Z file_id: '4716' file_name: IST-2017-904-v1+1_elife-23136-v2.pdf file_size: 5520359 relation: main_file - access_level: open_access checksum: a6d542253028f52e00aa29739ddffe8f content_type: application/pdf creator: system date_created: 2018-12-12T10:08:54Z date_updated: 2020-07-14T12:47:33Z file_id: '4717' file_name: IST-2017-904-v1+2_elife-23136-figures-v2.pdf file_size: 11242920 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '7082' pubrep_id: '904' quality_controlled: '1' scopus_import: 1 status: public title: Bacterial flagella grow through an injection diffusion mechanism 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: '2017' ... --- _id: '657' abstract: - lang: eng text: Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator. author: - first_name: Barbara full_name: Möller, Barbara last_name: Möller - first_name: Colette full_name: Ten Hove, Colette last_name: Ten Hove - first_name: Daoquan full_name: Xiang, Daoquan last_name: Xiang - first_name: Nerys full_name: Williams, Nerys last_name: Williams - first_name: Lorena full_name: López, Lorena last_name: López - first_name: Saiko full_name: Yoshida, Saiko id: 2E46069C-F248-11E8-B48F-1D18A9856A87 last_name: Yoshida - first_name: Margot full_name: Smit, Margot last_name: Smit - first_name: Raju full_name: Datla, Raju last_name: Datla - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers citation: ama: Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 2017;114(12):E2533-E2539. doi:10.1073/pnas.1616493114 apa: Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1616493114 chicago: Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1616493114. ieee: B. Möller et al., “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” PNAS, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017. ista: Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539. mla: Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:10.1073/pnas.1616493114. short: B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539. date_created: 2018-12-11T11:47:45Z date_published: 2017-03-21T00:00:00Z date_updated: 2021-01-12T08:08:02Z day: '21' department: - _id: JiFr doi: 10.1073/pnas.1616493114 external_id: pmid: - '28265057' intvolume: ' 114' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/ month: '03' oa: 1 oa_version: Submitted Version page: E2533 - E2539 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7076' quality_controlled: '1' scopus_import: 1 status: public title: Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '656' abstract: - lang: eng text: Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets. article_number: eaam9867 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867 apa: Novarino, G. (2017). Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aam9867 chicago: Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aam9867. ieee: G. Novarino, “Modeling Alzheimer’s disease in mice with human neurons,” Science Translational Medicine, vol. 9, no. 381. American Association for the Advancement of Science, 2017. ista: Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 9(381), eaam9867. mla: Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine, vol. 9, no. 381, eaam9867, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aam9867. short: G. Novarino, Science Translational Medicine 9 (2017). date_created: 2018-12-11T11:47:45Z date_published: 2017-03-15T00:00:00Z date_updated: 2021-01-12T08:07:59Z day: '15' department: - _id: GaNo doi: 10.1126/scitranslmed.aam9867 intvolume: ' 9' issue: '381' language: - iso: eng month: '03' oa_version: None publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '7079' quality_controlled: '1' scopus_import: 1 status: public title: Modeling Alzheimer's disease in mice with human neurons type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '658' abstract: - lang: eng text: 'With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object''s identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors "waiting" to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics.' article_number: '00008' article_processing_charge: Yes author: - first_name: Ralf full_name: Der, Ralf last_name: Der - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius citation: ama: Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008 apa: Der, R., & Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. Frontiers Research Foundation. https://doi.org/10.3389/fnbot.2017.00008 chicago: Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fnbot.2017.00008. ieee: R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” Frontiers in Neurorobotics, vol. 11, no. MAR. Frontiers Research Foundation, 2017. ista: Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008. mla: Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:10.3389/fnbot.2017.00008. short: R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017). date_created: 2018-12-11T11:47:45Z date_published: 2017-03-16T00:00:00Z date_updated: 2021-01-12T08:08:04Z day: '16' ddc: - '006' department: - _id: ChLa - _id: GaTk doi: 10.3389/fnbot.2017.00008 ec_funded: 1 file: - access_level: open_access checksum: b1bc43f96d1df3313c03032c2a46388d content_type: application/pdf creator: system date_created: 2018-12-12T10:18:49Z date_updated: 2020-07-14T12:47:33Z file_id: '5371' file_name: IST-2017-903-v1+1_fnbot-11-00008.pdf file_size: 8439566 relation: main_file file_date_updated: 2020-07-14T12:47:33Z has_accepted_license: '1' intvolume: ' 11' issue: MAR language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Frontiers in Neurorobotics publication_identifier: issn: - '16625218' publication_status: published publisher: Frontiers Research Foundation publist_id: '7078' pubrep_id: '903' quality_controlled: '1' scopus_import: 1 status: public title: Self organized behavior generation for musculoskeletal 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: 2EBD1598-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2017' ... --- _id: '659' abstract: - lang: eng text: Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching. article_number: '14832' article_processing_charge: No author: - first_name: Frieda full_name: Kage, Frieda last_name: Kage - first_name: Moritz full_name: Winterhoff, Moritz last_name: Winterhoff - first_name: Vanessa full_name: Dimchev, Vanessa last_name: Dimchev - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Tobias full_name: Thalheim, Tobias last_name: Thalheim - first_name: Anika full_name: Freise, Anika last_name: Freise - first_name: Stefan full_name: Brühmann, Stefan last_name: Brühmann - first_name: Jana full_name: Kollasser, Jana last_name: Kollasser - first_name: Jennifer full_name: Block, Jennifer last_name: Block - first_name: Georgi A full_name: Dimchev, Georgi A last_name: Dimchev - first_name: Matthias full_name: Geyer, Matthias last_name: Geyer - first_name: Hams full_name: Schnittler, Hams last_name: Schnittler - first_name: Cord full_name: Brakebusch, Cord last_name: Brakebusch - first_name: Theresia full_name: Stradal, Theresia last_name: Stradal - first_name: Marie full_name: Carlier, Marie last_name: Carlier - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Josef full_name: Käs, Josef last_name: Käs - first_name: Jan full_name: Faix, Jan last_name: Faix - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner citation: ama: Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832 apa: Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832 chicago: Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14832. ieee: F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832. mla: Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832. short: F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017). date_created: 2018-12-11T11:47:46Z date_published: 2017-03-22T00:00:00Z date_updated: 2021-01-12T08:08:06Z day: '22' ddc: - '570' department: - _id: MiSi doi: 10.1038/ncomms14832 file: - access_level: open_access checksum: dae30190291c3630e8102d8714a8d23e content_type: application/pdf creator: system date_created: 2018-12-12T10:14:21Z date_updated: 2020-07-14T12:47:34Z file_id: '5072' file_name: IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf file_size: 9523746 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 8' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '7075' pubrep_id: '902' quality_controlled: '1' scopus_import: 1 status: public title: FMNL formins boost lamellipodial force generation 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2017' ... --- _id: '660' abstract: - lang: eng text: Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth. acknowledgement: We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.). author: - first_name: Jamie full_name: Rickman, Jamie last_name: Rickman - first_name: Christian F full_name: Düllberg, Christian F id: 459064DC-F248-11E8-B48F-1D18A9856A87 last_name: Düllberg orcid: 0000-0001-6335-9748 - first_name: Nicholas full_name: Cade, Nicholas last_name: Cade - first_name: Lewis full_name: Griffin, Lewis last_name: Griffin - first_name: Thomas full_name: Surrey, Thomas last_name: Surrey citation: ama: Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 2017;114(13):3427-3432. doi:10.1073/pnas.1620274114 apa: Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., & Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1620274114 chicago: Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1620274114. ieee: J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” PNAS, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017. ista: Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432. mla: Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114. short: J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432. date_created: 2018-12-11T11:47:46Z date_published: 2017-03-28T00:00:00Z date_updated: 2021-01-12T08:08:09Z day: '28' department: - _id: MaLo doi: 10.1073/pnas.1620274114 external_id: pmid: - '28280102' intvolume: ' 114' issue: '13' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/ month: '03' oa: 1 oa_version: Submitted Version page: 3427 - 3432 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7073' quality_controlled: '1' scopus_import: 1 status: public title: Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '662' abstract: - lang: eng text: 'We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays.' article_number: '044107' author: - first_name: Liang full_name: Shi, Liang last_name: Shi - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Markus full_name: Rampp, Markus last_name: Rampp - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525 apa: Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4981525 chicago: Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute of Physics, 2017. https://doi.org/10.1063/1.4981525. ieee: L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American Institute of Physics, 2017. ista: Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107. mla: Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:10.1063/1.4981525. short: