--- _id: '11837' abstract: - lang: eng text: "Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1-1/e). (2) On the positive side we present (i) an O(sqrt n)-approximation algorithm for general concave externality functions,\r\n(ii) an O(\\log m)-approximation algorithm for linear externality functions, and (iii) an (1-1/e)\\frac{1}{6}-approximation algorithm for 2-hop step function externalities. We also improve the result from [6] for 1-hop step function externalities by giving a (1-1/e)/2-approximation algorithm." alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - 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: ' Martin' full_name: Starnberger, Martin last_name: Starnberger citation: ama: 'Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. Welfare maximization with friends-of-friends network externalities. In: 32nd International Symposium on Theoretical Aspects of Computer Science. Vol 30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:90-102. doi:10.4230/LIPICS.STACS.2015.90' apa: 'Bhattacharya, S., Dvorák, W., Henzinger, M. H., & Starnberger, Martin. (2015). Welfare maximization with friends-of-friends network externalities. In 32nd International Symposium on Theoretical Aspects of Computer Science (Vol. 30, pp. 90–102). Garching, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.STACS.2015.90' chicago: Bhattacharya, Sayan, Wolfgang Dvorák, Monika H Henzinger, and Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” In 32nd International Symposium on Theoretical Aspects of Computer Science, 30:90–102. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPICS.STACS.2015.90. ieee: S. Bhattacharya, W. Dvorák, M. H. Henzinger, and Martin Starnberger, “Welfare maximization with friends-of-friends network externalities,” in 32nd International Symposium on Theoretical Aspects of Computer Science, Garching, Germany, 2015, vol. 30, pp. 90–102. ista: 'Bhattacharya S, Dvorák W, Henzinger MH, Starnberger Martin. 2015. Welfare maximization with friends-of-friends network externalities. 32nd International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 30, 90–102.' mla: Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” 32nd International Symposium on Theoretical Aspects of Computer Science, vol. 30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPICS.STACS.2015.90. short: S. Bhattacharya, W. Dvorák, M.H. Henzinger, Martin Starnberger, in:, 32nd International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102. conference: end_date: 2015-03-07 location: Garching, Germany name: 'STACS: Symposium on Theoretical Aspects of Computer Science' start_date: 2015-03-04 date_created: 2022-08-12T11:39:40Z date_published: 2015-02-26T00:00:00Z date_updated: 2023-02-21T16:32:37Z day: '26' doi: 10.4230/LIPICS.STACS.2015.90 extern: '1' intvolume: ' 30' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.4230/LIPICS.STACS.2015.90 month: '02' oa: 1 oa_version: Published Version page: 90-102 publication: 32nd International Symposium on Theoretical Aspects of Computer Science publication_identifier: isbn: - 978-3-939897-78-1 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' related_material: record: - id: '11903' relation: later_version status: public scopus_import: '1' status: public title: Welfare maximization with friends-of-friends network externalities type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 30 year: '2015' ... --- _id: '11901' abstract: - lang: eng text: We consider auctions of indivisible items to unit-demand bidders with budgets. This setting was suggested as an expressive model for single sponsored search auctions. Prior work presented mechanisms that compute bidder-optimal outcomes and are truthful for a restricted set of inputs, i.e., inputs in so-called general position. This condition is easily violated. We provide the first mechanism that is truthful in expectation for all inputs and achieves for each bidder no worse utility than the bidder-optimal outcome. Additionally we give a complete characterization for which inputs mechanisms that compute bidder-optimal outcomes are truthful. article_processing_charge: No article_type: original author: - 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: Henzinger MH, Loitzenbauer V. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 2015;573:1-15. doi:10.1016/j.tcs.2015.01.033 apa: Henzinger, M. H., & Loitzenbauer, V. (2015). Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2015.01.033 chicago: Henzinger, Monika H, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science. Elsevier, 2015. https://doi.org/10.1016/j.tcs.2015.01.033. ieee: M. H. Henzinger and V. Loitzenbauer, “Truthful unit-demand auctions with budgets revisited,” Theoretical Computer Science, vol. 573. Elsevier, pp. 1–15, 2015. ista: Henzinger MH, Loitzenbauer V. 2015. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 573, 1–15. mla: Henzinger, Monika H., and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” Theoretical Computer Science, vol. 573, Elsevier, 2015, pp. 1–15, doi:10.1016/j.tcs.2015.01.033. short: M.H. Henzinger, V. Loitzenbauer, Theoretical Computer Science 573 (2015) 1–15. date_created: 2022-08-17T09:06:53Z date_published: 2015-03-30T00:00:00Z date_updated: 2023-02-17T14:50:04Z day: '30' doi: 10.1016/j.tcs.2015.01.033 extern: '1' intvolume: ' 573' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.tcs.2015.01.033 month: '03' oa: 1 oa_version: None page: 1-15 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Truthful unit-demand auctions with budgets revisited type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 573 year: '2015' ... --- _id: '121' abstract: - lang: eng text: We show that the simplest building blocks of origami-based materials - rigid, degree-four vertices - are generically multistable. The existence of two distinct branches of folding motion emerging from the flat state suggests at least bistability, but we show how nonlinearities in the folding motions allow generic vertex geometries to have as many as five stable states. In special geometries with collinear folds and symmetry, more branches emerge leading to as many as six stable states. Tuning the fold energy parameters, we show how monostability is also possible. Finally, we show how to program the stability features of a single vertex into a periodic fold tessellation. The resulting metasheets provide a previously unanticipated functionality - tunable and switchable shape and size via multistability. acknowledgement: B. G. C. acknowledges support from FOM, and S. W. and M. v. H. acknowledge support from NWO. article_number: '055503' author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Rémi full_name: Menaut, Rémi last_name: Menaut - first_name: Bryan full_name: Chen, Bryan last_name: Chen - first_name: Martin full_name: Van Hecke, Martin last_name: Van Hecke citation: ama: 'Waitukaitis SR, Menaut R, Chen B, Van Hecke M. Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. 2015;114(5). doi:10.1103/PhysRevLett.114.055503' apa: 'Waitukaitis, S. R., Menaut, R., Chen, B., & Van Hecke, M. (2015). Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.114.055503' chicago: 'Waitukaitis, Scott R, Rémi Menaut, Bryan Chen, and Martin Van Hecke. “Origami Multistability: From Single Vertices to Metasheets.” APS Physics, Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.114.055503.' ieee: 'S. R. Waitukaitis, R. Menaut, B. Chen, and M. Van Hecke, “Origami multistability: From single vertices to metasheets,” APS Physics, Physical Review Letters, vol. 114, no. 5. American Physical Society, 2015.' ista: 'Waitukaitis SR, Menaut R, Chen B, Van Hecke M. 2015. Origami multistability: From single vertices to metasheets. APS Physics, Physical Review Letters. 114(5), 055503.' mla: 'Waitukaitis, Scott R., et al. “Origami Multistability: From Single Vertices to Metasheets.” APS Physics, Physical Review Letters, vol. 114, no. 5, 055503, American Physical Society, 2015, doi:10.1103/PhysRevLett.114.055503.' short: S.R. Waitukaitis, R. Menaut, B. Chen, M. Van Hecke, APS Physics, Physical Review Letters 114 (2015). date_created: 2018-12-11T11:44:44Z date_published: 2015-02-04T00:00:00Z date_updated: 2021-01-12T06:49:07Z day: '04' doi: 10.1103/PhysRevLett.114.055503 extern: '1' external_id: arxiv: - '1408.1607' intvolume: ' 114' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.1607 month: '02' oa: 1 oa_version: Preprint publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7933' quality_controlled: '1' status: public title: 'Origami multistability: From single vertices to metasheets' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 114 year: '2015' ... --- _id: '1383' abstract: - lang: eng text: In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants. article_number: '15094' article_processing_charge: No article_type: original author: - first_name: Luo full_name: Yu, Luo last_name: Yu - first_name: Stefan full_name: Scholl, Stefan last_name: Scholl - first_name: Anett full_name: Doering, Anett last_name: Doering - first_name: Zhang full_name: Yi, Zhang last_name: Yi - first_name: Niloufer full_name: Irani, Niloufer last_name: Irani - first_name: Simone full_name: Di Rubbo, Simone last_name: Di Rubbo - first_name: Lutz full_name: Neumetzler, Lutz last_name: Neumetzler - first_name: Praveen full_name: Krishnamoorthy, Praveen last_name: Krishnamoorthy - first_name: Isabelle full_name: Van Houtte, Isabelle last_name: Van Houtte - first_name: Evelien full_name: Mylle, Evelien last_name: Mylle - first_name: Volker full_name: Bischoff, Volker last_name: Bischoff - first_name: Samantha full_name: Vernhettes, Samantha last_name: Vernhettes - first_name: Johan full_name: Winne, Johan last_name: Winne - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: York full_name: Stierhof, York last_name: Stierhof - first_name: Karin full_name: Schumacher, Karin last_name: Schumacher - first_name: Staffan full_name: Persson, Staffan last_name: Persson - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova citation: ama: Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7). doi:10.1038/nplants.2015.94 apa: Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94 chicago: Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing Group, 2015. https://doi.org/10.1038/nplants.2015.94. ieee: L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing Group, 2015. ista: Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094. mla: Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:10.1038/nplants.2015.94. short: L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015). date_created: 2018-12-11T11:51:42Z date_published: 2015-07-06T00:00:00Z date_updated: 2021-01-12T06:50:18Z day: '06' department: - _id: JiFr doi: 10.1038/nplants.2015.94 external_id: pmid: - '27250258' intvolume: ' 1' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/ month: '07' oa: 1 oa_version: Submitted Version pmid: 1 publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '5827' quality_controlled: '1' scopus_import: 1 status: public title: V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2015' ... --- _id: '1425' abstract: - lang: eng text: 'In this work we aim at extending the theoretical foundations of lifelong learning. Previous work analyzing this scenario is based on the assumption that learning tasks are sampled i.i.d. from a task environment or limited to strongly constrained data distributions. Instead, we study two scenarios when lifelong learning is possible, even though the observed tasks do not form an i.i.d. sample: first, when they are sampled from the same environment, but possibly with dependencies, and second, when the task environment is allowed to change over time in a consistent way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct generalization of the analogous previous result for the i.i.d. case. For the second scenario we propose to learn an inductive bias in form of a transfer procedure. We present a generalization bound and show on a toy example how it can be used to identify a beneficial transfer algorithm.' alternative_title: - Advances in Neural Information Processing Systems author: - first_name: Anastasia full_name: Pentina, Anastasia id: 42E87FC6-F248-11E8-B48F-1D18A9856A87 last_name: Pentina - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015. Neural Information Processing Systems; 2015:1540-1548.' apa: 'Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks (Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.' chicago: Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d. Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015. ieee: 'A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 2015, pp. 1540–1548.' ista: 'Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 2015, 1540–1548.' mla: Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d. Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48. short: A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015, pp. 1540–1548. conference: end_date: 2015-12-12 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2015-12-07 date_created: 2018-12-11T11:51:57Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:50:39Z day: '01' department: - _id: ChLa ec_funded: 1 intvolume: ' 2015' language: - iso: eng main_file_link: - open_access: '1' url: http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks month: '01' oa: 1 oa_version: None page: 1540 - 1548 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: Neural Information Processing Systems publist_id: '5781' quality_controlled: '1' scopus_import: 1 status: public title: Lifelong learning with non-i.i.d. tasks type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2015 year: '2015' ... --- _id: '1424' abstract: - lang: eng text: We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data. acknowledgement: This work was partially supported by the Austrian Science FUnd, project no. KLI 00012. alternative_title: - Advances in Neural Information Processing Systems author: - first_name: Roland full_name: Kwitt, Roland last_name: Kwitt - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Marc full_name: Niethammer, Marc last_name: Niethammer - first_name: Weili full_name: Lin, Weili last_name: Lin - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 citation: ama: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems; 2015:3070-3078.' apa: 'Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.' chicago: Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems, 2015. ieee: 'R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.' ista: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.' mla: Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective. Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78. short: R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems, 2015, pp. 3070–3078. conference: end_date: 2015-12-12 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2015-12-07 date_created: 2018-12-11T11:51:56Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:50:38Z day: '01' department: - _id: HeEd intvolume: ' 28' language: - iso: eng main_file_link: - open_access: '1' url: https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective month: '12' oa: 1 oa_version: Submitted Version page: 3070 - 3078 publication_status: published publisher: Neural Information Processing Systems publist_id: '5782' quality_controlled: '1' status: public title: Statistical topological data analysis-A kernel perspective type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2015' ... --- _id: '1430' abstract: - lang: eng text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse their runtime on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrence of new mutations is much longer than the time it takes for a new beneficial mutation to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a (1+1)-type process where the probability of accepting a new genotype (improvements or worsenings) depends on the change in fitness. We present an initial runtime analysis of SSWM, quantifying its performance for various parameters and investigating differences to the (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient. author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Jorge full_name: Heredia, Jorge last_name: Heredia - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime comparison of natural and artificial evolution. In: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462. doi:10.1145/2739480.2754758' apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps towards a runtime comparison of natural and artificial evolution. In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp. 1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758' chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62. ACM, 2015. https://doi.org/10.1145/2739480.2754758. ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards a runtime comparison of natural and artificial evolution,” in Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid, Spain, 2015, pp. 1455–1462. ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a runtime comparison of natural and artificial evolution. Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and evolutionary computation conference, 1455–1462.' mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758. short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp. 1455–1462. conference: end_date: 2015-07-15 location: Madrid, Spain name: 'GECCO: Genetic and evolutionary computation conference' start_date: 2015-07-11 date_created: 2018-12-11T11:51:58Z date_published: 2015-07-11T00:00:00Z date_updated: 2021-01-12T06:50:41Z day: '11' department: - _id: NiBa - _id: CaGu doi: 10.1145/2739480.2754758 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.06260 month: '07' oa: 1 oa_version: Preprint page: 1455 - 1462 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation publication_status: published publisher: ACM publist_id: '5768' quality_controlled: '1' scopus_import: 1 status: public title: First steps towards a runtime comparison of natural and artificial evolution type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1474' abstract: - lang: eng text: Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data. article_processing_charge: No author: - first_name: Anna full_name: Ferrara, Anna last_name: Ferrara - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Bin full_name: Liu, Bin last_name: Liu - first_name: Bogdan full_name: Warinschi, Bogdan last_name: Warinschi citation: ama: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. Policy privacy in cryptographic access control. In: IEEE; 2015:46-60. doi:10.1109/CSF.2015.11' apa: 'Ferrara, A., Fuchsbauer, G., Liu, B., & Warinschi, B. (2015). Policy privacy in cryptographic access control (pp. 46–60). Presented at the CSF: Computer Security Foundations, Verona, Italy: IEEE. https://doi.org/10.1109/CSF.2015.11' chicago: Ferrara, Anna, Georg Fuchsbauer, Bin Liu, and Bogdan Warinschi. “Policy Privacy in Cryptographic Access Control,” 46–60. IEEE, 2015. https://doi.org/10.1109/CSF.2015.11. ieee: 'A. Ferrara, G. Fuchsbauer, B. Liu, and B. Warinschi, “Policy privacy in cryptographic access control,” presented at the CSF: Computer Security Foundations, Verona, Italy, 2015, pp. 46–60.' ista: 'Ferrara A, Fuchsbauer G, Liu B, Warinschi B. 2015. Policy privacy in cryptographic access control. CSF: Computer Security Foundations, 46–60.' mla: Ferrara, Anna, et al. Policy Privacy in Cryptographic Access Control. IEEE, 2015, pp. 46–60, doi:10.1109/CSF.2015.11. short: A. Ferrara, G. Fuchsbauer, B. Liu, B. Warinschi, in:, IEEE, 2015, pp. 46–60. conference: end_date: 2015-07-17 location: Verona, Italy name: 'CSF: Computer Security Foundations' start_date: 2015-07-13 date_created: 2018-12-11T11:52:14Z date_published: 2015-09-04T00:00:00Z date_updated: 2021-01-12T06:50:59Z day: '04' department: - _id: KrPi doi: 10.1109/CSF.2015.11 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://epubs.surrey.ac.uk/808055/ month: '09' oa: 1 oa_version: Submitted Version page: 46-60 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: IEEE publist_id: '5722' quality_controlled: '1' status: public title: Policy privacy in cryptographic access control type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1473' abstract: - lang: eng text: In this paper we survey geometric and arithmetic techniques to study the cohomology of semiprojective hyperkähler manifolds including toric hyperkähler varieties, Nakajima quiver varieties and moduli spaces of Higgs bundles on Riemann surfaces. The resulting formulae for their Poincaré polynomials are combinatorial and representation theoretical in nature. In particular we will look at their Betti numbers and will establish some results and state some expectations on their asymptotic shape. author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Fernando full_name: Rodríguez Villegas, Fernando last_name: Rodríguez Villegas citation: ama: Hausel T, Rodríguez Villegas F. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015;2015(370):113-156. apa: Hausel, T., & Rodríguez Villegas, F. (2015). Cohomology of large semiprojective hyperkähler varieties. Asterisque. Societe Mathematique de France. chicago: Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque. Societe Mathematique de France, 2015. ieee: T. Hausel and F. Rodríguez Villegas, “Cohomology of large semiprojective hyperkähler varieties,” Asterisque, vol. 2015, no. 370. Societe Mathematique de France, pp. 113–156, 2015. ista: Hausel T, Rodríguez Villegas F. 2015. Cohomology of large semiprojective hyperkähler varieties. Asterisque. 2015(370), 113–156. mla: Hausel, Tamás, and Fernando Rodríguez Villegas. “Cohomology of Large Semiprojective Hyperkähler Varieties.” Asterisque, vol. 2015, no. 370, Societe Mathematique de France, 2015, pp. 113–56. short: T. Hausel, F. Rodríguez Villegas, Asterisque 2015 (2015) 113–156. date_created: 2018-12-11T11:52:13Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:50:59Z day: '01' extern: 1 intvolume: ' 2015' issue: '370' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1309.4914 month: '01' oa: 1 page: 113 - 156 publication: Asterisque publication_status: published publisher: Societe Mathematique de France publist_id: '5723' quality_controlled: 0 status: public title: Cohomology of large semiprojective hyperkähler varieties type: review volume: 2015 year: '2015' ... --- _id: '1483' abstract: - lang: eng text: Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes. author: - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Ulrich full_name: Bauer, Ulrich id: 2ADD483A-F248-11E8-B48F-1D18A9856A87 last_name: Bauer orcid: 0000-0002-9683-0724 - first_name: Roland full_name: Kwitt, Roland last_name: Kwitt citation: ama: 'Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:10.1109/CVPR.2015.7299106' apa: 'Reininghaus, J., Huber, S., Bauer, U., & Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. https://doi.org/10.1109/CVPR.2015.7299106' chicago: Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. https://doi.org/10.1109/CVPR.2015.7299106. ieee: 'J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.' ista: 'Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748.' mla: Reininghaus, Jan, et al. A Stable Multi-Scale Kernel for Topological Machine Learning. IEEE, 2015, pp. 4741–48, doi:10.1109/CVPR.2015.7299106. short: J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748. conference: end_date: 2015-06-12 location: Boston, MA, USA name: 'CVPR: Computer Vision and Pattern Recognition' start_date: 2015-06-07 date_created: 2018-12-11T11:52:17Z date_published: 2015-10-14T00:00:00Z date_updated: 2021-01-12T06:51:03Z day: '14' department: - _id: HeEd doi: 10.1109/CVPR.2015.7299106 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1412.6821 month: '10' oa: 1 oa_version: Preprint page: 4741 - 4748 publication_identifier: eisbn: - '978-1-4673-6964-0 ' publication_status: published publisher: IEEE publist_id: '5709' scopus_import: 1 status: public title: A stable multi-scale kernel for topological machine learning type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1498' abstract: - lang: eng text: Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea. alternative_title: - LIPIcs author: - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - 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: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: Dragoi C, Henzinger TA, Zufferey D. The need for language support for fault-tolerant distributed systems. 2015;32:90-102. doi:10.4230/LIPIcs.SNAPL.2015.90 apa: 'Dragoi, C., Henzinger, T. A., & Zufferey, D. (2015). The need for language support for fault-tolerant distributed systems. Presented at the SNAPL: Summit oN Advances in Programming Languages, Asilomar, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90' chicago: Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “The Need for Language Support for Fault-Tolerant Distributed Systems.” Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SNAPL.2015.90. ieee: C. Dragoi, T. A. Henzinger, and D. Zufferey, “The need for language support for fault-tolerant distributed systems,” vol. 32. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 90–102, 2015. ista: Dragoi C, Henzinger TA, Zufferey D. 2015. The need for language support for fault-tolerant distributed systems. 32, 90–102. mla: Dragoi, Cezara, et al. The Need for Language Support for Fault-Tolerant Distributed Systems. Vol. 32, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:10.4230/LIPIcs.SNAPL.2015.90. short: C. Dragoi, T.A. Henzinger, D. Zufferey, 32 (2015) 90–102. conference: end_date: 2015-05-06 location: Asilomar, CA, United States name: 'SNAPL: Summit oN Advances in Programming Languages' start_date: 2015-05-03 date_created: 2018-12-11T11:52:22Z date_published: 2015-01-01T00:00:00Z date_updated: 2020-08-11T10:09:14Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.4230/LIPIcs.SNAPL.2015.90 ec_funded: 1 file: - access_level: open_access checksum: cf5e94baa89a2dc4c5de01abc676eda8 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:02Z date_updated: 2020-07-14T12:44:58Z file_id: '5050' file_name: IST-2016-499-v1+1_9.pdf file_size: 489362 relation: main_file file_date_updated: 2020-07-14T12:44:58Z has_accepted_license: '1' intvolume: ' 32' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '01' oa: 1 oa_version: Published Version page: 90 - 102 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _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: - '978-3-939897-80-4 ' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5681' pubrep_id: '499' quality_controlled: '1' scopus_import: 1 series_title: Leibniz International Proceedings in Informatics status: public title: The need for language support for fault-tolerant distributed systems 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: 32 year: '2015' ... --- _id: '1497' abstract: - lang: eng text: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide. acknowledgement: "Austrian Science Fund [FWF P25185-B22, FWF F4302- B09, FWFW1207-B09]. Funding for open access charge: Austrian Science Fund.\r\nWe thank Florian Breitwieser for advice during the early stages of this project. High-throughput sequencing was conducted by the Biomedical Sequencing Facility (BSF) at CeMM in Vienna." article_number: e146 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: Tomasz full_name: Kulinski, Tomasz last_name: Kulinski - first_name: Philipp full_name: Guenzl, Philipp last_name: Guenzl - first_name: Philipp full_name: Bammer, Philipp last_name: Bammer - first_name: Denise full_name: Barlow, Denise last_name: Barlow - first_name: Florian full_name: Pauler, Florian last_name: Pauler - first_name: Quanah full_name: Hudson, Quanah last_name: Hudson citation: ama: Andergassen D, Dotter C, Kulinski T, et al. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 2015;43(21). doi:10.1093/nar/gkv727 apa: Andergassen, D., Dotter, C., Kulinski, T., Guenzl, P., Bammer, P., Barlow, D., … Hudson, Q. (2015). Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkv727 chicago: Andergassen, Daniel, Christoph Dotter, Tomasz Kulinski, Philipp Guenzl, Philipp Bammer, Denise Barlow, Florian Pauler, and Quanah Hudson. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research. Oxford University Press, 2015. https://doi.org/10.1093/nar/gkv727. ieee: D. Andergassen et al., “Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data,” Nucleic Acids Research, vol. 43, no. 21. Oxford University Press, 2015. ista: Andergassen D, Dotter C, Kulinski T, Guenzl P, Bammer P, Barlow D, Pauler F, Hudson Q. 2015. Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data. Nucleic Acids Research. 43(21), e146. mla: Andergassen, Daniel, et al. “Allelome.PRO, a Pipeline to Define Allele-Specific Genomic Features from High-Throughput Sequencing Data.” Nucleic Acids Research, vol. 43, no. 21, e146, Oxford University Press, 2015, doi:10.1093/nar/gkv727. short: D. Andergassen, C. Dotter, T. Kulinski, P. Guenzl, P. Bammer, D. Barlow, F. Pauler, Q. Hudson, Nucleic Acids Research 43 (2015). date_created: 2018-12-11T11:52:22Z date_published: 2015-07-21T00:00:00Z date_updated: 2021-01-12T06:51:09Z day: '21' ddc: - '570' department: - _id: GaNo doi: 10.1093/nar/gkv727 file: - access_level: open_access checksum: 385b83854fd0eb2e4f386867da2823e2 content_type: application/pdf creator: dernst date_created: 2018-12-20T14:18:57Z date_updated: 2020-07-14T12:44:58Z file_id: '5768' file_name: 2015_NucleicAcidsRes_Andergassen.pdf file_size: 6863297 relation: main_file file_date_updated: 2020-07-14T12:44:58Z has_accepted_license: '1' intvolume: ' 43' issue: '21' language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: Nucleic Acids Research publication_status: published publisher: Oxford University Press publist_id: '5682' quality_controlled: '1' scopus_import: 1 status: public title: Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data 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: 43 year: '2015' ... --- _id: '1499' abstract: - lang: eng text: "We consider weighted automata with both positive and negative integer weights on edges and\r\nstudy the problem of synchronization using adaptive strategies that may only observe whether\r\nthe current weight-level is negative or nonnegative. We show that the synchronization problem is decidable in polynomial time for deterministic weighted automata." acknowledgement: "The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement 601148 (CASSTING), EU FP7 FET project SENSATION, Sino-Danish Basic Research Center IDAE4CPS, the European Research Council (ERC) under grant agreement 267989 (QUAREM), the Austrian Science Fund (FWF) project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Czech Science Foundation under grant agreement P202/12/G061, and People Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734." alternative_title: - LIPIcs author: - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Kim full_name: Larsen, Kim last_name: Larsen - first_name: Simon full_name: Laursen, Simon last_name: Laursen - first_name: Jiří full_name: Srba, Jiří last_name: Srba citation: ama: 'Kretinsky J, Larsen K, Laursen S, Srba J. Polynomial time decidability of weighted synchronization under partial observability. In: Vol 42. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:142-154. doi:10.4230/LIPIcs.CONCUR.2015.142' apa: 'Kretinsky, J., Larsen, K., Laursen, S., & Srba, J. (2015). Polynomial time decidability of weighted synchronization under partial observability (Vol. 42, pp. 142–154). Presented at the CONCUR: Concurrency Theory, Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142' chicago: Kretinsky, Jan, Kim Larsen, Simon Laursen, and Jiří Srba. “Polynomial Time Decidability of Weighted Synchronization under Partial Observability,” 42:142–54. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.CONCUR.2015.142. ieee: 'J. Kretinsky, K. Larsen, S. Laursen, and J. Srba, “Polynomial time decidability of weighted synchronization under partial observability,” presented at the CONCUR: Concurrency Theory, Madrid, Spain, 2015, vol. 42, pp. 142–154.' ista: 'Kretinsky J, Larsen K, Laursen S, Srba J. 2015. Polynomial time decidability of weighted synchronization under partial observability. CONCUR: Concurrency Theory, LIPIcs, vol. 42, 142–154.' mla: Kretinsky, Jan, et al. Polynomial Time Decidability of Weighted Synchronization under Partial Observability. Vol. 42, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–54, doi:10.4230/LIPIcs.CONCUR.2015.142. short: J. Kretinsky, K. Larsen, S. Laursen, J. Srba, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 142–154. conference: end_date: 2015-09-04 location: Madrid, Spain name: 'CONCUR: Concurrency Theory' start_date: 2015-09-01 date_created: 2018-12-11T11:52:22Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:51:10Z day: '01' ddc: - '000' - '003' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPIcs.CONCUR.2015.142 ec_funded: 1 file: - access_level: open_access checksum: 49eb5021caafaabe5356c65b9c5f8c9c content_type: application/pdf creator: system date_created: 2018-12-12T10:08:12Z date_updated: 2020-07-14T12:44:58Z file_id: '4672' file_name: IST-2016-498-v1+1_32.pdf file_size: 623563 relation: main_file file_date_updated: 2020-07-14T12:44:58Z has_accepted_license: '1' intvolume: ' 42' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 142 - 154 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5680' pubrep_id: '498' quality_controlled: '1' scopus_import: 1 status: public title: Polynomial time decidability of weighted synchronization under partial observability 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: 42 year: '2015' ... --- _id: '1495' abstract: - lang: eng text: 'Motivated by biological questions, we study configurations of equal-sized disks in the Euclidean plane that neither pack nor cover. Measuring the quality by the probability that a random point lies in exactly one disk, we show that the regular hexagonal grid gives the maximum among lattice configurations. ' author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham - first_name: Vitaliy full_name: Kurlin, Vitaliy last_name: Kurlin citation: ama: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. Relaxed disk packing. In: Proceedings of the 27th Canadian Conference on Computational Geometry. Vol 2015-August. Queen’s University; 2015:128-135.' apa: 'Edelsbrunner, H., Iglesias Ham, M., & Kurlin, V. (2015). Relaxed disk packing. In Proceedings of the 27th Canadian Conference on Computational Geometry (Vol. 2015–August, pp. 128–135). Ontario, Canada: Queen’s University.' chicago: Edelsbrunner, Herbert, Mabel Iglesias Ham, and Vitaliy Kurlin. “Relaxed Disk Packing.” In Proceedings of the 27th Canadian Conference on Computational Geometry, 2015–August:128–35. Queen’s University, 2015. ieee: H. Edelsbrunner, M. Iglesias Ham, and V. Kurlin, “Relaxed disk packing,” in Proceedings of the 27th Canadian Conference on Computational Geometry, Ontario, Canada, 2015, vol. 2015–August, pp. 128–135. ista: 'Edelsbrunner H, Iglesias Ham M, Kurlin V. 2015. Relaxed disk packing. Proceedings of the 27th Canadian Conference on Computational Geometry. CCCG: Canadian Conference on Computational Geometry vol. 2015–August, 128–135.' mla: Edelsbrunner, Herbert, et al. “Relaxed Disk Packing.” Proceedings of the 27th Canadian Conference on Computational Geometry, vol. 2015–August, Queen’s University, 2015, pp. 128–35. short: H. Edelsbrunner, M. Iglesias Ham, V. Kurlin, in:, Proceedings of the 27th Canadian Conference on Computational Geometry, Queen’s University, 2015, pp. 128–135. conference: end_date: 2015-08-12 location: Ontario, Canada name: 'CCCG: Canadian Conference on Computational Geometry' start_date: 2015-08-10 date_created: 2018-12-11T11:52:21Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:09Z day: '01' department: - _id: HeEd ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1505.03402 month: '08' oa: 1 oa_version: Submitted Version page: 128-135 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Proceedings of the 27th Canadian Conference on Computational Geometry publication_status: published publisher: Queen's University publist_id: '5684' quality_controlled: '1' scopus_import: 1 status: public title: Relaxed disk packing type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2015-August year: '2015' ... --- _id: '1504' abstract: - lang: eng text: Let Q = (Q1, . . . , Qn) be a random vector drawn from the uniform distribution on the set of all n! permutations of {1, 2, . . . , n}. Let Z = (Z1, . . . , Zn), where Zj is the mean zero variance one random variable obtained by centralizing and normalizing Qj , j = 1, . . . , n. Assume that Xi , i = 1, . . . ,p are i.i.d. copies of 1/√ p Z and X = Xp,n is the p × n random matrix with Xi as its ith row. Then Sn = XX is called the p × n Spearman's rank correlation matrix which can be regarded as a high dimensional extension of the classical nonparametric statistic Spearman's rank correlation coefficient between two independent random variables. In this paper, we establish a CLT for the linear spectral statistics of this nonparametric random matrix model in the scenario of high dimension, namely, p = p(n) and p/n→c ∈ (0,∞) as n→∞.We propose a novel evaluation scheme to estimate the core quantity in Anderson and Zeitouni's cumulant method in [Ann. Statist. 36 (2008) 2553-2576] to bypass the so-called joint cumulant summability. In addition, we raise a two-step comparison approach to obtain the explicit formulae for the mean and covariance functions in the CLT. Relying on this CLT, we then construct a distribution-free statistic to test complete independence for components of random vectors. Owing to the nonparametric property, we can use this test on generally distributed random variables including the heavy-tailed ones. author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: Liang full_name: Lin, Liang last_name: Lin - first_name: Guangming full_name: Pan, Guangming last_name: Pan - first_name: Wang full_name: Zhou, Wang last_name: Zhou citation: ama: Bao Z, Lin L, Pan G, Zhou W. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 2015;43(6):2588-2623. doi:10.1214/15-AOS1353 apa: Bao, Z., Lin, L., Pan, G., & Zhou, W. (2015). Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/15-AOS1353 chicago: Bao, Zhigang, Liang Lin, Guangming Pan, and Wang Zhou. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/15-AOS1353. ieee: Z. Bao, L. Lin, G. Pan, and W. Zhou, “Spectral statistics of large dimensional spearman s rank correlation matrix and its application,” Annals of Statistics, vol. 43, no. 6. Institute of Mathematical Statistics, pp. 2588–2623, 2015. ista: Bao Z, Lin L, Pan G, Zhou W. 2015. Spectral statistics of large dimensional spearman s rank correlation matrix and its application. Annals of Statistics. 43(6), 2588–2623. mla: Bao, Zhigang, et al. “Spectral Statistics of Large Dimensional Spearman s Rank Correlation Matrix and Its Application.” Annals of Statistics, vol. 43, no. 6, Institute of Mathematical Statistics, 2015, pp. 2588–623, doi:10.1214/15-AOS1353. short: Z. Bao, L. Lin, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 2588–2623. date_created: 2018-12-11T11:52:24Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:51:14Z day: '01' doi: 10.1214/15-AOS1353 extern: '1' intvolume: ' 43' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1312.5119 month: '12' oa: 1 oa_version: Published Version page: 2588 - 2623 publication: Annals of Statistics publication_status: published publisher: Institute of Mathematical Statistics publist_id: '5674' quality_controlled: '1' status: public title: Spectral statistics of large dimensional spearman s rank correlation matrix and its application type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2015' ... --- _id: '1503' abstract: - lang: eng text: A Herman-Avila-Bochi type formula is obtained for the average sum of the top d Lyapunov exponents over a one-parameter family of double-struck G-cocycles, where double-struck G is the group that leaves a certain, non-degenerate Hermitian form of signature (c, d) invariant. The generic example of such a group is the pseudo-unitary group U(c, d) or, in the case c = d, the Hermitian-symplectic group HSp(2d) which naturally appears for cocycles related to Schrödinger operators. In the case d = 1, the formula for HSp(2d) cocycles reduces to the Herman-Avila-Bochi formula for SL(2, ℝ) cocycles. author: - first_name: Christian full_name: Sadel, Christian id: 4760E9F8-F248-11E8-B48F-1D18A9856A87 last_name: Sadel orcid: 0000-0001-8255-3968 citation: ama: Sadel C. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 2015;35(5):1582-1591. doi:10.1017/etds.2013.103 apa: Sadel, C. (2015). A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. Cambridge University Press. https://doi.org/10.1017/etds.2013.103 chicago: Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems. Cambridge University Press, 2015. https://doi.org/10.1017/etds.2013.103. ieee: C. Sadel, “A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles,” Ergodic Theory and Dynamical Systems, vol. 35, no. 5. Cambridge University Press, pp. 1582–1591, 2015. ista: Sadel C. 2015. A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles. Ergodic Theory and Dynamical Systems. 35(5), 1582–1591. mla: Sadel, Christian. “A Herman-Avila-Bochi Formula for Higher-Dimensional Pseudo-Unitary and Hermitian-Symplectic-Cocycles.” Ergodic Theory and Dynamical Systems, vol. 35, no. 5, Cambridge University Press, 2015, pp. 1582–91, doi:10.1017/etds.2013.103. short: C. Sadel, Ergodic Theory and Dynamical Systems 35 (2015) 1582–1591. date_created: 2018-12-11T11:52:24Z date_published: 2015-03-14T00:00:00Z date_updated: 2021-01-12T06:51:13Z day: '14' doi: 10.1017/etds.2013.103 extern: '1' intvolume: ' 35' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1307.8414 month: '03' oa: 1 oa_version: Preprint page: 1582 - 1591 publication: Ergodic Theory and Dynamical Systems publication_status: published publisher: Cambridge University Press publist_id: '5675' quality_controlled: '1' status: public title: A Herman-Avila-Bochi formula for higher-dimensional pseudo-unitary and Hermitian-symplectic-cocycles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2015' ... --- _id: '1510' abstract: - lang: eng text: 'The concept of well group in a special but important case captures homological properties of the zero set of a continuous map f from K to R^n on a compact space K that are invariant with respect to perturbations of f. The perturbations are arbitrary continuous maps within L_infty distance r from f for a given r > 0. The main drawback of the approach is that the computability of well groups was shown only when dim K = n or n = 1. Our contribution to the theory of well groups is twofold: on the one hand we improve on the computability issue, but on the other hand we present a range of examples where the well groups are incomplete invariants, that is, fail to capture certain important robust properties of the zero set. For the first part, we identify a computable subgroup of the well group that is obtained by cap product with the pullback of the orientation of R^n by f. In other words, well groups can be algorithmically approximated from below. When f is smooth and dim K < 2n-2, our approximation of the (dim K-n)th well group is exact. For the second part, we find examples of maps f, f'' from K to R^n with all well groups isomorphic but whose perturbations have different zero sets. We discuss on a possible replacement of the well groups of vector valued maps by an invariant of a better descriptive power and computability status. ' alternative_title: - LIPIcs 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. On computability and triviality of well groups. In: Vol 34. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:842-856. doi:10.4230/LIPIcs.SOCG.2015.842' apa: 'Franek, P., & Krcál, M. (2015). On computability and triviality of well groups (Vol. 34, pp. 842–856). Presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SOCG.2015.842' chicago: Franek, Peter, and Marek Krcál. “On Computability and Triviality of Well Groups,” 34:842–56. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. https://doi.org/10.4230/LIPIcs.SOCG.2015.842. ieee: 'P. Franek and M. Krcál, “On computability and triviality of well groups,” presented at the SoCG: Symposium on Computational Geometry, Eindhoven, Netherlands, 2015, vol. 34, pp. 842–856.' ista: 'Franek P, Krcál M. 2015. On computability and triviality of well groups. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 34, 842–856.' mla: Franek, Peter, and Marek Krcál. On Computability and Triviality of Well Groups. Vol. 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–56, doi:10.4230/LIPIcs.SOCG.2015.842. short: P. Franek, M. Krcál, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 842–856. conference: end_date: 2015-06-25 location: Eindhoven, Netherlands name: 'SoCG: Symposium on Computational Geometry' start_date: 2015-06-22 date_created: 2018-12-11T11:52:26Z date_published: 2015-06-11T00:00:00Z date_updated: 2023-02-21T17:02:57Z day: '11' ddc: - '510' department: - _id: UlWa - _id: HeEd doi: 10.4230/LIPIcs.SOCG.2015.842 ec_funded: 1 file: - access_level: open_access checksum: 49eb5021caafaabe5356c65b9c5f8c9c content_type: application/pdf creator: system date_created: 2018-12-12T10:13:19Z date_updated: 2020-07-14T12:44:59Z file_id: '5001' file_name: IST-2016-503-v1+1_32.pdf file_size: 623563 relation: main_file file_date_updated: 2020-07-14T12:44:59Z has_accepted_license: '1' intvolume: ' 34' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 842 - 856 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5667' pubrep_id: '503' quality_controlled: '1' related_material: record: - id: '1408' relation: later_version status: public scopus_import: 1 status: public title: On computability and triviality of well groups 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: 34 year: '2015' ... --- _id: '1505' abstract: - lang: eng text: This paper is aimed at deriving the universality of the largest eigenvalue of a class of high-dimensional real or complex sample covariance matrices of the form W N =Σ 1/2XX∗Σ 1/2 . Here, X = (xij )M,N is an M× N random matrix with independent entries xij , 1 ≤ i M,≤ 1 ≤ j ≤ N such that Exij = 0, E|xij |2 = 1/N . On dimensionality, we assume that M = M(N) and N/M → d ε (0, ∞) as N ∞→. For a class of general deterministic positive-definite M × M matrices Σ , under some additional assumptions on the distribution of xij 's, we show that the limiting behavior of the largest eigenvalue of W N is universal, via pursuing a Green function comparison strategy raised in [Probab. Theory Related Fields 154 (2012) 341-407, Adv. Math. 229 (2012) 1435-1515] by Erd″os, Yau and Yin for Wigner matrices and extended by Pillai and Yin [Ann. Appl. Probab. 24 (2014) 935-1001] to sample covariance matrices in the null case (&Epsi = I ). Consequently, in the standard complex case (Ex2 ij = 0), combing this universality property and the results known for Gaussian matrices obtained by El Karoui in [Ann. Probab. 35 (2007) 663-714] (nonsingular case) and Onatski in [Ann. Appl. Probab. 18 (2008) 470-490] (singular case), we show that after an appropriate normalization the largest eigenvalue of W N converges weakly to the type 2 Tracy-Widom distribution TW2 . Moreover, in the real case, we show that whenΣ is spiked with a fixed number of subcritical spikes, the type 1 Tracy-Widom limit TW1 holds for the normalized largest eigenvalue of W N , which extends a result of Féral and Péché in [J. Math. Phys. 50 (2009) 073302] to the scenario of nondiagonal Σ and more generally distributed X . In summary, we establish the Tracy-Widom type universality for the largest eigenvalue of generally distributed sample covariance matrices under quite light assumptions on &Sigma . Applications of these limiting results to statistical signal detection and structure recognition of separable covariance matrices are also discussed. acknowledgement: "B.Z. was supported in part by NSFC Grant 11071213, ZJNSF \ Grant R6090034 and SRFDP Grant 20100101110001. P.G. was supported in part by the Ministry of Education, Singapore, under Grant ARC 14/11. Z.W. was supported \ in part by the Ministry of Education, Singapore, under Grant ARC 14/11, \ and by a Grant R-155-000-131-112 at the National University of Singapore\r\n" author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: Guangming full_name: Pan, Guangming last_name: Pan - first_name: Wang full_name: Zhou, Wang last_name: Zhou citation: ama: Bao Z, Pan G, Zhou W. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 2015;43(1):382-421. doi:10.1214/14-AOS1281 apa: Bao, Z., Pan, G., & Zhou, W. (2015). Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/14-AOS1281 chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/14-AOS1281. ieee: Z. Bao, G. Pan, and W. Zhou, “Universality for the largest eigenvalue of sample covariance matrices with general population,” Annals of Statistics, vol. 43, no. 1. Institute of Mathematical Statistics, pp. 382–421, 2015. ista: Bao Z, Pan G, Zhou W. 2015. Universality for the largest eigenvalue of sample covariance matrices with general population. Annals of Statistics. 43(1), 382–421. mla: Bao, Zhigang, et al. “Universality for the Largest Eigenvalue of Sample Covariance Matrices with General Population.” Annals of Statistics, vol. 43, no. 1, Institute of Mathematical Statistics, 2015, pp. 382–421, doi:10.1214/14-AOS1281. short: Z. Bao, G. Pan, W. Zhou, Annals of Statistics 43 (2015) 382–421. date_created: 2018-12-11T11:52:25Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:51:14Z day: '01' department: - _id: LaEr doi: 10.1214/14-AOS1281 intvolume: ' 43' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1304.5690 month: '02' oa: 1 oa_version: Preprint page: 382 - 421 publication: Annals of Statistics publication_status: published publisher: Institute of Mathematical Statistics publist_id: '5672' quality_controlled: '1' status: public title: Universality for the largest eigenvalue of sample covariance matrices with general population type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 43 year: '2015' ... --- _id: '1508' abstract: - lang: eng text: We consider generalized Wigner ensembles and general β-ensembles with analytic potentials for any β ≥ 1. The recent universality results in particular assert that the local averages of consecutive eigenvalue gaps in the bulk of the spectrum are universal in the sense that they coincide with those of the corresponding Gaussian β-ensembles. In this article, we show that local averaging is not necessary for this result, i.e. we prove that the single gap distributions in the bulk are universal. In fact, with an additional step, our result can be extended to any C4(ℝ) potential. 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. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 2015;17(8):1927-2036. doi:10.4171/JEMS/548 apa: Erdös, L., & Yau, H. (2015). Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/548 chicago: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society. European Mathematical Society, 2015. https://doi.org/10.4171/JEMS/548. ieee: L. Erdös and H. Yau, “Gap universality of generalized Wigner and β ensembles,” Journal of the European Mathematical Society, vol. 17, no. 8. European Mathematical Society, pp. 1927–2036, 2015. ista: Erdös L, Yau H. 2015. Gap universality of generalized Wigner and β ensembles. Journal of the European Mathematical Society. 17(8), 1927–2036. mla: Erdös, László, and Horng Yau. “Gap Universality of Generalized Wigner and β Ensembles.” Journal of the European Mathematical Society, vol. 17, no. 8, European Mathematical Society, 2015, pp. 1927–2036, doi:10.4171/JEMS/548. short: L. Erdös, H. Yau, Journal of the European Mathematical Society 17 (2015) 1927–2036. date_created: 2018-12-11T11:52:26Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:15Z day: '01' department: - _id: LaEr doi: 10.4171/JEMS/548 intvolume: ' 17' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1211.3786 month: '08' oa: 1 oa_version: Preprint page: 1927 - 2036 publication: Journal of the European Mathematical Society publication_status: published publisher: European Mathematical Society publist_id: '5669' quality_controlled: '1' scopus_import: 1 status: public title: Gap universality of generalized Wigner and β ensembles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '1506' abstract: - lang: eng text: Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1). author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: Guangming full_name: Pan, Guangming last_name: Pan - first_name: Wang full_name: Zhou, Wang last_name: Zhou citation: ama: Bao Z, Pan G, Zhou W. The logarithmic law of random determinant. Bernoulli. 2015;21(3):1600-1628. doi:10.3150/14-BEJ615 apa: Bao, Z., Pan, G., & Zhou, W. (2015). The logarithmic law of random determinant. Bernoulli. Bernoulli Society for Mathematical Statistics and Probability. https://doi.org/10.3150/14-BEJ615 chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “The Logarithmic Law of Random Determinant.” Bernoulli. Bernoulli Society for Mathematical Statistics and Probability, 2015. https://doi.org/10.3150/14-BEJ615. ieee: Z. Bao, G. Pan, and W. Zhou, “The logarithmic law of random determinant,” Bernoulli, vol. 21, no. 3. Bernoulli Society for Mathematical Statistics and Probability, pp. 1600–1628, 2015. ista: Bao Z, Pan G, Zhou W. 2015. The logarithmic law of random determinant. Bernoulli. 21(3), 1600–1628. mla: Bao, Zhigang, et al. “The Logarithmic Law of Random Determinant.” Bernoulli, vol. 21, no. 3, Bernoulli Society for Mathematical Statistics and Probability, 2015, pp. 1600–28, doi:10.3150/14-BEJ615. short: Z. Bao, G. Pan, W. Zhou, Bernoulli 21 (2015) 1600–1628. date_created: 2018-12-11T11:52:25Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:14Z day: '01' department: - _id: LaEr doi: 10.3150/14-BEJ615 intvolume: ' 21' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1208.5823 month: '08' oa: 1 oa_version: Preprint page: 1600 - 1628 publication: Bernoulli publication_status: published publisher: Bernoulli Society for Mathematical Statistics and Probability publist_id: '5671' quality_controlled: '1' status: public title: The logarithmic law of random determinant type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2015' ... --- _id: '1513' abstract: - lang: eng text: "Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.\r\n\r\nIn this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. " article_processing_charge: No author: - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: 'Pal A, Vicoso B. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 2015;7(12):3259-3268. doi:10.1093/gbe/evv215' apa: 'Pal, A., & Vicoso, B. (2015). The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evv215' chicago: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution. Oxford University Press, 2015. https://doi.org/10.1093/gbe/evv215.' ieee: 'A. Pal and B. Vicoso, “The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression,” Genome Biology and Evolution, vol. 7, no. 12. Oxford University Press, pp. 3259–3268, 2015.' ista: 'Pal A, Vicoso B. 2015. The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression. Genome Biology and Evolution. 7(12), 3259–3268.' mla: 'Pal, Arka, and Beatriz Vicoso. “The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression.” Genome Biology and Evolution, vol. 7, no. 12, Oxford University Press, 2015, pp. 3259–68, doi:10.1093/gbe/evv215.' short: A. Pal, B. Vicoso, Genome Biology and Evolution 7 (2015) 3259–3268. date_created: 2018-12-11T11:52:27Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:51:18Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evv215 ec_funded: 1 file: - access_level: open_access checksum: 2b56b8c2e2a1d4cc3c9cb8daba26dd9b content_type: application/pdf creator: system date_created: 2018-12-12T10:17:29Z date_updated: 2020-07-14T12:45:00Z file_id: '5284' file_name: IST-2016-496-v1+1_Genome_Biol_Evol-2015-Pal-3259-68.pdf file_size: 858027 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 7' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 3259 - 3268 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Genome Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '5664' pubrep_id: '496' quality_controlled: '1' scopus_import: 1 status: public title: 'The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2015' ... --- _id: '1517' abstract: - lang: eng text: "We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.\r\n" article_number: '89' author: - first_name: Matthias full_name: Erbar, Matthias last_name: Erbar - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Michiel full_name: Renger, Michiel last_name: Renger citation: ama: Erbar M, Maas J, Renger M. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 2015;20. doi:10.1214/ECP.v20-4315 apa: Erbar, M., Maas, J., & Renger, M. (2015). From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/ECP.v20-4315 chicago: Erbar, Matthias, Jan Maas, and Michiel Renger. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2015. https://doi.org/10.1214/ECP.v20-4315. ieee: M. Erbar, J. Maas, and M. Renger, “From large deviations to Wasserstein gradient flows in multiple dimensions,” Electronic Communications in Probability, vol. 20. Institute of Mathematical Statistics, 2015. ista: Erbar M, Maas J, Renger M. 2015. From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability. 20, 89. mla: Erbar, Matthias, et al. “From Large Deviations to Wasserstein Gradient Flows in Multiple Dimensions.” Electronic Communications in Probability, vol. 20, 89, Institute of Mathematical Statistics, 2015, doi:10.1214/ECP.v20-4315. short: M. Erbar, J. Maas, M. Renger, Electronic Communications in Probability 20 (2015). date_created: 2018-12-11T11:52:29Z date_published: 2015-11-29T00:00:00Z date_updated: 2021-01-12T06:51:19Z day: '29' ddc: - '519' department: - _id: JaMa doi: 10.1214/ECP.v20-4315 file: - access_level: open_access checksum: 135741c17d3e1547ca696b6fbdcd559c content_type: application/pdf creator: system date_created: 2018-12-12T10:10:39Z date_updated: 2020-07-14T12:45:00Z file_id: '4828' file_name: IST-2016-494-v1+1_4315-23820-1-PB.pdf file_size: 230525 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 20' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Electronic Communications in Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '5660' pubrep_id: '494' quality_controlled: '1' scopus_import: 1 status: public title: From large deviations to Wasserstein gradient flows in multiple dimensions 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: 20 year: '2015' ... --- _id: '1519' abstract: - lang: eng text: Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so. 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: Maria full_name: Servedio, Maria last_name: Servedio citation: ama: Barton NH, Servedio M. The interpretation of selection coefficients. Evolution. 2015;69(5):1101-1112. doi:10.1111/evo.12641 apa: Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients. Evolution. Wiley. https://doi.org/10.1111/evo.12641 chicago: Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641. ieee: N. H. Barton and M. Servedio, “The interpretation of selection coefficients,” Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015. ista: Barton NH, Servedio M. 2015. The interpretation of selection coefficients. Evolution. 69(5), 1101–1112. mla: Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.” Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641. short: N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112. date_created: 2018-12-11T11:52:29Z date_published: 2015-03-19T00:00:00Z date_updated: 2021-01-12T06:51:20Z day: '19' ddc: - '570' department: - _id: NiBa doi: 10.1111/evo.12641 ec_funded: 1 file: - access_level: open_access checksum: fd8d23f476bc194419929b72ca265c02 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:34Z date_updated: 2020-07-14T12:45:00Z file_id: '4822' file_name: IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf file_size: 188872 relation: main_file - access_level: open_access checksum: b774911e70044641d556e258efcb52ef content_type: application/pdf creator: system date_created: 2018-12-12T10:10:35Z date_updated: 2020-07-14T12:45:00Z file_id: '4823' file_name: IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf file_size: 577415 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 69' issue: '5' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 1101 - 1112 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Evolution publication_status: published publisher: Wiley publist_id: '5656' pubrep_id: '560' quality_controlled: '1' scopus_import: 1 status: public title: The interpretation of selection coefficients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2015' ... --- _id: '1525' abstract: - lang: eng text: 'Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.' article_processing_charge: No article_type: original author: - first_name: Bruno full_name: Bauer, Bruno last_name: Bauer - first_name: Guido full_name: Blechl, Guido last_name: Blechl - first_name: Christoph full_name: Bock, Christoph last_name: Bock - first_name: Patrick full_name: Danowski, Patrick id: 2EBD1598-F248-11E8-B48F-1D18A9856A87 last_name: Danowski orcid: 0000-0002-6026-4409 - first_name: Andreas full_name: Ferus, Andreas last_name: Ferus - first_name: Anton full_name: Graschopf, Anton last_name: Graschopf - first_name: Thomas full_name: König, Thomas last_name: König - first_name: Katja full_name: Mayer, Katja last_name: Mayer - first_name: Falk full_name: Reckling, Falk last_name: Reckling - first_name: Katharina full_name: Rieck, Katharina last_name: Rieck - first_name: Peter full_name: Seitz, Peter last_name: Seitz - first_name: Herwig full_name: Stöger, Herwig last_name: Stöger - first_name: Elvira full_name: Welzig, Elvira last_name: Welzig citation: ama: Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 2015;68(3):580-607. doi:10.5281/zenodo.33178 apa: Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., … Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. Verein Österreichischer Bibliothekare. https://doi.org/10.5281/zenodo.33178 chicago: Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus, Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen. Verein Österreichischer Bibliothekare, 2015. https://doi.org/10.5281/zenodo.33178. ieee: B. Bauer et al., “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” VÖB Mitteilungen, vol. 68, no. 3. Verein Österreichischer Bibliothekare, pp. 580–607, 2015. ista: Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607. mla: Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” VÖB Mitteilungen, vol. 68, no. 3, Verein Österreichischer Bibliothekare, 2015, pp. 580–607, doi:10.5281/zenodo.33178. short: B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König, K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. Welzig, VÖB Mitteilungen 68 (2015) 580–607. date_created: 2018-12-11T11:52:31Z date_published: 2015-11-12T00:00:00Z date_updated: 2021-01-12T06:51:22Z day: '12' ddc: - '020' department: - _id: E-Lib doi: 10.5281/zenodo.33178 file: - access_level: open_access checksum: a495fe253bbc7615b1d60e9e85c94408 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:59Z date_updated: 2020-07-14T12:45:00Z file_id: '5317' file_name: IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf file_size: 931707 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 68' issue: '3' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 580 - 607 publication: VÖB Mitteilungen publication_status: published publisher: Verein Österreichischer Bibliothekare publist_id: '5648' pubrep_id: '720' quality_controlled: '1' scopus_import: 1 status: public title: Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA 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: 68 year: '2015' ... --- _id: '1539' abstract: - lang: eng text: 'Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ' article_number: '244103' author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 citation: ama: Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 2015;143(24). doi:10.1063/1.4937937 apa: Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/1.4937937 chicago: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937. ieee: J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015. ista: Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103. mla: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937. short: J. Ruess, Journal of Chemical Physics 143 (2015). date_created: 2018-12-11T11:52:36Z date_published: 2015-12-22T00:00:00Z date_updated: 2021-01-12T06:51:28Z day: '22' ddc: - '000' department: - _id: ToHe - _id: GaTk doi: 10.1063/1.4937937 ec_funded: 1 file: - access_level: open_access checksum: 838657118ae286463a2b7737319f35ce content_type: application/pdf creator: system date_created: 2018-12-12T10:07:43Z date_updated: 2020-07-14T12:45:01Z file_id: '4641' file_name: IST-2016-593-v1+1_Minimal_moment_equations.pdf file_size: 605355 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 143' issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Chemical Physics publication_status: published publisher: American Institute of Physics publist_id: '5632' pubrep_id: '593' quality_controlled: '1' scopus_import: 1 status: public title: Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 143 year: '2015' ... --- _id: '1534' abstract: - lang: eng text: PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity. article_number: '8822' author: - first_name: Hongzhe full_name: Wang, Hongzhe last_name: Wang - first_name: Kezhen full_name: Yang, Kezhen last_name: Yang - first_name: Junjie full_name: Zou, Junjie last_name: Zou - first_name: Lingling full_name: Zhu, Lingling last_name: Zhu - first_name: Zidian full_name: Xie, Zidian last_name: Xie - first_name: Miyoterao full_name: Morita, Miyoterao last_name: Morita - first_name: Masao full_name: Tasaka, Masao last_name: Tasaka - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Erich full_name: Grotewold, Erich last_name: Grotewold - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Fred