--- _id: '1127' abstract: - lang: eng text: "Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms controlling plant development. Auxin itself could change localization of PINs and\r\nthereby control direction of its own flow. We performed an expression profiling experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity which are transcriptionally\r\nregulated by auxin signalling. We identified several novel regulators and performed a detailed\r\ncharacterization of the transcription factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin transport processes such as gravitropism and leaf vascular pattern\r\nformation were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct targets of WRKY23, we performed consequential expression\r\nprofiling experiments using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23 line that is defunct in PIN re-arrangement. Among several genes mostly related to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER 1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1; At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits transcriptional behaviour, subcellular localization. Based on global expression data, we\r\ntried to identify ligand responsible for mechanism of signalling and suggest signalling partner\r\nand interactors. Additionally, we described role of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement, that could be a fundament for future studies in this\r\nfield.\r\nOur results provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork and characterised its mediatory role in plant development. We identified direct\r\neffectors of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement and\r\nPIN-dependent auxin transport processes." acknowledgement: I would like to first acknowledge my supervisor Jiří Friml for support, kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg forever. I would like to thank all past and present lab members for the friendship and friendly and scientific environment in the groups. It was so nice to cooperate with you, guys. There was always someone who helped me with experiments, troubleshoot issues coming from our work etc. At this place, I would like to thank especially to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became my tutor and guide through my PhD. From no one else during my entire professional career, I’ve learned that much. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Tomas full_name: Prat, Tomas id: 3DA3BFEE-F248-11E8-B48F-1D18A9856A87 last_name: Prat citation: ama: Prat T. Identification of novel regulators of PIN polarity and development of novel auxin sensor. 2017. apa: Prat, T. (2017). Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria. chicago: Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017. ieee: T. Prat, “Identification of novel regulators of PIN polarity and development of novel auxin sensor,” Institute of Science and Technology Austria, 2017. ista: Prat T. 2017. Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria. mla: Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017. short: T. Prat, Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:50:17Z date_published: 2017-01-12T00:00:00Z date_updated: 2023-09-19T10:39:33Z day: '12' ddc: - '580' degree_awarded: PhD department: - _id: JiFr file: - access_level: closed checksum: d192c7c6c5ea32c8432437286dc4909e content_type: application/pdf creator: dernst date_created: 2019-04-05T08:45:14Z date_updated: 2019-04-05T08:45:14Z file_id: '6209' file_name: IST_Austria_Thesis_Tomáš_Prát.pdf file_size: 10285946 relation: main_file - access_level: open_access checksum: bab18b52cf98145926042d8ed99fdb3b content_type: application/pdf creator: dernst date_created: 2021-02-22T11:52:56Z date_updated: 2021-02-22T11:52:56Z file_id: '9185' file_name: 2017_Thesis_Prat.pdf file_size: 9802991 relation: main_file success: 1 file_date_updated: 2021-02-22T11:52:56Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '131' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6233' related_material: record: - id: '449' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: Identification of novel regulators of PIN polarity and development of novel auxin sensor type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '2016' abstract: - lang: eng text: The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane. article_processing_charge: No author: - first_name: Abraham full_name: Martin Del Campo Sanchez, Abraham last_name: Martin Del Campo Sanchez - first_name: Sarah A full_name: Cepeda Humerez, Sarah A id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87 last_name: Cepeda Humerez - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 citation: ama: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306. doi:10.1111/sjos.12251 apa: Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251 chicago: Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251. ieee: A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” Scandinavian Journal of Statistics, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017. ista: Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306. mla: Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:10.1111/sjos.12251. short: A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306. date_created: 2018-12-11T11:55:13Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-19T15:13:27Z day: '01' department: - _id: GaTk doi: 10.1111/sjos.12251 external_id: arxiv: - '1410.1242' isi: - '000400985000001' intvolume: ' 44' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.1242 month: '06' oa: 1 oa_version: Preprint page: 285 - 306 publication: Scandinavian Journal of Statistics publication_identifier: issn: - '03036898' publication_status: published publisher: Wiley-Blackwell publist_id: '5060' quality_controlled: '1' related_material: record: - id: '6473' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Exact goodness-of-fit testing for the Ising model type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 44 year: '2017' ... --- _id: '1528' abstract: - lang: eng text: 'We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized.' acknowledgement: "Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 citation: ama: Bao Z, Erdös L. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 2017;167(3-4):673-776. doi:10.1007/s00440-015-0692-y apa: Bao, Z., & Erdös, L. (2017). Delocalization for a class of random block band matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-015-0692-y chicago: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” Probability Theory and Related Fields. Springer, 2017. https://doi.org/10.1007/s00440-015-0692-y. ieee: Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” Probability Theory and Related Fields, vol. 167, no. 3–4. Springer, pp. 673–776, 2017. ista: Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776. mla: Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” Probability Theory and Related Fields, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:10.1007/s00440-015-0692-y. short: Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776. date_created: 2018-12-11T11:52:32Z date_published: 2017-04-01T00:00:00Z date_updated: 2023-09-20T09:42:12Z day: '01' ddc: - '530' department: - _id: LaEr doi: 10.1007/s00440-015-0692-y ec_funded: 1 external_id: isi: - '000398842700004' file: - access_level: open_access checksum: 67afa85ff1e220cbc1f9f477a828513c content_type: application/pdf creator: system date_created: 2018-12-12T10:08:05Z date_updated: 2020-07-14T12:45:00Z file_id: '4665' file_name: IST-2016-489-v1+1_s00440-015-0692-y.pdf file_size: 1615755 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 167' isi: 1 issue: 3-4 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 673 - 776 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Probability Theory and Related Fields publication_identifier: issn: - '01788051' publication_status: published publisher: Springer publist_id: '5644' pubrep_id: '489' quality_controlled: '1' scopus_import: '1' status: public title: Delocalization for a class of random block band matrices 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 167 year: '2017' ... --- _id: '1433' abstract: - lang: eng text: Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology. article_processing_charge: No article_type: original author: - first_name: Ulrich full_name: Bauer, Ulrich last_name: Bauer - first_name: Michael full_name: Kerber, Michael last_name: Kerber - first_name: Jan full_name: Reininghaus, Jan last_name: Reininghaus - first_name: Hubert full_name: Wagner, Hubert id: 379CA8B8-F248-11E8-B48F-1D18A9856A87 last_name: Wagner citation: ama: Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 2017;78:76-90. doi:10.1016/j.jsc.2016.03.008 apa: Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. Academic Press. https://doi.org/10.1016/j.jsc.2016.03.008 chicago: Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation. Academic Press, 2017. https://doi.org/10.1016/j.jsc.2016.03.008. ieee: U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” Journal of Symbolic Computation, vol. 78. Academic Press, pp. 76–90, 2017. ista: Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90. mla: Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation, vol. 78, Academic Press, 2017, pp. 76–90, doi:10.1016/j.jsc.2016.03.008. short: U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90. date_created: 2018-12-11T11:51:59Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T09:42:40Z day: '01' department: - _id: HeEd doi: 10.1016/j.jsc.2016.03.008 ec_funded: 1 external_id: isi: - '000384396000005' intvolume: ' 78' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.jsc.2016.03.008 month: '01' oa: 1 oa_version: Published Version page: 76 - 90 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Journal of Symbolic Computation publication_identifier: issn: - ' 07477171' publication_status: published publisher: Academic Press publist_id: '5765' quality_controlled: '1' related_material: record: - id: '10894' relation: earlier_version status: public scopus_import: '1' status: public title: Phat - Persistent homology algorithms toolbox type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 78 year: '2017' ... --- _id: '1407' abstract: - lang: eng text: We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study. article_processing_charge: No author: - first_name: Mária full_name: Svoreňová, Mária last_name: Svoreňová - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ivana full_name: Cěrná, Ivana last_name: Cěrná - first_name: Cǎlin full_name: Belta, Cǎlin last_name: Belta citation: ama: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006' apa: 'Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006' chicago: 'Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006.' ieee: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2. Elsevier, pp. 230–253, 2017.' ista: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.' mla: 'Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006.' short: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.' date_created: 2018-12-11T11:51:50Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T09:43:09Z day: '01' department: - _id: ToHe - _id: KrCh doi: 10.1016/j.nahs.2016.04.006 ec_funded: 1 external_id: arxiv: - '1410.5387' isi: - '000390637000014' intvolume: ' 23' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.5387 month: '02' oa: 1 oa_version: Preprint page: 230 - 253 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: 'Nonlinear Analysis: Hybrid Systems' publication_status: published publisher: Elsevier publist_id: '5800' quality_controlled: '1' related_material: record: - id: '1689' relation: earlier_version status: public scopus_import: '1' status: public title: Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 23 year: '2017' ... --- _id: '1367' abstract: - lang: eng text: One of the major challenges in physically based modelling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes and particles. Applications range from fluids, through deformable bodies, to articulated solids. acknowledgement: This work was partly supported by the starting grants ADAPT and BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012, ERC-2014-StG_638176 and ERC-2011-ADG_20110209). article_processing_charge: No author: - first_name: Pierre full_name: Manteaux, Pierre last_name: Manteaux - 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: Rahul full_name: Narain, Rahul last_name: Narain - first_name: Stéphane full_name: Redon, Stéphane last_name: Redon - first_name: François full_name: Faure, François last_name: Faure - first_name: Marie full_name: Cani, Marie last_name: Cani citation: ama: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically based models in computer graphics. Computer Graphics Forum. 2017;36(6):312-337. doi:10.1111/cgf.12941 apa: Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., & Cani, M. (2017). Adaptive physically based models in computer graphics. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12941 chicago: Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum. Wiley-Blackwell, 2017. https://doi.org/10.1111/cgf.12941. ieee: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive physically based models in computer graphics,” Computer Graphics Forum, vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017. ista: Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically based models in computer graphics. Computer Graphics Forum. 36(6), 312–337. mla: Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37, doi:10.1111/cgf.12941. short: P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337. date_created: 2018-12-11T11:51:37Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-20T11:05:36Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12941 external_id: isi: - '000408634200019' file: - access_level: open_access checksum: 7676e9a9ead6d58c3000988c97deb2ef content_type: application/pdf creator: system date_created: 2018-12-12T10:16:21Z date_updated: 2020-07-14T12:44:47Z file_id: '5208' file_name: IST-2016-634-v1+1_starAdaptivity-cgf.pdf file_size: 1434439 relation: main_file file_date_updated: 2020-07-14T12:44:47Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '6' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 312 - 337 publication: Computer Graphics Forum publication_identifier: issn: - '01677055' publication_status: published publisher: Wiley-Blackwell publist_id: '5873' pubrep_id: '634' quality_controlled: '1' scopus_import: '1' status: public title: Adaptive physically based models in computer graphics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 36 year: '2017' ... --- _id: '1338' abstract: - lang: eng text: We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively. article_processing_charge: No author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Edmund full_name: Clarke, Edmund last_name: Clarke - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Leonid full_name: Ryzhyk, Leonid last_name: Ryzhyk - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta - first_name: Thorsten full_name: Tarrach, Thorsten id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87 last_name: Tarrach orcid: 0000-0003-4409-8487 citation: ama: Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 2017;50(2-3):97-139. doi:10.1007/s10703-016-0256-5 apa: Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., & Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-016-0256-5 chicago: Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Formal Methods in System Design. Springer, 2017. https://doi.org/10.1007/s10703-016-0256-5. ieee: P. Cerny et al., “From non-preemptive to preemptive scheduling using synchronization synthesis,” Formal Methods in System Design, vol. 50, no. 2–3. Springer, pp. 97–139, 2017. ista: Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139. mla: Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Formal Methods in System Design, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:10.1007/s10703-016-0256-5. short: P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139. date_created: 2018-12-11T11:51:27Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T11:13:51Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/s10703-016-0256-5 ec_funded: 1 external_id: isi: - '000399888900001' file: - access_level: open_access checksum: 1163dfd997e8212c789525d4178b1653 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:05Z date_updated: 2020-07-14T12:44:44Z file_id: '4985' file_name: IST-2016-656-v1+1_s10703-016-0256-5.pdf file_size: 1416170 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 50' isi: 1 issue: 2-3 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 97 - 139 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: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Formal Methods in System Design publication_status: published publisher: Springer publist_id: '5929' pubrep_id: '656' quality_controlled: '1' related_material: record: - id: '1729' relation: earlier_version status: public scopus_import: '1' status: public title: From non-preemptive to preemptive scheduling using synchronization synthesis 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 50 year: '2017' ... --- _id: '1351' abstract: - lang: eng text: The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights. article_processing_charge: No author: - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer. https://doi.org/10.1007/s00236-016-0278-x chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x. ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8. Springer, pp. 765–787, 2017. ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787. mla: Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x. short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787. date_created: 2018-12-11T11:51:32Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-20T11:06:03Z day: '01' ddc: - '006' - '576' department: - _id: ToHe - _id: CaGu - _id: NiBa doi: 10.1007/s00236-016-0278-x ec_funded: 1 external_id: isi: - '000414343200003' file: - access_level: open_access checksum: 4e661d9135d7f8c342e8e258dee76f3e content_type: application/pdf creator: dernst date_created: 2019-01-17T15:57:29Z date_updated: 2020-07-14T12:44:46Z file_id: '5841' file_name: 2017_ActaInformatica_Giacobbe.pdf file_size: 755241 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 54' isi: 1 issue: '8' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 765 - 787 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Acta Informatica publication_identifier: issn: - '00015903' publication_status: published publisher: Springer publist_id: '5898' pubrep_id: '649' quality_controlled: '1' related_material: record: - id: '1835' relation: earlier_version status: public scopus_import: '1' status: public title: Model checking the evolution of gene regulatory networks 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 54 year: '2017' ... --- _id: '1336' 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 the runtimes of EAs 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 occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (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. article_processing_charge: No author: - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Jorge full_name: Pérez Heredia, Jorge last_name: Pérez Heredia - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - 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, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1 apa: Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica. Springer. https://doi.org/10.1007/s00453-016-0212-1 chicago: Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica. Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1. ieee: T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2. Springer, pp. 681–713, 2017. ista: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713. mla: Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1. short: T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713. date_created: 2018-12-11T11:51:27Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T11:14:42Z day: '01' ddc: - '576' department: - _id: NiBa - _id: CaGu doi: 10.1007/s00453-016-0212-1 ec_funded: 1 external_id: isi: - '000400379500013' file: - access_level: open_access checksum: 7873f665a0c598ac747c908f34cb14b9 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:19Z date_updated: 2020-07-14T12:44:44Z file_id: '4805' file_name: IST-2016-658-v1+1_s00453-016-0212-1.pdf file_size: 710206 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 78' isi: 1 issue: '2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 681 - 713 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Algorithmica publication_identifier: issn: - '01784617' publication_status: published publisher: Springer publist_id: '5931' pubrep_id: '658' quality_controlled: '1' scopus_import: '1' status: public title: Towards a runtime comparison of natural and artificial evolution 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 78 year: '2017' ... --- _id: '1337' abstract: - lang: eng text: We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes. acknowledgement: 'Open access funding provided by Institute of Science and Technology (IST Austria). ' article_processing_charge: Yes (via OA deal) author: - first_name: Oskari H full_name: Ajanki, Oskari H id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87 last_name: Ajanki - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 2017;169(3-4):667-727. doi:10.1007/s00440-016-0740-2 apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2017). Universality for general Wigner-type matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-016-0740-2 chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” Probability Theory and Related Fields. Springer, 2017. https://doi.org/10.1007/s00440-016-0740-2. ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” Probability Theory and Related Fields, vol. 169, no. 3–4. Springer, pp. 667–727, 2017. ista: Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727. mla: Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” Probability Theory and Related Fields, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:10.1007/s00440-016-0740-2. short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727. date_created: 2018-12-11T11:51:27Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-20T11:14:17Z day: '01' ddc: - '510' - '530' department: - _id: LaEr doi: 10.1007/s00440-016-0740-2 ec_funded: 1 external_id: isi: - '000414358400002' file: - access_level: open_access checksum: 29f5a72c3f91e408aeb9e78344973803 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:25Z date_updated: 2020-07-14T12:44:44Z file_id: '4686' file_name: IST-2017-657-v1+2_s00440-016-0740-2.pdf file_size: 988843 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 169' isi: 1 issue: 3-4 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 667 - 727 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Probability Theory and Related Fields publication_identifier: issn: - '01788051' publication_status: published publisher: Springer publist_id: '5930' pubrep_id: '657' quality_controlled: '1' scopus_import: '1' status: public title: Universality for general Wigner-type matrices 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 169 year: '2017' ... --- _id: '1294' abstract: - lang: eng text: We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints. article_processing_charge: No author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera citation: ama: Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 2017;84:144-170. doi:10.1016/j.jcss.2016.09.009 apa: Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2017). Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.09.009 chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” Journal of Computer and System Sciences. Elsevier, 2017. https://doi.org/10.1016/j.jcss.2016.09.009. ieee: T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” Journal of Computer and System Sciences, vol. 84. Elsevier, pp. 144–170, 2017. ista: Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170. mla: Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” Journal of Computer and System Sciences, vol. 84, Elsevier, 2017, pp. 144–70, doi:10.1016/j.jcss.2016.09.009. short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170. date_created: 2018-12-11T11:51:12Z date_published: 2017-03-01T00:00:00Z date_updated: 2023-09-20T11:15:31Z day: '01' ddc: - '004' - '006' department: - _id: KrCh doi: 10.1016/j.jcss.2016.09.009 ec_funded: 1 external_id: isi: - '000388430000011' file: - access_level: open_access checksum: 91271b23cf884d7c06d33bef0cd623b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:30Z date_updated: 2020-07-14T12:44:42Z file_id: '4885' file_name: IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf file_size: 708657 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 84' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 144 - 170 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Journal of Computer and System Sciences publication_status: published publisher: Elsevier publist_id: '6009' pubrep_id: '717' quality_controlled: '1' related_material: record: - id: '2305' relation: earlier_version status: public scopus_import: '1' status: public title: Trading performance for stability in Markov decision processes 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 84 year: '2017' ... --- _id: '1228' abstract: - lang: eng text: Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD. acknowledgement: This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W. article_processing_charge: No article_type: review author: - first_name: Ulrich full_name: Sauerzopf, Ulrich last_name: Sauerzopf - first_name: Roberto full_name: Sacco, Roberto id: 42C9F57E-F248-11E8-B48F-1D18A9856A87 last_name: Sacco - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Marco full_name: Niello, Marco last_name: Niello - first_name: Ana full_name: Weidenauer, Ana last_name: Weidenauer - first_name: Nicole full_name: Praschak Rieder, Nicole last_name: Praschak Rieder - first_name: Harald full_name: Sitte, Harald last_name: Sitte - first_name: Matthaeus full_name: Willeit, Matthaeus last_name: Willeit citation: ama: Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 2017;45(1):45-57. doi:10.1111/ejn.13418 apa: Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.13418 