L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017). date_created: 2018-12-11T11:47:47Z date_published: 2017-04-01T00:00:00Z date_updated: 2021-01-12T08:08:15Z day: '01' department: - _id: BjHo doi: 10.1063/1.4981525 intvolume: ' 29' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.01714 month: '04' oa: 1 oa_version: Submitted Version project: - _id: 2511D90C-B435-11E9-9278-68D0E5697425 grant_number: SFB 963 TP A8 name: Astrophysical instability of currents and turbulences publication: Physics of Fluids publication_identifier: issn: - '10706631' publication_status: published publisher: American Institute of Physics publist_id: '7072' quality_controlled: '1' scopus_import: 1 status: public title: Hydrodynamic turbulence in quasi Keplerian rotating flows type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2017' ... --- _id: '663' abstract: - lang: eng text: 'In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. ' author: - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Sergiy full_name: Bogomolov, Sergiy last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Christian full_name: Schilling, Christian last_name: Schilling - first_name: Yu full_name: Jiang, Yu last_name: Jiang - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: Proceedings of the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814' apa: 'Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In Proceedings of the 20th International Conference on Hybrid Systems (pp. 163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814' chicago: Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems, 163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814. ieee: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United States, 2017, pp. 163–172. ista: 'Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.' mla: Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814. short: H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172. conference: end_date: 2017-04-20 location: Pittsburgh, PA, United States name: 'HSCC: Hybrid Systems Computation and Control ' start_date: 2017-04-18 date_created: 2018-12-11T11:47:47Z date_published: 2017-04-01T00:00:00Z date_updated: 2021-01-12T08:08:17Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1145/3049797.3049814 file: - access_level: open_access checksum: b7667434cbf5b5f0ade3bea1dbe5bf63 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:20Z date_updated: 2020-07-14T12:47:34Z file_id: '4873' file_name: IST-2017-817-v1+1_p163-kong.pdf file_size: 1650530 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 163 - 172 publication: Proceedings of the 20th International Conference on Hybrid Systems publication_identifier: isbn: - 978-145034590-3 publication_status: published publisher: ACM publist_id: '7067' pubrep_id: '817' quality_controlled: '1' scopus_import: 1 status: public title: Safety verification of nonlinear hybrid systems based on invariant clusters type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '667' abstract: - lang: eng text: Perinatal exposure to penicillin may result in longlasting gut and behavioral changes. article_number: '2786' author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. The antisocial side of antibiotics. Science Translational Medicine. 2017;9(387). doi:10.1126/scitranslmed.aan2786 apa: Novarino, G. (2017). The antisocial side of antibiotics. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786 chicago: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786. ieee: G. Novarino, “The antisocial side of antibiotics,” Science Translational Medicine, vol. 9, no. 387. American Association for the Advancement of Science, 2017. ista: Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786. mla: Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine, vol. 9, no. 387, 2786, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan2786. short: G. Novarino, Science Translational Medicine 9 (2017). date_created: 2018-12-11T11:47:48Z date_published: 2017-04-26T00:00:00Z date_updated: 2021-01-12T08:08:30Z day: '26' department: - _id: GaNo doi: 10.1126/scitranslmed.aan2786 intvolume: ' 9' issue: '387' language: - iso: eng month: '04' oa_version: None publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '7060' quality_controlled: '1' scopus_import: 1 status: public title: The antisocial side of antibiotics type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '668' abstract: - lang: eng text: Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading. article_type: original author: - first_name: Markus full_name: Horsthemke, Markus last_name: Horsthemke - first_name: Anne full_name: Bachg, Anne last_name: Bachg - first_name: Katharina full_name: Groll, Katharina last_name: Groll - first_name: Sven full_name: Moyzio, Sven last_name: Moyzio - first_name: Barbara full_name: Müther, Barbara last_name: Müther - first_name: Sandra full_name: Hemkemeyer, Sandra last_name: Hemkemeyer - first_name: Roland full_name: Wedlich Söldner, Roland last_name: Wedlich Söldner - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Sebastian full_name: Tacke, Sebastian last_name: Tacke - first_name: Martin full_name: Bähler, Martin last_name: Bähler - first_name: Peter full_name: Hanley, Peter last_name: Hanley citation: ama: Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 2017;292(17):7258-7273. doi:10.1074/jbc.M116.766923 apa: Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.766923 chicago: Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther, Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2017. https://doi.org/10.1074/jbc.M116.766923. ieee: M. Horsthemke et al., “Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” Journal of Biological Chemistry, vol. 292, no. 17. American Society for Biochemistry and Molecular Biology, pp. 7258–7273, 2017. ista: Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 292(17), 7258–7273. mla: Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry, vol. 292, no. 17, American Society for Biochemistry and Molecular Biology, 2017, pp. 7258–73, doi:10.1074/jbc.M116.766923. short: M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R. Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological Chemistry 292 (2017) 7258–7273. date_created: 2018-12-11T11:47:49Z date_published: 2017-04-28T00:00:00Z date_updated: 2021-01-12T08:08:34Z day: '28' ddc: - '570' department: - _id: MiSi doi: 10.1074/jbc.M116.766923 file: - access_level: open_access checksum: d488162874326a4bb056065fa549dc4a content_type: application/pdf creator: dernst date_created: 2019-10-24T15:25:42Z date_updated: 2020-07-14T12:47:37Z file_id: '6971' file_name: 2017_JBC_Horsthemke.pdf file_size: 5647880 relation: main_file file_date_updated: 2020-07-14T12:47:37Z has_accepted_license: '1' intvolume: ' 292' issue: '17' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 7258 - 7273 publication: Journal of Biological Chemistry publication_identifier: issn: - '00219258' publication_status: published publisher: American Society for Biochemistry and Molecular Biology publist_id: '7059' quality_controlled: '1' scopus_import: 1 status: public title: Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 292 year: '2017' ... --- _id: '669' abstract: - lang: eng text: 'The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. ' article_processing_charge: No article_type: original author: - first_name: Lukáš full_name: Synek, Lukáš last_name: Synek - first_name: Nemanja full_name: Vukašinović, Nemanja last_name: Vukašinović - first_name: Ivan full_name: Kulich, Ivan last_name: Kulich - first_name: Michal full_name: Hála, Michal last_name: Hála - first_name: Klára full_name: Aldorfová, Klára last_name: Aldorfová - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Viktor full_name: Žárský, Viktor last_name: Žárský citation: ama: Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 2017;174(1):223-240. doi:10.1104/pp.16.01282 apa: Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych, M., & Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01282 chicago: Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová, Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01282. ieee: L. Synek et al., “EXO70C2 is a key regulatory factor for optimal tip growth of pollen,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 223–240, 2017. ista: Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 174(1), 223–240. mla: Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 223–40, doi:10.1104/pp.16.01282. short: L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240. date_created: 2018-12-11T11:47:49Z date_published: 2017-05-01T00:00:00Z date_updated: 2021-01-12T08:08:35Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1104/pp.16.01282 external_id: pmid: - '28356503' file: - access_level: open_access checksum: 97155acc6aa5f0d0a78e0589a932fe02 content_type: application/pdf creator: dernst date_created: 2019-11-18T16:16:18Z date_updated: 2020-07-14T12:47:37Z file_id: '7041' file_name: 2017_PlantPhysio_Synek.pdf file_size: 2176903 relation: main_file file_date_updated: 2020-07-14T12:47:37Z has_accepted_license: '1' intvolume: ' 174' issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 223 - 240 pmid: 1 publication: Plant Physiology publication_identifier: issn: - '00320889' publication_status: published publisher: American Society of Plant Biologists publist_id: '7058' quality_controlled: '1' scopus_import: 1 status: public title: EXO70C2 is a key regulatory factor for optimal tip growth of pollen type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 174 year: '2017' ... --- _id: '671' abstract: - lang: eng text: Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation. article_processing_charge: Yes (in subscription journal) author: - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Vaquero full_name: Martinez, Vaquero last_name: Martinez - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. PNAS. 2017;114(18):4715-4720. doi:10.1073/pnas.1621239114 apa: Hilbe, C., Martinez, V., Chatterjee, K., & Nowak, M. (2017). Memory-n strategies of direct reciprocity. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1621239114 chicago: Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621239114. ieee: C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” PNAS, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017. ista: Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720. mla: Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” PNAS, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:10.1073/pnas.1621239114. short: C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720. date_created: 2018-12-11T11:47:50Z date_published: 2017-05-02T00:00:00Z date_updated: 2021-01-12T08:08:37Z day: '02' department: - _id: KrCh doi: 10.1073/pnas.1621239114 ec_funded: 1 external_id: pmid: - '28420786' intvolume: ' 114' issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/ month: '05' oa: 1 oa_version: Published Version page: 4715 - 4720 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _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: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7053' quality_controlled: '1' scopus_import: 1 status: public title: Memory-n strategies of direct reciprocity type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '670' abstract: - lang: eng text: We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears. article_processing_charge: No article_type: original author: - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: Damien full_name: Rohmer, Damien last_name: Rohmer - first_name: Stefanie full_name: Hahmann, Stefanie last_name: Hahmann citation: ama: Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. Computer Graphics Forum. 