full_name: Sack, Fred last_name: Sack - first_name: Jie full_name: Le, Jie last_name: Le citation: ama: Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 2015;6. doi:10.1038/ncomms9822 apa: Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9822 chicago: Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9822. ieee: H. Wang et al., “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822. mla: Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” Nature Communications, vol. 6, 8822, Nature Publishing Group, 2015, doi:10.1038/ncomms9822. short: H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015). date_created: 2018-12-11T11:52:34Z date_published: 2015-11-18T00:00:00Z date_updated: 2021-01-12T06:51:26Z day: '18' ddc: - '570' department: - _id: JiFr doi: 10.1038/ncomms9822 ec_funded: 1 file: - access_level: open_access checksum: 3c06735fc7cd7e482ca830cbd26001bf content_type: application/pdf creator: system date_created: 2018-12-12T10:17:07Z date_updated: 2020-07-14T12:45:01Z file_id: '5259' file_name: IST-2016-485-v1+1_ncomms9822.pdf file_size: 1852268 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5637' pubrep_id: '485' quality_controlled: '1' scopus_import: 1 status: public title: Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '1538' abstract: - lang: eng text: Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time. acknowledgement: 'J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ' author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Francesca full_name: Parise, Francesca last_name: Parise - first_name: Andreas full_name: Milias Argeitis, Andreas last_name: Milias Argeitis - first_name: Mustafa full_name: Khammash, Mustafa last_name: Khammash - first_name: John full_name: Lygeros, John last_name: Lygeros citation: ama: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112 apa: Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112 chicago: Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423947112. ieee: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015. ista: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153. mla: Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112. short: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153. date_created: 2018-12-11T11:52:36Z date_published: 2015-06-30T00:00:00Z date_updated: 2021-01-12T06:51:27Z day: '30' department: - _id: ToHe - _id: GaTk doi: 10.1073/pnas.1423947112 ec_funded: 1 external_id: pmid: - '26085136' intvolume: ' 112' issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/ month: '06' oa: 1 oa_version: Submitted Version page: 8148 - 8153 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5633' quality_controlled: '1' scopus_import: 1 status: public title: Iterative experiment design guides the characterization of a light-inducible gene expression circuit type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1535' abstract: - lang: eng text: Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress. acknowledgement: This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino. article_processing_charge: No article_type: original author: - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Andrea full_name: Marcantoni, Andrea last_name: Marcantoni - first_name: Emilio full_name: Carbone, Emilio last_name: Carbone citation: ama: Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 2015;8(2):149-161. doi:10.2174/1874467208666150507105443 apa: Vandael, D. H., Marcantoni, A., & Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. Bentham Science Publishers. https://doi.org/10.2174/1874467208666150507105443 chicago: Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology. Bentham Science Publishers, 2015. https://doi.org/10.2174/1874467208666150507105443. ieee: D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” Current Molecular Pharmacology, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015. ista: Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161. mla: Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” Current Molecular Pharmacology, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:10.2174/1874467208666150507105443. short: D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161. date_created: 2018-12-11T11:52:35Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:51:26Z day: '01' department: - _id: PeJo doi: 10.2174/1874467208666150507105443 external_id: pmid: - '25966692' intvolume: ' 8' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/ month: '10' oa: 1 oa_version: Submitted Version page: 149 - 161 pmid: 1 publication: Current Molecular Pharmacology publication_status: published publisher: Bentham Science Publishers publist_id: '5636' quality_controlled: '1' scopus_import: 1 status: public title: Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2015' ... --- _id: '1542' abstract: - lang: eng text: 'The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ' author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Golnaz full_name: Badkobeh, Golnaz last_name: Badkobeh - 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: Doğan full_name: Çörüş, Doğan last_name: Çörüş - first_name: Duccuong full_name: Dang, Duccuong last_name: Dang - first_name: Tobias full_name: Friedrich, Tobias last_name: Friedrich - first_name: Per full_name: Lehre, Per last_name: Lehre - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Andrew full_name: Sutton, Andrew last_name: Sutton - first_name: Barbora full_name: Trubenova, Barbora id: 42302D54-F248-11E8-B48F-1D18A9856A87 last_name: Trubenova orcid: 0000-0002-6873-2967 citation: ama: Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011 apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011 chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011. ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,” Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015. ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal of Theoretical Biology. 383, 28–43. mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011. short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383 (2015) 28–43. date_created: 2018-12-11T11:52:37Z date_published: 2015-10-21T00:00:00Z date_updated: 2021-01-12T06:51:29Z day: '21' ddc: - '570' department: - _id: NiBa - _id: CaGu doi: 10.1016/j.jtbi.2015.07.011 ec_funded: 1 file: - access_level: open_access checksum: 33b60ecfea60764756a9ee9df5eb65ca content_type: application/pdf creator: system date_created: 2018-12-12T10:16:53Z date_updated: 2020-07-14T12:45:01Z file_id: '5244' file_name: IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf file_size: 595307 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 383' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '10' oa: 1 oa_version: Published Version page: 28 - 43 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: ' Journal of Theoretical Biology' publication_status: published publisher: Elsevier publist_id: '5629' pubrep_id: '483' quality_controlled: '1' scopus_import: 1 status: public title: Toward a unifying framework for evolutionary processes 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: 383 year: '2015' ... --- _id: '1546' abstract: - lang: eng text: Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (<30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This "perimeter release model" provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course. acknowledgement: This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS. author: - first_name: Yukihiro full_name: Nakamura, Yukihiro last_name: Nakamura - first_name: Harumi full_name: Harada, Harumi id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87 last_name: Harada orcid: 0000-0001-7429-7896 - first_name: Naomi full_name: Kamasawa, Naomi last_name: Kamasawa - first_name: Ko full_name: Matsui, Ko last_name: Matsui - first_name: Jason full_name: Rothman, Jason last_name: Rothman - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: R Angus full_name: Silver, R Angus last_name: Silver - first_name: David full_name: Digregorio, David last_name: Digregorio - first_name: Tomoyuki full_name: Takahashi, Tomoyuki last_name: Takahashi citation: ama: Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 2015;85(1):145-158. doi:10.1016/j.neuron.2014.11.019 apa: Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.11.019 chicago: Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2014.11.019. ieee: Y. Nakamura et al., “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” Neuron, vol. 85, no. 1. Elsevier, pp. 145–158, 2015. ista: Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158. mla: Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” Neuron, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:10.1016/j.neuron.2014.11.019. short: Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158. date_created: 2018-12-11T11:52:39Z date_published: 2015-01-07T00:00:00Z date_updated: 2021-01-12T06:51:31Z day: '07' ddc: - '570' department: - _id: RySh doi: 10.1016/j.neuron.2014.11.019 file: - access_level: open_access checksum: 725f4d5be2dbb44b283ce722645ef37d content_type: application/pdf creator: system date_created: 2018-12-12T10:15:47Z date_updated: 2020-07-14T12:45:01Z file_id: '5170' file_name: IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf file_size: 3080111 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 85' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 145 - 158 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5625' pubrep_id: '482' quality_controlled: '1' scopus_import: 1 status: public title: Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 85 year: '2015' ... --- _id: '1544' abstract: - lang: eng text: 'Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.' author: - first_name: Phuong full_name: Nguyen, Phuong last_name: Nguyen - first_name: Christine full_name: Field, Christine last_name: Field - first_name: Aaron full_name: Groen, Aaron last_name: Groen - first_name: Timothy full_name: Mitchison, Timothy last_name: Mitchison - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from Its Components Parts. Vol 128. Academic Press; 2015:223-241. doi:10.1016/bs.mcb.2015.01.007' apa: Nguyen, P., Field, C., Groen, A., Mitchison, T., & Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In Building a Cell from its Components Parts (Vol. 128, pp. 223–241). Academic Press. https://doi.org/10.1016/bs.mcb.2015.01.007 chicago: Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In Building a Cell from Its Components Parts, 128:223–41. Academic Press, 2015. https://doi.org/10.1016/bs.mcb.2015.01.007. ieee: P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in Building a Cell from its Components Parts, vol. 128, Academic Press, 2015, pp. 223–241. ista: 'Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.' mla: Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” Building a Cell from Its Components Parts, vol. 128, Academic Press, 2015, pp. 223–41, doi:10.1016/bs.mcb.2015.01.007. short: P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241. date_created: 2018-12-11T11:52:38Z date_published: 2015-04-08T00:00:00Z date_updated: 2021-01-12T06:51:30Z day: '08' department: - _id: MaLo doi: 10.1016/bs.mcb.2015.01.007 external_id: pmid: - '25997350' intvolume: ' 128' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/ month: '04' oa: 1 oa_version: Submitted Version page: 223 - 241 pmid: 1 publication: Building a Cell from its Components Parts publication_status: published publisher: Academic Press publist_id: '5627' quality_controlled: '1' scopus_import: 1 status: public title: Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2015' ... --- _id: '1551' abstract: - lang: eng text: 'Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen''s genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system.' acknowledgement: We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM. author: - first_name: Leila full_name: El Masri, Leila id: 349A6E66-F248-11E8-B48F-1D18A9856A87 last_name: El Masri - first_name: Antoine full_name: Branca, Antoine last_name: Branca - first_name: Anna full_name: Sheppard, Anna last_name: Sheppard - first_name: Andrei full_name: Papkou, Andrei last_name: Papkou - first_name: David full_name: Laehnemann, David last_name: Laehnemann - first_name: Patrick full_name: Guenther, Patrick last_name: Guenther - first_name: Swantje full_name: Prahl, Swantje last_name: Prahl - first_name: Manja full_name: Saebelfeld, Manja last_name: Saebelfeld - first_name: Jacqueline full_name: Hollensteiner, Jacqueline last_name: Hollensteiner - first_name: Heiko full_name: Liesegang, Heiko last_name: Liesegang - first_name: Elzbieta full_name: Brzuszkiewicz, Elzbieta last_name: Brzuszkiewicz - first_name: Rolf full_name: Daniel, Rolf last_name: Daniel - first_name: Nico full_name: Michiels, Nico last_name: Michiels - first_name: Rebecca full_name: Schulte, Rebecca last_name: Schulte - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz - first_name: Philip full_name: Rosenstiel, Philip last_name: Rosenstiel - first_name: Arndt full_name: Telschow, Arndt last_name: Telschow - first_name: Erich full_name: Bornberg Bauer, Erich last_name: Bornberg Bauer - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg citation: ama: 'El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 2015;13(6):1-30. doi:10.1371/journal.pbio.1002169' apa: 'El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002169' chicago: 'El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002169.' ieee: 'L. El Masri et al., “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” PLoS Biology, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.' ista: 'El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.' mla: 'El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” PLoS Biology, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:10.1371/journal.pbio.1002169.' short: L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30. date_created: 2018-12-11T11:52:40Z date_published: 2015-06-04T00:00:00Z date_updated: 2021-01-12T06:51:33Z day: '04' ddc: - '570' department: - _id: SyCr doi: 10.1371/journal.pbio.1002169 ec_funded: 1 file: - access_level: open_access checksum: 30dee7a2c11ed09f2f5634655c0146f8 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:13Z date_updated: 2020-07-14T12:45:02Z file_id: '5063' file_name: IST-2016-481-v1+1_journal.pbio.1002169.pdf file_size: 3468956 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 13' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1 - 30 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '5620' pubrep_id: '481' quality_controlled: '1' scopus_import: 1 status: public title: 'Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes' 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: 13 year: '2015' ... --- _id: '1549' abstract: - lang: eng text: Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology. author: - first_name: Catherine full_name: Mckenzie, Catherine id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87 last_name: Mckenzie - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 citation: ama: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: Novel Chemical Tools to Study Ion Channel Biology. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:10.1007/978-1-4939-2845-3_6' apa: 'Mckenzie, C., Sanchez-Romero, I., & Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In Novel chemical tools to study ion channel biology (Vol. 869, pp. 101–117). Springer. https://doi.org/10.1007/978-1-4939-2845-3_6' chicago: 'Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In Novel Chemical Tools to Study Ion Channel Biology, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. https://doi.org/10.1007/978-1-4939-2845-3_6.' ieee: 'C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in Novel chemical tools to study ion channel biology, vol. 869, Springer, 2015, pp. 101–117.' ista: 'Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117.' mla: 'Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” Novel Chemical Tools to Study Ion Channel Biology, vol. 869, Springer, 2015, pp. 101–17, doi:10.1007/978-1-4939-2845-3_6.' short: C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117. date_created: 2018-12-11T11:52:39Z date_published: 2015-09-18T00:00:00Z date_updated: 2021-01-12T06:51:32Z day: '18' ddc: - '571' - '576' department: - _id: HaJa doi: 10.1007/978-1-4939-2845-3_6 file: - access_level: open_access checksum: bd1bfdf2423a0c3b6e7cabfa8b44bc0f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:02Z date_updated: 2020-07-14T12:45:01Z file_id: '4854' file_name: IST-2017-839-v1+1_mckenzie.pdf file_size: 1919655 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 869' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 101 - 117 publication: Novel chemical tools to study ion channel biology publication_identifier: isbn: - 978-1-4939-2844-6 publication_status: published publisher: Springer publist_id: '5622' pubrep_id: '839' quality_controlled: '1' scopus_import: 1 series_title: Advances in Experimental Medicine and Biology status: public title: 'Flipping the photoswitch: Ion channels under light control' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 869 year: '2015' ... --- _id: '1548' abstract: - lang: eng text: Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen. author: - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Christina full_name: Höfling, Christina last_name: Höfling - first_name: Momir full_name: Futo, Momir last_name: Futo - first_name: Jörn full_name: Scharsack, Jörn last_name: Scharsack - first_name: Joachim full_name: Kurtz, Joachim last_name: Kurtz citation: ama: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 2015;81(23):8135-8144. doi:10.1128/AEM.02051-15' apa: 'Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., & Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. American Society for Microbiology. https://doi.org/10.1128/AEM.02051-15' chicago: 'Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology. American Society for Microbiology, 2015. https://doi.org/10.1128/AEM.02051-15.' ieee: 'B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” Applied and Environmental Microbiology, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.' ista: 'Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.' mla: 'Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” Applied and Environmental Microbiology, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:10.1128/AEM.02051-15.' short: B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144. date_created: 2018-12-11T11:52:39Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:51:31Z day: '01' department: - _id: SyCr doi: 10.1128/AEM.02051-15 external_id: pmid: - '26386058' intvolume: ' 81' issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/ month: '12' oa: 1 oa_version: Submitted Version page: 8135 - 8144 pmid: 1 publication: Applied and Environmental Microbiology publication_status: published publisher: American Society for Microbiology publist_id: '5623' quality_controlled: '1' scopus_import: 1 status: public title: 'Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 81 year: '2015' ... --- _id: '1550' abstract: - lang: eng text: The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute. acknowledgement: "Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n" author: - first_name: Christian full_name: Mayer, Christian last_name: Mayer - first_name: Xavier full_name: Jaglin, Xavier last_name: Jaglin - first_name: Lucy full_name: Cobbs, Lucy last_name: Cobbs - first_name: Rachel full_name: Bandler, Rachel last_name: Bandler - first_name: Carmen full_name: Streicher, Carmen id: 36BCB99C-F248-11E8-B48F-1D18A9856A87 last_name: Streicher - first_name: Constance full_name: Cepko, Constance last_name: Cepko - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Gord full_name: Fishell, Gord last_name: Fishell citation: ama: Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 2015;87(5):989-998. doi:10.1016/j.neuron.2015.07.011 apa: Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2015.07.011 chicago: Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron. Elsevier, 2015. https://doi.org/10.1016/j.neuron.2015.07.011. ieee: C. Mayer et al., “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” Neuron, vol. 87, no. 5. Elsevier, pp. 989–998, 2015. ista: Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998. mla: Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” Neuron, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:10.1016/j.neuron.2015.07.011. short: C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998. date_created: 2018-12-11T11:52:40Z date_published: 2015-09-02T00:00:00Z date_updated: 2021-01-12T06:51:32Z day: '02' department: - _id: SiHi doi: 10.1016/j.neuron.2015.07.011 external_id: pmid: - '26299473' intvolume: ' 87' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/ month: '09' oa: 1 oa_version: Submitted Version page: 989 - 998 pmid: 1 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5621' quality_controlled: '1' scopus_import: 1 status: public title: Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 87 year: '2015' ... --- _id: '1547' abstract: - lang: eng text: Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice. author: - first_name: Fatemeh full_name: Mohammadi, Fatemeh id: 2C29581E-F248-11E8-B48F-1D18A9856A87 last_name: Mohammadi - first_name: Somayeh full_name: Moradi, Somayeh last_name: Moradi citation: ama: Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 2015;52(3):977-986. doi:10.4134/BKMS.2015.52.3.977 apa: Mohammadi, F., & Moradi, S. (2015). Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. Korean Mathematical Society. https://doi.org/10.4134/BKMS.2015.52.3.977 chicago: Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society. Korean Mathematical Society, 2015. https://doi.org/10.4134/BKMS.2015.52.3.977. ieee: F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” Bulletin of the Korean Mathematical Society, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015. ista: Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986. mla: Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” Bulletin of the Korean Mathematical Society, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:10.4134/BKMS.2015.52.3.977. short: F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986. date_created: 2018-12-11T11:52:39Z date_published: 2015-05-31T00:00:00Z date_updated: 2021-01-12T06:51:31Z day: '31' department: - _id: CaUh doi: 10.4134/BKMS.2015.52.3.977 intvolume: ' 52' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/0901.3015 month: '05' oa: 1 oa_version: Preprint page: 977 - 986 publication: Bulletin of the Korean Mathematical Society publication_identifier: eissn: - 2234-3016 publication_status: published publisher: Korean Mathematical Society publist_id: '5624' quality_controlled: '1' scopus_import: 1 status: public title: Resolution of unmixed bipartite graphs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 52 year: '2015' ... --- _id: '1556' abstract: - lang: eng text: The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators. author: - first_name: Yuebin full_name: Jia, Yuebin last_name: Jia - first_name: Huiyu full_name: Tian, Huiyu last_name: Tian - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Qianqian full_name: Yu, Qianqian last_name: Yu - first_name: Lei full_name: Wang, Lei last_name: Wang - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding citation: ama: Jia Y, Tian H, Li H, et al. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 2015;66(15):4631-4642. doi:10.1093/jxb/erv230 apa: Jia, Y., Tian, H., Li, H., Yu, Q., Wang, L., Friml, J., & Ding, Z. (2015). The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erv230 chicago: Jia, Yuebin, Huiyu Tian, Hongjiang Li, Qianqian Yu, Lei Wang, Jiří Friml, and Zhaojun Ding. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany. Oxford University Press, 2015. https://doi.org/10.1093/jxb/erv230. ieee: Y. Jia et al., “The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development,” Journal of Experimental Botany, vol. 66, no. 15. Oxford University Press, pp. 4631–4642, 2015. ista: Jia Y, Tian H, Li H, Yu Q, Wang L, Friml J, Ding Z. 2015. The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development. Journal of Experimental Botany. 66(15), 4631–4642. mla: Jia, Yuebin, et al. “The Arabidopsis Thaliana Elongator Complex Subunit 2 Epigenetically Affects Root Development.” Journal of Experimental Botany, vol. 66, no. 15, Oxford University Press, 2015, pp. 4631–42, doi:10.1093/jxb/erv230. short: Y. Jia, H. Tian, H. Li, Q. Yu, L. Wang, J. Friml, Z. Ding, Journal of Experimental Botany 66 (2015) 4631–4642. date_created: 2018-12-11T11:52:42Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:35Z day: '01' ddc: - '570' department: - _id: JiFr doi: 10.1093/jxb/erv230 file: - access_level: open_access checksum: 257919be0ce3d306185d3891ad7acf39 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:02Z date_updated: 2020-07-14T12:45:02Z file_id: '5051' file_name: IST-2016-480-v1+1_J._Exp._Bot.-2015-Jia-4631-42.pdf file_size: 7753043 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 66' issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 4631 - 4642 publication: Journal of Experimental Botany publication_status: published publisher: Oxford University Press publist_id: '5615' pubrep_id: '480' quality_controlled: '1' scopus_import: 1 status: public title: The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2015' ... --- _id: '1555' abstract: - lang: eng text: We show that incorporating spatial dispersal of individuals into a simple vaccination epidemic model may give rise to a model that exhibits rich dynamical behavior. Using an SIVS (susceptible-infected-vaccinated-susceptible) model as a basis, we describe the spread of an infectious disease in a population split into two regions. In each subpopulation, both forward and backward bifurcations can occur. This implies that for disconnected regions the two-patch system may admit several steady states. We consider traveling between the regions and investigate the impact of spatial dispersal of individuals on the model dynamics. We establish conditions for the existence of multiple nontrivial steady states in the system, and we study the structure of the equilibria. The mathematical analysis reveals an unusually rich dynamical behavior, not normally found in the simple epidemic models. In addition to the disease-free equilibrium, eight endemic equilibria emerge from backward transcritical and saddle-node bifurcation points, forming an interesting bifurcation diagram. Stability of steady states, their bifurcations, and the global dynamics are investigated with analytical tools, numerical simulations, and rigorous set-oriented numerical computations. acknowledgement: Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria (pawel.pilarczyk@ist.ac.at). This author’s work was partially supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 622033, by Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC), by the Portuguese national funds through Funda ̧caoparaaCiˆencia e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008), and by European Research Council through StG 259559 in the framework of the EPIDELAY project. article_processing_charge: No article_type: original author: - first_name: Diána full_name: Knipl, Diána last_name: Knipl - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk - first_name: Gergely full_name: Röst, Gergely last_name: Röst citation: ama: Knipl D, Pilarczyk P, Röst G. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 2015;14(2):980-1017. doi:10.1137/140993934 apa: Knipl, D., Pilarczyk, P., & Röst, G. (2015). Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/140993934 chicago: Knipl, Diána, Pawel Pilarczyk, and Gergely Röst. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems. Society for Industrial and Applied Mathematics , 2015. https://doi.org/10.1137/140993934. ieee: D. Knipl, P. Pilarczyk, and G. Röst, “Rich bifurcation structure in a two patch vaccination model,” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2. Society for Industrial and Applied Mathematics , pp. 980–1017, 2015. ista: Knipl D, Pilarczyk P, Röst G. 2015. Rich bifurcation structure in a two patch vaccination model. SIAM Journal on Applied Dynamical Systems. 14(2), 980–1017. mla: Knipl, Diána, et al. “Rich Bifurcation Structure in a Two Patch Vaccination Model.” SIAM Journal on Applied Dynamical Systems, vol. 14, no. 2, Society for Industrial and Applied Mathematics , 2015, pp. 980–1017, doi:10.1137/140993934. short: D. Knipl, P. Pilarczyk, G. Röst, SIAM Journal on Applied Dynamical Systems 14 (2015) 980–1017. date_created: 2018-12-11T11:52:42Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:51:34Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1137/140993934 ec_funded: 1 intvolume: ' 14' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://discovery.ucl.ac.uk/1473750/1/99393.pdf month: '01' oa: 1 oa_version: Published Version page: 980 - 1017 project: - _id: 255F06BE-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '622033' name: Persistent Homology - Images, Data and Maps publication: SIAM Journal on Applied Dynamical Systems publication_identifier: eissn: - 1536-0040 publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '5616' quality_controlled: '1' scopus_import: 1 status: public title: Rich bifurcation structure in a two patch vaccination model type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2015' ... --- _id: '1559' abstract: - lang: eng text: 'There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).' author: - 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: 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: Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 2015;112(51):15636-15641. doi:10.1073/pnas.1511366112 apa: Ibsen-Jensen, R., Chatterjee, K., & Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1511366112 chicago: Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511366112. ieee: R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” PNAS, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015. ista: Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641. mla: Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” PNAS, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:10.1073/pnas.1511366112. short: R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641. date_created: 2018-12-11T11:52:43Z date_published: 2015-12-22T00:00:00Z date_updated: 2021-01-12T06:51:36Z day: '22' department: - _id: KrCh doi: 10.1073/pnas.1511366112 external_id: pmid: - '26644569' intvolume: ' 112' issue: '51' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/ month: '12' oa: 1 oa_version: Submitted Version page: 15636 - 15641 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5612' quality_controlled: '1' scopus_import: 1 status: public title: Computational complexity of ecological and evolutionary spatial dynamics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1554' abstract: - lang: eng text: The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species. author: - first_name: Cheyang full_name: Liao, Cheyang last_name: Liao - first_name: Wouter full_name: Smet, Wouter last_name: Smet - first_name: Géraldine full_name: Brunoud, Géraldine last_name: Brunoud - first_name: Saiko full_name: Yoshida, Saiko id: 2E46069C-F248-11E8-B48F-1D18A9856A87 last_name: Yoshida - first_name: Teva full_name: Vernoux, Teva last_name: Vernoux - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers citation: ama: Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 2015;12(3):207-210. doi:10.1038/nmeth.3279 apa: Liao, C., Smet, W., Brunoud, G., Yoshida, S., Vernoux, T., & Weijers, D. (2015). Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.3279 chicago: Liao, Cheyang, Wouter Smet, Géraldine Brunoud, Saiko Yoshida, Teva Vernoux, and Dolf Weijers. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods. Nature Publishing Group, 2015. https://doi.org/10.1038/nmeth.3279. ieee: C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, and D. Weijers, “Reporters for sensitive and quantitative measurement of auxin response,” Nature Methods, vol. 12, no. 3. Nature Publishing Group, pp. 207–210, 2015. ista: Liao C, Smet W, Brunoud G, Yoshida S, Vernoux T, Weijers D. 2015. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods. 12(3), 207–210. mla: Liao, Cheyang, et al. “Reporters for Sensitive and Quantitative Measurement of Auxin Response.” Nature Methods, vol. 12, no. 3, Nature Publishing Group, 2015, pp. 207–10, doi:10.1038/nmeth.3279. short: C. Liao, W. Smet, G. Brunoud, S. Yoshida, T. Vernoux, D. Weijers, Nature Methods 12 (2015) 207–210. date_created: 2018-12-11T11:52:41Z date_published: 2015-02-26T00:00:00Z date_updated: 2021-01-12T06:51:34Z day: '26' department: - _id: JiFr doi: 10.1038/nmeth.3279 external_id: pmid: - '25643149' intvolume: ' 12' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344836/ month: '02' oa: 1 oa_version: Submitted Version page: 207 - 210 pmid: 1 publication: Nature Methods publication_status: published publisher: Nature Publishing Group publist_id: '5617' quality_controlled: '1' scopus_import: 1 status: public title: Reporters for sensitive and quantitative measurement of auxin response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2015' ... --- _id: '1565' abstract: - lang: eng text: Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release. acknowledgement: "This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support." author: - first_name: Daniela full_name: Gavello, Daniela last_name: Gavello - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Sara full_name: Gosso, Sara last_name: Gosso - first_name: Emilio full_name: Carbone, Emilio last_name: Carbone - first_name: Valentina full_name: Carabelli, Valentina last_name: Carabelli citation: ama: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 2015;593(22):4835-4853. doi:10.1113/JP271078 apa: Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., & Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/JP271078 chicago: Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology. Wiley-Blackwell, 2015. https://doi.org/10.1113/JP271078. ieee: D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” Journal of Physiology, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015. ista: Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853. mla: Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” Journal of Physiology, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:10.1113/JP271078. short: D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853. date_created: 2018-12-11T11:52:45Z date_published: 2015-11-15T00:00:00Z date_updated: 2021-01-12T06:51:38Z day: '15' department: - _id: PeJo doi: 10.1113/JP271078 external_id: pmid: - '26282459' intvolume: ' 593' issue: '22' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/ month: '11' oa: 1 oa_version: Submitted Version page: 4835 - 4853 pmid: 1 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '5606' quality_controlled: '1' scopus_import: 1 status: public title: Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 593 year: '2015' ... --- _id: '1564' article_number: '145' author: - first_name: Matthieu full_name: Gilson, Matthieu last_name: Gilson - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Friedemann full_name: Zenke, Friedemann last_name: Zenke citation: ama: 'Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145' apa: 'Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145' chicago: 'Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.' ieee: 'M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.' ista: 'Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.' mla: 'Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.' short: M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015). date_created: 2018-12-11T11:52:45Z date_published: 2015-11-30T00:00:00Z date_updated: 2021-01-12T06:51:37Z day: '30' ddc: - '570' department: - _id: GaTk doi: 10.3389/fncom.2015.00145 ec_funded: 1 file: - access_level: open_access checksum: cea73b6d3ef1579f32da10b82f4de4fd content_type: application/pdf creator: system date_created: 2018-12-12T10:12:09Z date_updated: 2020-07-14T12:45:02Z file_id: '4927' file_name: IST-2016-479-v1+1_fncom-09-00145.pdf file_size: 187038 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 9' issue: '11' 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 publication: Frontiers in Computational Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '5607' pubrep_id: '479' quality_controlled: '1' scopus_import: 1 status: public title: 'Editorial: Emergent neural computation from the interaction of different forms of plasticity' 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: 9 year: '2015' ... --- _id: '1574' abstract: - lang: eng text: Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level. acknowledgement: 'of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ' article_number: '8821' author: - first_name: Qian full_name: Chen, Qian last_name: Chen - first_name: Yang full_name: Liu, Yang last_name: Liu - first_name: Steven full_name: Maere, Steven last_name: Maere - first_name: Eunkyoung full_name: Lee, Eunkyoung last_name: Lee - first_name: Gert full_name: Van Isterdael, Gert last_name: Van Isterdael - first_name: Zidian full_name: Xie, Zidian last_name: Xie - first_name: Wei full_name: Xuan, Wei last_name: Xuan - first_name: Jessica full_name: Lucas, Jessica last_name: Lucas - first_name: Valya full_name: Vassileva, Valya last_name: Vassileva - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Niko full_name: Geldner, Niko last_name: Geldner - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jie full_name: Le, Jie last_name: Le - first_name: Hidehiro full_name: Fukaki, Hidehiro last_name: Fukaki - first_name: Erich full_name: Grotewold, Erich last_name: Grotewold - first_name: Chuanyou full_name: Li, Chuanyou last_name: Li - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Fred full_name: Sack, Fred last_name: Sack - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: ama: Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821 apa: Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821 chicago: Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821. ieee: Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821. mla: Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821. short: Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015). date_created: 2018-12-11T11:52:48Z date_published: 2015-11-18T00:00:00Z date_updated: 2021-01-12T06:51:42Z day: '18' ddc: - '580' department: - _id: EvBe - _id: JiFr doi: 10.1038/ncomms9821 file: - access_level: open_access checksum: 8ff5c108899b548806e1cb7a302fe76d content_type: application/pdf creator: system date_created: 2018-12-12T10:14:32Z date_updated: 2020-07-14T12:45:02Z file_id: '5085' file_name: IST-2016-477-v1+1_ncomms9821.pdf file_size: 1701815 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5597' pubrep_id: '477' quality_controlled: '1' scopus_import: 1 status: public title: A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '1575' abstract: - lang: eng text: The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space. acknowledgement: M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie). article_number: '7526' author: - first_name: Mélanie full_name: Chabaud, Mélanie last_name: Chabaud - first_name: Mélina full_name: Heuzé, Mélina last_name: Heuzé - first_name: Marine full_name: Bretou, Marine last_name: Bretou - first_name: Pablo full_name: Vargas, Pablo last_name: Vargas - first_name: Paolo full_name: Maiuri, Paolo last_name: Maiuri - first_name: Paola full_name: Solanes, Paola last_name: Solanes - first_name: Mathieu full_name: Maurin, Mathieu last_name: Maurin - first_name: Emmanuel full_name: Terriac, Emmanuel last_name: Terriac - first_name: Maël full_name: Le Berre, Maël last_name: Le Berre - first_name: Danielle full_name: Lankar, Danielle last_name: Lankar - first_name: Tristan full_name: Piolot, Tristan last_name: Piolot - first_name: Robert full_name: Adelstein, Robert last_name: Adelstein - first_name: Yingfan full_name: Zhang, Yingfan last_name: Zhang - 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: Jordan full_name: Jacobelli, Jordan last_name: Jacobelli - first_name: Olivier full_name: Bénichou, Olivier last_name: Bénichou - first_name: Raphaël full_name: Voituriez, Raphaël last_name: Voituriez - first_name: Matthieu full_name: Piel, Matthieu last_name: Piel - first_name: Ana full_name: Lennon Duménil, Ana last_name: Lennon Duménil citation: ama: Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 2015;6. doi:10.1038/ncomms8526 apa: Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms8526 chicago: Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526. ieee: M. Chabaud et al., “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526. mla: Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications, vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526. short: M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015). date_created: 2018-12-11T11:52:48Z date_published: 2015-06-25T00:00:00Z date_updated: 2021-01-12T06:51:42Z day: '25' ddc: - '570' department: - _id: MiSi doi: 10.1038/ncomms8526 file: - access_level: open_access checksum: bae12e86be2adb28253f890b8bba8315 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:58Z date_updated: 2020-07-14T12:45:02Z file_id: '4915' file_name: IST-2016-476-v1+1_ncomms8526.pdf file_size: 4530215 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5596' pubrep_id: '476' quality_controlled: '1' scopus_import: 1 status: public title: Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '1569' abstract: - lang: eng text: Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development. acknowledgement: 'This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ' author: - first_name: Siamsa full_name: Doyle, Siamsa last_name: Doyle - first_name: Ash full_name: Haegera, Ash last_name: Haegera - first_name: Thomas full_name: Vain, Thomas last_name: Vain - first_name: Adeline full_name: Rigala, Adeline last_name: Rigala - first_name: Corrado full_name: Viotti, Corrado last_name: Viotti - first_name: Małgorzata full_name: Łangowskaa, Małgorzata last_name: Łangowskaa - first_name: Qian full_name: Maa, Qian last_name: Maa - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Natasha full_name: Raikhel, Natasha last_name: Raikhel - first_name: Glenn full_name: Hickse, Glenn last_name: Hickse - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert citation: ama: Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112 apa: Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112 chicago: Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112. ieee: S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015. ista: Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815. mla: Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112. short: S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815. date_created: 2018-12-11T11:52:46Z date_published: 2015-02-17T00:00:00Z date_updated: 2021-01-12T06:51:39Z day: '17' department: - _id: JiFr doi: 10.1073/pnas.1424856112 ec_funded: 1 intvolume: ' 112' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/ month: '02' oa: 1 oa_version: Published Version page: E806 - E815 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5602' quality_controlled: '1' scopus_import: 1 status: public title: An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1570' abstract: - lang: eng text: Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution. 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. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112 apa: Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112 chicago: Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1508400112. ieee: R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015. ista: Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232. mla: Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112. short: R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232. date_created: 2018-12-11T11:52:47Z date_published: 2015-11-10T00:00:00Z date_updated: 2021-01-12T06:51:40Z day: '10' department: - _id: ChLa - _id: GaTk doi: 10.1073/pnas.1508400112 ec_funded: 1 external_id: pmid: - '26504200' intvolume: ' 112' issue: '45' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/ month: '11' oa: 1 oa_version: Submitted Version page: E6224 - E6232 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5601' quality_controlled: '1' scopus_import: 1 status: public title: Novel plasticity rule can explain the development of sensorimotor intelligence type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1572' abstract: - lang: eng text: "We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n" author: - first_name: Michele full_name: Correggi, Michele last_name: Correggi - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0 apa: Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0 chicago: Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0. ieee: M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015. ista: Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307. mla: Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0. short: M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307. date_created: 2018-12-11T11:52:47Z date_published: 2015-06-23T00:00:00Z date_updated: 2021-01-12T06:51:41Z day: '23' department: - _id: RoSe doi: 10.1007/s00220-015-2402-0 intvolume: ' 339' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1312.7873 month: '06' oa: 1 oa_version: Preprint page: 279 - 307 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '5599' quality_controlled: '1' scopus_import: 1 status: public title: Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2015' ... --- _id: '1573' abstract: - lang: eng text: We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau. author: - first_name: Thomas full_name: Chen, Thomas last_name: Chen - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Nataša full_name: Pavlović, Nataša last_name: Pavlović - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552 apa: Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552 chicago: Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015. https://doi.org/10.1002/cpa.21552. ieee: T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015. ista: Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884. mla: Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552. short: T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884. date_created: 2018-12-11T11:52:48Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:51:41Z day: '01' department: - _id: RoSe doi: 10.1002/cpa.21552 intvolume: ' 68' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.3168 month: '10' oa: 1 oa_version: Preprint page: 1845 - 1884 project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley publist_id: '5598' quality_controlled: '1' scopus_import: 1 status: public title: Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2015' ... --- _id: '1580' abstract: - lang: eng text: Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs. article_processing_charge: No article_type: original author: - first_name: Oscar full_name: Brenes, Oscar last_name: Brenes - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Emilio full_name: Carbone, Emilio last_name: Carbone - first_name: Pier full_name: Montarolo, Pier last_name: Montarolo - first_name: Mirella full_name: Ghirardi, Mirella last_name: Ghirardi citation: ama: Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046 apa: Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M. (2015). Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046 chicago: Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046. ieee: O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience, vol. 311. Elsevier, pp. 430–443, 2015. ista: Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 311, 430–443. mla: Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp. 430–43, doi:10.1016/j.neuroscience.2015.10.046. short: O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience 311 (2015) 430–443. date_created: 2018-12-11T11:52:50Z date_published: 2015-12-17T00:00:00Z date_updated: 2021-01-12T06:51:44Z day: '17' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuroscience.2015.10.046 file: - access_level: open_access checksum: af2c4c994718c7be417eba0dc746aac9 content_type: application/pdf creator: dernst date_created: 2020-05-15T06:50:20Z date_updated: 2020-07-14T12:45:02Z file_id: '7849' file_name: 2015_Neuroscience_Brenes.pdf file_size: 5563015 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 311' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version page: 430 - 443 publication: Neuroscience publication_status: published publisher: Elsevier publist_id: '5591' quality_controlled: '1' scopus_import: 1 status: public title: Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons 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: 311 year: '2015' ... --- _id: '1577' abstract: - lang: eng text: Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes. acknowledgement: "This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript." article_processing_charge: No article_type: original author: - first_name: Antonio full_name: Carvalho, Antonio last_name: Carvalho - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Claudia full_name: Russo, Claudia last_name: Russo - first_name: Bonnielin full_name: Swenor, Bonnielin last_name: Swenor - first_name: Andrew full_name: Clark, Andrew last_name: Clark citation: ama: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455. doi:10.1073/pnas.1516543112 apa: Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1516543112 chicago: Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112. ieee: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015. ista: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455. mla: Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:10.1073/pnas.1516543112. short: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455. date_created: 2018-12-11T11:52:49Z date_published: 2015-10-06T00:00:00Z date_updated: 2021-01-12T06:51:43Z day: '06' department: - _id: BeVi doi: 10.1073/pnas.1516543112 external_id: pmid: - '26385968' intvolume: ' 112' issue: '40' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/ month: '10' oa: 1 oa_version: Published Version page: 12450 - 12455 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5594' quality_controlled: '1' scopus_import: 1 status: public title: Birth of a new gene on the Y chromosome of Drosophila melanogaster type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1579' abstract: - lang: eng text: We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality. acknowledgement: "This research was supported in part by NSF grant DMS-915211 and the Institut Mittag-Leffler.\r\n" article_processing_charge: No author: - first_name: Christopher full_name: Brooks, Christopher last_name: Brooks - first_name: Abraham full_name: Martin Del Campo Sanchez, Abraham id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87 last_name: Martin Del Campo Sanchez - first_name: Frank full_name: Sottile, Frank last_name: Sottile citation: ama: Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8 apa: Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8 chicago: Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/S0002-9947-2014-06192-8. ieee: C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of Schubert problems of lines are at least alternating,” Transactions of the American Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp. 4183–4206, 2015. ista: Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 367(6), 4183–4206. mla: Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society, vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8. short: C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American Mathematical Society 367 (2015) 4183–4206. date_created: 2018-12-11T11:52:50Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:51:43Z day: '01' department: - _id: CaUh doi: 10.1090/S0002-9947-2014-06192-8 intvolume: ' 367' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1207.4280 month: '06' oa: 1 oa_version: Preprint page: 4183 - 4206 publication: Transactions of the American Mathematical Society publication_status: published publisher: American Mathematical Society publist_id: '5592' quality_controlled: '1' scopus_import: 1 status: public title: Galois groups of Schubert problems of lines are at least alternating type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 367 year: '2015' ... --- _id: '1589' abstract: - lang: eng text: We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices. article_number: '18589' article_type: original author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Younghae full_name: Do, Younghae last_name: Do - first_name: Ying full_name: Lai, Ying last_name: Lai citation: ama: Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589 apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep18589 chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589. ieee: S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature Publishing Group, 2015. ista: Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589. mla: Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589, Nature Publishing Group, 2015, doi:10.1038/srep18589. short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015). date_created: 2018-12-11T11:52:53Z date_published: 2015-12-21T00:00:00Z date_updated: 2021-01-12T06:51:48Z day: '21' ddc: - '530' - '540' department: - _id: BjHo doi: 10.1038/srep18589 file: - access_level: open_access checksum: 927e151674347661ce36eae2818dafdc content_type: application/pdf creator: system date_created: 2018-12-12T10:13:49Z date_updated: 2020-07-14T12:45:03Z file_id: '5036' file_name: IST-2016-472-v1+1_srep18589.pdf file_size: 2771236 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '5582' pubrep_id: '472' quality_controlled: '1' scopus_import: 1 status: public title: Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system 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: 5 year: '2015' ... --- _id: '1584' abstract: - lang: eng text: We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights. author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Dominik full_name: Kaaser, Dominik last_name: Kaaser - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(5):429-442. doi:10.1016/j.comgeo.2015.01.004' apa: 'Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2015.01.004' chicago: 'Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004.' ieee: 'T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Reprint of: Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 5. Elsevier, pp. 429–442, 2015.' ista: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(5), 429–442.' mla: 'Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier, 2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.' short: 'T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 429–442.' date_created: 2018-12-11T11:52:51Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T10:05:22Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.comgeo.2015.01.004 file: - access_level: open_access checksum: 5b33719a86f7f4c8e5dc62c1b6893f49 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:36Z date_updated: 2020-07-14T12:45:03Z file_id: '5292' file_name: IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf file_size: 508379 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 48' issue: '5' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 429 - 442 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '5587' pubrep_id: '475' quality_controlled: '1' related_material: record: - id: '1582' relation: other status: public scopus_import: 1 status: public title: 'Reprint of: Weighted straight skeletons in the plane' 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: 48 year: '2015' ... --- _id: '1582' abstract: - lang: eng text: We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights. author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Dominik full_name: Kaaser, Dominik last_name: Kaaser - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(2):120-133. doi:10.1016/j.comgeo.2014.08.006' apa: 'Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.006' chicago: 'Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.006.' ieee: 'T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 2. Elsevier, pp. 120–133, 2015.' ista: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(2), 120–133.' mla: 'Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 2, Elsevier, 2015, pp. 120–33, doi:10.1016/j.comgeo.2014.08.006.' short: 'T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 120–133.' date_created: 2018-12-11T11:52:51Z date_published: 2015-02-01T00:00:00Z date_updated: 2023-02-23T10:05:27Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.comgeo.2014.08.006 file: - access_level: open_access checksum: c1ef67f6ec925e12f73a96b8fe285ab4 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:28Z date_updated: 2020-07-14T12:45:02Z file_id: '5215' file_name: IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf file_size: 505987 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 48' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 120 - 133 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '5589' pubrep_id: '474' quality_controlled: '1' related_material: record: - id: '1584' relation: other status: public scopus_import: 1 status: public title: Weighted straight skeletons in the plane 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: 48 year: '2015' ... --- _id: '1583' abstract: - lang: eng text: We study the characteristics of straight skeletons of monotone polygonal chains and use them to devise an algorithm for computing positively weighted straight skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space, where n denotes the number of vertices of the polygon. author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Dominik full_name: Kaaser, Dominik last_name: Kaaser - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: Biedl T, Held M, Huber S, Kaaser D, Palfrader P. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 2015;115(2):243-247. doi:10.1016/j.ipl.2014.09.021 apa: Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.021 chicago: Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.021. ieee: T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “A simple algorithm for computing positively weighted straight skeletons of monotone polygons,” Information Processing Letters, vol. 115, no. 2. Elsevier, pp. 243–247, 2015. ista: Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 115(2), 243–247. mla: Biedl, Therese, et al. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters, vol. 115, no. 2, Elsevier, 2015, pp. 243–47, doi:10.1016/j.ipl.2014.09.021. short: T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Information Processing Letters 115 (2015) 243–247. date_created: 2018-12-11T11:52:51Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:51:45Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.ipl.2014.09.021 file: - access_level: open_access checksum: 2779a648610c9b5c86d0b51a62816d23 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:45Z date_updated: 2020-07-14T12:45:03Z file_id: '5367' file_name: IST-2016-473-v1+1_1-s2.0-S0020019014001987-main.pdf file_size: 270137 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 115' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 243 - 247 publication: Information Processing Letters publication_status: published publisher: Elsevier publist_id: '5588' pubrep_id: '473' quality_controlled: '1' scopus_import: 1 status: public title: A simple algorithm for computing positively weighted straight skeletons of monotone polygons 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: 115 year: '2015' ... --- _id: '1587' abstract: - lang: eng text: We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme. article_number: '062506' article_processing_charge: No article_type: original author: - first_name: Pedro full_name: Amaro, Pedro last_name: Amaro - first_name: Filippo full_name: Fratini, Filippo last_name: Fratini - first_name: Laleh full_name: Safari, Laleh id: 3C325E5E-F248-11E8-B48F-1D18A9856A87 last_name: Safari - first_name: Aldo full_name: Antognini, Aldo last_name: Antognini - first_name: Paul full_name: Indelicato, Paul last_name: Indelicato - first_name: Randolf full_name: Pohl, Randolf last_name: Pohl - first_name: José full_name: Santos, José last_name: Santos citation: ama: Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 2015;92(6). doi:10.1103/PhysRevA.92.062506 apa: Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R., & Santos, J. (2015). Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506 chicago: Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato, Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506. ieee: P. Amaro et al., “Quantum interference shifts in laser spectroscopy with elliptical polarization,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6. American Physical Society, 2015. ista: Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J. 2015. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506. mla: Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506. short: P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015). date_created: 2018-12-11T11:52:53Z date_published: 2015-12-31T00:00:00Z date_updated: 2021-01-12T06:51:47Z day: '31' department: - _id: MiLe doi: 10.1103/PhysRevA.92.062506 ec_funded: 1 external_id: arxiv: - '1511.03585' intvolume: ' 92' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.03585 month: '12' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '5584' quality_controlled: '1' scopus_import: 1 status: public title: Quantum interference shifts in laser spectroscopy with elliptical polarization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1593' abstract: - lang: eng text: 'Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.' author: - first_name: Petra full_name: Žádníková, Petra last_name: Žádníková - first_name: Dajo full_name: Smet, Dajo last_name: Smet - first_name: Qiang full_name: Zhu, Qiang id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87 last_name: Zhu - first_name: Dominique full_name: Van Der Straeten, Dominique last_name: Van Der Straeten - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 2015;6(4). doi:10.3389/fpls.2015.00218' apa: 'Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E. (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218' chicago: 'Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fpls.2015.00218.' ieee: 'P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.' ista: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 6(4).' mla: 'Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6, no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218.' short: P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers in Plant Science 6 (2015). date_created: 2018-12-11T11:52:55Z date_published: 2015-04-14T00:00:00Z date_updated: 2021-01-12T06:51:50Z day: '14' ddc: - '570' department: - _id: EvBe doi: 10.3389/fpls.2015.00218 ec_funded: 1 file: - access_level: open_access checksum: c454d642e18dfa86820b97a86cd6d3cc content_type: application/pdf creator: system date_created: 2018-12-12T10:15:23Z date_updated: 2020-07-14T12:45:03Z file_id: '5142' file_name: IST-2016-471-v1+1_fpls-06-00218.pdf file_size: 965690 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 6' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '5578' pubrep_id: '471' quality_controlled: '1' scopus_import: 1 status: public title: 'Strategies of seedlings to overcome their sessile nature: Auxin in mobility control' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '1595' abstract: - lang: eng text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth.' acknowledgement: 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]. alternative_title: - LNCS author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Michael full_name: Pelsmajer, Michael last_name: Pelsmajer - first_name: Marcus full_name: Schaefer, Marcus last_name: Schaefer citation: ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol 9411. Springer; 2015:99-110. doi:10.1007/978-3-319-27261-0_9' apa: 'Fulek, R., Pelsmajer, M., & Schaefer, M. (2015). Hanani-Tutte for radial planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA: Springer. https://doi.org/10.1007/978-3-319-27261-0_9' chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity,” 9411:99–110. Springer, 2015. https://doi.org/10.1007/978-3-319-27261-0_9. ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA, 2015, vol. 9411, pp. 99–110.' ista: 'Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.' mla: Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity. Vol. 9411, Springer, 2015, pp. 99–110, doi:10.1007/978-3-319-27261-0_9. short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110. conference: end_date: 2015-09-26 location: Los Angeles, CA, USA name: 'GD: Graph Drawing and Network Visualization' start_date: 2015-09-24 date_created: 2018-12-11T11:52:55Z date_published: 2015-11-27T00:00:00Z date_updated: 2023-02-21T16:23:36Z day: '27' ddc: - '510' department: - _id: UlWa doi: 10.1007/978-3-319-27261-0_9 ec_funded: 1 file: - access_level: open_access checksum: 685f91bd077a951ba067d42cce75409e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:36Z date_updated: 2020-07-14T12:45:03Z file_id: '4697' file_name: IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf file_size: 330135 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 9411' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 99 - 110 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5576' pubrep_id: '594' quality_controlled: '1' related_material: record: - id: '1113' relation: later_version status: public - id: '1164' relation: later_version status: public scopus_import: 1 status: public title: Hanani-Tutte for radial planarity type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9411 year: '2015' ... --- _id: '1590' abstract: - lang: eng text: 'The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Oswin full_name: Aichholzer, Oswin last_name: Aichholzer - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Thomas full_name: Hackl, Thomas last_name: Hackl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader - first_name: Birgit full_name: Vogtenhuber, Birgit last_name: Vogtenhuber citation: ama: 'Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:335-347. doi:10.1007/978-3-319-27261-0_28' apa: 'Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P., & Vogtenhuber, B. (2015). Representing directed trees as straight skeletons. In Graph Drawing and Network Visualization (Vol. 9411, pp. 335–347). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_28' chicago: Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber, Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight Skeletons.” In Graph Drawing and Network Visualization, 9411:335–47. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_28. ieee: O. Aichholzer et al., “Representing directed trees as straight skeletons,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–347. ista: 'Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 335–347.' mla: Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–47, doi:10.1007/978-3-319-27261-0_28. short: O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347. conference: end_date: 2015-09-26 location: Los Angeles, CA, United States name: 'GD: International Symposium on Graph Drawing' start_date: 2015-09-24 date_created: 2018-12-11T11:52:54Z date_published: 2015-11-27T00:00:00Z date_updated: 2022-01-28T09:10:37Z day: '27' department: - _id: HeEd doi: 10.1007/978-3-319-27261-0_28 intvolume: ' 9411' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1508.01076 month: '11' oa: 1 oa_version: Preprint page: 335 - 347 publication: Graph Drawing and Network Visualization publication_identifier: eisbn: - 978-3-319-27261-0 isbn: - 978-3-319-27260-3 publication_status: published publisher: Springer Nature publist_id: '5581' quality_controlled: '1' scopus_import: '1' status: public title: Representing directed trees as straight skeletons type: book_chapter user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9411 year: '2015' ... --- _id: '1596' abstract: - lang: eng text: Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi < j the intersection Ci and (Ci ∩ Cj)\⋃i<l<jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon. alternative_title: - LNCS article_processing_charge: No author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Radoš full_name: Radoičić, Radoš last_name: Radoičić citation: ama: 'Fulek R, Radoičić R. Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:373-379. doi:10.1007/978-3-319-27261-0_31' apa: 'Fulek, R., & Radoičić, R. (2015). Vertical visibility among parallel polygons in three dimensions. In Graph Drawing and Network Visualization (Vol. 9411, pp. 373–379). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_31' chicago: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” In Graph Drawing and Network Visualization, 9411:373–79. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_31. ieee: R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in three dimensions,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–379. ista: 'Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 373–379.' mla: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–79, doi:10.1007/978-3-319-27261-0_31. short: R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 373–379. conference: end_date: 2015-09-26 location: Los Angeles, CA, United States name: 'GD: Graph Drawing and Network Visualization' start_date: 2015-09-24 date_created: 2018-12-11T11:52:56Z date_published: 2015-11-27T00:00:00Z date_updated: 2022-01-28T09:20:50Z day: '27' ddc: - '510' department: - _id: UlWa doi: 10.1007/978-3-319-27261-0_31 ec_funded: 1 file: - access_level: open_access checksum: eec04f86c5921d04f025d5791db9b965 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:06Z date_updated: 2020-07-14T12:45:04Z file_id: '5258' file_name: IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf file_size: 312992 relation: main_file file_date_updated: 2020-07-14T12:45:04Z has_accepted_license: '1' intvolume: ' 9411' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 373 - 379 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Graph Drawing and Network Visualization publication_identifier: isbn: - 978-3-319-27260-3 publication_status: published publisher: Springer Nature publist_id: '5575' pubrep_id: '595' quality_controlled: '1' scopus_import: '1' status: public title: Vertical visibility among parallel polygons in three dimensions type: book_chapter user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9411 year: '2015' ... --- _id: '1601' abstract: - lang: eng text: We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata. alternative_title: - LNCS article_processing_charge: No author: - first_name: Tomáš full_name: Babiak, Tomáš last_name: Babiak - first_name: František full_name: Blahoudek, František last_name: Blahoudek - first_name: Alexandre full_name: Duret Lutz, Alexandre last_name: Duret Lutz - first_name: Joachim full_name: Klein, Joachim last_name: Klein - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Daniel full_name: Mueller, Daniel last_name: Mueller - first_name: David full_name: Parker, David last_name: Parker - first_name: Jan full_name: Strejček, Jan last_name: Strejček citation: ama: 'Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format. In: Vol 9206. Springer; 2015:479-486. doi:10.1007/978-3-319-21690-4_31' apa: 'Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller, D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_31' chicago: Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein, Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata Format,” 9206:479–86. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_31. ieee: 'T. Babiak et al., “The Hanoi omega-automata format,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 479–486.' ista: 'Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification, LNCS, vol. 9206, 479–486.' mla: Babiak, Tomáš, et al. The Hanoi Omega-Automata Format. Vol. 9206, Springer, 2015, pp. 479–86, doi:10.1007/978-3-319-21690-4_31. short: T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller, D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486. conference: end_date: 2015-07-24 location: San Francisco, CA, United States name: 'CAV: Computer Aided Verification' start_date: 2015-07-18 date_created: 2018-12-11T11:52:57Z date_published: 2015-07-16T00:00:00Z date_updated: 2021-01-12T06:51:54Z day: '16' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-319-21690-4_31 ec_funded: 1 file: - access_level: open_access checksum: 5885236fa88a439baba9ac6f3e801e93 content_type: application/pdf creator: dernst date_created: 2020-05-15T08:38:12Z date_updated: 2020-07-14T12:45:04Z file_id: '7850' file_name: 2015_CAV_Babiak.pdf file_size: 1651779 relation: main_file file_date_updated: 2020-07-14T12:45:04Z has_accepted_license: '1' intvolume: ' 9206' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 479 - 486 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5566' quality_controlled: '1' scopus_import: 1 status: public title: The Hanoi omega-automata format type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9206 year: '2015' ... --- _id: '1605' abstract: - lang: eng text: Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model. acknowledgement: This work was partly supported by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/). alternative_title: - LNCS article_processing_charge: No author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Grégory full_name: Batt, Grégory last_name: Batt - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35. doi:10.1007/978-3-319-26287-1_2' apa: 'Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu, R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol. 9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2' chicago: Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,” 9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2. ieee: 'S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu, “Abstraction-based parameter synthesis for multiaffine systems,” presented at the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.' ista: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference, LNCS, vol. 9434, 19–35.' mla: Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2. short: S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:, Springer, 2015, pp. 19–35. conference: end_date: 2015-11-19 location: Haifa, Israel name: 'HVC: Haifa Verification Conference' start_date: 2015-11-17 date_created: 2018-12-11T11:52:59Z date_published: 2015-11-28T00:00:00Z date_updated: 2021-01-12T06:51:56Z day: '28' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-26287-1_2 ec_funded: 1 file: - access_level: open_access checksum: 3aab260f3f34641d622030ba22645b3e content_type: application/pdf creator: dernst date_created: 2020-05-15T08:43:19Z date_updated: 2020-07-14T12:45:05Z file_id: '7851' file_name: 2015_LNCS_Bogomolov.pdf file_size: 1053207 relation: main_file file_date_updated: 2020-07-14T12:45:05Z has_accepted_license: '1' intvolume: ' 9434' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 19 - 35 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5561' quality_controlled: '1' scopus_import: 1 status: public title: Abstraction-based parameter synthesis for multiaffine systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9434 year: '2015' ... --- _id: '1609' abstract: - lang: eng text: The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound. acknowledgement: 'This research was supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.' 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: Moshe full_name: Vardi, Moshe last_name: Vardi citation: ama: 'Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic components. In: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:108-120. doi:10.1007/978-3-662-47666-6_9' apa: 'Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis from probabilistic components. In 42nd International Colloquium (Vol. 9135, pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9' chicago: Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity of Synthesis from Probabilistic Components.” In 42nd International Colloquium, 9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9. ieee: K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol. 9135, pp. 108–120. ista: 'Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic components. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 108–120.' mla: Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic Components.” 42nd International Colloquium, vol. 9135, Springer Nature, 2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9. short: K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 108–120. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: Automata, Languages and Programming' start_date: 2015-07-06 date_created: 2018-12-11T11:53:00Z date_published: 2015-06-20T00:00:00Z date_updated: 2022-02-01T15:04:44Z day: '20' department: - _id: KrCh doi: 10.1007/978-3-662-47666-6_9 ec_funded: 1 intvolume: ' 9135' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.04844 month: '06' oa: 1 oa_version: Preprint page: 108 - 120 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: 42nd International Colloquium publication_identifier: isbn: - 978-3-662-47665-9 publication_status: published publisher: Springer Nature publist_id: '5557' quality_controlled: '1' scopus_import: '1' status: public title: The complexity of synthesis from probabilistic components type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9135 year: '2015' ... --- _id: '1615' abstract: - lang: eng text: Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches. acknowledgement: This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry. author: - first_name: Matthieu full_name: Hammer, Matthieu last_name: Hammer - first_name: Dilja full_name: Krueger Burg, Dilja last_name: Krueger Burg - first_name: Liam full_name: Tuffy, Liam last_name: Tuffy - first_name: Benjamin full_name: Cooper, Benjamin last_name: Cooper - first_name: Holger full_name: Taschenberger, Holger last_name: Taschenberger - first_name: Sarit full_name: Goswami, Sarit id: 3A578F32-F248-11E8-B48F-1D18A9856A87 last_name: Goswami - first_name: Hannelore full_name: Ehrenreich, Hannelore last_name: Ehrenreich - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Frederique full_name: Varoqueaux, Frederique last_name: Varoqueaux - first_name: Jeong full_name: Rhee, Jeong last_name: Rhee - first_name: Nils full_name: Brose, Nils last_name: Brose citation: ama: Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011 apa: Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2015.09.011 chicago: Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011. ieee: M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13, no. 3. Cell Press, pp. 516–523, 2015. ista: Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523. mla: Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011. short: M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523. date_created: 2018-12-11T11:53:02Z date_published: 2015-10-20T00:00:00Z date_updated: 2021-01-12T06:52:01Z day: '20' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.celrep.2015.09.011 file: - access_level: open_access checksum: 44d30fbb543774b076b4938bd36af9d7 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:23Z date_updated: 2020-07-14T12:45:07Z file_id: '5005' file_name: IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf file_size: 2314406 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 13' issue: '3' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 516 - 523 publication: Cell Reports publication_status: published publisher: Cell Press publist_id: '5551' pubrep_id: '470' quality_controlled: '1' scopus_import: 1 status: public title: Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism 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: 13 year: '2015' ... --- _id: '1614' abstract: - lang: eng text: 'GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. ' author: - first_name: Michael full_name: Strüber, Michael last_name: Strüber - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Marlene full_name: Bartos, Marlene last_name: Bartos citation: ama: Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 2015;112(4):1220-1225. doi:10.1073/pnas.1412996112 apa: Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112 chicago: Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112. ieee: M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015. ista: Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225. mla: Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112. short: M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225. date_created: 2018-12-11T11:53:02Z date_published: 2015-01-27T00:00:00Z date_updated: 2021-01-12T06:52:01Z day: '27' ddc: - '570' department: - _id: PeJo doi: 10.1073/pnas.1412996112 ec_funded: 1 external_id: pmid: - '25583495' file: - access_level: open_access checksum: 6703309a1f58493cf5a704211fb6ebed content_type: application/pdf creator: dernst date_created: 2019-01-17T07:52:40Z date_updated: 2020-07-14T12:45:07Z file_id: '5838' file_name: 2015_PNAS_Strueber.pdf file_size: 1280860 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 112' issue: '4' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 1220 - 1225 pmid: 1 project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5552' quality_controlled: '1' scopus_import: 1 status: public title: Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1611' abstract: - lang: eng text: Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue. author: - first_name: Jason full_name: Whitfield, Jason last_name: Whitfield - first_name: William full_name: Zhang, William last_name: Zhang - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Ben full_name: Clifton, Ben last_name: Clifton - first_name: Johanna full_name: Radziejewski, Johanna last_name: Radziejewski - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Colin full_name: Jackson, Colin last_name: Jackson citation: ama: Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 2015;24(9):1412-1422. doi:10.1002/pro.2721 apa: Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721 chicago: Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721. ieee: J. Whitfield et al., “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” Protein Science, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015. ista: Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422. mla: Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721. short: J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422. date_created: 2018-12-11T11:53:01Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:00Z day: '01' department: - _id: HaJa doi: 10.1002/pro.2721 external_id: pmid: - '26061224' intvolume: ' 24' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/ month: '09' oa: 1 oa_version: Submitted Version page: 1412 - 1422 pmid: 1 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) publication: Protein Science publication_status: published publisher: Wiley publist_id: '5555' quality_controlled: '1' scopus_import: 1 status: public title: Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2015' ... --- _id: '1624' abstract: - lang: eng text: Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions. acknowledgement: 'The research was supported by the Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton foundation is gratefully acknowledged.' article_number: '17147' author: - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ben full_name: Adlam, Ben last_name: Adlam - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift updating and repulsion. Scientific Reports. 2015;5. doi:10.1038/srep17147 apa: Pavlogiannis, A., Chatterjee, K., Adlam, B., & Nowak, M. (2015). Cellular cooperation with shift updating and repulsion. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep17147 chicago: Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep17147. ieee: A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation with shift updating and repulsion,” Scientific Reports, vol. 5. Nature Publishing Group, 2015. ista: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation with shift updating and repulsion. Scientific Reports. 5, 17147. mla: Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports, vol. 5, 17147, Nature Publishing Group, 2015, doi:10.1038/srep17147. short: A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5 (2015). date_created: 2018-12-11T11:53:06Z date_published: 2015-11-25T00:00:00Z date_updated: 2021-01-12T06:52:05Z day: '25' ddc: - '000' department: - _id: KrCh doi: 10.1038/srep17147 ec_funded: 1 file: - access_level: open_access checksum: 38e06d8310d2087cae5f6d4d4bfe082b content_type: application/pdf creator: system date_created: 2018-12-12T10:12:29Z date_updated: 2020-07-14T12:45:07Z file_id: '4947' file_name: IST-2016-466-v1+1_srep17147.pdf file_size: 1021931 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '11' 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' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '5536' pubrep_id: '466' quality_controlled: '1' scopus_import: 1 status: public title: Cellular cooperation with shift updating and repulsion 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: 5 year: '2015' ... --- _id: '1623' abstract: - lang: eng text: "Background\r\nPhotosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.\r\n" article_number: '193' author: - first_name: Petter full_name: Hammar, Petter last_name: Hammar - first_name: Andreas full_name: Angermayr, Andreas id: 4677C796-F248-11E8-B48F-1D18A9856A87 last_name: Angermayr orcid: 0000-0001-8619-2223 - first_name: Staffan full_name: Sjostrom, Staffan last_name: Sjostrom - first_name: Josefin full_name: Van Der Meer, Josefin last_name: Van Der Meer - first_name: Klaas full_name: Hellingwerf, Klaas last_name: Hellingwerf - first_name: Elton full_name: Hudson, Elton last_name: Hudson - first_name: Hakaan full_name: Joensson, Hakaan last_name: Joensson citation: ama: Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 2015;8(1). doi:10.1186/s13068-015-0380-2 apa: Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K., Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. BioMed Central. https://doi.org/10.1186/s13068-015-0380-2 chicago: Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer, Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2. ieee: P. Hammar et al., “Single-cell screening of photosynthetic growth and lactate production by cyanobacteria,” Biotechnology for Biofuels, vol. 8, no. 1. BioMed Central, 2015. ista: Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E, Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 8(1), 193. mla: Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol. 8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2. short: P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E. Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015). date_created: 2018-12-11T11:53:05Z date_published: 2015-11-25T00:00:00Z date_updated: 2021-01-12T06:52:04Z day: '25' ddc: - '570' department: - _id: ToBo doi: 10.1186/s13068-015-0380-2 file: - access_level: open_access checksum: 172b0b6f4eb2e5c22b7cec1d57dc0107 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:11Z date_updated: 2020-07-14T12:45:07Z file_id: '4796' file_name: IST-2016-467-v1+1_s13068-015-0380-2.pdf file_size: 2914089 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Biotechnology for Biofuels publication_status: published publisher: BioMed Central publist_id: '5537' pubrep_id: '467' quality_controlled: '1' scopus_import: 1 status: public title: Single-cell screening of photosynthetic growth and lactate production by cyanobacteria 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: 8 year: '2015' ... --- _id: '1628' abstract: - lang: eng text: We propose a method for fabricating deformable objects with spatially varying elasticity using 3D printing. Using a single, relatively stiff printer material, our method designs an assembly of smallscale microstructures that have the effect of a softer material at the object scale, with properties depending on the microstructure used in each part of the object. We build on work in the area of metamaterials, using numerical optimization to design tiled microstructures with desired properties, but with the key difference that our method designs families of related structures that can be interpolated to smoothly vary the material properties over a wide range. To create an object with spatially varying elastic properties, we tile the object's interior with microstructures drawn from these families, generating a different microstructure for each cell using an efficient algorithm to select compatible structures for neighboring cells. We show results computed for both 2D and 3D objects, validating several 2D and 3D printed structures using standard material tests as well as demonstrating various example applications. article_number: '136' article_processing_charge: No author: - first_name: Christian full_name: Schumacher, Christian last_name: Schumacher - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Jan full_name: Rys, Jan last_name: Rys - first_name: Steve full_name: Marschner, Steve last_name: Marschner - first_name: Chiara full_name: Daraio, Chiara last_name: Daraio - first_name: Markus full_name: Gross, Markus last_name: Gross citation: ama: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:10.1145/2766926' apa: 'Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., & Gross, M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766926' chicago: Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio, and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766926. ieee: 'C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross, “Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.' ista: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 136.' mla: Schumacher, Christian, et al. Microstructures to Control Elasticity in 3D Printing. Vol. 34, no. 4, 136, ACM, 2015, doi:10.1145/2766926. short: C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, USA name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:07Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:06Z day: '01' department: - _id: BeBi doi: 10.1145/2766926 intvolume: ' 34' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/2766926 month: '08' oa: 1 oa_version: Published Version publication_status: published publisher: ACM publist_id: '5529' quality_controlled: '1' scopus_import: 1 status: public title: Microstructures to control elasticity in 3D printing type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1634' abstract: - lang: eng text: Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart. article_number: '149' author: - first_name: Fang full_name: Da, Fang last_name: Da - first_name: Christopher full_name: Batty, Christopher last_name: Batty - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Eitan full_name: Grinspun, Eitan last_name: Grinspun citation: ama: 'Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. In: Vol 34. ACM; 2015. doi:10.1145/2767003' apa: 'Da, F., Batty, C., Wojtan, C., & Grinspun, E. (2015). Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2767003' chicago: 'Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2767003.' ieee: 'F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.' ista: 'Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 149.' mla: 'Da, Fang, et al. Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams. Vol. 34, no. 4, 149, ACM, 2015, doi:10.1145/2767003.' short: F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:09Z date_published: 2015-07-27T00:00:00Z date_updated: 2023-02-23T10:07:42Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1145/2767003 ec_funded: 1 file: - access_level: open_access checksum: 57b07d78d2d612a8052744b37d4a71fa content_type: application/pdf creator: system date_created: 2018-12-12T10:11:14Z date_updated: 2020-07-14T12:45:07Z file_id: '4867' file_name: IST-2016-608-v1+1_doublebubbles.pdf file_size: 8973215 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication_status: published publisher: ACM publist_id: '5521' pubrep_id: '608' quality_controlled: '1' scopus_import: 1 status: public title: 'Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1636' abstract: - lang: eng text: "Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem that appears in many areas of Computer Science. It can be equivalently stated as computing a homomorphism R→ΓΓ between two relational structures, e.g. between two directed graphs. Analyzing its complexity has been a prominent research direction, especially for the fixed template CSPs where the right side ΓΓ is fixed and the left side R is unconstrained.\r\n\r\nFar fewer results are known for the hybrid setting that restricts both sides simultaneously. It assumes that R belongs to a certain class of relational structures (called a structural restriction in this paper). We study which structural restrictions are effective, i.e. there exists a fixed template ΓΓ (from a certain class of languages) for which the problem is tractable when R is restricted, and NP-hard otherwise. We provide a characterization for structural restrictions that are closed under inverse homomorphisms. The criterion is based on the chromatic number of a relational structure defined in this paper; it generalizes the standard chromatic number of a graph.\r\n\r\nAs our main tool, we use the algebraic machinery developed for fixed template CSPs. To apply it to our case, we introduce a new construction called a “lifted language”. We also give a characterization for structural restrictions corresponding to minor-closed families of graphs, extend results to certain Valued CSPs (namely conservative valued languages), and state implications for (valued) CSPs with ordered variables and for the maximum weight independent set problem on some restricted families of graphs." alternative_title: - LNCS article_processing_charge: No author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek - first_name: Rustem full_name: Takhanov, Rustem last_name: Takhanov citation: ama: 'Kolmogorov V, Rolinek M, Takhanov R. Effectiveness of structural restrictions for hybrid CSPs. In: 26th International Symposium. Vol 9472. Springer Nature; 2015:566-577. doi:10.1007/978-3-662-48971-0_48' apa: 'Kolmogorov, V., Rolinek, M., & Takhanov, R. (2015). Effectiveness of structural restrictions for hybrid CSPs. In 26th International Symposium (Vol. 9472, pp. 566–577). Nagoya, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-48971-0_48' chicago: Kolmogorov, Vladimir, Michal Rolinek, and Rustem Takhanov. “Effectiveness of Structural Restrictions for Hybrid CSPs.” In 26th International Symposium, 9472:566–77. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48971-0_48. ieee: V. Kolmogorov, M. Rolinek, and R. Takhanov, “Effectiveness of structural restrictions for hybrid CSPs,” in 26th International Symposium, Nagoya, Japan, 2015, vol. 9472, pp. 566–577. ista: 'Kolmogorov V, Rolinek M, Takhanov R. 2015. Effectiveness of structural restrictions for hybrid CSPs. 26th International Symposium. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 9472, 566–577.' mla: Kolmogorov, Vladimir, et al. “Effectiveness of Structural Restrictions for Hybrid CSPs.” 26th International Symposium, vol. 9472, Springer Nature, 2015, pp. 566–77, doi:10.1007/978-3-662-48971-0_48. short: V. Kolmogorov, M. Rolinek, R. Takhanov, in:, 26th International Symposium, Springer Nature, 2015, pp. 566–577. conference: end_date: 2015-12-11 location: Nagoya, Japan name: 'ISAAC: International Symposium on Algorithms and Computation' start_date: 2015-12-09 date_created: 2018-12-11T11:53:10Z date_published: 2015-12-01T00:00:00Z date_updated: 2022-02-01T15:12:35Z day: '01' department: - _id: VlKo doi: 10.1007/978-3-662-48971-0_48 ec_funded: 1 external_id: arxiv: - '1504.07067' intvolume: ' 9472' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.07067 month: '12' oa: 1 oa_version: Preprint page: 566 - 577 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: 26th International Symposium publication_identifier: isbn: - 978-3-662-48970-3 publication_status: published publisher: Springer Nature publist_id: '5519' quality_controlled: '1' scopus_import: '1' status: public title: Effectiveness of structural restrictions for hybrid CSPs type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9472 year: '2015' ... --- _id: '1632' abstract: - lang: eng text: "This paper presents a liquid simulation technique that enforces the incompressibility condition using a stream function solve instead of a pressure projection. Previous methods have used stream function techniques for the simulation of detailed single-phase flows, but a formulation for liquid simulation has proved elusive in part due to the free surface boundary conditions. In this paper, we introduce a stream function approach to liquid simulations with novel boundary conditions for free surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach increases the dimension of the linear system necessary to enforce incompressibility, it provides interesting and surprising benefits. First, the resulting flow is guaranteed to be divergence-free regardless of the accuracy of the solve. Second, our free-surface boundary conditions guarantee divergence-free motion even in the un-simulated air phase, which enables two-phase flow simulation by only computing a single phase. We implemented this method using a variant of FLIP simulation which only samples particles within a narrow band of the liquid surface, and we illustrate the effectiveness of our method for detailed two-phase flow simulations with complex boundaries, detailed bubble interactions, and two-way solid-fluid coupling." acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014 realFlow and ERC-2014- StG-638176 BigSplash. alternative_title: - ACM Transactions on Graphics article_number: '53' author: - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Ando R, Thuerey N, Wojtan C. A stream function solver for liquid simulations. In: Vol 34. ACM; 2015. doi:10.1145/2766935' apa: 'Ando, R., Thuerey, N., & Wojtan, C. (2015). A stream function solver for liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766935' chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver for Liquid Simulations,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766935. ieee: 'R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.' ista: 'Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 53.' mla: Ando, Ryoichi, et al. A Stream Function Solver for Liquid Simulations. Vol. 34, no. 4, 53, ACM, 2015, doi:10.1145/2766935. short: R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, USA name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:09Z date_published: 2015-07-27T00:00:00Z date_updated: 2023-02-23T10:07:37Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1145/2766935 file: - access_level: open_access checksum: 7a9afdfaba9209157ce19376e15bc90b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:52Z date_updated: 2020-07-14T12:45:07Z file_id: '4909' file_name: IST-2016-610-v1+1_vecpotential.pdf file_size: 21831121 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication_status: published publisher: ACM publist_id: '5523' pubrep_id: '610' quality_controlled: '1' scopus_import: 1 status: public title: A stream function solver for liquid simulations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1630' abstract: - lang: eng text: We present a method to learn and propagate shape placements in 2D polygonal scenes from a few examples provided by a user. The placement of a shape is modeled as an oriented bounding box. Simple geometric relationships between this bounding box and nearby scene polygons define a feature set for the placement. The feature sets of all example placements are then used to learn a probabilistic model over all possible placements and scenes. With this model, we can generate a new set of placements with similar geometric relationships in any given scene. We introduce extensions that enable propagation and generation of shapes in 3D scenes, as well as the application of a learned modeling session to large scenes without additional user interaction. These concepts allow us to generate complex scenes with thousands of objects with relatively little user interaction. acknowledgement: This publication is based upon work supported by the KAUST Office of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no. P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23). article_number: '108' author: - first_name: Paul full_name: Guerrero, Paul last_name: Guerrero - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer - first_name: Peter full_name: Wonka, Peter last_name: Wonka citation: ama: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. Learning shape placements by example. In: Vol 34. ACM; 2015. doi:10.1145/2766933' apa: 'Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2015). Learning shape placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766933' chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning Shape Placements by Example,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766933. ieee: 'P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.' ista: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 108.' mla: Guerrero, Paul, et al. Learning Shape Placements by Example. Vol. 34, no. 4, 108, ACM, 2015, doi:10.1145/2766933. short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:08Z date_published: 2015-07-27T00:00:00Z date_updated: 2021-01-12T06:52:07Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1145/2766933 file: - access_level: open_access checksum: 8b05a51e372c9b0b5af9a00098a9538b content_type: application/pdf creator: system date_created: 2018-12-12T10:07:49Z date_updated: 2020-07-14T12:45:07Z file_id: '4647' file_name: IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf file_size: 11902290 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version 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_status: published publisher: ACM publist_id: '5525' pubrep_id: '576' quality_controlled: '1' scopus_import: 1 status: public title: Learning shape placements by example type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1640' abstract: - lang: eng text: Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: This work was supported by the European Research Council Starting Independent Research grant (ERC-2007-Stg-207362-HCPO to E.B., M.S., C.C.), by the Ghent University Multidisciplinary Research Partnership ‘Biotechnology for a Sustainable Economy’ no.01MRB510W, by the Research Foundation—Flanders (grant 3G033711 to J.