chicago: Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” European Journal of Neuroscience. Wiley-Blackwell, 2017. https://doi.org/10.1111/ejn.13418. ieee: U. Sauerzopf et al., “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” European Journal of Neuroscience, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017. ista: Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57. mla: Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” European Journal of Neuroscience, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:10.1111/ejn.13418. short: U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57. date_created: 2018-12-11T11:50:50Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:16:01Z day: '01' ddc: - '616' department: - _id: GaNo doi: 10.1111/ejn.13418 external_id: isi: - '000392487100005' pmid: - '27690184' file: - access_level: open_access checksum: c572cf02be8fbb7020cfcfb892182e4c content_type: application/pdf creator: system date_created: 2018-12-12T10:10:48Z date_updated: 2020-07-14T12:44:39Z file_id: '4838' file_name: IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf file_size: 169145 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 45' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 45 - 57 pmid: 1 publication: European Journal of Neuroscience publication_status: published publisher: Wiley-Blackwell publist_id: '6106' pubrep_id: '738' quality_controlled: '1' scopus_import: '1' status: public title: Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 45 year: '2017' ... --- _id: '1213' abstract: - lang: eng text: Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin. acknowledged_ssus: - _id: Bio acknowledgement: Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell). alternative_title: - Methods in Cell Biology article_processing_charge: No author: - first_name: Natalia full_name: Baranova, Natalia id: 38661662-F248-11E8-B48F-1D18A9856A87 last_name: Baranova orcid: 0000-0002-3086-9124 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: 'Baranova NS, Loose M. Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. Cytokinesis. Vol 137. Academic Press; 2017:355-370. doi:10.1016/bs.mcb.2016.03.036' apa: Baranova, N. S., & Loose, M. (2017). Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), Cytokinesis (Vol. 137, pp. 355–370). Academic Press. https://doi.org/10.1016/bs.mcb.2016.03.036 chicago: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In Cytokinesis, edited by Arnaud Echard, 137:355–70. Academic Press, 2017. https://doi.org/10.1016/bs.mcb.2016.03.036. ieee: N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers,” in Cytokinesis, vol. 137, A. Echard, Ed. Academic Press, 2017, pp. 355–370. ista: 'Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol. 137, 355–370.' mla: Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” Cytokinesis, edited by Arnaud Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:10.1016/bs.mcb.2016.03.036. short: N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370. date_created: 2018-12-11T11:50:45Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-20T11:16:30Z day: '01' department: - _id: MaLo doi: 10.1016/bs.mcb.2016.03.036 ec_funded: 1 editor: - first_name: 'Arnaud ' full_name: 'Echard, Arnaud ' last_name: Echard external_id: isi: - '000403542900022' intvolume: ' 137' isi: 1 language: - iso: eng month: '12' oa_version: None page: 355 - 370 project: - _id: 2596EAB6-B435-11E9-9278-68D0E5697425 grant_number: ALTF 2015-1163 name: Synthesis of bacterial cell wall - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Cytokinesis publication_identifier: issn: - 0091679X publication_status: published publisher: Academic Press publist_id: '6134' quality_controlled: '1' scopus_import: '1' status: public title: Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 137 year: '2017' ... --- _id: '1198' abstract: - lang: eng text: We consider a model of fermions interacting via point interactions, defined via a certain weighted Dirichlet form. While for two particles the interaction corresponds to infinite scattering length, the presence of further particles effectively decreases the interaction strength. We show that the model becomes trivial in the thermodynamic limit, in the sense that the free energy density at any given particle density and temperature agrees with the corresponding expression for non-interacting particles. acknowledgement: 'Open access funding provided by Institute of Science and Technology (IST Austria). ' article_processing_charge: Yes (via OA deal) author: - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Moser T, Seiringer R. Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. 2017;107(3):533-552. doi:10.1007/s11005-016-0915-x apa: Moser, T., & Seiringer, R. (2017). Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0915-x chicago: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s11005-016-0915-x. ieee: T. Moser and R. Seiringer, “Triviality of a model of particles with point interactions in the thermodynamic limit,” Letters in Mathematical Physics, vol. 107, no. 3. Springer, pp. 533–552, 2017. ista: Moser T, Seiringer R. 2017. Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. 107(3), 533–552. mla: Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics, vol. 107, no. 3, Springer, 2017, pp. 533–52, doi:10.1007/s11005-016-0915-x. short: T. Moser, R. Seiringer, Letters in Mathematical Physics 107 (2017) 533–552. date_created: 2018-12-11T11:50:40Z date_published: 2017-03-01T00:00:00Z date_updated: 2023-09-20T11:18:13Z day: '01' ddc: - '510' - '539' department: - _id: RoSe doi: 10.1007/s11005-016-0915-x external_id: isi: - '000394280200007' file: - access_level: open_access checksum: c0c835def162c1bc52f978fad26e3c2f content_type: application/pdf creator: system date_created: 2018-12-12T10:17:40Z date_updated: 2020-07-14T12:44:38Z file_id: '5296' file_name: IST-2016-723-v1+1_s11005-016-0915-x.pdf file_size: 587207 relation: main_file file_date_updated: 2020-07-14T12:44:38Z has_accepted_license: '1' intvolume: ' 107' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: ' 533 - 552' project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Letters in Mathematical Physics publication_identifier: issn: - '03779017' publication_status: published publisher: Springer publist_id: '6152' pubrep_id: '723' quality_controlled: '1' related_material: record: - id: '52' relation: dissertation_contains status: public scopus_import: '1' status: public title: Triviality of a model of particles with point interactions in the thermodynamic limit 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 107 year: '2017' ... --- _id: '1207' abstract: - lang: eng text: The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix. article_processing_charge: Yes (via OA deal) author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 2017;349(3):947-990. doi:10.1007/s00220-016-2805-6 apa: Bao, Z., Erdös, L., & Schnelli, K. (2017). Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2805-6 chicago: Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition of Random Matrices on Optimal Scale.” Communications in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s00220-016-2805-6. ieee: Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices on optimal scale,” Communications in Mathematical Physics, vol. 349, no. 3. Springer, pp. 947–990, 2017. ista: Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 349(3), 947–990. mla: Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.” Communications in Mathematical Physics, vol. 349, no. 3, Springer, 2017, pp. 947–90, doi:10.1007/s00220-016-2805-6. short: Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349 (2017) 947–990. date_created: 2018-12-11T11:50:43Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T11:16:57Z day: '01' ddc: - '530' department: - _id: LaEr doi: 10.1007/s00220-016-2805-6 ec_funded: 1 external_id: isi: - '000393696700005' file: - access_level: open_access checksum: ddff79154c3daf27237de5383b1264a9 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:47Z date_updated: 2020-07-14T12:44:39Z file_id: '5102' file_name: IST-2016-722-v1+1_s00220-016-2805-6.pdf file_size: 1033743 relation: main_file file_date_updated: 2020-07-14T12:44:39Z has_accepted_license: '1' intvolume: ' 349' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 947 - 990 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Communications in Mathematical Physics publication_identifier: issn: - '00103616' publication_status: published publisher: Springer publist_id: '6141' pubrep_id: '722' quality_controlled: '1' scopus_import: '1' status: public title: Local law of addition of random matrices on optimal scale 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 349 year: '2017' ... --- _id: '1196' abstract: - lang: eng text: 'We define the . model-measuring problem: given a model . M and specification . ϕ, what is the maximal distance . ρ such that all models . M'' within distance . ρ from . M satisfy (or violate) . ϕ. The model-measuring problem presupposes a distance function on models. We concentrate on . automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification; robustness problems that measure how much a model can be perturbed without violating the specification; and parameter synthesis for hybrid systems. We show that for automatic distance functions, and (a) . ω-regular linear-time, (b) . ω-regular branching-time, and (c) hybrid specifications, the model-measuring problem can be solved.We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for word, tree, and hybrid automata by the . optimal-value question for the weighted versions of these automata. For automata over words and trees, we consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. For hybrid automata, we consider monotonic (parametric) hybrid automata, a hybrid counterpart of (discrete) weighted automata.We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications. Further, we propose the modeling framework for model measuring to ease the specification and reduce the likelihood of errors in modeling.Finally, we present a variant of the model-measuring problem, called the . model-repair problem. The model-repair problem applies to models that do not satisfy the specification; it can be used to derive restrictions, under which the model satisfies the specification, i.e., to repair the model.' acknowledgement: "This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund1 (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.\r\nA Technical Report of this article is available via: https://repository.ist.ac.at/171/" article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop citation: ama: 'Henzinger TA, Otop J. Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. 2017;23:166-190. doi:10.1016/j.nahs.2016.09.001' apa: 'Henzinger, T. A., & Otop, J. (2017). Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.09.001' chicago: 'Henzinger, Thomas A, and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.09.001.' ieee: 'T. A. Henzinger and J. Otop, “Model measuring for discrete and hybrid systems,” Nonlinear Analysis: Hybrid Systems, vol. 23. Elsevier, pp. 166–190, 2017.' ista: 'Henzinger TA, Otop J. 2017. Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. 23, 166–190.' mla: 'Henzinger, Thomas A., and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” Nonlinear Analysis: Hybrid Systems, vol. 23, Elsevier, 2017, pp. 166–90, doi:10.1016/j.nahs.2016.09.001.' short: 'T.A. Henzinger, J. Otop, Nonlinear Analysis: Hybrid Systems 23 (2017) 166–190.' date_created: 2018-12-11T11:50:39Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T11:18:50Z day: '01' department: - _id: ToHe doi: 10.1016/j.nahs.2016.09.001 ec_funded: 1 external_id: isi: - '000390637000011' intvolume: ' 23' isi: 1 language: - iso: eng month: '02' oa_version: None page: 166 - 190 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 publication: 'Nonlinear Analysis: Hybrid Systems' publication_status: published publisher: Elsevier publist_id: '6154' quality_controlled: '1' scopus_import: '1' status: public title: Model measuring for discrete and hybrid systems type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 23 year: '2017' ... --- _id: '1199' abstract: - lang: eng text: Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects. article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. How does epistasis influence the response to selection? Heredity. 2017;118:96-109. doi:10.1038/hdy.2016.109 apa: Barton, N. H. (2017). How does epistasis influence the response to selection? Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109 chicago: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109. ieee: N. H. Barton, “How does epistasis influence the response to selection?,” Heredity, vol. 118. Nature Publishing Group, pp. 96–109, 2017. ista: Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109. mla: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109. short: N.H. Barton, Heredity 118 (2017) 96–109. date_created: 2018-12-11T11:50:40Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:17:47Z day: '01' department: - _id: NiBa doi: 10.1038/hdy.2016.109 ec_funded: 1 external_id: isi: - '000392229100011' intvolume: ' 118' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/ month: '01' oa: 1 oa_version: Submitted Version page: 96 - 109 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Heredity publication_status: published publisher: Nature Publishing Group publist_id: '6151' quality_controlled: '1' related_material: record: - id: '9710' relation: research_data status: public scopus_import: '1' status: public title: How does epistasis influence the response to selection? type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2017' ... --- _id: '1208' abstract: - lang: eng text: We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd. article_processing_charge: No author: - first_name: Piotr full_name: Zwiernik, Piotr last_name: Zwiernik - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Donald full_name: Richards, Donald last_name: Richards citation: ama: 'Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society Series B: Statistical Methodology. 2017;79(4):1269-1292. doi:10.1111/rssb.12217' apa: 'Zwiernik, P., Uhler, C., & Richards, D. (2017). Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. Wiley-Blackwell. https://doi.org/10.1111/rssb.12217' chicago: 'Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical Methodology. Wiley-Blackwell, 2017. https://doi.org/10.1111/rssb.12217.' ieee: 'P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for linear Gaussian covariance models,” Journal of the Royal Statistical Society. Series B: Statistical Methodology, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292, 2017.' ista: 'Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. 79(4), 1269–1292.' mla: 'Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical Methodology, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:10.1111/rssb.12217.' short: 'P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society. Series B: Statistical Methodology 79 (2017) 1269–1292.' date_created: 2018-12-11T11:50:43Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-20T11:17:21Z day: '01' department: - _id: CaUh doi: 10.1111/rssb.12217 external_id: isi: - '000411712300012' intvolume: ' 79' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.5604 month: '09' oa: 1 oa_version: Submitted Version page: 1269 - 1292 project: - _id: 2530CA10-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 903-N35 name: 'Gaussian Graphical Models: Theory and Applications' publication: 'Journal of the Royal Statistical Society. Series B: Statistical Methodology' publication_identifier: issn: - '13697412' publication_status: published publisher: Wiley-Blackwell publist_id: '6142' quality_controlled: '1' scopus_import: '1' status: public title: Maximum likelihood estimation for linear Gaussian covariance models type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 79 year: '2017' ... --- _id: '1174' abstract: - lang: eng text: Security of cryptographic applications is typically defined by security games. The adversary, within certain resources, cannot win with probability much better than 0 (for unpredictability applications, like one-way functions) or much better than 1/2 (indistinguishability applications for instance encryption schemes). In so called squared-friendly applications the winning probability of the adversary, for different values of the application secret randomness, is not only close to 0 or 1/2 on average, but also concentrated in the sense that its second central moment is small. The class of squared-friendly applications, which contains all unpredictability applications and many indistinguishability applications, is particularly important for key derivation. Barak et al. observed that for square-friendly applications one can beat the "RT-bound", extracting secure keys with significantly smaller entropy loss. In turn Dodis and Yu showed that in squared-friendly applications one can directly use a "weak" key, which has only high entropy, as a secure key. In this paper we give sharp lower bounds on square security assuming security for "weak" keys. We show that any application which is either (a) secure with weak keys or (b) allows for entropy savings for keys derived by universal hashing, must be square-friendly. Quantitatively, our lower bounds match the positive results of Dodis and Yu and Barak et al. (TCC\'13, CRYPTO\'11) Hence, they can be understood as a general characterization of squared-friendly applications. While the positive results on squared-friendly applications where derived by one clever application of the Cauchy-Schwarz Inequality, for tight lower bounds we need more machinery. In our approach we use convex optimization techniques and some theory of circular matrices. alternative_title: - LIPIcs article_number: '57' article_processing_charge: No author: - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Skórski M. Lower bounds on key derivation for square-friendly applications. In: Vol 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.STACS.2017.57' apa: 'Skórski, M. (2017). Lower bounds on key derivation for square-friendly applications (Vol. 66). Presented at the STACS: Symposium on Theoretical Aspects of Computer Science, Hannover, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2017.57' chicago: Skórski, Maciej. “Lower Bounds on Key Derivation for Square-Friendly Applications,” Vol. 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.STACS.2017.57. ieee: 'M. Skórski, “Lower bounds on key derivation for square-friendly applications,” presented at the STACS: Symposium on Theoretical Aspects of Computer Science, Hannover, Germany, 2017, vol. 66.' ista: 'Skórski M. 2017. Lower bounds on key derivation for square-friendly applications. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 66, 57.' mla: Skórski, Maciej. Lower Bounds on Key Derivation for Square-Friendly Applications. Vol. 66, 57, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.STACS.2017.57. short: M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-03-11 location: Hannover, Germany name: 'STACS: Symposium on Theoretical Aspects of Computer Science' start_date: 2017-03-08 date_created: 2018-12-11T11:50:32Z date_published: 2017-03-01T00:00:00Z date_updated: 2023-09-20T11:23:15Z day: '01' department: - _id: KrPi doi: 10.4230/LIPIcs.STACS.2017.57 ec_funded: 1 external_id: isi: - '000521077300057' intvolume: ' 66' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://drops.dagstuhl.de/opus/volltexte/2017/6976 month: '03' oa: 1 oa_version: Submitted Version project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6180' quality_controlled: '1' scopus_import: '1' status: public title: Lower bounds on key derivation for square-friendly applications type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 66 year: '2017' ... --- _id: '1176' abstract: - lang: eng text: The algorithm Argon2i-B of Biryukov, Dinu and Khovratovich is currently being considered by the IRTF (Internet Research Task Force) as a new de-facto standard for password hashing. An older version (Argon2i-A) of the same algorithm was chosen as the winner of the recent Password Hashing Competition. An important competitor to Argon2i-B is the recently introduced Balloon Hashing (BH) algorithm of Corrigan-Gibs, Boneh and Schechter. A key security desiderata for any such algorithm is that evaluating it (even using a custom device) requires a large amount of memory amortized across multiple instances. Alwen and Blocki (CRYPTO 2016) introduced a class of theoretical attacks against Argon2i-A and BH. While these attacks yield large asymptotic reductions in the amount of memory, it was not, a priori, clear if (1) they can be extended to the newer Argon2i-B, (2) the attacks are effective on any algorithm for practical parameter ranges (e.g., 1GB of memory) and (3) if they can be effectively instantiated against any algorithm under realistic hardware constrains. In this work we answer all three of these questions in the affirmative for all three algorithms. This is also the first work to analyze the security of Argon2i-B. In more detail, we extend the theoretical attacks of Alwen and Blocki (CRYPTO 2016) to the recent Argon2i-B proposal demonstrating severe asymptotic deficiencies in its security. Next we introduce several novel heuristics for improving the attack's concrete memory efficiency even when on-chip memory bandwidth is bounded. We then simulate our attacks on randomly sampled Argon2i-A, Argon2i-B and BH instances and measure the resulting memory consumption for various practical parameter ranges and for a variety of upperbounds on the amount of parallelism available to the attacker. Finally we describe, implement, and test a new heuristic for applying the Alwen-Blocki attack to functions employing a technique developed by Corrigan-Gibs et al. for improving concrete security of memory-hard functions. We analyze the collected data and show the effects various parameters have on the memory consumption of the attack. In particular, we can draw several interesting conclusions about the level of security provided by these functions. · For the Alwen-Blocki attack to fail against practical memory parameters, Argon2i-B must be instantiated with more than 10 passes on memory - beyond the "paranoid" parameter setting in the current IRTF proposal. · The technique of Corrigan-Gibs for improving security can also be overcome by the Alwen-Blocki attack under realistic hardware constraints. · On a positive note, both the asymptotic and concrete security of Argon2i-B seem to improve on that of Argon2i-A. article_number: '7961977' 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: Jeremiah full_name: Blocki, Jeremiah last_name: Blocki citation: ama: 'Alwen JF, Blocki J. Towards practical attacks on Argon2i and balloon hashing. In: IEEE; 2017. doi:10.1109/EuroSP.2017.47' apa: 'Alwen, J. F., & Blocki, J. (2017). Towards practical attacks on Argon2i and balloon hashing. Presented at the EuroS&P: European Symposium on Security and Privacy, Paris, France: IEEE. https://doi.org/10.1109/EuroSP.2017.47' chicago: Alwen, Joel F, and Jeremiah Blocki. “Towards Practical Attacks on Argon2i and Balloon Hashing.” IEEE, 2017. https://doi.org/10.1109/EuroSP.2017.47. ieee: 'J. F. Alwen and J. Blocki, “Towards practical attacks on Argon2i and balloon hashing,” presented at the EuroS&P: European Symposium on Security and Privacy, Paris, France, 2017.' ista: 'Alwen JF, Blocki J. 2017. Towards practical attacks on Argon2i and balloon hashing. EuroS&P: European Symposium on Security and Privacy, 7961977.' mla: Alwen, Joel F., and Jeremiah Blocki. Towards Practical Attacks on Argon2i and Balloon Hashing. 7961977, IEEE, 2017, doi:10.1109/EuroSP.2017.47. short: J.F. Alwen, J. Blocki, in:, IEEE, 2017. conference: end_date: 2017-04-28 location: Paris, France name: 'EuroS&P: European Symposium on Security and Privacy' start_date: 2017-04-26 date_created: 2018-12-11T11:50:33Z date_published: 2017-07-03T00:00:00Z date_updated: 2023-09-20T11:22:25Z day: '03' department: - _id: KrPi doi: 10.1109/EuroSP.2017.47 external_id: isi: - '000424197300011' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/759 month: '07' oa: 1 oa_version: Submitted Version publication_identifier: isbn: - 978-150905761-0 publication_status: published publisher: IEEE publist_id: '6178' quality_controlled: '1' scopus_import: '1' status: public title: Towards practical attacks on Argon2i and balloon hashing type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '1187' abstract: - lang: eng text: We construct efficient authentication protocols and message authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work—starting with the (Formula presented.) protocol of Hopper and Blum in 2001—until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle attacks. A MAC implies such a (two-round) protocol. article_processing_charge: No article_type: original author: - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - 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: Daniele full_name: Venturi, Daniele last_name: Venturi - first_name: David full_name: Cash, David last_name: Cash - first_name: Abhishek full_name: Jain, Abhishek last_name: Jain citation: ama: Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. Efficient authentication from hard learning problems. Journal of Cryptology. 2017;30(4):1238-1275. doi:10.1007/s00145-016-9247-3 apa: Kiltz, E., Pietrzak, K. Z., Venturi, D., Cash, D., & Jain, A. (2017). Efficient authentication from hard learning problems. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-016-9247-3 chicago: Kiltz, Eike, Krzysztof Z Pietrzak, Daniele Venturi, David Cash, and Abhishek Jain. “Efficient Authentication from Hard Learning Problems.” Journal of Cryptology. Springer, 2017. https://doi.org/10.1007/s00145-016-9247-3. ieee: E. Kiltz, K. Z. Pietrzak, D. Venturi, D. Cash, and A. Jain, “Efficient authentication from hard learning problems,” Journal of Cryptology, vol. 30, no. 4. Springer, pp. 1238–1275, 2017. ista: Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. 2017. Efficient authentication from hard learning problems. Journal of Cryptology. 