2017;36(2):95-106. doi:10.1111/cgf.13110 apa: Schreck, C., Rohmer, D., & Hahmann, S. (2017). Interactive paper tearing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13110 chicago: Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” Computer Graphics Forum. Wiley, 2017. https://doi.org/10.1111/cgf.13110. ieee: C. Schreck, D. Rohmer, and S. Hahmann, “Interactive paper tearing,” Computer Graphics Forum, vol. 36, no. 2. Wiley, pp. 95–106, 2017. ista: Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106. mla: Schreck, Camille, et al. “Interactive Paper Tearing.” Computer Graphics Forum, vol. 36, no. 2, Wiley, 2017, pp. 95–106, doi:10.1111/cgf.13110. short: C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106. date_created: 2018-12-11T11:47:49Z date_published: 2017-05-01T00:00:00Z date_updated: 2021-01-12T08:08:37Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.13110 intvolume: ' 36' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf month: '05' oa: 1 oa_version: Published Version page: 95 - 106 project: - _id: 25357BD2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 24352-N23 name: 'Deep Pictures: Creating Visual and Haptic Vector Images' publication: Computer Graphics Forum publication_identifier: issn: - '01677055' publication_status: published publisher: Wiley publist_id: '7056' quality_controlled: '1' scopus_import: 1 status: public title: Interactive paper tearing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2017' ... --- _id: '672' abstract: - lang: eng text: Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration. article_processing_charge: Yes author: - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner - first_name: Matthias full_name: Mehling, Matthias id: 3C23B994-F248-11E8-B48F-1D18A9856A87 last_name: Mehling orcid: 0000-0001-8599-1226 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Vaahtomeri K, Brown M, Hauschild R, et al. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 2017;19(5):902-909. doi:10.1016/j.celrep.2017.04.027 apa: Vaahtomeri, K., Brown, M., Hauschild, R., de Vries, I., Leithner, A. F., Mehling, M., … Sixt, M. K. (2017). Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.027 chicago: Vaahtomeri, Kari, Markus Brown, Robert Hauschild, Ingrid de Vries, Alexander F Leithner, Matthias Mehling, Walter Kaufmann, and Michael K Sixt. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.027. ieee: K. Vaahtomeri et al., “Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia,” Cell Reports, vol. 19, no. 5. Cell Press, pp. 902–909, 2017. ista: Vaahtomeri K, Brown M, Hauschild R, de Vries I, Leithner AF, Mehling M, Kaufmann W, Sixt MK. 2017. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 19(5), 902–909. mla: Vaahtomeri, Kari, et al. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports, vol. 19, no. 5, Cell Press, 2017, pp. 902–09, doi:10.1016/j.celrep.2017.04.027. short: K. Vaahtomeri, M. Brown, R. Hauschild, I. de Vries, A.F. Leithner, M. Mehling, W. Kaufmann, M.K. Sixt, Cell Reports 19 (2017) 902–909. date_created: 2018-12-11T11:47:50Z date_published: 2017-05-02T00:00:00Z date_updated: 2023-02-23T12:50:09Z day: '02' ddc: - '570' department: - _id: MiSi - _id: Bio - _id: EM-Fac doi: 10.1016/j.celrep.2017.04.027 ec_funded: 1 file: - access_level: open_access checksum: 8fdddaab1f1d76a6ec9ca94dcb6b07a2 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:54Z date_updated: 2020-07-14T12:47:38Z file_id: '5109' file_name: IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf file_size: 2248814 relation: main_file file_date_updated: 2020-07-14T12:47:38Z has_accepted_license: '1' intvolume: ' 19' issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 902 - 909 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) publication: Cell Reports publication_identifier: issn: - '22111247' publication_status: published publisher: Cell Press publist_id: '7052' pubrep_id: '900' quality_controlled: '1' scopus_import: 1 status: public title: Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2017' ... --- _id: '674' abstract: - lang: eng text: Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo. author: - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Veronika full_name: Bierbaum, Veronika id: 3FD04378-F248-11E8-B48F-1D18A9856A87 last_name: Bierbaum - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Teresa full_name: Tarrant, Teresa last_name: Tarrant - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Schwarz J, Bierbaum V, Vaahtomeri K, et al. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 2017;27(9):1314-1325. doi:10.1016/j.cub.2017.04.004 apa: Schwarz, J., Bierbaum, V., Vaahtomeri, K., Hauschild, R., Brown, M., de Vries, I., … Sixt, M. K. (2017). Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.04.004 chicago: Schwarz, Jan, Veronika Bierbaum, Kari Vaahtomeri, Robert Hauschild, Markus Brown, Ingrid de Vries, Alexander F Leithner, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.04.004. ieee: J. Schwarz et al., “Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6,” Current Biology, vol. 27, no. 9. Cell Press, pp. 1314–1325, 2017. ista: Schwarz J, Bierbaum V, Vaahtomeri K, Hauschild R, Brown M, de Vries I, Leithner AF, Reversat A, Merrin J, Tarrant T, Bollenbach MT, Sixt MK. 2017. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 27(9), 1314–1325. mla: Schwarz, Jan, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology, vol. 27, no. 9, Cell Press, 2017, pp. 1314–25, doi:10.1016/j.cub.2017.04.004. short: J. Schwarz, V. Bierbaum, K. Vaahtomeri, R. Hauschild, M. Brown, I. de Vries, A.F. Leithner, A. Reversat, J. Merrin, T. Tarrant, M.T. Bollenbach, M.K. Sixt, Current Biology 27 (2017) 1314–1325. date_created: 2018-12-11T11:47:51Z date_published: 2017-05-09T00:00:00Z date_updated: 2023-02-23T12:50:44Z day: '09' department: - _id: MiSi - _id: Bio - _id: NanoFab doi: 10.1016/j.cub.2017.04.004 ec_funded: 1 intvolume: ' 27' issue: '9' language: - iso: eng month: '05' oa_version: None page: 1314 - 1325 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Cell Press publist_id: '7050' quality_controlled: '1' scopus_import: 1 status: public title: Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6 type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2017' ... --- _id: '677' abstract: - lang: eng text: The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR. author: - first_name: Claudio full_name: Lademann, Claudio last_name: Lademann - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Boris full_name: Pfander, Boris last_name: Pfander - first_name: Stefan full_name: Jentsch, Stefan last_name: Jentsch citation: ama: Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 2017;19(7):1294-1303. doi:10.1016/j.celrep.2017.04.051 apa: Lademann, C., Renkawitz, J., Pfander, B., & Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.051 chicago: Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.051. ieee: C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” Cell Reports, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017. ista: Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303. mla: Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:10.1016/j.celrep.2017.04.051. short: C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303. date_created: 2018-12-11T11:47:52Z date_published: 2017-05-16T00:00:00Z date_updated: 2021-01-12T08:08:57Z day: '16' ddc: - '570' department: - _id: MiSi doi: 10.1016/j.celrep.2017.04.051 file: - access_level: open_access checksum: efc7287d9c6354983cb151880e9ad72a content_type: application/pdf creator: system date_created: 2018-12-12T10:15:48Z date_updated: 2020-07-14T12:47:40Z file_id: '5171' file_name: IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf file_size: 3005610 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 19' issue: '7' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1294 - 1303 publication: Cell Reports publication_identifier: issn: - '22111247' publication_status: published publisher: Cell Press publist_id: '7046' pubrep_id: '899' quality_controlled: '1' scopus_import: 1 status: public title: The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2017' ... --- _id: '678' abstract: - lang: eng text: The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development. author: - first_name: Nicoletta full_name: Petridou, Nicoletta id: 2A003F6C-F248-11E8-B48F-1D18A9856A87 last_name: Petridou orcid: 0000-0002-8451-1195 - first_name: Zoltan P full_name: Spiro, Zoltan P id: 426AD026-F248-11E8-B48F-1D18A9856A87 last_name: Spiro - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Petridou N, Spiro ZP, Heisenberg C-PJ. Multiscale force sensing in development. Nature Cell Biology. 2017;19(6):581-588. doi:10.1038/ncb3524 apa: Petridou, N., Spiro, Z. P., & Heisenberg, C.-P. J. (2017). Multiscale force sensing in development. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3524 chicago: Petridou, Nicoletta, Zoltan P Spiro, and Carl-Philipp J Heisenberg. “Multiscale Force Sensing in Development.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3524. ieee: N. Petridou, Z. P. Spiro, and C.-P. J. Heisenberg, “Multiscale force sensing in development,” Nature Cell Biology, vol. 19, no. 6. Nature Publishing Group, pp. 581–588, 2017. ista: Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588. mla: Petridou, Nicoletta, et al. “Multiscale Force Sensing in Development.” Nature Cell Biology, vol. 19, no. 6, Nature Publishing Group, 2017, pp. 581–88, doi:10.1038/ncb3524. short: N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588. date_created: 2018-12-11T11:47:53Z date_published: 2017-05-31T00:00:00Z date_updated: 2021-01-12T08:08:59Z day: '31' department: - _id: CaHe doi: 10.1038/ncb3524 intvolume: ' 19' issue: '6' language: - iso: eng month: '05' oa_version: None page: 581 - 588 project: - _id: 25236028-B435-11E9-9278-68D0E5697425 grant_number: ALTF534-2016 name: The generation and function of anisotropic tissue tension in zebrafish epiboly (EMBO Fellowship) publication: Nature Cell Biology publication_identifier: issn: - '14657392' publication_status: published publisher: Nature Publishing Group publist_id: '7040' quality_controlled: '1' scopus_import: 1 status: public title: Multiscale force sensing in development type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2017' ... --- _id: '681' abstract: - lang: eng text: Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information. In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile where all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players' objective, then the objective of every player is violated. We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games. We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games. article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Emmanuel full_name: Filiot, Emmanuel last_name: Filiot - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: ama: Chatterjee K, Doyen L, Filiot E, Raskin J. Doomsday equilibria for omega-regular games. Information and Computation. 