-A.O.), by the Austrian Science Fund (FWF01_I1774S) to K.Ö.,E.B., and by the Interuniversity Attraction Poles Programme (IUAP P7/29 ‘MARS’) initiated by the Belgian Science Policy Office. I.D.C. and S.V. are post-doctoral fellows of the Research Foundation—Flanders (FWO). This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF). article_number: '8717' author: - first_name: Mária full_name: Šimášková, Mária last_name: Šimášková - first_name: José full_name: O'Brien, José last_name: O'Brien - first_name: Mamoona full_name: Khan-Djamei, Mamoona id: 391B5BBC-F248-11E8-B48F-1D18A9856A87 last_name: Khan-Djamei - first_name: Giel full_name: Van Noorden, Giel last_name: Van Noorden - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Anne full_name: Vieten, Anne last_name: Vieten - first_name: Inge full_name: De Clercq, Inge last_name: De Clercq - first_name: Johanna full_name: Van Haperen, Johanna last_name: Van Haperen - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Klára full_name: Hoyerová, Klára last_name: Hoyerová - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Frank full_name: Van Breusegem, Frank last_name: Van Breusegem - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack - first_name: Angus full_name: Murphy, Angus last_name: Murphy - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Šimášková M, O’Brien J, Khan-Djamei M, et al. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 2015;6. doi:10.1038/ncomms9717 apa: Šimášková, M., O’Brien, J., Khan-Djamei, M., Van Noorden, G., Ötvös, K., Vieten, A., … Benková, E. (2015). Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9717 chicago: Šimášková, Mária, José O’Brien, Mamoona Khan-Djamei, Giel Van Noorden, Krisztina Ötvös, Anne Vieten, Inge De Clercq, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9717. ieee: M. Šimášková et al., “Cytokinin response factors regulate PIN-FORMED auxin transporters,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Šimášková M, O’Brien J, Khan-Djamei M, Van Noorden G, Ötvös K, Vieten A, De Clercq I, Van Haperen J, Cuesta C, Hoyerová K, Vanneste S, Marhavý P, Wabnik KT, Van Breusegem F, Nowack M, Murphy A, Friml J, Weijers D, Beeckman T, Benková E. 2015. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 6, 8717. mla: Šimášková, Mária, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” Nature Communications, vol. 6, 8717, Nature Publishing Group, 2015, doi:10.1038/ncomms9717. short: M. Šimášková, J. O’Brien, M. Khan-Djamei, G. Van Noorden, K. Ötvös, A. Vieten, I. De Clercq, J. Van Haperen, C. Cuesta, K. Hoyerová, S. Vanneste, P. Marhavý, K.T. Wabnik, F. Van Breusegem, M. Nowack, A. Murphy, J. Friml, D. Weijers, T. Beeckman, E. Benková, Nature Communications 6 (2015). date_created: 2018-12-11T11:53:12Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:52:11Z day: '01' ddc: - '580' department: - _id: EvBe - _id: JiFr doi: 10.1038/ncomms9717 ec_funded: 1 file: - access_level: open_access checksum: c2c84bca37401435fedf76bad0ba0579 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:36Z date_updated: 2020-07-14T12:45:08Z file_id: '5358' file_name: IST-2018-1020-v1+1_Simaskova_et_al_NatCom_2015.pdf file_size: 1471217 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5513' pubrep_id: '1020' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinin response factors regulate PIN-FORMED auxin transporters type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '1642' abstract: - lang: eng text: The Hanani-Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this result to clustered graphs with two disjoint clusters, and show that a straightforward extension to flat clustered graphs with three or more disjoint clusters is not possible. For general clustered graphs we show a variant of the Hanani-Tutte theorem in the case when each cluster induces a connected subgraph. Di Battista and Frati proved that clustered planarity of embedded clustered graphs whose every face is incident to at most five vertices can be tested in polynomial time. We give a new and short proof of this result, using the matroid intersection algorithm. acknowledgement: e research leading to these results has received funding fromthe People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no [291734], and ESF Eurogiga project GraDR as GAˇCRGIG/11/E023. article_number: 'P4.24 ' article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Igor full_name: Malinovič, Igor last_name: Malinovič - first_name: Dömötör full_name: Pálvölgyi, Dömötör last_name: Pálvölgyi citation: ama: Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. Clustered planarity testing revisited. Electronic Journal of Combinatorics. 2015;22(4). doi:10.37236/5002 apa: Fulek, R., Kynčl, J., Malinovič, I., & Pálvölgyi, D. (2015). Clustered planarity testing revisited. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/5002 chicago: Fulek, Radoslav, Jan Kynčl, Igor Malinovič, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2015. https://doi.org/10.37236/5002. ieee: R. Fulek, J. Kynčl, I. Malinovič, and D. Pálvölgyi, “Clustered planarity testing revisited,” Electronic Journal of Combinatorics, vol. 22, no. 4. Electronic Journal of Combinatorics, 2015. ista: Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. 2015. Clustered planarity testing revisited. Electronic Journal of Combinatorics. 22(4), P4.24. mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” Electronic Journal of Combinatorics, vol. 22, no. 4, P4.24, Electronic Journal of Combinatorics, 2015, doi:10.37236/5002. short: R. Fulek, J. Kynčl, I. Malinovič, D. Pálvölgyi, Electronic Journal of Combinatorics 22 (2015). date_created: 2018-12-11T11:53:12Z date_published: 2015-11-13T00:00:00Z date_updated: 2023-02-21T16:03:02Z day: '13' ddc: - '514' - '516' department: - _id: UlWa doi: 10.37236/5002 ec_funded: 1 external_id: arxiv: - '1305.4519' file: - access_level: open_access checksum: 40b5920b49ee736694f59f39588ee206 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:03Z date_updated: 2020-07-14T12:45:08Z file_id: '5120' file_name: IST-2016-714-v1+1_5002-15499-3-PB.pdf file_size: 443655 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 22' issue: '4' 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 publication: Electronic Journal of Combinatorics publication_identifier: eissn: - 1077-8926 publication_status: published publisher: Electronic Journal of Combinatorics publist_id: '5511' pubrep_id: '714' quality_controlled: '1' related_material: record: - id: '10793' relation: earlier_version status: public scopus_import: '1' status: public title: Clustered planarity testing revisited type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2015' ... --- _id: '1639' abstract: - lang: eng text: In this paper the optimal transport and the metamorphosis perspectives are combined. For a pair of given input images geodesic paths in the space of images are defined as minimizers of a resulting path energy. To this end, the underlying Riemannian metric measures the rate of transport cost and the rate of viscous dissipation. Furthermore, the model is capable to deal with strongly varying image contrast and explicitly allows for sources and sinks in the transport equations which are incorporated in the metric related to the metamorphosis approach by Trouvé and Younes. In the non-viscous case with source term existence of geodesic paths is proven in the space of measures. The proposed model is explored on the range from merely optimal transport to strongly dissipative dynamics. For this model a robust and effective variational time discretization of geodesic paths is proposed. This requires to minimize a discrete path energy consisting of a sum of consecutive image matching functionals. These functionals are defined on corresponding pairs of intensity functions and on associated pairwise matching deformations. Existence of time discrete geodesics is demonstrated. Furthermore, a finite element implementation is proposed and applied to instructive test cases and to real images. In the non-viscous case this is compared to the algorithm proposed by Benamou and Brenier including a discretization of the source term. Finally, the model is generalized to define discrete weighted barycentres with applications to textures and objects. acknowledgement: The authors acknowledge support of the Collaborative Research Centre 1060 funded by the German Science foundation. This work is further supported by the King Abdullah University for Science and Technology (KAUST) Award No. KUK-I1-007-43 and the EPSRC grant Nr. EP/M00483X/1. author: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Martin full_name: Rumpf, Martin last_name: Rumpf - first_name: Carola full_name: Schönlieb, Carola last_name: Schönlieb - first_name: Stefan full_name: Simon, Stefan last_name: Simon citation: ama: 'Maas J, Rumpf M, Schönlieb C, Simon S. A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. 2015;49(6):1745-1769. doi:10.1051/m2an/2015043' apa: 'Maas, J., Rumpf, M., Schönlieb, C., & Simon, S. (2015). A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2015043' chicago: 'Maas, Jan, Martin Rumpf, Carola Schönlieb, and Stefan Simon. “A Generalized Model for Optimal Transport of Images Including Dissipation and Density Modulation.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2015. https://doi.org/10.1051/m2an/2015043.' ieee: 'J. Maas, M. Rumpf, C. Schönlieb, and S. Simon, “A generalized model for optimal transport of images including dissipation and density modulation,” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 49, no. 6. EDP Sciences, pp. 1745–1769, 2015.' ista: 'Maas J, Rumpf M, Schönlieb C, Simon S. 2015. A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. 49(6), 1745–1769.' mla: 'Maas, Jan, et al. “A Generalized Model for Optimal Transport of Images Including Dissipation and Density Modulation.” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 49, no. 6, EDP Sciences, 2015, pp. 1745–69, doi:10.1051/m2an/2015043.' short: 'J. Maas, M. Rumpf, C. Schönlieb, S. Simon, ESAIM: Mathematical Modelling and Numerical Analysis 49 (2015) 1745–1769.' date_created: 2018-12-11T11:53:11Z date_published: 2015-11-01T00:00:00Z date_updated: 2021-01-12T06:52:10Z day: '01' department: - _id: JaMa doi: 10.1051/m2an/2015043 external_id: arxiv: - '1504.01988' intvolume: ' 49' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.01988 month: '11' oa: 1 oa_version: Preprint page: 1745 - 1769 publication: 'ESAIM: Mathematical Modelling and Numerical Analysis' publication_status: published publisher: EDP Sciences publist_id: '5514' quality_controlled: '1' scopus_import: 1 status: public title: A generalized model for optimal transport of images including dissipation and density modulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2015' ... --- _id: '1646' abstract: - lang: eng text: 'A pseudorandom function (PRF) is a keyed function F : K × X → Y where, for a random key k ∈ K, the function F(k, ·) is indistinguishable from a uniformly random function, given black-box access. A key-homomorphic PRF has the additional feature that for any keys k, k'' and any input x, we have F(k+k'', x) = F(k, x)⊕F(k'', x) for some group operations +,⊕ on K and Y, respectively. A constrained PRF for a family of setsS ⊆ P(X) has the property that, given any key k and set S ∈ S, one can efficiently compute a “constrained” key kS that enables evaluation of F(k, x) on all inputs x ∈ S, while the values F(k, x) for x /∈ S remain pseudorandom even given kS. In this paper we construct PRFs that are simultaneously constrained and key homomorphic, where the homomorphic property holds even for constrained keys. We first show that the multilinear map-based bit-fixing and circuit-constrained PRFs of Boneh and Waters (Asiacrypt 2013) can be modified to also be keyhomomorphic. We then show that the LWE-based key-homomorphic PRFs of Banerjee and Peikert (Crypto 2014) are essentially already prefix-constrained PRFs, using a (non-obvious) definition of constrained keys and associated group operation. Moreover, the constrained keys themselves are pseudorandom, and the constraining and evaluation functions can all be computed in low depth. As an application of key-homomorphic constrained PRFs,we construct a proxy re-encryption schemewith fine-grained access control. This scheme allows storing encrypted data on an untrusted server, where each file can be encrypted relative to some attributes, so that only parties whose constrained keys match the attributes can decrypt. Moreover, the server can re-key (arbitrary subsets of) the ciphertexts without learning anything about the plaintexts, thus permitting efficient and finegrained revocation.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Abishek full_name: Banerjee, Abishek last_name: Banerjee - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Chris full_name: Peikert, Chris last_name: Peikert - 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: Sophie full_name: Stevens, Sophie last_name: Stevens citation: ama: 'Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. Key-homomorphic constrained pseudorandom functions. In: 12th Theory of Cryptography Conference. Vol 9015. Springer Nature; 2015:31-60. doi:10.1007/978-3-662-46497-7_2' apa: 'Banerjee, A., Fuchsbauer, G., Peikert, C., Pietrzak, K. Z., & Stevens, S. (2015). Key-homomorphic constrained pseudorandom functions. In 12th Theory of Cryptography Conference (Vol. 9015, pp. 31–60). Warsaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-662-46497-7_2' chicago: Banerjee, Abishek, Georg Fuchsbauer, Chris Peikert, Krzysztof Z Pietrzak, and Sophie Stevens. “Key-Homomorphic Constrained Pseudorandom Functions.” In 12th Theory of Cryptography Conference, 9015:31–60. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-46497-7_2. ieee: A. Banerjee, G. Fuchsbauer, C. Peikert, K. Z. Pietrzak, and S. Stevens, “Key-homomorphic constrained pseudorandom functions,” in 12th Theory of Cryptography Conference, Warsaw, Poland, 2015, vol. 9015, pp. 31–60. ista: 'Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. 2015. Key-homomorphic constrained pseudorandom functions. 12th Theory of Cryptography Conference. TCC: Theory of Cryptography Conference, LNCS, vol. 9015, 31–60.' mla: Banerjee, Abishek, et al. “Key-Homomorphic Constrained Pseudorandom Functions.” 12th Theory of Cryptography Conference, vol. 9015, Springer Nature, 2015, pp. 31–60, doi:10.1007/978-3-662-46497-7_2. short: A. Banerjee, G. Fuchsbauer, C. Peikert, K.Z. Pietrzak, S. Stevens, in:, 12th Theory of Cryptography Conference, Springer Nature, 2015, pp. 31–60. conference: end_date: 2015-03-25 location: Warsaw, Poland name: 'TCC: Theory of Cryptography Conference' start_date: 2015-03-23 date_created: 2018-12-11T11:53:14Z date_published: 2015-03-01T00:00:00Z date_updated: 2022-02-03T08:41:46Z day: '01' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-662-46497-7_2 ec_funded: 1 file: - access_level: open_access checksum: 3c5093bda5783c89beaacabf1aa0e60e content_type: application/pdf creator: system date_created: 2018-12-12T10:15:17Z date_updated: 2020-07-14T12:45:08Z file_id: '5136' file_name: IST-2016-679-v1+1_180.pdf file_size: 450665 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9015' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2015/180 month: '03' oa: 1 oa_version: Submitted Version page: 31 - 60 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: 12th Theory of Cryptography Conference publication_identifier: isbn: - 978-3-662-46496-0 publication_status: published publisher: Springer Nature publist_id: '5505' pubrep_id: '679' quality_controlled: '1' scopus_import: '1' status: public title: Key-homomorphic constrained pseudorandom functions type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9015 year: '2015' ... --- _id: '1648' abstract: - lang: eng text: Generalized Selective Decryption (GSD), introduced by Panjwani [TCC’07], is a game for a symmetric encryption scheme Enc that captures the difficulty of proving adaptive security of certain protocols, most notably the Logical Key Hierarchy (LKH) multicast encryption protocol. In the GSD game there are n keys k1,..., kn, which the adversary may adaptively corrupt (learn); moreover, it can ask for encryptions Encki (kj) of keys under other keys. The adversary’s task is to distinguish keys (which it cannot trivially compute) from random. Proving the hardness of GSD assuming only IND-CPA security of Enc is surprisingly hard. Using “complexity leveraging” loses a factor exponential in n, which makes the proof practically meaningless. We can think of the GSD game as building a graph on n vertices, where we add an edge i → j when the adversary asks for an encryption of kj under ki. If restricted to graphs of depth ℓ, Panjwani gave a reduction that loses only a factor exponential in ℓ (not n). To date, this is the only non-trivial result known for GSD. In this paper we give almost-polynomial reductions for large classes of graphs. Most importantly, we prove the security of the GSD game restricted to trees losing only a quasi-polynomial factor n3 log n+5. Trees are an important special case capturing real-world protocols like the LKH protocol. Our new bound improves upon Panjwani’s on some LKH variants proposed in the literature where the underlying tree is not balanced. Our proof builds on ideas from the “nested hybrids” technique recently introduced by Fuchsbauer et al. [Asiacrypt’14] for proving the adaptive security of constrained PRFs. alternative_title: - LNCS author: - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Zahra full_name: Jafargholi, Zahra last_name: Jafargholi - 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: 'Fuchsbauer G, Jafargholi Z, Pietrzak KZ. A quasipolynomial reduction for generalized selective decryption on trees. In: Vol 9215. Springer; 2015:601-620. doi:10.1007/978-3-662-47989-6_29' apa: 'Fuchsbauer, G., Jafargholi, Z., & Pietrzak, K. Z. (2015). A quasipolynomial reduction for generalized selective decryption on trees (Vol. 9215, pp. 601–620). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-47989-6_29' chicago: Fuchsbauer, Georg, Zahra Jafargholi, and Krzysztof Z Pietrzak. “A Quasipolynomial Reduction for Generalized Selective Decryption on Trees,” 9215:601–20. Springer, 2015. https://doi.org/10.1007/978-3-662-47989-6_29. ieee: 'G. Fuchsbauer, Z. Jafargholi, and K. Z. Pietrzak, “A quasipolynomial reduction for generalized selective decryption on trees,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2015, vol. 9215, pp. 601–620.' ista: 'Fuchsbauer G, Jafargholi Z, Pietrzak KZ. 2015. A quasipolynomial reduction for generalized selective decryption on trees. CRYPTO: International Cryptology Conference, LNCS, vol. 9215, 601–620.' mla: Fuchsbauer, Georg, et al. A Quasipolynomial Reduction for Generalized Selective Decryption on Trees. Vol. 9215, Springer, 2015, pp. 601–20, doi:10.1007/978-3-662-47989-6_29. short: G. Fuchsbauer, Z. Jafargholi, K.Z. Pietrzak, in:, Springer, 2015, pp. 601–620. conference: end_date: 2015-08-20 location: Santa Barbara, CA, USA name: 'CRYPTO: International Cryptology Conference' start_date: 2015-08-16 date_created: 2018-12-11T11:53:14Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:14Z day: '01' ddc: - '004' department: - _id: KrPi doi: 10.1007/978-3-662-47989-6_29 ec_funded: 1 file: - access_level: open_access checksum: 99b76b3263d5082554d0a9cbdeca3a22 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:31Z date_updated: 2020-07-14T12:45:08Z file_id: '5015' file_name: IST-2016-674-v1+1_389.pdf file_size: 505618 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9215' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 601 - 620 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5502' pubrep_id: '674' quality_controlled: '1' scopus_import: 1 status: public title: A quasipolynomial reduction for generalized selective decryption on trees 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: 9215 year: '2015' ... --- _id: '1649' abstract: - lang: eng text: 'We extend a commitment scheme based on the learning with errors over rings (RLWE) problem, and present efficient companion zeroknowledge proofs of knowledge. Our scheme maps elements from the ring (or equivalently, n elements from ' alternative_title: - LNCS author: - first_name: Fabrice full_name: Benhamouda, Fabrice last_name: Benhamouda - first_name: Stephan full_name: Krenn, Stephan last_name: Krenn - first_name: Vadim full_name: Lyubashevsky, Vadim last_name: Lyubashevsky - 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: Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. Efficient zero-knowledge proofs for commitments from learning with errors over rings. 2015;9326:305-325. doi:10.1007/978-3-319-24174-6_16 apa: 'Benhamouda, F., Krenn, S., Lyubashevsky, V., & Pietrzak, K. Z. (2015). Efficient zero-knowledge proofs for commitments from learning with errors over rings. Presented at the ESORICS: European Symposium on Research in Computer Security, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-24174-6_16' chicago: Benhamouda, Fabrice, Stephan Krenn, Vadim Lyubashevsky, and Krzysztof Z Pietrzak. “Efficient Zero-Knowledge Proofs for Commitments from Learning with Errors over Rings.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-24174-6_16. ieee: F. Benhamouda, S. Krenn, V. Lyubashevsky, and K. Z. Pietrzak, “Efficient zero-knowledge proofs for commitments from learning with errors over rings,” vol. 9326. Springer, pp. 305–325, 2015. ista: Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. 2015. Efficient zero-knowledge proofs for commitments from learning with errors over rings. 9326, 305–325. mla: Benhamouda, Fabrice, et al. Efficient Zero-Knowledge Proofs for Commitments from Learning with Errors over Rings. Vol. 9326, Springer, 2015, pp. 305–25, doi:10.1007/978-3-319-24174-6_16. short: F. Benhamouda, S. Krenn, V. Lyubashevsky, K.Z. Pietrzak, 9326 (2015) 305–325. conference: end_date: 2015-09-25 location: Vienna, Austria name: 'ESORICS: European Symposium on Research in Computer Security' start_date: 2015-09-21 date_created: 2018-12-11T11:53:15Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:52:14Z day: '01' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-319-24174-6_16 ec_funded: 1 file: - access_level: open_access checksum: 6eac4a485b2aa644b2d3f753ed0b280b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:28Z date_updated: 2020-07-14T12:45:08Z file_id: '4883' file_name: IST-2016-678-v1+1_889.pdf file_size: 494239 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9326' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '01' oa: 1 oa_version: Published Version page: 305 - 325 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5501' pubrep_id: '678' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Efficient zero-knowledge proofs for commitments from learning with errors over rings 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: 9326 year: '2015' ... --- _id: '1644' abstract: - lang: eng text: Increasing the computational complexity of evaluating a hash function, both for the honest users as well as for an adversary, is a useful technique employed for example in password-based cryptographic schemes to impede brute-force attacks, and also in so-called proofs of work (used in protocols like Bitcoin) to show that a certain amount of computation was performed by a legitimate user. A natural approach to adjust the complexity of a hash function is to iterate it c times, for some parameter c, in the hope that any query to the scheme requires c evaluations of the underlying hash function. However, results by Dodis et al. (Crypto 2012) imply that plain iteration falls short of achieving this goal, and designing schemes which provably have such a desirable property remained an open problem. This paper formalizes explicitly what it means for a given scheme to amplify the query complexity of a hash function. In the random oracle model, the goal of a secure query-complexity amplifier (QCA) scheme is captured as transforming, in the sense of indifferentiability, a random oracle allowing R queries (for the adversary) into one provably allowing only r < R queries. Turned around, this means that making r queries to the scheme requires at least R queries to the actual random oracle. Second, a new scheme, called collision-free iteration, is proposed and proven to achieve c-fold QCA for both the honest parties and the adversary, for any fixed parameter c. alternative_title: - LNCS author: - first_name: Grégory full_name: Demay, Grégory last_name: Demay - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Ueli full_name: Maurer, Ueli last_name: Maurer - first_name: Björn full_name: Tackmann, Björn last_name: Tackmann citation: ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Query-complexity amplification for random oracles. In: Vol 9063. Springer; 2015:159-180. doi:10.1007/978-3-319-17470-9_10' apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2015). Query-complexity amplification for random oracles (Vol. 9063, pp. 159–180). Presented at the ICITS: International Conference on Information Theoretic Security, Lugano, Switzerland: Springer. https://doi.org/10.1007/978-3-319-17470-9_10' chicago: Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Query-Complexity Amplification for Random Oracles,” 9063:159–80. Springer, 2015. https://doi.org/10.1007/978-3-319-17470-9_10. ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Query-complexity amplification for random oracles,” presented at the ICITS: International Conference on Information Theoretic Security, Lugano, Switzerland, 2015, vol. 9063, pp. 159–180.' ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2015. Query-complexity amplification for random oracles. ICITS: International Conference on Information Theoretic Security, LNCS, vol. 9063, 159–180.' mla: Demay, Grégory, et al. Query-Complexity Amplification for Random Oracles. Vol. 9063, Springer, 2015, pp. 159–80, doi:10.1007/978-3-319-17470-9_10. short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, Springer, 2015, pp. 159–180. conference: end_date: 2015-05-05 location: Lugano, Switzerland name: 'ICITS: International Conference on Information Theoretic Security' start_date: 2015-05-02 date_created: 2018-12-11T11:53:13Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:52:13Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-17470-9_10 ec_funded: 1 intvolume: ' 9063' language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2015/315 month: '01' oa: 1 oa_version: Submitted Version page: 159 - 180 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5507' quality_controlled: '1' scopus_import: 1 status: public title: Query-complexity amplification for random oracles type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9063 year: '2015' ... --- _id: '1647' abstract: - lang: eng text: Round-optimal blind signatures are notoriously hard to construct in the standard model, especially in the malicious-signer model, where blindness must hold under adversarially chosen keys. This is substantiated by several impossibility results. The only construction that can be termed theoretically efficient, by Garg and Gupta (Eurocrypt’14), requires complexity leveraging, inducing an exponential security loss. We present a construction of practically efficient round-optimal blind signatures in the standard model. It is conceptually simple and builds on the recent structure-preserving signatures on equivalence classes (SPSEQ) from Asiacrypt’14. While the traditional notion of blindness follows from standard assumptions, we prove blindness under adversarially chosen keys under an interactive variant of DDH. However, we neither require non-uniform assumptions nor complexity leveraging. We then show how to extend our construction to partially blind signatures and to blind signatures on message vectors, which yield a construction of one-show anonymous credentials à la “anonymous credentials light” (CCS’13) in the standard model. Furthermore, we give the first SPS-EQ construction under noninteractive assumptions and show how SPS-EQ schemes imply conventional structure-preserving signatures, which allows us to apply optimality results for the latter to SPS-EQ. alternative_title: - LNCS article_processing_charge: No author: - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Christian full_name: Hanser, Christian last_name: Hanser - first_name: Daniel full_name: Slamanig, Daniel last_name: Slamanig citation: ama: 'Fuchsbauer G, Hanser C, Slamanig D. Practical round-optimal blind signatures in the standard model. In: Vol 9216. Springer; 2015:233-253. doi:10.1007/978-3-662-48000-7_12' apa: 'Fuchsbauer, G., Hanser, C., & Slamanig, D. (2015). Practical round-optimal blind signatures in the standard model (Vol. 9216, pp. 233–253). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_12' chicago: Fuchsbauer, Georg, Christian Hanser, and Daniel Slamanig. “Practical Round-Optimal Blind Signatures in the Standard Model,” 9216:233–53. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_12. ieee: 'G. Fuchsbauer, C. Hanser, and D. Slamanig, “Practical round-optimal blind signatures in the standard model,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 233–253.' ista: 'Fuchsbauer G, Hanser C, Slamanig D. 2015. Practical round-optimal blind signatures in the standard model. CRYPTO: International Cryptology Conference, LNCS, vol. 9216, 233–253.' mla: Fuchsbauer, Georg, et al. Practical Round-Optimal Blind Signatures in the Standard Model. Vol. 9216, Springer, 2015, pp. 233–53, doi:10.1007/978-3-662-48000-7_12. short: G. Fuchsbauer, C. Hanser, D. Slamanig, in:, Springer, 2015, pp. 233–253. conference: end_date: 2015-08-20 location: Santa Barbara, CA, United States name: 'CRYPTO: International Cryptology Conference' start_date: 2015-08-16 date_created: 2018-12-11T11:53:14Z date_published: 2015-08-01T00:00:00Z date_updated: 2023-02-21T16:44:51Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-662-48000-7_12 ec_funded: 1 intvolume: ' 9216' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2015/626.pdf month: '08' oa: 1 oa_version: Submitted Version page: 233 - 253 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5503' quality_controlled: '1' related_material: record: - id: '1225' relation: later_version status: public scopus_import: 1 status: public title: Practical round-optimal blind signatures in the standard model type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9216 year: '2015' ... --- _id: '1654' abstract: - lang: eng text: "HMAC and its variant NMAC are the most popular approaches to deriving a MAC (and more generally, a PRF) from a cryptographic hash function. Despite nearly two decades of research, their exact security still remains far from understood in many different contexts. Indeed, recent works have re-surfaced interest for {\\em generic} attacks, i.e., attacks that treat the compression function of the underlying hash function as a black box.\r\n\r\nGeneric security can be proved in a model where the underlying compression function is modeled as a random function -- yet, to date, the question of proving tight, non-trivial bounds on the generic security of HMAC/NMAC even as a PRF remains a challenging open question.\r\n\r\nIn this paper, we ask the question of whether a small modification to HMAC and NMAC can allow us to exactly characterize the security of the resulting constructions, while only incurring little penalty with respect to efficiency. To this end, we present simple variants of NMAC and HMAC, for which we prove tight bounds on the generic PRF security, expressed in terms of numbers of construction and compression function queries necessary to break the construction. All of our constructions are obtained via a (near) {\\em black-box} modification of NMAC and HMAC, which can be interpreted as an initial step of key-dependent message pre-processing.\r\n\r\nWhile our focus is on PRF security, a further attractive feature of our new constructions is that they clearly defeat all recent generic attacks against properties such as state recovery and universal forgery. These exploit properties of the so-called ``functional graph'' which are not directly accessible in our new constructions. " alternative_title: - LNCS author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - 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: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: Gazi P, Pietrzak KZ, Tessaro S. Generic security of NMAC and HMAC with input whitening. 2015;9453:85-109. doi:10.1007/978-3-662-48800-3_4 apa: 'Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). Generic security of NMAC and HMAC with input whitening. Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48800-3_4' chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “Generic Security of NMAC and HMAC with Input Whitening.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48800-3_4. ieee: P. Gazi, K. Z. Pietrzak, and S. Tessaro, “Generic security of NMAC and HMAC with input whitening,” vol. 9453. Springer, pp. 85–109, 2015. ista: Gazi P, Pietrzak KZ, Tessaro S. 2015. Generic security of NMAC and HMAC with input whitening. 9453, 85–109. mla: Gazi, Peter, et al. Generic Security of NMAC and HMAC with Input Whitening. Vol. 9453, Springer, 2015, pp. 85–109, doi:10.1007/978-3-662-48800-3_4. short: P. Gazi, K.Z. Pietrzak, S. Tessaro, 9453 (2015) 85–109. conference: end_date: 2015-12-03 location: Auckland, New Zealand name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security' start_date: 2015-11-29 date_created: 2018-12-11T11:53:17Z date_published: 2015-12-30T00:00:00Z date_updated: 2021-01-12T06:52:16Z day: '30' ddc: - '004' - '005' department: - _id: KrPi doi: 10.1007/978-3-662-48800-3_4 ec_funded: 1 file: - access_level: open_access checksum: d1e53203db2d8573a560995ccdffac62 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:09Z date_updated: 2020-07-14T12:45:08Z file_id: '4732' file_name: IST-2016-676-v1+1_881.pdf file_size: 512071 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9453' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version page: 85 - 109 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5496' pubrep_id: '676' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Generic security of NMAC and HMAC with input whitening type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9453 year: '2015' ... --- _id: '1650' abstract: - lang: eng text: "We consider the task of deriving a key with high HILL entropy (i.e., being computationally indistinguishable from a key with high min-entropy) from an unpredictable source.\r\n\r\nPrevious to this work, the only known way to transform unpredictability into a key that was ϵ indistinguishable from having min-entropy was via pseudorandomness, for example by Goldreich-Levin (GL) hardcore bits. This approach has the inherent limitation that from a source with k bits of unpredictability entropy one can derive a key of length (and thus HILL entropy) at most k−2log(1/ϵ) bits. In many settings, e.g. when dealing with biometric data, such a 2log(1/ϵ) bit entropy loss in not an option. Our main technical contribution is a theorem that states that in the high entropy regime, unpredictability implies HILL entropy. Concretely, any variable K with |K|−d bits of unpredictability entropy has the same amount of so called metric entropy (against real-valued, deterministic distinguishers), which is known to imply the same amount of HILL entropy. The loss in circuit size in this argument is exponential in the entropy gap d, and thus this result only applies for small d (i.e., where the size of distinguishers considered is exponential in d).\r\n\r\nTo overcome the above restriction, we investigate if it’s possible to first “condense” unpredictability entropy and make the entropy gap small. We show that any source with k bits of unpredictability can be condensed into a source of length k with k−3 bits of unpredictability entropy. Our condenser simply “abuses" the GL construction and derives a k bit key from a source with k bits of unpredicatibily. The original GL theorem implies nothing when extracting that many bits, but we show that in this regime, GL still behaves like a “condenser" for unpredictability. This result comes with two caveats (1) the loss in circuit size is exponential in k and (2) we require that the source we start with has no HILL entropy (equivalently, one can efficiently check if a guess is correct). We leave it as an intriguing open problem to overcome these restrictions or to prove they’re inherent." alternative_title: - LNCS author: - first_name: Maciej full_name: Skórski, Maciej last_name: Skórski - first_name: Alexander full_name: Golovnev, Alexander last_name: Golovnev - 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: 'Skórski M, Golovnev A, Pietrzak KZ. Condensed unpredictability . In: Vol 9134. Springer; 2015:1046-1057. doi:10.1007/978-3-662-47672-7_85' apa: 'Skórski, M., Golovnev, A., & Pietrzak, K. Z. (2015). Condensed unpredictability (Vol. 9134, pp. 1046–1057). Presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan: Springer. https://doi.org/10.1007/978-3-662-47672-7_85' chicago: Skórski, Maciej, Alexander Golovnev, and Krzysztof Z Pietrzak. “Condensed Unpredictability ,” 9134:1046–57. Springer, 2015. https://doi.org/10.1007/978-3-662-47672-7_85. ieee: 'M. Skórski, A. Golovnev, and K. Z. Pietrzak, “Condensed unpredictability ,” presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 1046–1057.' ista: 'Skórski M, Golovnev A, Pietrzak KZ. 2015. Condensed unpredictability . ICALP: Automata, Languages and Programming, LNCS, vol. 9134, 1046–1057.' mla: Skórski, Maciej, et al. Condensed Unpredictability . Vol. 9134, Springer, 2015, pp. 1046–57, doi:10.1007/978-3-662-47672-7_85. short: M. Skórski, A. Golovnev, K.Z. Pietrzak, in:, Springer, 2015, pp. 1046–1057. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: Automata, Languages and Programming' start_date: 2015-07-06 date_created: 2018-12-11T11:53:15Z date_published: 2015-06-20T00:00:00Z date_updated: 2021-01-12T06:52:15Z day: '20' ddc: - '000' - '005' department: - _id: KrPi doi: 10.1007/978-3-662-47672-7_85 ec_funded: 1 file: - access_level: open_access checksum: e808c7eecb631336fc9f9bf2e8d4ecae content_type: application/pdf creator: system date_created: 2018-12-12T10:08:32Z date_updated: 2020-07-14T12:45:08Z file_id: '4693' file_name: IST-2016-675-v1+1_384.pdf file_size: 525503 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9134' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1046 - 1057 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5500' pubrep_id: '675' quality_controlled: '1' scopus_import: 1 status: public title: 'Condensed unpredictability ' 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: 9134 year: '2015' ... --- _id: '1651' abstract: - lang: eng text: Cryptographic e-cash allows off-line electronic transactions between a bank, users and merchants in a secure and anonymous fashion. A plethora of e-cash constructions has been proposed in the literature; however, these traditional e-cash schemes only allow coins to be transferred once between users and merchants. Ideally, we would like users to be able to transfer coins between each other multiple times before deposit, as happens with physical cash. “Transferable” e-cash schemes are the solution to this problem. Unfortunately, the currently proposed schemes are either completely impractical or do not achieve the desirable anonymity properties without compromises, such as assuming the existence of a trusted “judge” who can trace all coins and users in the system. This paper presents the first efficient and fully anonymous transferable e-cash scheme without any trusted third parties. We start by revising the security and anonymity properties of transferable e-cash to capture issues that were previously overlooked. For our construction we use the recently proposed malleable signatures by Chase et al. to allow the secure and anonymous transfer of coins, combined with a new efficient double-spending detection mechanism. Finally, we discuss an instantiation of our construction. acknowledgement: Work done as an intern in Microsoft Research Redmond and as a student at Brown University, where supported by NSF grant 0964379. Supported by the European Research Council, ERC Starting Grant (259668-PSPC). alternative_title: - LNCS article_processing_charge: No author: - first_name: Foteini full_name: Baldimtsi, Foteini last_name: Baldimtsi - first_name: Melissa full_name: Chase, Melissa last_name: Chase - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Markulf full_name: Kohlweiss, Markulf last_name: Kohlweiss citation: ama: 'Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. Anonymous transferable e-cash. In: Public-Key Cryptography - PKC 2015. Vol 9020. Springer; 2015:101-124. doi:10.1007/978-3-662-46447-2_5' apa: 'Baldimtsi, F., Chase, M., Fuchsbauer, G., & Kohlweiss, M. (2015). Anonymous transferable e-cash. In Public-Key Cryptography - PKC 2015 (Vol. 9020, pp. 101–124). Gaithersburg, MD, United States: Springer. https://doi.org/10.1007/978-3-662-46447-2_5' chicago: Baldimtsi, Foteini, Melissa Chase, Georg Fuchsbauer, and Markulf Kohlweiss. “Anonymous Transferable E-Cash.” In Public-Key Cryptography - PKC 2015, 9020:101–24. Springer, 2015. https://doi.org/10.1007/978-3-662-46447-2_5. ieee: F. Baldimtsi, M. Chase, G. Fuchsbauer, and M. Kohlweiss, “Anonymous transferable e-cash,” in Public-Key Cryptography - PKC 2015, Gaithersburg, MD, United States, 2015, vol. 9020, pp. 101–124. ista: 'Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. 2015. Anonymous transferable e-cash. Public-Key Cryptography - PKC 2015. PKC: Public Key Crypography, LNCS, vol. 9020, 101–124.' mla: Baldimtsi, Foteini, et al. “Anonymous Transferable E-Cash.” Public-Key Cryptography - PKC 2015, vol. 9020, Springer, 2015, pp. 101–24, doi:10.1007/978-3-662-46447-2_5. short: F. Baldimtsi, M. Chase, G. Fuchsbauer, M. Kohlweiss, in:, Public-Key Cryptography - PKC 2015, Springer, 2015, pp. 101–124. conference: end_date: 2015-04-01 location: Gaithersburg, MD, United States name: 'PKC: Public Key Crypography' start_date: 2015-03-30 date_created: 2018-12-11T11:53:15Z date_published: 2015-03-17T00:00:00Z date_updated: 2022-05-23T10:08:37Z day: '17' department: - _id: KrPi doi: 10.1007/978-3-662-46447-2_5 ec_funded: 1 intvolume: ' 9020' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/978-3-662-46447-2_5 month: '03' oa: 1 oa_version: Published Version page: 101 - 124 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Public-Key Cryptography - PKC 2015 publication_identifier: isbn: - 978-3-662-46446-5 publication_status: published publisher: Springer publist_id: '5499' quality_controlled: '1' scopus_import: '1' status: public title: Anonymous transferable e-cash type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9020 year: '2015' ... --- _id: '1652' abstract: - lang: eng text: We develop new theoretical tools for proving lower-bounds on the (amortized) complexity of certain functions in models of parallel computation. We apply the tools to construct a class of functions with high amortized memory complexity in the parallel Random Oracle Model (pROM); a variant of the standard ROM allowing for batches of simultaneous queries. In particular we obtain a new, more robust, type of Memory-Hard Functions (MHF); a security primitive which has recently been gaining acceptance in practice as an effective means of countering brute-force attacks on security relevant functions. Along the way we also demonstrate an important shortcoming of previous definitions of MHFs and give a new definition addressing the problem. The tools we develop represent an adaptation of the powerful pebbling paradigm (initially introduced by Hewitt and Paterson [HP70] and Cook [Coo73]) to a simple and intuitive parallel setting. We define a simple pebbling game Gp over graphs which aims to abstract parallel computation in an intuitive way. As a conceptual contribution we define a measure of pebbling complexity for graphs called cumulative complexity (CC) and show how it overcomes a crucial shortcoming (in the parallel setting) exhibited by more traditional complexity measures used in the past. As a main technical contribution we give an explicit construction of a constant in-degree family of graphs whose CC in Gp approaches maximality to within a polylogarithmic factor for any graph of equal size (analogous to the graphs of Tarjan et. al. [PTC76, LT82] for sequential pebbling games). Finally, for a given graph G and related function fG, we derive a lower-bound on the amortized memory complexity of fG in the pROM in terms of the CC of G in the game Gp. author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Vladimir full_name: Serbinenko, Vladimir last_name: Serbinenko citation: ama: 'Alwen JF, Serbinenko V. High parallel complexity graphs and memory-hard functions. In: Proceedings of the 47th Annual ACM Symposium on Theory of Computing. ACM; 2015:595-603. doi:10.1145/2746539.2746622' apa: 'Alwen, J. F., & Serbinenko, V. (2015). High parallel complexity graphs and memory-hard functions. In Proceedings of the 47th annual ACM symposium on Theory of computing (pp. 595–603). Portland, OR, United States: ACM. https://doi.org/10.1145/2746539.2746622' chicago: Alwen, Joel F, and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” In Proceedings of the 47th Annual ACM Symposium on Theory of Computing, 595–603. ACM, 2015. https://doi.org/10.1145/2746539.2746622. ieee: J. F. Alwen and V. Serbinenko, “High parallel complexity graphs and memory-hard functions,” in Proceedings of the 47th annual ACM symposium on Theory of computing, Portland, OR, United States, 2015, pp. 595–603. ista: 'Alwen JF, Serbinenko V. 2015. High parallel complexity graphs and memory-hard functions. Proceedings of the 47th annual ACM symposium on Theory of computing. STOC: Symposium on the Theory of Computing, 595–603.' mla: Alwen, Joel F., and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603, doi:10.1145/2746539.2746622. short: J.F. Alwen, V. Serbinenko, in:, Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603. conference: end_date: 2015-06-17 location: Portland, OR, United States name: 'STOC: Symposium on the Theory of Computing' start_date: 2015-06-14 date_created: 2018-12-11T11:53:16Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:52:16Z day: '01' department: - _id: KrPi doi: 10.1145/2746539.2746622 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2014/238 month: '06' oa: 1 oa_version: Submitted Version page: 595 - 603 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Proceedings of the 47th annual ACM symposium on Theory of computing publication_status: published publisher: ACM publist_id: '5498' quality_controlled: '1' scopus_import: 1 status: public title: High parallel complexity graphs and memory-hard functions type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1660' abstract: - lang: eng text: We study the pattern frequency vector for runs in probabilistic Vector Addition Systems with States (pVASS). Intuitively, each configuration of a given pVASS is assigned one of finitely many patterns, and every run can thus be seen as an infinite sequence of these patterns. The pattern frequency vector assigns to each run the limit of pattern frequencies computed for longer and longer prefixes of the run. If the limit does not exist, then the vector is undefined. We show that for one-counter pVASS, the pattern frequency vector is defined and takes one of finitely many values for almost all runs. Further, these values and their associated probabilities can be approximated up to an arbitrarily small relative error in polynomial time. For stable two-counter pVASS, we show the same result, but we do not provide any upper complexity bound. As a byproduct of our study, we discover counterexamples falsifying some classical results about stochastic Petri nets published in the 80s. alternative_title: - LICS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Stefan full_name: Kiefer, Stefan last_name: Kiefer - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Brázdil T, Kiefer S, Kučera A, Novotný P. Long-run average behaviour of probabilistic vector addition systems. In: IEEE; 2015:44-55. doi:10.1109/LICS.2015.15' apa: 'Brázdil, T., Kiefer, S., Kučera, A., & Novotný, P. (2015). Long-run average behaviour of probabilistic vector addition systems (pp. 44–55). Presented at the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.15' chicago: Brázdil, Tomáš, Stefan Kiefer, Antonín Kučera, and Petr Novotný. “Long-Run Average Behaviour of Probabilistic Vector Addition Systems,” 44–55. IEEE, 2015. https://doi.org/10.1109/LICS.2015.15. ieee: 'T. Brázdil, S. Kiefer, A. Kučera, and P. Novotný, “Long-run average behaviour of probabilistic vector addition systems,” presented at the LICS: Logic in Computer Science, Kyoto, Japan, 2015, pp. 44–55.' ista: 'Brázdil T, Kiefer S, Kučera A, Novotný P. 2015. Long-run average behaviour of probabilistic vector addition systems. LICS: Logic in Computer Science, LICS, , 44–55.' mla: Brázdil, Tomáš, et al. Long-Run Average Behaviour of Probabilistic Vector Addition Systems. IEEE, 2015, pp. 44–55, doi:10.1109/LICS.2015.15. short: T. Brázdil, S. Kiefer, A. Kučera, P. Novotný, in:, IEEE, 2015, pp. 44–55. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:19Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:52:20Z day: '01' department: - _id: KrCh doi: 10.1109/LICS.2015.15 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1505.02655 month: '07' oa: 1 oa_version: Preprint page: 44 - 55 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: IEEE publist_id: '5490' quality_controlled: '1' scopus_import: 1 status: public title: Long-run average behaviour of probabilistic vector addition systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1665' abstract: - lang: eng text: Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome. article_processing_charge: No article_type: original author: - first_name: Dan full_name: Landau, Dan last_name: Landau - first_name: Eugen full_name: Tausch, Eugen last_name: Tausch - first_name: Amaro full_name: Taylor Weiner, Amaro last_name: Taylor Weiner - first_name: Chip full_name: Stewart, Chip last_name: Stewart - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Jasmin full_name: Bahlo, Jasmin last_name: Bahlo - first_name: Sandra full_name: Kluth, Sandra last_name: Kluth - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Michael full_name: Lawrence, Michael last_name: Lawrence - first_name: Sebastian full_name: Böttcher, Sebastian last_name: Böttcher - first_name: Scott full_name: Carter, Scott last_name: Carter - first_name: Kristian full_name: Cibulskis, Kristian last_name: Cibulskis - first_name: Daniel full_name: Mertens, Daniel last_name: Mertens - first_name: Carrie full_name: Sougnez, Carrie last_name: Sougnez - first_name: Mara full_name: Rosenberg, Mara last_name: Rosenberg - first_name: Julian full_name: Hess, Julian last_name: Hess - first_name: Jennifer full_name: Edelmann, Jennifer last_name: Edelmann - first_name: Sabrina full_name: Kless, Sabrina last_name: Kless - first_name: Michael full_name: Kneba, Michael last_name: Kneba - first_name: Matthias full_name: Ritgen, Matthias last_name: Ritgen - first_name: Anna full_name: Fink, Anna last_name: Fink - first_name: Kirsten full_name: Fischer, Kirsten last_name: Fischer - first_name: Stacey full_name: Gabriel, Stacey last_name: Gabriel - first_name: Eric full_name: Lander, Eric last_name: Lander - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Hartmut full_name: Döhner, Hartmut last_name: Döhner - first_name: Michael full_name: Hallek, Michael last_name: Hallek - first_name: Donna full_name: Neuberg, Donna last_name: Neuberg - first_name: Gad full_name: Getz, Gad last_name: Getz - first_name: Stephan full_name: Stilgenbauer, Stephan last_name: Stilgenbauer - first_name: Catherine full_name: Wu, Catherine last_name: Wu citation: ama: Landau D, Tausch E, Taylor Weiner A, et al. Mutations driving CLL and their evolution in progression and relapse. Nature. 2015;526(7574):525-530. doi:10.1038/nature15395 apa: Landau, D., Tausch, E., Taylor Weiner, A., Stewart, C., Reiter, J., Bahlo, J., … Wu, C. (2015). Mutations driving CLL and their evolution in progression and relapse. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15395 chicago: Landau, Dan, Eugen Tausch, Amaro Taylor Weiner, Chip Stewart, Johannes Reiter, Jasmin Bahlo, Sandra Kluth, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15395. ieee: D. Landau et al., “Mutations driving CLL and their evolution in progression and relapse,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 525–530, 2015. ista: Landau D, Tausch E, Taylor Weiner A, Stewart C, Reiter J, Bahlo J, Kluth S, Božić I, Lawrence M, Böttcher S, Carter S, Cibulskis K, Mertens D, Sougnez C, Rosenberg M, Hess J, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K, Gabriel S, Lander E, Nowak M, Döhner H, Hallek M, Neuberg D, Getz G, Stilgenbauer S, Wu C. 2015. Mutations driving CLL and their evolution in progression and relapse. Nature. 526(7574), 525–530. mla: Landau, Dan, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 525–30, doi:10.1038/nature15395. short: D. Landau, E. Tausch, A. Taylor Weiner, C. Stewart, J. Reiter, J. Bahlo, S. Kluth, I. Božić, M. Lawrence, S. Böttcher, S. Carter, K. Cibulskis, D. Mertens, C. Sougnez, M. Rosenberg, J. Hess, J. Edelmann, S. Kless, M. Kneba, M. Ritgen, A. Fink, K. Fischer, S. Gabriel, E. Lander, M. Nowak, H. Döhner, M. Hallek, D. Neuberg, G. Getz, S. Stilgenbauer, C. Wu, Nature 526 (2015) 525–530. date_created: 2018-12-11T11:53:21Z date_published: 2015-10-22T00:00:00Z date_updated: 2021-01-12T06:52:23Z day: '22' department: - _id: KrCh doi: 10.1038/nature15395 ec_funded: 1 external_id: pmid: - '26466571' intvolume: ' 526' issue: '7574' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815041/ month: '10' oa: 1 oa_version: Submitted Version page: 525 - 530 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: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5484' quality_controlled: '1' scopus_import: 1 status: public title: Mutations driving CLL and their evolution in progression and relapse type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 526 year: '2015' ... --- _id: '1667' abstract: - lang: eng text: We consider parametric version of fixed-delay continuoustime Markov chains (or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay transitions are specified by parameters, rather than concrete values. Our goal is to synthesize values of these parameters that, for a given cost function, minimise expected total cost incurred before reaching a given set of target states. We show that under mild assumptions, optimal values of parameters can be effectively approximated using translation to a Markov decision process (MDP) whose actions correspond to discretized values of these parameters. To this end we identify and overcome several interesting phenomena arising in systems with fixed delays. acknowledgement: 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 n∘ [291734]. This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the Czech Science Foundation, grant No. 15-17564S, and by the CAS/SAFEA International Partnership Program for Creative Research Teams. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: L'Uboš full_name: Korenčiak, L'Uboš last_name: Korenčiak - first_name: Jan full_name: Krčál, Jan last_name: Krčál - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny - first_name: Vojtěch full_name: Řehák, Vojtěch last_name: Řehák citation: ama: Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 2015;9259:141-159. doi:10.1007/978-3-319-22264-6_10 apa: 'Brázdil, T., Korenčiak, L., Krčál, J., Novotný, P., & Řehák, V. (2015). Optimizing performance of continuous-time stochastic systems using timeout synthesis. Presented at the QEST: Quantitative Evaluation of Systems, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-22264-6_10' chicago: Brázdil, Tomáš, L’Uboš Korenčiak, Jan Krčál, Petr Novotný, and Vojtěch Řehák. “Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22264-6_10. ieee: T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, and V. Řehák, “Optimizing performance of continuous-time stochastic systems using timeout synthesis,” vol. 9259. Springer, pp. 141–159, 2015. ista: Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. 2015. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 9259, 141–159. mla: Brázdil, Tomáš, et al. Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis. Vol. 9259, Springer, 2015, pp. 141–59, doi:10.1007/978-3-319-22264-6_10. short: T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, V. Řehák, 9259 (2015) 141–159. conference: end_date: 2015-09-03 location: Madrid, Spain name: 'QEST: Quantitative Evaluation of Systems' start_date: 2015-09-01 date_created: 2018-12-11T11:53:22Z date_published: 2015-08-22T00:00:00Z date_updated: 2021-01-12T06:52:24Z day: '22' department: - _id: KrCh doi: 10.1007/978-3-319-22264-6_10 ec_funded: 1 intvolume: ' 9259' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.4777 month: '08' oa: 1 oa_version: Preprint page: 141 - 159 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5482' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Optimizing performance of continuous-time stochastic systems using timeout synthesis type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9259 year: '2015' ... --- _id: '1664' abstract: - lang: eng text: Over a century of research into the origin of turbulence in wall-bounded shear flows has resulted in a puzzling picture in which turbulence appears in a variety of different states competing with laminar background flow. At moderate flow speeds, turbulence is confined to localized patches; it is only at higher speeds that the entire flow becomes turbulent. The origin of the different states encountered during this transition, the front dynamics of the turbulent regions and the transformation to full turbulence have yet to be explained. By combining experiments, theory and computer simulations, here we uncover a bifurcation scenario that explains the transformation to fully turbulent pipe flow and describe the front dynamics of the different states encountered in the process. Key to resolving this problem is the interpretation of the flow as a bistable system with nonlinear propagation (advection) of turbulent fronts. These findings bridge the gap between our understanding of the onset of turbulence and fully turbulent flows. acknowledgement: We acknowledge the Deutsche Forschungsgemeinschaft (Project No. FOR 1182), and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. B.S. acknowledges financial support from the Chinese State Scholarship Fund under grant number 2010629145. B.S. acknowledges support from the International Max Planck Research School for the Physics of Biological and Complex Systems and the Göttingen Graduate School for Neurosciences and Molecular Biosciences. We acknowledge computing resources from GWDG (Gesellschaft für wissenschaftliche Datenverarbeitung Göttingen) and the Jülich Supercomputing Centre (grant HGU16) where the simulations were performed. author: - first_name: Dwight full_name: Barkley, Dwight last_name: Barkley - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Mukund full_name: Vasudevan, Mukund id: 3C5A959A-F248-11E8-B48F-1D18A9856A87 last_name: Vasudevan - first_name: Grégoire M full_name: Lemoult, Grégoire M id: 4787FE80-F248-11E8-B48F-1D18A9856A87 last_name: Lemoult - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. The rise of fully turbulent flow. Nature. 2015;526(7574):550-553. doi:10.1038/nature15701 apa: Barkley, D., Song, B., Vasudevan, M., Lemoult, G. M., Avila, M., & Hof, B. (2015). The rise of fully turbulent flow. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15701 chicago: Barkley, Dwight, Baofang Song, Mukund Vasudevan, Grégoire M Lemoult, Marc Avila, and Björn Hof. “The Rise of Fully Turbulent Flow.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15701. ieee: D. Barkley, B. Song, M. Vasudevan, G. M. Lemoult, M. Avila, and B. Hof, “The rise of fully turbulent flow,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 550–553, 2015. ista: Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. 2015. The rise of fully turbulent flow. Nature. 526(7574), 550–553. mla: Barkley, Dwight, et al. “The Rise of Fully Turbulent Flow.