30(4), 1238–1275. mla: Kiltz, Eike, et al. “Efficient Authentication from Hard Learning Problems.” Journal of Cryptology, vol. 30, no. 4, Springer, 2017, pp. 1238–75, doi:10.1007/s00145-016-9247-3. short: E. Kiltz, K.Z. Pietrzak, D. Venturi, D. Cash, A. Jain, Journal of Cryptology 30 (2017) 1238–1275. date_created: 2018-12-11T11:50:37Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-20T11:20:58Z day: '01' ddc: - '000' department: - _id: KrPi doi: 10.1007/s00145-016-9247-3 ec_funded: 1 external_id: isi: - '000410788600007' file: - access_level: open_access checksum: c647520d115b772a1682fc06fa273eb1 content_type: application/pdf creator: dernst date_created: 2020-05-14T16:30:17Z date_updated: 2020-07-14T12:44:37Z file_id: '7843' file_name: 2017_JournalCrypto_Kiltz.pdf file_size: 516959 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 1238 - 1275 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Journal of Cryptology publication_status: published publisher: Springer publist_id: '6166' quality_controlled: '1' related_material: record: - id: '3238' relation: earlier_version status: public scopus_import: '1' status: public title: Efficient authentication from hard learning problems type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2017' ... --- _id: '1192' abstract: - lang: eng text: The main result of this paper is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even Δ-matroid constraints allows us to extend the tractability result to a larger class of Δ-matroids that includes many classes that were known to be tractable before, namely co-independent, compact, local and binary. article_processing_charge: No author: - first_name: Alexandr full_name: Kazda, Alexandr id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87 last_name: Kazda - 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 citation: ama: 'Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar Boolean CSPs. In: SIAM; 2017:307-326. doi:10.1137/1.9781611974782.20' apa: 'Kazda, A., Kolmogorov, V., & Rolinek, M. (2017). Even delta-matroids and the complexity of planar Boolean CSPs (pp. 307–326). Presented at the SODA: Symposium on Discrete Algorithms, Barcelona, Spain: SIAM. https://doi.org/10.1137/1.9781611974782.20' chicago: Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs,” 307–26. SIAM, 2017. https://doi.org/10.1137/1.9781611974782.20. ieee: 'A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar Boolean CSPs,” presented at the SODA: Symposium on Discrete Algorithms, Barcelona, Spain, 2017, pp. 307–326.' ista: 'Kazda A, Kolmogorov V, Rolinek M. 2017. Even delta-matroids and the complexity of planar Boolean CSPs. SODA: Symposium on Discrete Algorithms, 307–326.' mla: Kazda, Alexandr, et al. Even Delta-Matroids and the Complexity of Planar Boolean CSPs. SIAM, 2017, pp. 307–26, doi:10.1137/1.9781611974782.20. short: A. Kazda, V. Kolmogorov, M. Rolinek, in:, SIAM, 2017, pp. 307–326. conference: end_date: 2017-01019 location: Barcelona, Spain name: 'SODA: Symposium on Discrete Algorithms' start_date: 2017-01-16 date_created: 2018-12-11T11:50:38Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:20:26Z day: '01' department: - _id: VlKo doi: 10.1137/1.9781611974782.20 ec_funded: 1 external_id: isi: - '000426965800020' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1602.03124 month: '01' oa: 1 oa_version: Submitted Version page: 307 - 326 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: isbn: - 978-161197478-2 publication_status: published publisher: SIAM publist_id: '6159' quality_controlled: '1' related_material: record: - id: '6032' relation: later_version status: public status: public title: Even delta-matroids and the complexity of planar Boolean CSPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '1178' abstract: - lang: eng text: 'For any pair (X, Z) of correlated random variables we can think of Z as a randomized function of X. If the domain of Z is small, one can make this function computationally efficient by allowing it to be only approximately correct. In folklore this problem is known as simulating auxiliary inputs. This idea of simulating auxiliary information turns out to be a very usefull tool, finding applications in complexity theory, cryptography, pseudorandomness and zero-knowledge. In this paper we revisit this problem, achieving the following results: (a) We present a novel boosting algorithm for constructing the simulator. This boosting proof is of independent interest, as it shows how to handle “negative mass” issues when constructing probability measures by shifting distinguishers in descent algorithms. Our technique essentially fixes the flaw in the TCC’14 paper “How to Fake Auxiliary Inputs”. (b) The complexity of our simulator is better than in previous works, including results derived from the uniform min-max theorem due to Vadhan and Zheng. To achieve (s,ϵ) -indistinguishability we need the complexity O(s⋅25ℓϵ−2) in time/circuit size, which improve previous bounds by a factor of ϵ−2. In particular, with we get meaningful provable security for the EUROCRYPT’09 leakage-resilient stream cipher instantiated with a standard 256-bit block cipher, like ' acknowledgement: This work was supported by the National Science Center, Poland (2015/17/N/ST6/03564). alternative_title: - LNCS article_processing_charge: No author: - first_name: Maciej full_name: Skórski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skórski citation: ama: 'Skórski M. Simulating auxiliary inputs, revisited. In: Vol 9985. Springer; 2017:159-179. doi:10.1007/978-3-662-53641-4_7' apa: 'Skórski, M. (2017). Simulating auxiliary inputs, revisited (Vol. 9985, pp. 159–179). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-662-53641-4_7' chicago: Skórski, Maciej. “Simulating Auxiliary Inputs, Revisited,” 9985:159–79. Springer, 2017. https://doi.org/10.1007/978-3-662-53641-4_7. ieee: 'M. Skórski, “Simulating auxiliary inputs, revisited,” presented at the TCC: Theory of Cryptography Conference, 2017, vol. 9985, pp. 159–179.' ista: 'Skórski M. 2017. Simulating auxiliary inputs, revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 9985, 159–179.' mla: Skórski, Maciej. Simulating Auxiliary Inputs, Revisited. Vol. 9985, Springer, 2017, pp. 159–79, doi:10.1007/978-3-662-53641-4_7. short: M. Skórski, in:, Springer, 2017, pp. 159–179. conference: name: 'TCC: Theory of Cryptography Conference' date_created: 2018-12-11T11:50:34Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:21:57Z day: '01' doi: 10.1007/978-3-662-53641-4_7 extern: '1' external_id: isi: - '000390176000007' intvolume: ' 9985' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: 'https://eprint.iacr.org/2016/808.pdf ' month: '01' oa: 1 oa_version: Submitted Version page: 159 - 179 publication_status: published publisher: Springer publist_id: '6176' quality_controlled: '1' status: public title: Simulating auxiliary inputs, revisited type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 9985 year: '2017' ... --- _id: '1180' abstract: - lang: eng text: In this article we define an algebraic vertex of a generalized polyhedron and show that the set of algebraic vertices is the smallest set of points needed to define the polyhedron. We prove that the indicator function of a generalized polytope P is a linear combination of indicator functions of simplices whose vertices are algebraic vertices of P. We also show that the indicator function of any generalized polyhedron is a linear combination, with integer coefficients, of indicator functions of cones with apices at algebraic vertices and line-cones. The concept of an algebraic vertex is closely related to the Fourier–Laplace transform. We show that a point v is an algebraic vertex of a generalized polyhedron P if and only if the tangent cone of P, at v, has non-zero Fourier–Laplace transform. article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Imre full_name: Bárány, Imre last_name: Bárány - first_name: Sinai full_name: Robins, Sinai last_name: Robins citation: ama: Akopyan A, Bárány I, Robins S. Algebraic vertices of non-convex polyhedra. Advances in Mathematics. 2017;308:627-644. doi:10.1016/j.aim.2016.12.026 apa: Akopyan, A., Bárány, I., & Robins, S. (2017). Algebraic vertices of non-convex polyhedra. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2016.12.026 chicago: Akopyan, Arseniy, Imre Bárány, and Sinai Robins. “Algebraic Vertices of Non-Convex Polyhedra.” Advances in Mathematics. Academic Press, 2017. https://doi.org/10.1016/j.aim.2016.12.026. ieee: A. Akopyan, I. Bárány, and S. Robins, “Algebraic vertices of non-convex polyhedra,” Advances in Mathematics, vol. 308. Academic Press, pp. 627–644, 2017. ista: Akopyan A, Bárány I, Robins S. 2017. Algebraic vertices of non-convex polyhedra. Advances in Mathematics. 308, 627–644. mla: Akopyan, Arseniy, et al. “Algebraic Vertices of Non-Convex Polyhedra.” Advances in Mathematics, vol. 308, Academic Press, 2017, pp. 627–44, doi:10.1016/j.aim.2016.12.026. short: A. Akopyan, I. Bárány, S. Robins, Advances in Mathematics 308 (2017) 627–644. date_created: 2018-12-11T11:50:34Z date_published: 2017-02-21T00:00:00Z date_updated: 2023-09-20T11:21:27Z day: '21' department: - _id: HeEd doi: 10.1016/j.aim.2016.12.026 ec_funded: 1 external_id: isi: - '000409292900015' intvolume: ' 308' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1508.07594 month: '02' oa: 1 oa_version: Submitted Version page: 627 - 644 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Advances in Mathematics publication_identifier: issn: - '00018708' publication_status: published publisher: Academic Press publist_id: '6173' quality_controlled: '1' scopus_import: '1' status: public title: Algebraic vertices of non-convex polyhedra type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 308 year: '2017' ... --- _id: '1159' abstract: - lang: eng text: Auxin steers numerous physiological processes in plants, making the tight control of its endogenous levels and spatiotemporal distribution a necessity. This regulation is achieved by different mechanisms, including auxin biosynthesis, metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic acid (c-CA) as a novel and unique addition to a small group of endogenous molecules affecting in planta auxin concentrations. c-CA is the photo-isomerization product of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes characteristic for high auxin levels, including inhibition of primary root growth, induction of root hairs, and promotion of adventitious and lateral rooting. By molecular docking and receptor binding assays, we showed that c-CA itself is neither an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux. Auxin signaling reporters detected changes in spatiotemporal distribution of the auxin response along the root of c-CA-treated plants, and long-distance auxin transport assays showed no inhibition of rootward auxin transport. Overall, these results suggest that the phenotypes of c-CA-treated plants are the consequence of a local change in auxin accumulation, induced by the inhibition of auxin efflux. This work reveals a novel mechanism how plants may regulate auxin levels and adds a novel, naturally occurring molecule to the chemical toolbox for the studies of auxin homeostasis. article_processing_charge: No article_type: original author: - first_name: Ward full_name: Steenackers, Ward last_name: Steenackers - first_name: Petr full_name: Klíma, Petr last_name: Klíma - first_name: Mussa full_name: Quareshy, Mussa last_name: Quareshy - first_name: Igor full_name: Cesarino, Igor last_name: Cesarino - first_name: Robert full_name: Kumpf, Robert last_name: Kumpf - first_name: Sander full_name: Corneillie, Sander last_name: Corneillie - first_name: Pedro full_name: Araújo, Pedro last_name: Araújo - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Geert full_name: Goeminne, Geert last_name: Goeminne - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Joshua full_name: Blakeslee, Joshua last_name: Blakeslee - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Richard full_name: Napier, Richard last_name: Napier - first_name: Wout full_name: Boerjan, Wout last_name: Boerjan - first_name: Bartel full_name: Vanholme, Bartel last_name: Vanholme citation: ama: Steenackers W, Klíma P, Quareshy M, et al. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 2017;173(1):552-565. doi:10.1104/pp.16.00943 apa: Steenackers, W., Klíma, P., Quareshy, M., Cesarino, I., Kumpf, R., Corneillie, S., … Vanholme, B. (2017). Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00943 chicago: Steenackers, Ward, Petr Klíma, Mussa Quareshy, Igor Cesarino, Robert Kumpf, Sander Corneillie, Pedro Araújo, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.00943. ieee: W. Steenackers et al., “Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation,” Plant Physiology, vol. 173, no. 1. American Society of Plant Biologists, pp. 552–565, 2017. ista: Steenackers W, Klíma P, Quareshy M, Cesarino I, Kumpf R, Corneillie S, Araújo P, Viaene T, Goeminne G, Nowack M, Ljung K, Friml J, Blakeslee J, Novák O, Zažímalová E, Napier R, Boerjan W, Vanholme B. 2017. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 173(1), 552–565. mla: Steenackers, Ward, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology, vol. 173, no. 1, American Society of Plant Biologists, 2017, pp. 552–65, doi:10.1104/pp.16.00943. short: W. Steenackers, P. Klíma, M. Quareshy, I. Cesarino, R. Kumpf, S. Corneillie, P. Araújo, T. Viaene, G. Goeminne, M. Nowack, K. Ljung, J. Friml, J. Blakeslee, O. Novák, E. Zažímalová, R. Napier, W. Boerjan, B. Vanholme, Plant Physiology 173 (2017) 552–565. date_created: 2018-12-11T11:50:28Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:29:17Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1104/pp.16.00943 ec_funded: 1 external_id: isi: - '000394135800041' pmid: - '27837086' file: - access_level: open_access checksum: fd4d1cfe7ed70e54bb12ae3881f3fb91 content_type: application/pdf creator: dernst date_created: 2019-11-18T16:12:25Z date_updated: 2020-07-14T12:44:36Z file_id: '7040' file_name: 2016_PlantPhysi_Steenackers.pdf file_size: 4109142 relation: main_file file_date_updated: 2020-07-14T12:44:36Z has_accepted_license: '1' intvolume: ' 173' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 552 - 565 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plant Physiology publication_identifier: issn: - 0032-0889 publication_status: published publisher: American Society of Plant Biologists publist_id: '6199' quality_controlled: '1' scopus_import: '1' status: public title: Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 173 year: '2017' ... --- _id: '1169' abstract: - lang: eng text: Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies. article_processing_charge: No author: - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak orcid: 0000-0002-2519-824X - first_name: Richard full_name: Kollár, Richard last_name: Kollár citation: ama: Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946 apa: Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946 chicago: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193946. ieee: S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp. 367–374, 2017. ista: Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374. mla: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America, 2017, pp. 367–74, doi:10.1534/genetics.116.193946. short: S. Novak, R. Kollár, Genetics 205 (2017) 367–374. date_created: 2018-12-11T11:50:31Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:24:21Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1534/genetics.116.193946 ec_funded: 1 external_id: isi: - '000393677300025' file: - access_level: open_access checksum: 7c8ab79cda1f92760bbbbe0f53175bfc content_type: application/pdf creator: system date_created: 2018-12-12T10:10:43Z date_updated: 2020-07-14T12:44:37Z file_id: '4833' file_name: IST-2016-727-v1+1_SFC_Genetics_final.pdf file_size: 361500 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 205' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 367 - 374 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: Genetics publication_identifier: issn: - '00166731' publication_status: published publisher: Genetics Society of America publist_id: '6188' pubrep_id: '727' quality_controlled: '1' scopus_import: '1' status: public title: Spatial gene frequency waves under genotype dependent dispersal type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 205 year: '2017' ... --- _id: '1160' abstract: - lang: eng text: 'We investigate fundamental nonlinear dynamics of ferrofluidic Taylor-Couette flow - flow confined be-tween two concentric independently rotating cylinders - consider small aspect ratio by solving the ferro-hydrodynamical equations, carrying out systematic bifurcation analysis. Without magnetic field, we find steady flow patterns, previously observed with a simple fluid, such as those containing normal one- or two vortex cells, as well as anomalous one-cell and twin-cell flow states. However, when a symmetry-breaking transverse magnetic field is present, all flow states exhibit stimulated, finite two-fold mode. Various bifurcations between steady and unsteady states can occur, corresponding to the transitions between the two-cell and one-cell states. While unsteady, axially oscillating flow states can arise, we also detect the emergence of new unsteady flow states. In particular, we uncover two new states: one contains only the azimuthally oscillating solution in the configuration of the twin-cell flow state, and an-other a rotating flow state. Topologically, these flow states are a limit cycle and a quasiperiodic solution on a two-torus, respectively. Emergence of new flow states in addition to observed ones with classical fluid, indicates that richer but potentially more controllable dynamics in ferrofluidic flows, as such flow states depend on the external magnetic field.' article_number: '40012' article_processing_charge: No 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. Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. 2017;7. doi:10.1038/srep40012 apa: Altmeyer, S., Do, Y., & Lai, Y. (2017). Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep40012 chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Dynamics of Ferrofluidic Flow in the Taylor-Couette System with a Small Aspect Ratio.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep40012. ieee: S. Altmeyer, Y. Do, and Y. Lai, “Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio,” Scientific Reports, vol. 7. Nature Publishing Group, 2017. ista: Altmeyer S, Do Y, Lai Y. 2017. Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. 7, 40012. mla: Altmeyer, Sebastian, et al. “Dynamics of Ferrofluidic Flow in the Taylor-Couette System with a Small Aspect Ratio.” Scientific Reports, vol. 7, 40012, Nature Publishing Group, 2017, doi:10.1038/srep40012. short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 7 (2017). date_created: 2018-12-11T11:50:28Z date_published: 2017-01-06T00:00:00Z date_updated: 2023-09-20T11:28:49Z day: '06' ddc: - '532' department: - _id: BjHo doi: 10.1038/srep40012 external_id: isi: - '000391269700001' file: - access_level: open_access checksum: 694aa70399444570825099c1a7ec91f2 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:16Z date_updated: 2020-07-14T12:44:36Z file_id: '4802' file_name: IST-2017-743-v1+1_srep40012.pdf file_size: 4546835 relation: main_file file_date_updated: 2020-07-14T12:44:36Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Scientific Reports publication_identifier: issn: - '20452322' publication_status: published publisher: Nature Publishing Group publist_id: '6198' pubrep_id: '743' quality_controlled: '1' scopus_import: '1' status: public title: Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2017' ... --- _id: '1162' abstract: - lang: eng text: Selected universal experimental properties of high-temperature superconducting (HTS) cuprates have been singled out in the last decade. One of the pivotal challenges in this field is the designation of a consistent interpretation framework within which we can describe quantitatively the universal features of those systems. Here we analyze in a detailed manner the principal experimental data and compare them quantitatively with the approach based on a single-band model of strongly correlated electrons supplemented with strong antiferromagnetic (super)exchange interaction (the so-called t−J−U model). The model rationale is provided by estimating its microscopic parameters on the basis of the three-band approach for the Cu-O plane. We use our original full Gutzwiller wave-function solution by going beyond the renormalized mean-field theory (RMFT) in a systematic manner. Our approach reproduces very well the observed hole doping (δ) dependence of the kinetic-energy gain in the superconducting phase, one of the principal non-Bardeen-Cooper-Schrieffer features of the cuprates. The calculated Fermi velocity in the nodal direction is practically δ-independent and its universal value agrees very well with that determined experimentally. Also, a weak doping dependence of the Fermi wave vector leads to an almost constant value of the effective mass in a pure superconducting phase which is both observed in experiment and reproduced within our approach. An assessment of the currently used models (t−J, Hubbard) is carried out and the results of the canonical RMFT as a zeroth-order solution are provided for comparison to illustrate the necessity of the introduced higher-order contributions. article_number: '024506' article_processing_charge: No author: - first_name: Jozef full_name: Spałek, Jozef last_name: Spałek - first_name: Michał full_name: Zegrodnik, Michał last_name: Zegrodnik - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 citation: ama: Spałek J, Zegrodnik M, Kaczmarczyk J. Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. 2017;95(2). doi:10.1103/PhysRevB.95.024506 apa: Spałek, J., Zegrodnik, M., & Kaczmarczyk, J. (2017). Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.95.024506 chicago: Spałek, Jozef, Michał Zegrodnik, and Jan Kaczmarczyk. “Universal Properties of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.024506. ieee: J. Spałek, M. Zegrodnik, and J. Kaczmarczyk, “Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment,” Physical Review B - Condensed Matter and Materials Physics, vol. 95, no. 2. American Physical Society, 2017. ista: Spałek J, Zegrodnik M, Kaczmarczyk J. 2017. Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. 95(2), 024506. mla: Spałek, Jozef, et al. “Universal Properties of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.” Physical Review B - Condensed Matter and Materials Physics, vol. 95, no. 2, 024506, American Physical Society, 2017, doi:10.1103/PhysRevB.95.024506. short: J. Spałek, M. Zegrodnik, J. Kaczmarczyk, Physical Review B - Condensed Matter and Materials Physics 95 (2017). date_created: 2018-12-11T11:50:29Z date_published: 2017-01-13T00:00:00Z date_updated: 2023-09-20T11:25:56Z day: '13' department: - _id: MiLe doi: 10.1103/PhysRevB.95.024506 ec_funded: 1 external_id: isi: - '000391852800006' intvolume: ' 95' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.03247 month: '01' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review B - Condensed Matter and Materials Physics publication_identifier: issn: - '24699950' publication_status: published publisher: American Physical Society publist_id: '6195' quality_controlled: '1' scopus_import: '1' status: public title: Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 95 year: '2017' ... --- _id: '1152' abstract: - lang: eng text: We propose a new memetic strategy that can solve the multi-physics, complex inverse problems, formulated as the multi-objective optimization ones, in which objectives are misfits between the measured and simulated states of various governing processes. The multi-deme structure of the strategy allows for both, intensive, relatively cheap exploration with a moderate accuracy and more accurate search many regions of Pareto set in parallel. The special type of selection operator prefers the coherent alternative solutions, eliminating artifacts appearing in the particular processes. The additional accuracy increment is obtained by the parallel convex searches applied to the local scalarizations of the misfit vector. The strategy is dedicated for solving ill-conditioned problems, for which inverting the single physical process can lead to the ambiguous results. The skill of the selection in artifact elimination is shown on the benchmark problem, while the whole strategy was applied for identification of oil deposits, where the misfits are related to various frequencies of the magnetic and electric waves of the magnetotelluric measurements. 2016 Elsevier B.V. article_processing_charge: No author: - first_name: Ewa P full_name: Gajda-Zagorska, Ewa P id: 47794CF0-F248-11E8-B48F-1D18A9856A87 last_name: Gajda-Zagorska - first_name: Robert full_name: Schaefer, Robert last_name: Schaefer - first_name: Maciej full_name: Smołka, Maciej last_name: Smołka - first_name: David full_name: Pardo, David last_name: Pardo - first_name: Julen full_name: Alvarez Aramberri, Julen last_name: Alvarez Aramberri citation: ama: Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. 2017;18:85-94. doi:10.1016/j.jocs.2016.06.007 apa: Gajda-Zagorska, E. P., Schaefer, R., Smołka, M., Pardo, D., & Alvarez Aramberri, J. (2017). A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.06.007 chicago: Gajda-Zagorska, Ewa P, Robert Schaefer, Maciej Smołka, David Pardo, and Julen Alvarez Aramberri. “A Multi Objective Memetic Inverse Solver Reinforced by Local Optimization Methods.” Journal of Computational Science. Elsevier, 2017. https://doi.org/10.1016/j.jocs.2016.06.007. ieee: E. P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, and J. Alvarez Aramberri, “A multi objective memetic inverse solver reinforced by local optimization methods,” Journal of Computational Science, vol. 18. Elsevier, pp. 85–94, 2017. ista: Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. 2017. A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. 