2017;254:296-315. doi:10.1016/j.ic.2016.10.012 apa: Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J. (2017). Doomsday equilibria for omega-regular games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.012 chicago: Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean Raskin. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.012. ieee: K. Chatterjee, L. Doyen, E. Filiot, and J. Raskin, “Doomsday equilibria for omega-regular games,” Information and Computation, vol. 254. Elsevier, pp. 296–315, 2017. ista: Chatterjee K, Doyen L, Filiot E, Raskin J. 2017. Doomsday equilibria for omega-regular games. Information and Computation. 254, 296–315. mla: Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation, vol. 254, Elsevier, 2017, pp. 296–315, doi:10.1016/j.ic.2016.10.012. short: K. Chatterjee, L. Doyen, E. Filiot, J. Raskin, Information and Computation 254 (2017) 296–315. date_created: 2018-12-11T11:47:53Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-21T16:06:02Z day: '01' department: - _id: KrCh doi: 10.1016/j.ic.2016.10.012 ec_funded: 1 external_id: arxiv: - '1311.3238' intvolume: ' 254' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.3238 month: '06' oa: 1 oa_version: Submitted Version page: 296 - 315 project: - _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 - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Information and Computation publication_identifier: issn: - '08905401' publication_status: published publisher: Elsevier publist_id: '7036' quality_controlled: '1' related_material: record: - id: '10885' relation: earlier_version status: public scopus_import: '1' status: public title: Doomsday equilibria for omega-regular games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 254 year: '2017' ... --- _id: '6841' abstract: - lang: eng text: In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified. author: - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Martius GS, Lampert C. Extrapolation and learning equations. In: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations; 2017.' apa: 'Martius, G. S., & Lampert, C. (2017). Extrapolation and learning equations. In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. Toulon, France: International Conference on Learning Representations.' chicago: Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations, 2017. ieee: G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, Toulon, France, 2017. ista: 'Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations.' mla: Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017. short: G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017. conference: end_date: 2017-04-26 location: Toulon, France name: 'ICLR: International Conference on Learning Representations' start_date: 2017-04-24 date_created: 2019-09-01T22:01:00Z date_published: 2017-02-21T00:00:00Z date_updated: 2021-01-12T08:09:17Z day: '21' department: - _id: ChLa ec_funded: 1 external_id: arxiv: - '1610.02995' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.02995 month: '02' oa: 1 oa_version: Preprint project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings publication_status: published publisher: International Conference on Learning Representations quality_controlled: '1' scopus_import: 1 status: public title: Extrapolation and learning equations type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '684' abstract: - lang: eng text: We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic. article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Nir full_name: Piterman, Nir last_name: Piterman citation: ama: Chatterjee K, Piterman N. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 2017;82(2):420-452. doi:10.1017/jsl.2016.71 apa: Chatterjee, K., & Piterman, N. (2017). Obligation blackwell games and p-automata. Journal of Symbolic Logic. Cambridge University Press. https://doi.org/10.1017/jsl.2016.71 chicago: Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic. Cambridge University Press, 2017. https://doi.org/10.1017/jsl.2016.71. ieee: K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” Journal of Symbolic Logic, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017. ista: Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452. mla: Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:10.1017/jsl.2016.71. short: K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452. date_created: 2018-12-11T11:47:54Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-04-16T12:10:53Z day: '01' department: - _id: KrCh doi: 10.1017/jsl.2016.71 intvolume: ' 82' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1206.5174 month: '06' oa: 1 oa_version: Submitted Version page: 420 - 452 publication: Journal of Symbolic Logic publication_identifier: eissn: - 1943-5886 issn: - 0022-4812 publication_status: published publisher: Cambridge University Press publist_id: '7026' quality_controlled: '1' scopus_import: '1' status: public title: Obligation blackwell games and p-automata type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2017' ... --- _id: '685' abstract: - lang: eng text: By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube. author: - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. 2017;145:26-31. doi:10.1016/j.mod.2017.03.005 apa: Briscoe, J., & Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.005 chicago: Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.005. ieee: J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” Mechanisms of Development, vol. 145. Elsevier, pp. 26–31, 2017. ista: Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31. mla: Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 26–31, doi:10.1016/j.mod.2017.03.005. short: J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31. date_created: 2018-12-11T11:47:55Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:20Z day: '01' ddc: - '571' department: - _id: AnKi doi: 10.1016/j.mod.2017.03.005 ec_funded: 1 external_id: pmid: - '28366718' file: - access_level: open_access checksum: 727043d2e4199fbef6b3704e6d1ac105 content_type: application/pdf creator: dernst date_created: 2019-04-17T07:58:48Z date_updated: 2020-07-14T12:47:42Z file_id: '6335' file_name: 2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf file_size: 652313 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 145' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 26 - 31 pmid: 1 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord publication: Mechanisms of Development publication_identifier: issn: - '09254773' publication_status: published publisher: Elsevier publist_id: '7025' pubrep_id: '985' quality_controlled: '1' scopus_import: 1 status: public title: The physics of development 100 years after D'Arcy Thompson's “on growth and form” type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 145 year: '2017' ... --- _id: '688' abstract: - lang: eng text: 'We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. ' alternative_title: - LIPIcs author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: 'Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:10.4230/LIPIcs.SoCG.2017.39' apa: 'Edelsbrunner, H., & Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.39' chicago: Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.39. ieee: H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916. ista: Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916. mla: Edelsbrunner, Herbert, and Hubert Wagner. Topological Data Analysis with Bregman Divergences. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:10.4230/LIPIcs.SoCG.2017.39. short: H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916. conference: end_date: 2017-07-07 location: Brisbane, Australia name: Symposium on Computational Geometry, SoCG start_date: 2017-07-04 date_created: 2018-12-11T11:47:56Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:26Z day: '01' ddc: - '514' - '516' department: - _id: HeEd - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2017.39 file: - access_level: open_access checksum: 067ab0cb3f962bae6c3af6bf0094e0f3 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:03Z date_updated: 2020-07-14T12:47:42Z file_id: '4856' file_name: IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf file_size: 990546 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 77' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 391-3916 publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7021' pubrep_id: '895' quality_controlled: '1' scopus_import: 1 status: public title: Topological data analysis with Bregman divergences 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2017' ... --- _id: '687' abstract: - lang: eng text: Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs. author: - first_name: Ben full_name: Davison, Ben id: 4634AB1E-F248-11E8-B48F-1D18A9856A87 last_name: Davison orcid: 0000-0002-8944-4390 citation: ama: Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053 apa: Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053 chicago: Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053. ieee: B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017. ista: Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703. mla: Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053. short: B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703. date_created: 2018-12-11T11:47:55Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:24Z day: '01' department: - _id: TaHa doi: 10.1093/qmath/haw053 ec_funded: 1 intvolume: ' 68' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1311.7172 month: '06' oa: 1 oa_version: Submitted Version page: 635 - 703 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Quarterly Journal of Mathematics publication_identifier: issn: - '00335606' publication_status: published publisher: Oxford University Press publist_id: '7022' quality_controlled: '1' scopus_import: 1 status: public title: The critical CoHA of a quiver with potential type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2017' ... --- _id: '686' abstract: - lang: eng text: Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology. author: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006' apa: 'Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006' chicago: 'Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006.' ieee: 'C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017.' ista: 'Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.' mla: 'Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.' short: C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37. date_created: 2018-12-11T11:47:55Z date_published: 2017-06-01T00:00:00Z date_updated: 2021-01-12T08:09:23Z day: '01' department: - _id: CaHe doi: 10.1016/j.mod.2017.03.006 intvolume: ' 145' language: - iso: eng month: '06' oa_version: None page: 32 - 37 publication: Mechanisms of Development publication_identifier: issn: - '09254773' publication_status: published publisher: Elsevier publist_id: '7024' quality_controlled: '1' scopus_import: 1 status: public title: 'D''Arcy Thompson''s ‘on growth and form’: From soap bubbles to tissue self organization' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 145 year: '2017' ... --- _id: '689' abstract: - lang: eng text: Rett syndrome modeling in monkey mirrors the human disorder. article_number: eaan8196 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196 apa: Novarino, G. (2017). Rett syndrome modeling goes simian. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan8196 chicago: Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan8196. ieee: G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017. ista: Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196. mla: Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan8196. short: G. Novarino, Science Translational Medicine 9 (2017). date_created: 2018-12-11T11:47:56Z date_published: 2017-06-07T00:00:00Z date_updated: 2021-01-12T08:09:29Z day: '07' department: - _id: GaNo doi: 10.1126/scitranslmed.aan8196 intvolume: ' 9' issue: '393' language: - iso: eng month: '06' oa_version: None publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '7019' quality_controlled: '1' scopus_import: 1 status: public title: Rett syndrome modeling goes simian type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '693' abstract: - lang: eng text: 'Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ' article_processing_charge: Yes (in subscription journal) author: - first_name: Takafumi full_name: Miki, Takafumi last_name: Miki - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Gerardo full_name: Malagon, Gerardo last_name: Malagon - first_name: Laura full_name: Gomez, Laura last_name: Gomez - first_name: Katsuhiko full_name: Tabuchi, Katsuhiko last_name: Tabuchi - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Alain full_name: Marty, Alain last_name: Marty citation: ama: Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114 apa: Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114 chicago: Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114. ieee: T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017. ista: Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255. mla: Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114. short: T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255. date_created: 2018-12-11T11:47:57Z date_published: 2017-06-27T00:00:00Z date_updated: 2023-02-23T12:54:57Z day: '27' ddc: - '570' department: - _id: EM-Fac - _id: RySh doi: 10.1073/pnas.1704470114 external_id: pmid: - '28607047' file: - access_level: open_access checksum: 2ab75d554f3df4a34d20fa8040589b7e content_type: application/pdf creator: kschuh date_created: 2020-01-03T13:27:29Z date_updated: 2020-07-14T12:47:44Z file_id: '7223' file_name: 2017_PNAS_Miki.pdf file_size: 2721544 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 114' issue: '26' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: E5246 - E5255 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7013' quality_controlled: '1' scopus_import: 1 status: public title: Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '694' abstract: - lang: eng text: A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells. article_type: original author: - first_name: Astrid full_name: Veß, Astrid last_name: Veß - first_name: Ulrich full_name: Blache, Ulrich last_name: Blache - first_name: Laura full_name: Leitner, Laura last_name: Leitner - first_name: Angela full_name: Kurz, Angela last_name: Kurz - first_name: Anja full_name: Ehrenpfordt, Anja last_name: Ehrenpfordt - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Guido full_name: Posern, Guido last_name: Posern citation: ama: Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 2017;130(13):2172-2184. doi:10.1242/jcs.200899 apa: Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., & Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.200899 chicago: Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.200899. ieee: A. Veß et al., “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” Journal of Cell Science, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017. ista: Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184. mla: Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:10.1242/jcs.200899. short: A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184. date_created: 2018-12-11T11:47:58Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:09:41Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1242/jcs.200899 external_id: pmid: - '28515231' file: - access_level: open_access checksum: 42c81a0a4fc3128883b391c3af3f74bc content_type: application/pdf creator: dernst date_created: 2019-10-24T09:43:56Z date_updated: 2020-07-14T12:47:45Z file_id: '6966' file_name: 2017_CellScience_Vess.pdf file_size: 10847596 relation: main_file file_date_updated: 2020-07-14T12:47:45Z has_accepted_license: '1' intvolume: ' 130' issue: '13' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 2172 - 2184 pmid: 1 publication: Journal of Cell Science publication_identifier: issn: - '00219533' publication_status: published publisher: Company of Biologists publist_id: '7008' quality_controlled: '1' scopus_import: 1 status: public title: A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 130 year: '2017' ... --- _id: '697' abstract: - lang: eng text: 'De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. ' alternative_title: - LIPIcs article_number: '39' author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.ICALP.2017.39' apa: 'Pietrzak, K. Z., & Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2017.39' chicago: Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ICALP.2017.39. ieee: 'K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.' ista: 'Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.' mla: Pietrzak, Krzysztof Z., and Maciej Skórski. Non Uniform Attacks against Pseudoentropy. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.ICALP.2017.39. short: K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-07-14 location: Warsaw, Poland name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2017-07-10 date_created: 2018-12-11T11:47:59Z date_published: 2017-07-01T00:00:00Z date_updated: 2021-01-12T08:11:15Z day: '01' ddc: - '005' department: - _id: KrPi doi: 10.4230/LIPIcs.ICALP.2017.39 ec_funded: 1 file: - access_level: open_access checksum: e95618a001692f1af2d68f5fde43bc1f content_type: application/pdf creator: system date_created: 2018-12-12T10:08:40Z date_updated: 2020-07-14T12:47:46Z file_id: '4701' file_name: IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf file_size: 601004 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 80' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7003' pubrep_id: '893' quality_controlled: '1' scopus_import: 1 status: public title: Non uniform attacks against pseudoentropy 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 80 year: '2017' ... --- _id: '698' abstract: - lang: eng text: 'Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. ' author: - first_name: Yejun full_name: Wang, Yejun last_name: Wang - first_name: Mallika full_name: Nagarajan, Mallika last_name: Nagarajan - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Gv full_name: Shivashankar, Gv last_name: Shivashankar citation: ama: Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825 apa: Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825 chicago: Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell. American Society for Cell Biology, 2017. https://doi.org/10.1091/mbc.E16-12-0825. ieee: Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” Molecular Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017. ista: Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009. mla: Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825. short: Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009. date_created: 2018-12-11T11:47:59Z date_published: 2017-07-07T00:00:00Z date_updated: 2021-01-12T08:11:17Z day: '07' ddc: - '519' department: - _id: CaUh doi: 10.1091/mbc.E16-12-0825 file: - access_level: open_access checksum: de01dac9e30970cfa6ae902480a4e04d content_type: application/pdf creator: system date_created: 2018-12-12T10:10:53Z date_updated: 2020-07-14T12:47:46Z file_id: '4844' file_name: IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf file_size: 1086097 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 28' issue: '14' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '07' oa: 1 oa_version: Published Version page: 1997 - 2009 project: - _id: 2530CA10-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 903-N35 name: 'Gaussian Graphical Models: Theory and Applications' publication: Molecular Biology of the Cell publication_identifier: issn: - '10591524' publication_status: published publisher: American Society for Cell Biology publist_id: '7001' pubrep_id: '892' quality_controlled: '1' scopus_import: 1 status: public title: Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2017' ... --- _id: '699' abstract: - lang: eng text: 'In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. ' author: - first_name: Carl full_name: Veller, Carl last_name: Veller - first_name: Laura full_name: Hayward, Laura last_name: Hayward - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X citation: ama: Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114 apa: Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114 chicago: Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114. ieee: C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017. ista: Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405. mla: Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114. short: C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405. date_created: 2018-12-11T11:48:00Z date_published: 2017-07-03T00:00:00Z date_updated: 2021-01-12T08:11:21Z day: '03' department: - _id: KrCh doi: 10.1073/pnas.1702020114 external_id: pmid: - '28630336' intvolume: ' 114' issue: '27' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/ month: '07' oa: 1 oa_version: Submitted Version page: E5396 - E5405 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7002' quality_controlled: '1' scopus_import: 1 status: public title: The red queen and king in finite populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2017' ... --- _id: '700' abstract: - lang: eng text: Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs. article_number: '012404' author: - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Vahid full_name: Salari, Vahid last_name: Salari - first_name: Jack full_name: Tuszynski, Jack last_name: Tuszynski - first_name: Michal full_name: Cifra, Michal last_name: Cifra - first_name: Christoph full_name: Simon, Christoph last_name: Simon citation: ama: Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.012404 apa: Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., & Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.012404 chicago: Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.012404. ieee: S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017. ista: Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404. mla: Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.012404. short: S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017). date_created: 2018-12-11T11:48:00Z date_published: 2017-07-12T00:00:00Z date_updated: 2023-02-23T12:56:35Z day: '12' department: - _id: JoFi doi: 10.1103/PhysRevE.96.012404 ec_funded: 1 intvolume: ' 96' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/pdf/1612.07061.pdf month: '07' oa: 1 oa_version: Submitted Version project: - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics' publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics ' publication_identifier: issn: - '24700045' publication_status: published publisher: American Institute of Physics publist_id: '6997' quality_controlled: '1' scopus_import: 1 status: public title: Optomechanical proposal for monitoring microtubule mechanical vibrations type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 96 year: '2017' ... --- _id: '701' abstract: - lang: eng text: A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2. author: - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 citation: ama: Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 2017;24(3):1-44. apa: Kynčl, J., & Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. International Press. chicago: Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics. International Press, 2017. ieee: J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” The Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, pp. 1–44, 2017. ista: Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44. mla: Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics, vol. 24, no. 3, International Press, 2017, pp. 1–44. short: J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44. date_created: 2018-12-11T11:48:00Z date_published: 2017-07-14T00:00:00Z date_updated: 2021-01-12T08:11:28Z day: '14' ddc: - '500' department: - _id: UlWa file: - access_level: open_access checksum: a431e573e31df13bc0f66de3061006ec content_type: application/pdf creator: system date_created: 2018-12-12T10:14:25Z date_updated: 2020-07-14T12:47:47Z file_id: '5077' file_name: IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf file_size: 544042 relation: main_file file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' intvolume: ' 24' issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 1-44 publication: The Electronic Journal of Combinatorics publication_identifier: issn: - '10778926' publication_status: published publisher: International Press publist_id: '6996' pubrep_id: '984' quality_controlled: '1' status: public title: On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2017' ... --- _id: '702' abstract: - lang: eng text: "Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n" author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 2017;9(399):eaao0972. doi:10.1126/scitranslmed.aao0972 apa: Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao0972 chicago: Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao0972. ieee: G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” Science Translational Medicine, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017. ista: Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972. mla: Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:10.1126/scitranslmed.aao0972. short: G. Novarino, Science Translational Medicine 9 (2017) eaao0972. date_created: 2018-12-11T11:48:01Z date_published: 2017-07-19T00:00:00Z date_updated: 2021-01-12T08:11:31Z day: '19' department: - _id: GaNo doi: 10.1126/scitranslmed.aao0972 intvolume: ' 9' issue: '399' language: - iso: eng month: '07' oa_version: None page: eaao0972 publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '6993' quality_controlled: '1' scopus_import: 1 status: public title: The riddle of CHD8 haploinsufficiency in autism spectrum disorder type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '706' abstract: - lang: eng text: A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse. author: - first_name: Xiaoqi full_name: Geng, Xiaoqi id: 3395256A-F248-11E8-B48F-1D18A9856A87 last_name: Geng - first_name: Tomohiko full_name: Maruo, Tomohiko last_name: Maruo - first_name: Kenji full_name: Mandai, Kenji last_name: Mandai - first_name: Irwan full_name: Supriyanto, Irwan last_name: Supriyanto - first_name: Muneaki full_name: Miyata, Muneaki last_name: Miyata - first_name: Shotaro full_name: Sakakibara, Shotaro last_name: Sakakibara - first_name: Akira full_name: Mizoguchi, Akira last_name: Mizoguchi - first_name: Yoshimi full_name: Takai, Yoshimi last_name: Takai - first_name: Masahiro full_name: Mori, Masahiro last_name: Mori citation: ama: Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 2017;22(8):715-722. doi:10.1111/gtc.12508 apa: Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. Wiley-Blackwell. https://doi.org/10.1111/gtc.12508 chicago: Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells. Wiley-Blackwell, 2017. https://doi.org/10.1111/gtc.12508. ieee: X. Geng et al., “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” Genes to Cells, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017. ista: Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722. mla: Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:10.1111/gtc.12508. short: X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722. date_created: 2018-12-11T11:48:02Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:11:37Z day: '01' department: - _id: PeJo doi: 10.1111/gtc.12508 intvolume: ' 22' issue: '8' language: - iso: eng month: '08' oa_version: None page: 715 - 722 publication: Genes to Cells publication_identifier: issn: - '13569597' publication_status: published publisher: Wiley-Blackwell publist_id: '6987' quality_controlled: '1' scopus_import: 1 status: public title: Roles of afadin in functional differentiations of hippocampal mossy fiber synapse type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2017' ... --- _id: '707' abstract: - lang: eng text: We answer a question of M. Gromov on the waist of the unit ball. author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Roman full_name: Karasev, Roman last_name: Karasev citation: ama: Akopyan A, Karasev R. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 2017;49(4):690-693. doi:10.1112/blms.12062 apa: Akopyan, A., & Karasev, R. (2017). A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. Wiley-Blackwell. https://doi.org/10.1112/blms.12062 chicago: Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society. Wiley-Blackwell, 2017. https://doi.org/10.1112/blms.12062. ieee: A. Akopyan and R. Karasev, “A tight estimate for the waist of the ball ,” Bulletin of the London Mathematical Society, vol. 49, no. 4. Wiley-Blackwell, pp. 690–693, 2017. ista: Akopyan A, Karasev R. 2017. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 49(4), 690–693. mla: Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society, vol. 49, no. 4, Wiley-Blackwell, 2017, pp. 690–93, doi:10.1112/blms.12062. short: A. Akopyan, R. Karasev, Bulletin of the London Mathematical Society 49 (2017) 690–693. date_created: 2018-12-11T11:48:02Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:11:41Z day: '01' department: - _id: HeEd doi: 10.1112/blms.12062 ec_funded: 1 intvolume: ' 49' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1608.06279 month: '08' oa: 1 oa_version: Preprint page: 690 - 693 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Bulletin of the London Mathematical Society publication_identifier: issn: - '00246093' publication_status: published publisher: Wiley-Blackwell publist_id: '6982' quality_controlled: '1' scopus_import: 1 status: public title: 'A tight estimate for the waist of the ball ' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2017' ... --- _id: '708' abstract: - lang: eng text: 'In the developing and adult brain, oligodendrocyte precursor cells (OPCs) are influenced by neuronal activity: they are involved in synaptic signaling with neurons, and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing. An important question that has been unanswered is whether OPCs can discriminate different patterns of neuronal activity and respond to them in a distinct way. Here, we demonstrate in brain slices that the pattern of neuronal activity determines the functional changes triggered at synapses between axons and OPCs. Furthermore, we show that stimulation of the corpus callosum at different frequencies in vivo affects proliferation and differentiation of OPCs in a dissimilar way. Our findings suggest that neurons do not influence OPCs in “all-or-none” fashion but use their firing pattern to tune the response and behavior of these nonneuronal cells.' article_number: e2001993 author: - first_name: Balint full_name: Nagy, Balint id: 30F830CE-02D1-11E9-9BAA-DAF4881429F2 last_name: Nagy orcid: 0000-0002-4002-4686 - first_name: Anahit full_name: Hovhannisyan, Anahit last_name: Hovhannisyan - first_name: Ruxandra full_name: Barzan, Ruxandra last_name: Barzan - first_name: Ting full_name: Chen, Ting last_name: Chen - first_name: Maria full_name: Kukley, Maria last_name: Kukley citation: ama: Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 2017;15(8). doi:10.1371/journal.pbio.2001993 apa: Nagy, B., Hovhannisyan, A., Barzan, R., Chen, T., & Kukley, M. (2017). Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001993 chicago: Nagy, Balint, Anahit Hovhannisyan, Ruxandra Barzan, Ting Chen, and Maria Kukley. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001993. ieee: B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, and M. Kukley, “Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum,” PLoS Biology, vol. 15, no. 8. Public Library of Science, 2017. ista: Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. 2017. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 15(8), e2001993. mla: Nagy, Balint, et al. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology, vol. 15, no. 8, e2001993, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001993. short: B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, M. Kukley, PLoS Biology 15 (2017). date_created: 2018-12-11T11:48:03Z date_published: 2017-08-22T00:00:00Z date_updated: 2021-01-12T08:11:45Z day: '22' ddc: - '576' - '610' department: - _id: SaSi doi: 10.1371/journal.pbio.2001993 file: - access_level: open_access checksum: 0c974f430682dc832ea7b27ab5a93124 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:35Z date_updated: 2020-07-14T12:47:49Z file_id: '5156' file_name: IST-2017-889-v1+1_journal.pbio.2001993.pdf file_size: 18155365 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 15' issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: PLoS Biology publication_identifier: issn: - '15449173' publication_status: published publisher: Public Library of Science publist_id: '6983' pubrep_id: '889' quality_controlled: '1' scopus_import: 1 status: public title: Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum 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: 15 year: '2017' ... --- _id: '709' abstract: - lang: eng text: Adipose tissues play key roles in energy homeostasis. Brown adipocytes and beige adipocytes in white adipose tissue (WAT) share the similar characters of thermogenesis, both of them could be potential targets for obesity management. Several thermo-sensitive transient receptor potential channels (thermoTRPs) are shown to be involved in adipocyte biology. However, the expression pattern of thermoTRPs in adipose tissues from obese mice is still unknown. The mRNA expression of thermoTRPs in subcutaneous WAT (sWAT) and interscapular brown adipose tissue (iBAT) from lean and obese mice were measured using reverse transcriptase-quantitative PCRs (RT-qPCR). The results demonstrated that all 10 thermoTRPs are expressed in both iBAT and sWAT, and without significant difference in the mRNA expression level of thermoTRPs between these two tissues. Moreover, Trpv1 and Trpv3 mRNA expression levels in both iBAT and sWAT were significantly decreased in high fat diet (HFD)-induced obese mice and db/db (leptin receptor deficient) mice. Trpm2 mRNA expression level was significantly decreased only in sWAT from HFD-induced obese mice and db/db mice. On the other hand, Trpv2 and Trpv4 mRNA expression levels in iBAT and sWAT were significantly increased in HFD-induced obese mice and db/db mice. Taken together, we conclude that all 10 thermoTRPs are expressed in iBAT and sWAT. And several thermoTRPs differentially expressed in adipose tissues from HFD-induced obese mice and db/db mice, suggesting a potential involvement in anti-obesity regulations. author: - first_name: Wuping full_name: Sun, Wuping last_name: Sun - first_name: Chen full_name: Li, Chen last_name: Li - first_name: Yonghong full_name: Zhang, Yonghong last_name: Zhang - first_name: Changyu full_name: Jiang, Changyu last_name: Jiang - first_name: Ming-Zhu full_name: Zhai, Ming-Zhu id: 34009CFA-F248-11E8-B48F-1D18A9856A87 last_name: Zhai - first_name: Qian full_name: Zhou, Qian last_name: Zhou - first_name: Lizu full_name: Xiao, Lizu last_name: Xiao - first_name: Qiwen full_name: Deng, Qiwen last_name: Deng citation: ama: Sun W, Li C, Zhang Y, et al. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 2017;41(8):908-913. doi:10.1002/cbin.10783 apa: Sun, W., Li, C., Zhang, Y., Jiang, C., Zhai, M.-Z., Zhou, Q., … Deng, Q. (2017). Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. Wiley-Blackwell. https://doi.org/10.1002/cbin.10783 chicago: Sun, Wuping, Chen Li, Yonghong Zhang, Changyu Jiang, Ming-Zhu Zhai, Qian Zhou, Lizu Xiao, and Qiwen Deng. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International. Wiley-Blackwell, 2017. https://doi.org/10.1002/cbin.10783. ieee: W. Sun et al., “Gene expression changes of thermo sensitive transient receptor potential channels in obese mice,” Cell Biology International, vol. 41, no. 8. Wiley-Blackwell, pp. 908–913, 2017. ista: Sun W, Li C, Zhang Y, Jiang C, Zhai M-Z, Zhou Q, Xiao L, Deng Q. 2017. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 41(8), 908–913. mla: Sun, Wuping, et al. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International, vol. 41, no. 8, Wiley-Blackwell, 2017, pp. 908–13, doi:10.1002/cbin.10783. short: W. Sun, C. Li, Y. Zhang, C. Jiang, M.-Z. Zhai, Q. Zhou, L. Xiao, Q. Deng, Cell Biology International 41 (2017) 908–913. date_created: 2018-12-11T11:48:04Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:11:47Z day: '01' department: - _id: RySh doi: 10.1002/cbin.10783 intvolume: ' 41' issue: '8' language: - iso: eng month: '08' oa_version: None page: 908 - 913 publication: Cell Biology International publication_identifier: issn: - '10656995' publication_status: published publisher: Wiley-Blackwell publist_id: '6981' quality_controlled: '1' scopus_import: 1 status: public title: Gene expression changes of thermo sensitive transient receptor potential channels in obese mice type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2017' ... --- _id: '710' abstract: - lang: eng text: 'We revisit the problem of estimating entropy of discrete distributions from independent samples, studied recently by Acharya, Orlitsky, Suresh and Tyagi (SODA 2015), improving their upper and lower bounds on the necessary sample size n. For estimating Renyi entropy of order alpha, up to constant accuracy and error probability, we show the following * Upper bounds n = O(1) 2^{(1-1/alpha)H_alpha} for integer alpha>1, as the worst case over distributions with Renyi entropy equal to H_alpha. * Lower bounds n = Omega(1) K^{1-1/alpha} for any real alpha>1, with the constant being an inverse polynomial of the accuracy, as the worst case over all distributions on K elements. Our upper bounds essentially replace the alphabet size by a factor exponential in the entropy, which offers improvements especially in low or medium entropy regimes (interesting for example in anomaly detection). As for the lower bounds, our proof explicitly shows how the complexity depends on both alphabet and accuracy, partially solving the open problem posted in previous works. The argument for upper bounds derives a clean identity for the variance of falling-power sum of a multinomial distribution. Our approach for lower bounds utilizes convex optimization to find a distribution with possibly worse estimation performance, and may be of independent interest as a tool to work with Le Cam’s two point method. ' alternative_title: - LIPIcs article_number: '20' author: - first_name: Maciej full_name: Obremski, Maciej last_name: Obremski - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Obremski M, Skórski M. Renyi entropy estimation revisited. In: Vol 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20' apa: 'Obremski, M., & Skórski, M. (2017). Renyi entropy estimation revisited (Vol. 81). Presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20' chicago: Obremski, Maciej, and Maciej Skórski. “Renyi Entropy Estimation Revisited,” Vol. 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20. ieee: M. Obremski and M. Skórski, “Renyi entropy estimation revisited,” presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA, 2017, vol. 81. ista: Obremski M, Skórski M. 2017. Renyi entropy estimation revisited. 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, LIPIcs, vol. 81, 20. mla: Obremski, Maciej, and Maciej Skórski. Renyi Entropy Estimation Revisited. Vol. 81, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20. short: M. Obremski, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-18 location: Berkeley, USA name: 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX start_date: 2017-08-18 date_created: 2018-12-11T11:48:04Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:11:50Z day: '01' ddc: - '005' - '600' department: - _id: KrPi doi: 10.4230/LIPIcs.APPROX-RANDOM.2017.20 ec_funded: 1 file: - access_level: open_access checksum: 89225c7dcec2c93838458c9102858985 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:10Z date_updated: 2020-07-14T12:47:49Z file_id: '4991' file_name: IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf file_size: 604813 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 81' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6979' pubrep_id: '888' quality_controlled: '1' scopus_import: 1 status: public title: Renyi entropy estimation revisited 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2017' ... --- _id: '713' abstract: - lang: eng text: To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta. article_number: e25125 author: - first_name: Daniel full_name: Andergassen, Daniel last_name: Andergassen - first_name: Christoph full_name: Dotter, Christoph id: 4C66542E-F248-11E8-B48F-1D18A9856A87 last_name: Dotter - first_name: Dyniel full_name: Wenzel, Dyniel last_name: Wenzel - first_name: Verena full_name: Sigl, Verena last_name: Sigl - first_name: Philipp full_name: Bammer, Philipp last_name: Bammer - first_name: Markus full_name: Muckenhuber, Markus last_name: Muckenhuber - first_name: Daniela full_name: Mayer, Daniela last_name: Mayer - first_name: Tomasz full_name: Kulinski, Tomasz last_name: Kulinski - first_name: Hans full_name: Theussl, Hans last_name: Theussl - first_name: Josef full_name: Penninger, Josef last_name: Penninger - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Denise full_name: Barlow, Denise last_name: Barlow - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler - first_name: Quanah full_name: Hudson, Quanah last_name: Hudson citation: ama: Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 2017;6. doi:10.7554/eLife.25125 apa: Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber, M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25125 chicago: Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25125. ieee: D. Andergassen et al., “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 6, e25125. mla: Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife, vol. 6, e25125, eLife Sciences Publications, 2017, doi:10.7554/eLife.25125. short: D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber, D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler, Q. Hudson, ELife 6 (2017). date_created: 2018-12-11T11:48:05Z date_published: 2017-08-14T00:00:00Z date_updated: 2021-01-12T08:11:57Z day: '14' ddc: - '576' department: - _id: GaNo - _id: SiHi doi: 10.7554/eLife.25125 file: - access_level: open_access checksum: 1ace3462e64a971b9ead896091829549 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:36Z date_updated: 2020-07-14T12:47:50Z file_id: '5020' file_name: IST-2017-885-v1+1_elife-25125-figures-v2.pdf file_size: 6399510 relation: main_file - access_level: open_access checksum: 6241dc31eeb87b03facadec3a53a6827 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:36Z date_updated: 2020-07-14T12:47:50Z file_id: '5021' file_name: IST-2017-885-v1+2_elife-25125-v2.pdf file_size: 4264398 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications publist_id: '6971' pubrep_id: '885' quality_controlled: '1' scopus_import: 1 status: public title: Mapping the mouse Allelome reveals tissue specific regulation of allelic expression 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: '2017' ... --- _id: '711' abstract: - lang: eng text: Nested weighted automata (NWA) present a robust and convenient automata-theoretic formalism for quantitative specifications. Previous works have considered NWA that processed input words only in the forward direction. It is natural to allow the automata to process input words backwards as well, for example, to measure the maximal or average time between a response and the preceding request. We therefore introduce and study bidirectional NWA that can process input words in both directions. First, we show that bidirectional NWA can express interesting quantitative properties that are not expressible by forward-only NWA. Second, for the fundamental decision problems of emptiness and universality, we establish decidability and complexity results for the new framework which match the best-known results for the special case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality is achieved at no additional computational complexity. This is in stark contrast to the unweighted case, where bidirectional finite automata are no more expressive but exponentially more succinct than their forward-only counterparts. alternative_title: - LIPIcs article_number: '5' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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: Jan full_name: Otop, Jan last_name: Otop citation: ama: 'Chatterjee K, Henzinger TA, Otop J. Bidirectional nested weighted automata. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.5' apa: 'Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Bidirectional nested weighted automata (Vol. 85). Presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Bidirectional Nested Weighted Automata,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5. ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Bidirectional nested weighted automata,” presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany, 2017, vol. 85. ista: Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 5. mla: Chatterjee, Krishnendu, et al. Bidirectional Nested Weighted Automata. Vol. 85, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.5. short: K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-08 location: Berlin, Germany name: 28th International Conference on Concurrency Theory, CONCUR start_date: 2017-09-05 date_created: 2018-12-11T11:48:04Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:11:53Z day: '01' ddc: - '004' - '005' department: - _id: KrCh - _id: ToHe doi: 10.4230/LIPIcs.CONCUR.2017.5 file: - access_level: open_access checksum: d2bda4783821a6358333fe27f11f4737 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:02Z date_updated: 2020-07-14T12:47:49Z file_id: '4661' file_name: IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf file_size: 570294 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 85' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6976' pubrep_id: '886' quality_controlled: '1' scopus_import: 1 status: public title: Bidirectional nested weighted automata 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: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 85 year: '2017' ... --- _id: '712' abstract: - lang: eng text: 'We establish a weak–strong uniqueness principle for solutions to entropy-dissipating reaction–diffusion equations: As long as a strong solution to the reaction–diffusion equation exists, any weak solution and even any renormalized solution must coincide with this strong solution. Our assumptions on the reaction rates are just the entropy condition and local Lipschitz continuity; in particular, we do not impose any growth restrictions on the reaction rates. Therefore, our result applies to any single reversible reaction with mass-action kinetics as well as to systems of reversible reactions with mass-action kinetics satisfying the detailed balance condition. Renormalized solutions are known to exist globally in time for reaction–diffusion equations with entropy-dissipating reaction rates; in contrast, the global-in-time existence of weak solutions is in general still an open problem–even for smooth data–, thereby motivating the study of renormalized solutions. The key ingredient of our result is a careful adjustment of the usual relative entropy functional, whose evolution cannot be controlled properly for weak solutions or renormalized solutions.' author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: 'Fischer JL. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 2017;159:181-207. doi:10.1016/j.na.2017.03.001' apa: 'Fischer, J. L. (2017). Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. Elsevier. https://doi.org/10.1016/j.na.2017.03.001' chicago: 'Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications. Elsevier, 2017. https://doi.org/10.1016/j.na.2017.03.001.' ieee: 'J. L. Fischer, “Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations,” Nonlinear Analysis: Theory, Methods and Applications, vol. 159. Elsevier, pp. 181–207, 2017.' ista: 'Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207.' mla: 'Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications, vol. 159, Elsevier, 2017, pp. 181–207, doi:10.1016/j.na.2017.03.001.' short: 'J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207.' date_created: 2018-12-11T11:48:05Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:11:55Z day: '01' department: - _id: JuFi doi: 10.1016/j.na.2017.03.001 intvolume: ' 159' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1703.00730 month: '08' oa: 1 oa_version: Submitted Version page: 181 - 207 publication: 'Nonlinear Analysis: Theory, Methods and Applications' publication_identifier: issn: - 0362546X publication_status: published publisher: Elsevier publist_id: '6975' quality_controlled: '1' scopus_import: 1 status: public title: Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2017' ... --- _id: '714' abstract: - lang: eng text: Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients. acknowledgement: This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU). article_processing_charge: No article_type: original author: - first_name: Gabriela full_name: Brailoiu, Gabriela last_name: Brailoiu - first_name: Elena full_name: Deliu, Elena id: 37A40D7E-F248-11E8-B48F-1D18A9856A87 last_name: Deliu orcid: 0000-0002-7370-5293 - first_name: Jeffrey full_name: Barr, Jeffrey last_name: Barr - first_name: Linda full_name: Console Bram, Linda last_name: Console Bram - first_name: Alexandra full_name: Ciuciu, Alexandra last_name: Ciuciu - first_name: Mary full_name: Abood, Mary last_name: Abood - first_name: Ellen full_name: Unterwald, Ellen last_name: Unterwald - first_name: Eugen full_name: Brǎiloiu, Eugen last_name: Brǎiloiu citation: ama: Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 2017;178:7-14. doi:10.1016/j.drugalcdep.2017.04.015 apa: Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. Elsevier. https://doi.org/10.1016/j.drugalcdep.2017.04.015 chicago: Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence. Elsevier, 2017. https://doi.org/10.1016/j.drugalcdep.2017.04.015. ieee: G. Brailoiu et al., “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” Drug and Alcohol Dependence, vol. 178. Elsevier, pp. 7–14, 2017. ista: Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14. mla: Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence, vol. 178, Elsevier, 2017, pp. 7–14, doi:10.1016/j.drugalcdep.2017.04.015. short: G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14. date_created: 2018-12-11T11:48:05Z date_published: 2017-09-01T00:00:00Z date_updated: 2021-01-12T08:12:00Z day: '01' department: - _id: GaNo doi: 10.1016/j.drugalcdep.2017.04.015 external_id: pmid: - '28623807' intvolume: ' 178' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705 month: '09' oa: 1 oa_version: Submitted Version page: 7 - 14 pmid: 1 publication: Drug and Alcohol Dependence publication_identifier: issn: - '03768716' publication_status: published publisher: Elsevier publist_id: '6967' quality_controlled: '1' scopus_import: 1 status: public title: HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 178 year: '2017' ... --- _id: '715' abstract: - lang: eng text: D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome. article_number: aao4218 author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Novarino G. More excitation for Rett syndrome. Science Translational Medicine. 2017;9(405). doi:10.1126/scitranslmed.aao4218 apa: Novarino, G. (2017). More excitation for Rett syndrome. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218 chicago: Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218. ieee: G. Novarino, “More excitation for Rett syndrome,” Science Translational Medicine, vol. 9, no. 405. American Association for the Advancement of Science, 2017. ista: Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218. mla: Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aao4218. short: G. Novarino, Science Translational Medicine 9 (2017). date_created: 2018-12-11T11:48:06Z date_published: 2017-08-30T00:00:00Z date_updated: 2021-01-12T08:12:04Z day: '30' department: - _id: GaNo doi: 10.1126/scitranslmed.aao4218 intvolume: ' 9' issue: '405' language: - iso: eng month: '08' oa_version: None publication: Science Translational Medicine publication_identifier: issn: - '19466234' publication_status: published publisher: American Association for the Advancement of Science publist_id: '6968' quality_controlled: '1' scopus_import: 1 status: public title: More excitation for Rett syndrome type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2017' ... --- _id: '716' abstract: - lang: eng text: 'Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.' article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Yaron full_name: Velner, Yaron last_name: Velner citation: ama: Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):34. doi:10.1145/3121408 apa: Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408 chicago: Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408. ieee: K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017. ista: Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34. mla: Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408. short: K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34. date_created: 2018-12-11T11:48:06Z date_published: 2017-09-01T00:00:00Z date_updated: 2021-01-12T08:12:08Z day: '01' department: - _id: KrCh doi: 10.1145/3121408 ec_funded: 1 external_id: arxiv: - '1201.2829' intvolume: ' 64' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1201.2829 month: '09' oa: 1 oa_version: Preprint page: '34' project: - _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 - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Journal of the ACM publication_identifier: issn: - '00045411' publication_status: published publisher: ACM publist_id: '6964' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of mean-payoff pushdown games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 64 year: '2017' ...