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 550–53, doi:10.1038/nature15701. short: D. Barkley, B. Song, M. Vasudevan, G.M. Lemoult, M. Avila, B. Hof, Nature 526 (2015) 550–553. date_created: 2018-12-11T11:53:20Z date_published: 2015-10-21T00:00:00Z date_updated: 2021-01-12T06:52:22Z day: '21' department: - _id: BjHo doi: 10.1038/nature15701 ec_funded: 1 intvolume: ' 526' issue: '7574' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1510.09143 month: '10' oa: 1 oa_version: Preprint page: 550 - 553 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5485' quality_controlled: '1' scopus_import: 1 status: public title: The rise of fully turbulent flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 526 year: '2015' ... --- _id: '1672' abstract: - lang: eng text: Composable notions of incoercibility aim to forbid a coercer from using anything beyond the coerced parties’ inputs and outputs to catch them when they try to deceive him. Existing definitions are restricted to weak coercion types, and/or are not universally composable. Furthermore, they often make too strong assumptions on the knowledge of coerced parties—e.g., they assume they known the identities and/or the strategies of other coerced parties, or those of corrupted parties— which makes them unsuitable for applications of incoercibility such as e-voting, where colluding adversarial parties may attempt to coerce honest voters, e.g., by offering them money for a promised vote, and use their own view to check that the voter keeps his end of the bargain. In this work we put forward the first universally composable notion of incoercible multi-party computation, which satisfies the above intuition and does not assume collusions among coerced parties or knowledge of the corrupted set. We define natural notions of UC incoercibility corresponding to standard coercion-types, i.e., receipt-freeness and resistance to full-active coercion. Importantly, our suggested notion has the unique property that it builds on top of the well studied UC framework by Canetti instead of modifying it. This guarantees backwards compatibility, and allows us to inherit results from the rich UC literature. We then present MPC protocols which realize our notions of UC incoercibility given access to an arguably minimal setup—namely honestly generate tamper-proof hardware performing a very simple cryptographic operation—e.g., a smart card. This is, to our knowledge, the first proposed construction of an MPC protocol (for more than two parties) that is incoercibly secure and universally composable, and therefore the first construction of a universally composable receipt-free e-voting protocol. acknowledgement: Joël Alwen was supported by the ERC starting grant (259668-PSPC). Rafail Ostrovsky was supported in part by NSF grants 09165174, 1065276, 1118126 and 1136174, US-Israel BSF grant 2008411, OKAWA Foundation Research Award, IBM Faculty Research Award, Xerox Faculty Research Award, B. John Garrick Foundation Award, Teradata Research Award, Lockheed-Martin Corporation Research Award, and the Defense Advanced Research Projects Agency through the U.S. Office of Naval Research under Contract N00014 -11 -1-0392. The views expressed are those of the author and do not reflect the official policy or position of the Department of Defense or the U.S. Government. Vassilis Zikas was supported in part by the Swiss National Science Foundation (SNF) via the Ambizione grant PZ00P-2142549. alternative_title: - LNCS article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Rafail full_name: Ostrovsky, Rafail last_name: Ostrovsky - first_name: Hongsheng full_name: Zhou, Hongsheng last_name: Zhou - first_name: Vassilis full_name: Zikas, Vassilis last_name: Zikas citation: ama: 'Alwen JF, Ostrovsky R, Zhou H, Zikas V. Incoercible multi-party computation and universally composable receipt-free voting. In: Advances in Cryptology - CRYPTO 2015. Vol 9216. Lecture Notes in Computer Science. Springer; 2015:763-780. doi:10.1007/978-3-662-48000-7_37' apa: 'Alwen, J. F., Ostrovsky, R., Zhou, H., & Zikas, V. (2015). Incoercible multi-party computation and universally composable receipt-free voting. In Advances in Cryptology - CRYPTO 2015 (Vol. 9216, pp. 763–780). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_37' chicago: Alwen, Joel F, Rafail Ostrovsky, Hongsheng Zhou, and Vassilis Zikas. “Incoercible Multi-Party Computation and Universally Composable Receipt-Free Voting.” In Advances in Cryptology - CRYPTO 2015, 9216:763–80. Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_37. ieee: J. F. Alwen, R. Ostrovsky, H. Zhou, and V. Zikas, “Incoercible multi-party computation and universally composable receipt-free voting,” in Advances in Cryptology - CRYPTO 2015, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 763–780. ista: 'Alwen JF, Ostrovsky R, Zhou H, Zikas V. 2015. Incoercible multi-party computation and universally composable receipt-free voting. Advances in Cryptology - CRYPTO 2015. CRYPTO: International Cryptology ConferenceLecture Notes in Computer Science, LNCS, vol. 9216, 763–780.' mla: Alwen, Joel F., et al. “Incoercible Multi-Party Computation and Universally Composable Receipt-Free Voting.” Advances in Cryptology - CRYPTO 2015, vol. 9216, Springer, 2015, pp. 763–80, doi:10.1007/978-3-662-48000-7_37. short: J.F. Alwen, R. Ostrovsky, H. Zhou, V. Zikas, in:, Advances in Cryptology - CRYPTO 2015, Springer, 2015, pp. 763–780. conference: end_date: 2015-08-20 location: Santa Barbara, CA, United States name: 'CRYPTO: International Cryptology Conference' start_date: 2015-08-16 date_created: 2018-12-11T11:53:23Z date_published: 2015-08-01T00:00:00Z date_updated: 2022-06-07T09:51:55Z day: '01' ddc: - '000' department: - _id: KrPi doi: 10.1007/978-3-662-48000-7_37 ec_funded: 1 file: - access_level: open_access checksum: 5b6649e80d1f781a8910f7cce6427f78 content_type: application/pdf creator: dernst date_created: 2020-05-15T08:55:29Z date_updated: 2020-07-14T12:45:11Z file_id: '7853' file_name: 2015_CRYPTO_Alwen.pdf file_size: 397363 relation: main_file file_date_updated: 2020-07-14T12:45:11Z has_accepted_license: '1' intvolume: ' 9216' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 763 - 780 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Advances in Cryptology - CRYPTO 2015 publication_identifier: eisbn: - 978-3-662-48000-7 isbn: - 978-3-662-47999-5 publication_status: published publisher: Springer publist_id: '5476' quality_controlled: '1' scopus_import: '1' series_title: Lecture Notes in Computer Science status: public title: Incoercible multi-party computation and universally composable receipt-free voting type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9216 year: '2015' ... --- _id: '1669' abstract: - lang: eng text: Computational notions of entropy (a.k.a. pseudoentropy) have found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The most important tools to argue about pseudoentropy are chain rules, which quantify by how much (in terms of quantity and quality) the pseudoentropy of a given random variable X decreases when conditioned on some other variable Z (think for example of X as a secret key and Z as information leaked by a side-channel). In this paper we give a very simple and modular proof of the chain rule for HILL pseudoentropy, improving best known parameters. Our version allows for increasing the acceptable length of leakage in applications up to a constant factor compared to the best previous bounds. As a contribution of independent interest, we provide a comprehensive study of all known versions of the chain rule, comparing their worst-case strength and limitations. alternative_title: - LNCS 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 last_name: Skórski citation: ama: Pietrzak KZ, Skórski M. The chain rule for HILL pseudoentropy, revisited. 2015;9230:81-98. doi:10.1007/978-3-319-22174-8_5 apa: 'Pietrzak, K. Z., & Skórski, M. (2015). The chain rule for HILL pseudoentropy, revisited. Presented at the LATINCRYPT: Cryptology and Information Security in Latin America, Guadalajara, Mexico: Springer. https://doi.org/10.1007/978-3-319-22174-8_5' chicago: Pietrzak, Krzysztof Z, and Maciej Skórski. “The Chain Rule for HILL Pseudoentropy, Revisited.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22174-8_5. ieee: K. Z. Pietrzak and M. Skórski, “The chain rule for HILL pseudoentropy, revisited,” vol. 9230. Springer, pp. 81–98, 2015. ista: Pietrzak KZ, Skórski M. 2015. The chain rule for HILL pseudoentropy, revisited. 9230, 81–98. mla: Pietrzak, Krzysztof Z., and Maciej Skórski. The Chain Rule for HILL Pseudoentropy, Revisited. Vol. 9230, Springer, 2015, pp. 81–98, doi:10.1007/978-3-319-22174-8_5. short: K.Z. Pietrzak, M. Skórski, 9230 (2015) 81–98. conference: end_date: 2015-08-26 location: Guadalajara, Mexico name: 'LATINCRYPT: Cryptology and Information Security in Latin America' start_date: 2015-08-23 date_created: 2018-12-11T11:53:22Z date_published: 2015-08-15T00:00:00Z date_updated: 2021-01-12T06:52:24Z day: '15' ddc: - '005' department: - _id: KrPi doi: 10.1007/978-3-319-22174-8_5 ec_funded: 1 file: - access_level: open_access checksum: 8cd4215b83efba720e8cf27c23ff4781 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:29Z date_updated: 2020-07-14T12:45:11Z file_id: '5351' file_name: IST-2016-669-v1+1_599.pdf file_size: 443340 relation: main_file file_date_updated: 2020-07-14T12:45:11Z has_accepted_license: '1' intvolume: ' 9230' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 81 - 98 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5480' pubrep_id: '669' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: The chain rule for HILL pseudoentropy, revisited type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9230 year: '2015' ... --- _id: '1671' abstract: - lang: eng text: This paper studies the concrete security of PRFs and MACs obtained by keying hash functions based on the sponge paradigm. One such hash function is KECCAK, selected as NIST’s new SHA-3 standard. In contrast to other approaches like HMAC, the exact security of keyed sponges is not well understood. Indeed, recent security analyses delivered concrete security bounds which are far from existing attacks. This paper aims to close this gap. We prove (nearly) exact bounds on the concrete PRF security of keyed sponges using a random permutation. These bounds are tight for the most relevant ranges of parameters, i.e., for messages of length (roughly) l ≤ min{2n/4, 2r} blocks, where n is the state size and r is the desired output length; and for l ≤ q queries (to the construction or the underlying permutation). Moreover, we also improve standard-model bounds. As an intermediate step of independent interest, we prove tight bounds on the PRF security of the truncated CBC-MAC construction, which operates as plain CBC-MAC, but only returns a prefix of the output. alternative_title: - LNCS author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - 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: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: 'Gazi P, Pietrzak KZ, Tessaro S. The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC. In: Vol 9215. Springer; 2015:368-387. doi:10.1007/978-3-662-47989-6_18' apa: 'Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC (Vol. 9215, pp. 368–387). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-47989-6_18' chicago: 'Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “The Exact PRF Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC,” 9215:368–87. Springer, 2015. https://doi.org/10.1007/978-3-662-47989-6_18.' ieee: 'P. Gazi, K. Z. Pietrzak, and S. Tessaro, “The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9215, pp. 368–387.' ista: 'Gazi P, Pietrzak KZ, Tessaro S. 2015. The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC. CRYPTO: International Cryptology Conference, LNCS, vol. 9215, 368–387.' mla: 'Gazi, Peter, et al. The Exact PRF Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC. Vol. 9215, Springer, 2015, pp. 368–87, doi:10.1007/978-3-662-47989-6_18.' short: P. Gazi, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2015, pp. 368–387. conference: end_date: 2015-08-20 location: Santa Barbara, CA, United States name: 'CRYPTO: International Cryptology Conference' start_date: 2015-08-16 date_created: 2018-12-11T11:53:23Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:25Z day: '01' ddc: - '004' - '005' department: - _id: KrPi doi: 10.1007/978-3-662-47989-6_18 ec_funded: 1 file: - access_level: open_access checksum: 17d854227b3b753fd34f5d29e5b5a32e content_type: application/pdf creator: system date_created: 2018-12-12T10:10:38Z date_updated: 2020-07-14T12:45:11Z file_id: '4827' file_name: IST-2016-673-v1+1_053.pdf file_size: 592296 relation: main_file file_date_updated: 2020-07-14T12:45:11Z has_accepted_license: '1' intvolume: ' 9215' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 368 - 387 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5478' pubrep_id: '673' quality_controlled: '1' scopus_import: 1 status: public title: 'The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9215 year: '2015' ... --- _id: '1673' abstract: - lang: eng text: 'When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement-that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two. ' acknowledgement: 'K.C. gratefully acknowledges support from ERC Start grant no. (279307: Graph Games), Austrian Science Fund (FWF) grant no. P23499-N23, and FWF NFN grant no. S11407-N23 (RiSE). ' article_number: '20150114' author: - first_name: Ben full_name: Adlam, Ben last_name: Adlam - 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: 'Adlam B, Chatterjee K, Nowak M. Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2015;471(2181). doi:10.1098/rspa.2015.0114' apa: 'Adlam, B., Chatterjee, K., & Nowak, M. (2015). Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2015.0114' chicago: 'Adlam, Ben, Krishnendu Chatterjee, and Martin Nowak. “Amplifiers of Selection.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2015. https://doi.org/10.1098/rspa.2015.0114.' ieee: 'B. Adlam, K. Chatterjee, and M. Nowak, “Amplifiers of selection,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no. 2181. Royal Society of London, 2015.' ista: 'Adlam B, Chatterjee K, Nowak M. 2015. Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 471(2181), 20150114.' mla: 'Adlam, Ben, et al. “Amplifiers of Selection.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no. 2181, 20150114, Royal Society of London, 2015, doi:10.1098/rspa.2015.0114.' short: 'B. Adlam, K. Chatterjee, M. Nowak, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 471 (2015).' date_created: 2018-12-11T11:53:24Z date_published: 2015-09-08T00:00:00Z date_updated: 2021-01-12T06:52:26Z day: '08' ddc: - '000' department: - _id: KrCh doi: 10.1098/rspa.2015.0114 ec_funded: 1 file: - access_level: open_access checksum: e613d94d283c776322403a28aad11bdd content_type: application/pdf creator: kschuh date_created: 2019-04-18T12:39:56Z date_updated: 2020-07-14T12:45:11Z file_id: '6342' file_name: 2015_rspa_Adlam.pdf file_size: 391466 relation: main_file file_date_updated: 2020-07-14T12:45:11Z has_accepted_license: '1' intvolume: ' 471' issue: '2181' language: - iso: eng month: '09' 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 Royal Society A: Mathematical, Physical and Engineering Sciences' publication_status: published publisher: Royal Society of London publist_id: '5477' quality_controlled: '1' scopus_import: 1 status: public title: Amplifiers of selection type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2015' ... --- _id: '1668' abstract: - lang: eng text: "We revisit the security (as a pseudorandom permutation) of cascading-based constructions for block-cipher key-length extension. Previous works typically considered the extreme case where the adversary is given the entire codebook of the construction, the only complexity measure being the number qe of queries to the underlying ideal block cipher, representing adversary’s secret-key-independent computation. Here, we initiate a systematic study of the more natural case of an adversary restricted to adaptively learning a number qc of plaintext/ciphertext pairs that is less than the entire codebook. For any such qc, we aim to determine the highest number of block-cipher queries qe the adversary can issue without being able to successfully distinguish the construction (under a secret key) from a random permutation.\r\nMore concretely, we show the following results for key-length extension schemes using a block cipher with n-bit blocks and κ-bit keys:\r\nPlain cascades of length ℓ=2r+1 are secure whenever qcqre≪2r(κ+n), qc≪2κ and qe≪22κ. The bound for r=1 also applies to two-key triple encryption (as used within Triple DES).\r\nThe r-round XOR-cascade is secure as long as qcqre≪2r(κ+n), matching an attack by Gaži (CRYPTO 2013).\r\nWe fully characterize the security of Gaži and Tessaro’s two-call " alternative_title: - LNCS author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Jooyoung full_name: Lee, Jooyoung last_name: Lee - first_name: Yannick full_name: Seurin, Yannick last_name: Seurin - first_name: John full_name: Steinberger, John last_name: Steinberger - first_name: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: 'Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 2015;9054:319-341. doi:10.1007/978-3-662-48116-5_16' apa: 'Gazi, P., Lee, J., Seurin, Y., Steinberger, J., & Tessaro, S. (2015). Relaxing full-codebook security: A refined analysis of key-length extension schemes. Presented at the FSE: Fast Software Encryption, Istanbul, Turkey: Springer. https://doi.org/10.1007/978-3-662-48116-5_16' chicago: 'Gazi, Peter, Jooyoung Lee, Yannick Seurin, John Steinberger, and Stefano Tessaro. “Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48116-5_16.' ieee: 'P. Gazi, J. Lee, Y. Seurin, J. Steinberger, and S. Tessaro, “Relaxing full-codebook security: A refined analysis of key-length extension schemes,” vol. 9054. Springer, pp. 319–341, 2015.' ista: 'Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. 2015. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 9054, 319–341.' mla: 'Gazi, Peter, et al. Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes. Vol. 9054, Springer, 2015, pp. 319–41, doi:10.1007/978-3-662-48116-5_16.' short: P. Gazi, J. Lee, Y. Seurin, J. Steinberger, S. Tessaro, 9054 (2015) 319–341. conference: end_date: 2015-03-11 location: Istanbul, Turkey name: 'FSE: Fast Software Encryption' start_date: 2015-03-08 date_created: 2018-12-11T11:53:22Z date_published: 2015-08-12T00:00:00Z date_updated: 2020-08-11T10:09:26Z day: '12' department: - _id: KrPi doi: 10.1007/978-3-662-48116-5_16 ec_funded: 1 intvolume: ' 9054' language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2015/397 month: '08' oa: 1 oa_version: Submitted Version page: 319 - 341 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5481' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: 'Relaxing full-codebook security: A refined analysis of key-length extension schemes' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9054 year: '2015' ... --- _id: '1674' abstract: - lang: eng text: We consider N × N random matrices of the form H = W + V where W is a real symmetric Wigner matrix and V a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W and we choose V so that the eigenvalues of W and V are typically of the same order. For a large class of diagonal matrices V, we show that the rescaled distribution of the extremal eigenvalues is given by the Tracy-Widom distribution F1 in the limit of large N. Our proofs also apply to the complex Hermitian setting, i.e. when W is a complex Hermitian Wigner matrix. article_number: '1550018' author: - first_name: Jioon full_name: Lee, Jioon last_name: Lee - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Lee J, Schnelli K. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 2015;27(8). doi:10.1142/S0129055X1550018X apa: Lee, J., & Schnelli, K. (2015). Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X1550018X chicago: Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.” Reviews in Mathematical Physics. World Scientific Publishing, 2015. https://doi.org/10.1142/S0129055X1550018X. ieee: J. Lee and K. Schnelli, “Edge universality for deformed Wigner matrices,” Reviews in Mathematical Physics, vol. 27, no. 8. World Scientific Publishing, 2015. ista: Lee J, Schnelli K. 2015. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 27(8), 1550018. mla: Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.” Reviews in Mathematical Physics, vol. 27, no. 8, 1550018, World Scientific Publishing, 2015, doi:10.1142/S0129055X1550018X. short: J. Lee, K. Schnelli, Reviews in Mathematical Physics 27 (2015). date_created: 2018-12-11T11:53:24Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:26Z day: '01' department: - _id: LaEr doi: 10.1142/S0129055X1550018X intvolume: ' 27' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.8015 month: '09' oa: 1 oa_version: Preprint publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '5475' quality_controlled: '1' scopus_import: 1 status: public title: Edge universality for deformed Wigner matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2015' ... --- _id: '1679' article_number: '091102' author: - first_name: Grégoire M full_name: Lemoult, Grégoire M id: 4787FE80-F248-11E8-B48F-1D18A9856A87 last_name: Lemoult - first_name: Philipp full_name: Maier, Philipp id: 384F7C04-F248-11E8-B48F-1D18A9856A87 last_name: Maier - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Lemoult GM, Maier P, Hof B. Taylor’s Forest. Physics of Fluids. 2015;27(9). doi:10.1063/1.4930850 apa: Lemoult, G. M., Maier, P., & Hof, B. (2015). Taylor’s Forest. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4930850 chicago: Lemoult, Grégoire M, Philipp Maier, and Björn Hof. “Taylor’s Forest.” Physics of Fluids. American Institute of Physics, 2015. https://doi.org/10.1063/1.4930850. ieee: G. M. Lemoult, P. Maier, and B. Hof, “Taylor’s Forest,” Physics of Fluids, vol. 27, no. 9. American Institute of Physics, 2015. ista: Lemoult GM, Maier P, Hof B. 2015. Taylor’s Forest. Physics of Fluids. 27(9), 091102. mla: Lemoult, Grégoire M., et al. “Taylor’s Forest.” Physics of Fluids, vol. 27, no. 9, 091102, American Institute of Physics, 2015, doi:10.1063/1.4930850. short: G.M. Lemoult, P. Maier, B. Hof, Physics of Fluids 27 (2015). date_created: 2018-12-11T11:53:26Z date_published: 2015-09-24T00:00:00Z date_updated: 2021-01-12T06:52:28Z day: '24' ddc: - '532' department: - _id: BjHo doi: 10.1063/1.4930850 file: - access_level: open_access checksum: 604bba3c2496aadb3efcff77de01ce6c content_type: application/pdf creator: system date_created: 2018-12-12T10:13:35Z date_updated: 2020-07-14T12:45:12Z file_id: '5019' file_name: IST-2017-748-v1+1_1.4930850.pdf file_size: 872366 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 27' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Physics of Fluids publication_status: published publisher: American Institute of Physics publist_id: '5469' pubrep_id: '748' quality_controlled: '1' scopus_import: 1 status: public title: Taylor's Forest 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: 27 year: '2015' ... --- _id: '1684' abstract: - lang: eng text: Many species groups, including mammals and many insects, determine sex using heteromorphic sex chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY sex chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in sex chromosome karyotypes among flies. We identify over a dozen different sex chromosome configurations, and the small dot chromosome is repeatedly used as the sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated sex chromosomes, others in which a different chromosome replaced the dot as a sex chromosome or in which up to three chromosomal elements became incorporated into the sex chromosomes, and others yet with female heterogamety (ZW sex chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting sex-specific selective pressures. These species thus provide a rich resource to study sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of sex chromosomes in diverse fly taxa. acknowledgement: "This research was funded by NIH grants (R01GM076007 and R01GM093182) to DB. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\r\nWe thank the people listed in S2 Table for samples, Jere Schweikert for identifying Tephritid species, and Zaak Walton for technical assistance." article_number: e1002078 author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: Vicoso B, Bachtrog D. Numerous transitions of sex chromosomes in Diptera. PLoS Biology. 2015;13(4). doi:10.1371/journal.pbio.1002078 apa: Vicoso, B., & Bachtrog, D. (2015). Numerous transitions of sex chromosomes in Diptera. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002078 chicago: Vicoso, Beatriz, and Doris Bachtrog. “Numerous Transitions of Sex Chromosomes in Diptera.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002078. ieee: B. Vicoso and D. Bachtrog, “Numerous transitions of sex chromosomes in Diptera,” PLoS Biology, vol. 13, no. 4. Public Library of Science, 2015. ista: Vicoso B, Bachtrog D. 2015. Numerous transitions of sex chromosomes in Diptera. PLoS Biology. 13(4), e1002078. mla: Vicoso, Beatriz, and Doris Bachtrog. “Numerous Transitions of Sex Chromosomes in Diptera.” PLoS Biology, vol. 13, no. 4, e1002078, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002078. short: B. Vicoso, D. Bachtrog, PLoS Biology 13 (2015). date_created: 2018-12-11T11:53:27Z date_published: 2015-04-16T00:00:00Z date_updated: 2021-01-12T06:52:30Z day: '16' ddc: - '570' doi: 10.1371/journal.pbio.1002078 extern: '1' file: - access_level: open_access checksum: 92a300d7b97eafb477885303f7632fe1 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:05Z date_updated: 2020-07-14T12:45:12Z file_id: '4858' file_name: IST-2016-492-v1+1_journal.pbio.1002078.pdf file_size: 1104701 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 13' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '5463' pubrep_id: '492' quality_controlled: '1' status: public title: Numerous transitions of sex chromosomes in Diptera 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: 13 year: '2015' ... --- _id: '1687' abstract: - lang: eng text: Guided cell movement is essential for development and integrity of animals and crucially involved in cellular immune responses. Leukocytes are professional migratory cells that can navigate through most types of tissues and sense a wide range of directional cues. The responses of these cells to attractants have been mainly explored in tissue culture settings. How leukocytes make directional decisions in situ, within the challenging environment of a tissue maze, is less understood. Here we review recent advances in how leukocytes sense chemical cues in complex tissue settings and make links with paradigms of directed migration in development and Dictyostelium discoideum amoebae. author: - first_name: Milka full_name: Sarris, Milka last_name: Sarris - 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: 'Sarris M, Sixt MK. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 2015;36(10):93-102. doi:10.1016/j.ceb.2015.08.001' apa: 'Sarris, M., & Sixt, M. K. (2015). Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.08.001' chicago: 'Sarris, Milka, and Michael K Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.08.001.' ieee: 'M. Sarris and M. K. Sixt, “Navigating in tissue mazes: Chemoattractant interpretation in complex environments,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 93–102, 2015.' ista: 'Sarris M, Sixt MK. 2015. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 36(10), 93–102.' mla: 'Sarris, Milka, and Michael K. Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 93–102, doi:10.1016/j.ceb.2015.08.001.' short: M. Sarris, M.K. Sixt, Current Opinion in Cell Biology 36 (2015) 93–102. date_created: 2018-12-11T11:53:28Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:31Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1016/j.ceb.2015.08.001 ec_funded: 1 file: - access_level: open_access checksum: c29973924b790aab02fdd91857759cfb content_type: application/pdf creator: system date_created: 2018-12-12T10:11:21Z date_updated: 2020-07-14T12:45:12Z file_id: '4875' file_name: IST-2016-445-v1+1_1-s2.0-S0955067415001064-main.pdf file_size: 797964 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 36' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 93 - 102 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '5458' pubrep_id: '445' quality_controlled: '1' scopus_import: 1 status: public title: 'Navigating in tissue mazes: Chemoattractant interpretation in complex environments' 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: 36 year: '2015' ... --- _id: '1685' abstract: - lang: eng text: "Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3.\r\nOur techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest." alternative_title: - LNCS author: - first_name: Vincent full_name: Cohen Addad, Vincent last_name: Cohen Addad - first_name: Arnaud N full_name: De Mesmay, Arnaud N id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87 last_name: De Mesmay citation: ama: 'Cohen Addad V, de Mesmay AN. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. In: Vol 9294. Springer; 2015:386-398. doi:10.1007/978-3-662-48350-3_33' apa: 'Cohen Addad, V., & de Mesmay, A. N. (2015). A fixed parameter tractable approximation scheme for the optimal cut graph of a surface (Vol. 9294, pp. 386–398). Presented at the ESA: European Symposium on Algorithms, Patras, Greece: Springer. https://doi.org/10.1007/978-3-662-48350-3_33' chicago: Cohen Addad, Vincent, and Arnaud N de Mesmay. “A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface,” 9294:386–98. Springer, 2015. https://doi.org/10.1007/978-3-662-48350-3_33. ieee: 'V. Cohen Addad and A. N. de Mesmay, “A fixed parameter tractable approximation scheme for the optimal cut graph of a surface,” presented at the ESA: European Symposium on Algorithms, Patras, Greece, 2015, vol. 9294, pp. 386–398.' ista: 'Cohen Addad V, de Mesmay AN. 2015. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. ESA: European Symposium on Algorithms, LNCS, vol. 9294, 386–398.' mla: Cohen Addad, Vincent, and Arnaud N. de Mesmay. A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface. Vol. 9294, Springer, 2015, pp. 386–98, doi:10.1007/978-3-662-48350-3_33. short: V. Cohen Addad, A.N. de Mesmay, in:, Springer, 2015, pp. 386–398. conference: end_date: 2015-09-16 location: Patras, Greece name: 'ESA: European Symposium on Algorithms' start_date: 2015-09-14 date_created: 2018-12-11T11:53:27Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:31Z day: '01' department: - _id: UlWa doi: 10.1007/978-3-662-48350-3_33 ec_funded: 1 intvolume: ' 9294' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1507.01688 month: '09' oa: 1 oa_version: Preprint page: 386 - 398 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5462' quality_controlled: '1' scopus_import: 1 status: public title: A fixed parameter tractable approximation scheme for the optimal cut graph of a surface type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9294 year: '2015' ... --- _id: '1688' abstract: - lang: eng text: 'We estimate the selection constant in the following geometric selection theorem by Pach: For every positive integer d, there is a constant (Formula presented.) such that whenever (Formula presented.) are n-element subsets of (Formula presented.), we can find a point (Formula presented.) and subsets (Formula presented.) for every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices determined by (Formula presented.) simplices with one vertex in each Yi. We show a super-exponentially decreasing upper bound (Formula presented.). The ideas used in the proof of the upper bound also help us to prove Pach’s theorem with (Formula presented.), which is a lower bound doubly exponentially decreasing in d (up to some polynomial in the exponent). For comparison, Pach’s original approach yields a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem with (Formula presented.). In our construction for the upper bound, we use the fact that the minimum solid angle of every d-simplex is super-exponentially small. This fact was previously unknown and might be of independent interest. For the lower bound, we improve the ‘separation’ part of the argument by showing that in one of the key steps only d+1 separations are necessary, compared to 2d separations in the original proof. We also provide a measure version of Pach’s theorem.' acknowledgement: R. K. was supported by the Russian Foundation for Basic Research Grant 15-31-20403 (mol_a_ved) and grant 15-01-99563. J. K., Z. P., and M. T. were partially supported by ERC Advanced Research Grant No. 267165 (DISCONV) and by the project CE-ITI (GAČR P202/12/G061) of the Czech Science Foundation. J. K. was also partially supported by Swiss National Science Foundation Grants 200021-137574 and 200020-14453. P. P., Z. P., and M. T. were partially supported by the Charles University Grant GAUK 421511. P. P. was also partially supported by the Charles University Grant SVV-2014-260107. Z. P. was also partially supported by the Charles University Grant SVV-2014-260103. author: - first_name: Roman full_name: Karasev, Roman last_name: Karasev - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Pavel full_name: Paták, Pavel last_name: Paták - first_name: Zuzana full_name: Patakova, Zuzana 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 citation: ama: Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 2015;54(3):610-636. doi:10.1007/s00454-015-9720-z apa: Karasev, R., Kynčl, J., Paták, P., Patakova, Z., & Tancer, M. (2015). Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9720-z chicago: Karasev, Roman, Jan Kynčl, Pavel Paták, Zuzana Patakova, and Martin Tancer. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9720-z. ieee: R. Karasev, J. Kynčl, P. Paták, Z. Patakova, and M. Tancer, “Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex,” Discrete & Computational Geometry, vol. 54, no. 3. Springer, pp. 610–636, 2015. ista: Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. 2015. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 54(3), 610–636. mla: Karasev, Roman, et al. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry, vol. 54, no. 3, Springer, 2015, pp. 610–36, doi:10.1007/s00454-015-9720-z. short: R. Karasev, J. Kynčl, P. Paták, Z. Patakova, M. Tancer, Discrete & Computational Geometry 54 (2015) 610–636. date_created: 2018-12-11T11:53:28Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:32Z day: '01' department: - _id: UlWa doi: 10.1007/s00454-015-9720-z intvolume: ' 54' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1403.8147 month: '10' oa: 1 oa_version: Preprint page: 610 - 636 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5457' quality_controlled: '1' scopus_import: 1 status: public title: Bounds for Pach's selection theorem and for the minimum solid angle in a simplex type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2015' ...