18, 85–94. mla: Gajda-Zagorska, Ewa P., et al. “A Multi Objective Memetic Inverse Solver Reinforced by Local Optimization Methods.” Journal of Computational Science, vol. 18, Elsevier, 2017, pp. 85–94, doi:10.1016/j.jocs.2016.06.007. short: E.P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, J. Alvarez Aramberri, Journal of Computational Science 18 (2017) 85–94. date_created: 2018-12-11T11:50:26Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-20T11:29:44Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1016/j.jocs.2016.06.007 external_id: isi: - '000393528700009' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2019-01-18T08:43:16Z date_updated: 2019-01-18T08:43:16Z file_id: '5842' file_name: 2016_jocs_ewa.pdf file_size: 1083911 relation: main_file success: 1 file_date_updated: 2019-01-18T08:43:16Z has_accepted_license: '1' intvolume: ' 18' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 85 - 94 publication: Journal of Computational Science publication_identifier: issn: - '18777503' publication_status: published publisher: Elsevier publist_id: '6206' quality_controlled: '1' scopus_import: '1' status: public title: A multi objective memetic inverse solver reinforced by local optimization methods type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 18 year: '2017' ... --- _id: '1168' abstract: - lang: eng text: Optimum experimental design theory has recently been extended for parameter estimation in copula models. The use of these models allows one to gain in flexibility by considering the model parameter set split into marginal and dependence parameters. However, this separation also leads to the natural issue of estimating only a subset of all model parameters. In this work, we treat this problem with the application of the (Formula presented.)-optimality to copula models. First, we provide an extension of the corresponding equivalence theory. Then, we analyze a wide range of flexible copula models to highlight the usefulness of (Formula presented.)-optimality in many possible scenarios. Finally, we discuss how the usage of the introduced design criterion also relates to the more general issue of copula selection and optimal design for model discrimination. acknowledgement: 'This work has been supported by the project ANR-2011-IS01-001-01 “DESIRE” and Austrian Science Fund (FWF) I833-N18. Open access funding is provided by the Austrian Science Fund (FWF). ' article_processing_charge: No author: - first_name: Elisa full_name: Perrone, Elisa id: 2A5F8724-F248-11E8-B48F-1D18A9856A87 last_name: Perrone orcid: 0000-0003-0370-9835 - first_name: Andreas full_name: Rappold, Andreas last_name: Rappold - first_name: Werner full_name: Müller, Werner last_name: Müller citation: ama: Perrone E, Rappold A, Müller W. D inf s optimality in copula models. Statistical Methods and Applications. 2017;26(3):403-418. doi:10.1007/s10260-016-0375-6 apa: Perrone, E., Rappold, A., & Müller, W. (2017). D inf s optimality in copula models. Statistical Methods and Applications. Springer. https://doi.org/10.1007/s10260-016-0375-6 chicago: Perrone, Elisa, Andreas Rappold, and Werner Müller. “D Inf s Optimality in Copula Models.” Statistical Methods and Applications. Springer, 2017. https://doi.org/10.1007/s10260-016-0375-6. ieee: E. Perrone, A. Rappold, and W. Müller, “D inf s optimality in copula models,” Statistical Methods and Applications, vol. 26, no. 3. Springer, pp. 403–418, 2017. ista: Perrone E, Rappold A, Müller W. 2017. D inf s optimality in copula models. Statistical Methods and Applications. 26(3), 403–418. mla: Perrone, Elisa, et al. “D Inf s Optimality in Copula Models.” Statistical Methods and Applications, vol. 26, no. 3, Springer, 2017, pp. 403–18, doi:10.1007/s10260-016-0375-6. short: E. Perrone, A. Rappold, W. Müller, Statistical Methods and Applications 26 (2017) 403–418. date_created: 2018-12-11T11:50:31Z date_published: 2017-08-01T00:00:00Z date_updated: 2023-09-20T11:25:09Z day: '01' ddc: - '519' department: - _id: CaUh doi: 10.1007/s10260-016-0375-6 external_id: isi: - '000407973200004' file: - access_level: open_access checksum: 0b2d1b647ca96e9ef13a14b8b6775e0f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:13Z date_updated: 2020-07-14T12:44:37Z file_id: '5199' file_name: IST-2017-739-v1+2_10260_2016_375_MOESM1_ESM.pdf file_size: 56664 relation: main_file - access_level: open_access checksum: 3321ef34e02e28acfc427f77cf32812a content_type: application/pdf creator: system date_created: 2018-12-12T10:16:14Z date_updated: 2020-07-14T12:44:37Z file_id: '5200' file_name: IST-2017-739-v1+3_s10260-016-0375-6.pdf file_size: 688953 relation: main_file file_date_updated: 2020-07-14T12:44:37Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 403 - 418 publication: Statistical Methods and Applications publication_status: published publisher: Springer publist_id: '6189' pubrep_id: '739' quality_controlled: '1' scopus_import: '1' status: public title: D inf s optimality in copula models 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 26 year: '2017' ... --- _id: '1163' abstract: - lang: eng text: 'We investigate the effect of the electron-hole (e-h) symmetry breaking on d-wave superconductivity induced by non-local effects of correlations in the generalized Hubbard model. The symmetry breaking is introduced in a two-fold manner: by the next-to-nearest neighbor hopping of electrons and by the charge-bond interaction - the off-diagonal term of the Coulomb potential. Both terms lead to a pronounced asymmetry of the superconducting order parameter. The next-to-nearest neighbor hopping enhances superconductivity for h-doping, while diminishes it for e-doping. The charge-bond interaction alone leads to the opposite effect and, additionally, to the kinetic-energy gain upon condensation in the underdoped regime. With both terms included, with similar amplitudes, the height of the superconducting dome and the critical doping remain in favor of h-doping. The influence of the charge-bond interaction on deviations from symmetry of the shape of the gap at the Fermi surface in the momentum space is briefly discussed.' article_number: '085604' article_processing_charge: No author: - first_name: Marcin full_name: Wysokiński, Marcin last_name: Wysokiński - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 citation: ama: 'Wysokiński M, Kaczmarczyk J. Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. 2017;29(8). doi:10.1088/1361-648X/aa532f' apa: 'Wysokiński, M., & Kaczmarczyk, J. (2017). Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/1361-648X/aa532f' chicago: 'Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2017. https://doi.org/10.1088/1361-648X/aa532f.' ieee: 'M. Wysokiński and J. Kaczmarczyk, “Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms,” Journal of Physics: Condensed Matter, vol. 29, no. 8. IOP Publishing Ltd., 2017.' ista: 'Wysokiński M, Kaczmarczyk J. 2017. Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. 29(8), 085604.' mla: 'Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal of Physics: Condensed Matter, vol. 29, no. 8, 085604, IOP Publishing Ltd., 2017, doi:10.1088/1361-648X/aa532f.' short: 'M. Wysokiński, J. Kaczmarczyk, Journal of Physics: Condensed Matter 29 (2017).' date_created: 2018-12-11T11:50:29Z date_published: 2017-01-16T00:00:00Z date_updated: 2023-09-20T11:25:32Z day: '16' department: - _id: MiLe doi: 10.1088/1361-648X/aa532f ec_funded: 1 external_id: isi: - '000393955500001' intvolume: ' 29' isi: 1 issue: '8' language: - iso: eng month: '01' oa_version: None project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'Journal of Physics: Condensed Matter' publication_identifier: issn: - '09538984' publication_status: published publisher: IOP Publishing Ltd. publist_id: '6194' quality_controlled: '1' scopus_import: '1' status: public title: Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 29 year: '2017' ... --- _id: '1173' abstract: - lang: eng text: We introduce the Voronoi functional of a triangulation of a finite set of points in the Euclidean plane and prove that among all geometric triangulations of the point set, the Delaunay triangulation maximizes the functional. This result neither extends to topological triangulations in the plane nor to geometric triangulations in three and higher dimensions. acknowledgement: This research is partially supported by the Russian Government under the Mega Project 11.G34.31.0053, by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by RFBR grant 11-01-00735, and by NSF grants DMS-1101688, DMS-1400876. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Alexey full_name: Glazyrin, Alexey last_name: Glazyrin - first_name: Oleg full_name: Musin, Oleg last_name: Musin - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Edelsbrunner H, Glazyrin A, Musin O, Nikitenko A. The Voronoi functional is maximized by the Delaunay triangulation in the plane. Combinatorica. 2017;37(5):887-910. doi:10.1007/s00493-016-3308-y apa: Edelsbrunner, H., Glazyrin, A., Musin, O., & Nikitenko, A. (2017). The Voronoi functional is maximized by the Delaunay triangulation in the plane. Combinatorica. Springer. https://doi.org/10.1007/s00493-016-3308-y chicago: Edelsbrunner, Herbert, Alexey Glazyrin, Oleg Musin, and Anton Nikitenko. “The Voronoi Functional Is Maximized by the Delaunay Triangulation in the Plane.” Combinatorica. Springer, 2017. https://doi.org/10.1007/s00493-016-3308-y. ieee: H. Edelsbrunner, A. Glazyrin, O. Musin, and A. Nikitenko, “The Voronoi functional is maximized by the Delaunay triangulation in the plane,” Combinatorica, vol. 37, no. 5. Springer, pp. 887–910, 2017. ista: Edelsbrunner H, Glazyrin A, Musin O, Nikitenko A. 2017. The Voronoi functional is maximized by the Delaunay triangulation in the plane. Combinatorica. 37(5), 887–910. mla: Edelsbrunner, Herbert, et al. “The Voronoi Functional Is Maximized by the Delaunay Triangulation in the Plane.” Combinatorica, vol. 37, no. 5, Springer, 2017, pp. 887–910, doi:10.1007/s00493-016-3308-y. short: H. Edelsbrunner, A. Glazyrin, O. Musin, A. Nikitenko, Combinatorica 37 (2017) 887–910. date_created: 2018-12-11T11:50:32Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-20T11:23:53Z day: '01' department: - _id: HeEd doi: 10.1007/s00493-016-3308-y ec_funded: 1 external_id: isi: - '000418056000005' intvolume: ' 37' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1411.6337 month: '10' oa: 1 oa_version: Submitted Version page: 887 - 910 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: Combinatorica publication_identifier: issn: - '02099683' publication_status: published publisher: Springer publist_id: '6182' quality_controlled: '1' scopus_import: '1' status: public title: The Voronoi functional is maximized by the Delaunay triangulation in the plane type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2017' ... --- _id: '1161' abstract: - lang: eng text: Coordinated changes of cell shape are often the result of the excitable, wave-like dynamics of the actin cytoskeleton. New work shows that, in migrating cells, protrusion waves arise from mechanochemical crosstalk between adhesion sites, membrane tension and the actin protrusive machinery. article_processing_charge: No author: - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - 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: 'Müller J, Sixt MK. Cell migration: Making the waves. Current Biology. 2017;27(1):R24-R25. doi:10.1016/j.cub.2016.11.035' apa: 'Müller, J., & Sixt, M. K. (2017). Cell migration: Making the waves. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2016.11.035' chicago: 'Müller, Jan, and Michael K Sixt. “Cell Migration: Making the Waves.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2016.11.035.' ieee: 'J. Müller and M. K. Sixt, “Cell migration: Making the waves,” Current Biology, vol. 27, no. 1. Cell Press, pp. R24–R25, 2017.' ista: 'Müller J, Sixt MK. 2017. Cell migration: Making the waves. Current Biology. 27(1), R24–R25.' mla: 'Müller, Jan, and Michael K. Sixt. “Cell Migration: Making the Waves.” Current Biology, vol. 27, no. 1, Cell Press, 2017, pp. R24–25, doi:10.1016/j.cub.2016.11.035.' short: J. Müller, M.K. Sixt, Current Biology 27 (2017) R24–R25. date_created: 2018-12-11T11:50:29Z date_published: 2017-01-09T00:00:00Z date_updated: 2023-09-20T11:28:19Z day: '09' department: - _id: MiSi doi: 10.1016/j.cub.2016.11.035 external_id: isi: - '000391902500010' intvolume: ' 27' isi: 1 issue: '1' language: - iso: eng month: '01' oa_version: None page: R24 - R25 publication: Current Biology publication_identifier: issn: - '09609822' publication_status: published publisher: Cell Press publist_id: '6197' quality_controlled: '1' scopus_import: '1' status: public title: 'Cell migration: Making the waves' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 27 year: '2017' ... --- _id: '1116' abstract: - lang: eng text: "Time-triggered switched networks are a deterministic communication infrastructure used by real-time distributed embedded systems. Due to the criticality of the applications running over them, developers need to ensure that end-to-end communication is dependable and predictable. Traditional approaches assume static networks that are not flexible to changes caused by reconfigurations or, more importantly, faults, which are dealt with in the application using redundancy. We adopt the concept of handling faults in the switches from non-real-time networks while maintaining the required predictability. \r\n\r\nWe study a class of forwarding schemes that can handle various types of failures. We consider probabilistic failures. We study a class of forwarding schemes that can handle various types of failures. We consider probabilistic failures. For a given network with a forwarding scheme and a constant ℓ, we compute the {\\em score} of the scheme, namely the probability (induced by faults) that at least ℓ messages arrive on time. We reduce the scoring problem to a reachability problem on a Markov chain with a "product-like" structure. Its special structure allows us to reason about it symbolically, and reduce the scoring problem to #SAT. Our solution is generic and can be adapted to different networks and other contexts. Also, we show the computational complexity of the scoring problem is #P-complete, and we study methods to estimate the score. We evaluate the effectiveness of our techniques with an implementation. " alternative_title: - LNCS article_processing_charge: No author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Shubham full_name: Goel, Shubham last_name: Goel - 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: Guillermo full_name: Rodríguez Navas, Guillermo last_name: Rodríguez Navas citation: ama: 'Avni G, Goel S, Henzinger TA, Rodríguez Navas G. Computing scores of forwarding schemes in switched networks with probabilistic faults. In: Vol 10206. Springer; 2017:169-187. doi:10.1007/978-3-662-54580-5_10' apa: 'Avni, G., Goel, S., Henzinger, T. A., & Rodríguez Navas, G. (2017). Computing scores of forwarding schemes in switched networks with probabilistic faults (Vol. 10206, pp. 169–187). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54580-5_10' chicago: Avni, Guy, Shubham Goel, Thomas A Henzinger, and Guillermo Rodríguez Navas. “Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic Faults,” 10206:169–87. Springer, 2017. https://doi.org/10.1007/978-3-662-54580-5_10. ieee: 'G. Avni, S. Goel, T. A. Henzinger, and G. Rodríguez Navas, “Computing scores of forwarding schemes in switched networks with probabilistic faults,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10206, pp. 169–187.' ista: 'Avni G, Goel S, Henzinger TA, Rodríguez Navas G. 2017. Computing scores of forwarding schemes in switched networks with probabilistic faults. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10206, 169–187.' mla: Avni, Guy, et al. Computing Scores of Forwarding Schemes in Switched Networks with Probabilistic Faults. Vol. 10206, Springer, 2017, pp. 169–87, doi:10.1007/978-3-662-54580-5_10. short: G. Avni, S. Goel, T.A. Henzinger, G. Rodríguez Navas, in:, Springer, 2017, pp. 169–187. conference: end_date: 2017-04-29 location: Uppsala, Sweden name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2017-04-22 date_created: 2018-12-11T11:50:14Z date_published: 2017-03-31T00:00:00Z date_updated: 2023-09-20T11:32:43Z day: '31' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-662-54580-5_10 external_id: isi: - '000440733400010' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:08:37Z date_updated: 2018-12-12T10:08:37Z file_id: '4698' file_name: IST-2017-758-v1+1_tacas-cr.pdf file_size: 321800 relation: main_file file_date_updated: 2018-12-12T10:08:37Z has_accepted_license: '1' intvolume: ' 10206' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 169 - 187 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '6246' pubrep_id: '758' quality_controlled: '1' scopus_import: '1' status: public title: Computing scores of forwarding schemes in switched networks with probabilistic faults type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10206 year: '2017' ... --- _id: '1118' abstract: - lang: eng text: Sharp wave-ripple (SWR) oscillations play a key role in memory consolidation during non-rapid eye movement sleep, immobility, and consummatory behavior. However, whether temporally modulated synaptic excitation or inhibition underlies the ripples is controversial. To address this question, we performed simultaneous recordings of excitatory and inhibitory postsynaptic currents (EPSCs and IPSCs) and local field potentials (LFPs) in the CA1 region of awake mice in vivo. During SWRs, inhibition dominated over excitation, with a peak conductance ratio of 4.1 ± 0.5. Furthermore, the amplitude of SWR-associated IPSCs was positively correlated with SWR magnitude, whereas that of EPSCs was not. Finally, phase analysis indicated that IPSCs were phase-locked to individual ripple cycles, whereas EPSCs were uniformly distributed in phase space. Optogenetic inhibition indicated that PV+ interneurons provided a major contribution to SWR-associated IPSCs. Thus, phasic inhibition, but not excitation, shapes SWR oscillations in the hippocampal CA1 region in vivo. acknowledged_ssus: - _id: M-Shop - _id: ScienComp - _id: PreCl article_processing_charge: No author: - first_name: Jian full_name: Gan, Jian id: 3614E438-F248-11E8-B48F-1D18A9856A87 last_name: Gan - first_name: Shih-Ming full_name: Weng, Shih-Ming id: 2F9C5AC8-F248-11E8-B48F-1D18A9856A87 last_name: Weng - first_name: Alejandro full_name: Pernia-Andrade, Alejandro id: 36963E98-F248-11E8-B48F-1D18A9856A87 last_name: Pernia-Andrade - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. 2017;93(2):308-314. doi:10.1016/j.neuron.2016.12.018 apa: Gan, J., Weng, S.-M., Pernia-Andrade, A., Csicsvari, J. L., & Jonas, P. M. (2017). Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2016.12.018 chicago: Gan, Jian, Shih-Ming Weng, Alejandro Pernia-Andrade, Jozsef L Csicsvari, and Peter M Jonas. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice in Vivo.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2016.12.018. ieee: J. Gan, S.-M. Weng, A. Pernia-Andrade, J. L. Csicsvari, and P. M. Jonas, “Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo,” Neuron, vol. 93, no. 2. Elsevier, pp. 308–314, 2017. ista: Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. 2017. Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. 93(2), 308–314. mla: Gan, Jian, et al. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice in Vivo.” Neuron, vol. 93, no. 2, Elsevier, 2017, pp. 308–14, doi:10.1016/j.neuron.2016.12.018. short: J. Gan, S.-M. Weng, A. Pernia-Andrade, J.L. Csicsvari, P.M. Jonas, Neuron 93 (2017) 308–314. date_created: 2018-12-11T11:50:15Z date_published: 2017-01-18T00:00:00Z date_updated: 2023-09-20T11:31:48Z day: '18' ddc: - '571' department: - _id: PeJo - _id: JoCs doi: 10.1016/j.neuron.2016.12.018 ec_funded: 1 external_id: isi: - '000396428200010' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:08:56Z date_updated: 2018-12-12T10:08:56Z file_id: '4719' file_name: IST-2017-752-v1+1_1-s2.0-S0896627316309606-main.pdf file_size: 2738950 relation: main_file file_date_updated: 2018-12-12T10:08:56Z has_accepted_license: '1' intvolume: ' 93' isi: 1 issue: '2' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 308 - 314 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: Neuron publication_status: published publisher: Elsevier publist_id: '6244' pubrep_id: '752' quality_controlled: '1' scopus_import: '1' status: public title: Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 93 year: '2017' ... --- _id: '1117' abstract: - lang: eng text: 'GABAergic synapses in brain circuits generate inhibitory output signals with submillisecond latency and temporal precision. Whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Here, we examined the Ca^2+ sensor of exocytosis at GABAergic basket cell (BC) to Purkinje cell (PC) synapses in cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ∼10%, identifying Syt2 as the major Ca^2+ sensor at BC-PC synapses. Differential adenovirus-mediated rescue revealed that Syt2 triggered release with shorter latency and higher temporal precision and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as release sensor at BC-PC synapses ensures fast and efficient feedforward inhibition in cerebellar microcircuits. #bioimagingfacility-author' acknowledged_ssus: - _id: Bio - _id: PreCl article_processing_charge: No author: - first_name: Chong full_name: Chen, Chong id: 3DFD581A-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Itaru full_name: Arai, Itaru id: 32A73F6C-F248-11E8-B48F-1D18A9856A87 last_name: Arai - first_name: Rachel full_name: Satterield, Rachel last_name: Satterield - first_name: Samuel full_name: Young, Samuel last_name: Young - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Chen C, Arai itaru, Satterield R, Young S, Jonas PM. Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 2017;18(3):723-736. doi:10.1016/j.celrep.2016.12.067 apa: Chen, C., Arai, itaru, Satterield, R., Young, S., & Jonas, P. M. (2017). Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2016.12.067 chicago: Chen, Chong, itaru Arai, Rachel Satterield, Samuel Young, and Peter M Jonas. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2016.12.067. ieee: C. Chen, itaru Arai, R. Satterield, S. Young, and P. M. Jonas, “Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse,” Cell Reports, vol. 18, no. 3. Cell Press, pp. 723–736, 2017. ista: Chen C, Arai itaru, Satterield R, Young S, Jonas PM. 2017. Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse. Cell Reports. 18(3), 723–736. mla: Chen, Chong, et al. “Synaptotagmin 2 Is the Fast Ca2+ Sensor at a Central Inhibitory Synapse.” Cell Reports, vol. 18, no. 3, Cell Press, 2017, pp. 723–36, doi:10.1016/j.celrep.2016.12.067. short: C. Chen, itaru Arai, R. Satterield, S. Young, P.M. Jonas, Cell Reports 18 (2017) 723–736. date_created: 2018-12-11T11:50:14Z date_published: 2017-01-17T00:00:00Z date_updated: 2023-09-20T11:32:15Z day: '17' ddc: - '571' department: - _id: PeJo doi: 10.1016/j.celrep.2016.12.067 ec_funded: 1 external_id: isi: - '000396470600013' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:16:09Z date_updated: 2018-12-12T10:16:09Z file_id: '5195' file_name: IST-2017-751-v1+1_1-s2.0-S2211124716317740-main.pdf file_size: 4427591 relation: main_file file_date_updated: 2018-12-12T10:16:09Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '3' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 723 - 736 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: Cell Reports publication_identifier: issn: - '22111247' publication_status: published publisher: Cell Press publist_id: '6245' pubrep_id: '751' quality_controlled: '1' related_material: record: - id: '324' relation: dissertation_contains status: public scopus_import: '1' status: public title: Synaptotagmin 2 is the fast Ca2+ sensor at a central inhibitory synapse 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 18 year: '2017' ... --- _id: '1132' abstract: - lang: eng text: The hippocampus is thought to initiate systems-wide mnemonic processes through the reactivation of previously acquired spatial and episodic memory traces, which can recruit the entorhinal cortex as a first stage of memory redistribution to other brain areas. Hippocampal reactivation occurs during sharp wave-ripples, in which synchronous network firing encodes sequences of places.We investigated the coordination of this replay by recording assembly activity simultaneously in the CA1 region of the hippocampus and superficial layers of the medial entorhinal cortex. We found that entorhinal cell assemblies can replay trajectories independently of the hippocampus and sharp wave-ripples. This suggests that the hippocampus is not the sole initiator of spatial and episodic memory trace reactivation. Memory systems involved in these processes may include nonhierarchical, parallel components. article_processing_charge: No author: - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Charlotte full_name: Boccara, Charlotte id: 3FC06552-F248-11E8-B48F-1D18A9856A87 last_name: Boccara orcid: 0000-0001-7237-5109 - first_name: Federico full_name: Stella, Federico id: 39AF1E74-F248-11E8-B48F-1D18A9856A87 last_name: Stella orcid: 0000-0001-9439-3148 - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: O’Neill J, Boccara CN, Stella F, Schönenberger P, Csicsvari JL. Superficial layers of the medial entorhinal cortex replay independently of the hippocampus. Science. 2017;355(6321):184-188. doi:10.1126/science.aag2787 apa: O’Neill, J., Boccara, C. N., Stella, F., Schönenberger, P., & Csicsvari, J. L. (2017). Superficial layers of the medial entorhinal cortex replay independently of the hippocampus. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag2787 chicago: O’Neill, Joseph, Charlotte N. Boccara, Federico Stella, Philipp Schönenberger, and Jozsef L Csicsvari. “Superficial Layers of the Medial Entorhinal Cortex Replay Independently of the Hippocampus.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aag2787. ieee: J. O’Neill, C. N. Boccara, F. Stella, P. Schönenberger, and J. L. Csicsvari, “Superficial layers of the medial entorhinal cortex replay independently of the hippocampus,” Science, vol. 355, no. 6321. American Association for the Advancement of Science, pp. 184–188, 2017. ista: O’Neill J, Boccara CN, Stella F, Schönenberger P, Csicsvari JL. 2017. Superficial layers of the medial entorhinal cortex replay independently of the hippocampus. Science. 355(6321), 184–188. mla: O’Neill, Joseph, et al. “Superficial Layers of the Medial Entorhinal Cortex Replay Independently of the Hippocampus.” Science, vol. 355, no. 6321, American Association for the Advancement of Science, 2017, pp. 184–88, doi:10.1126/science.aag2787. short: J. O’Neill, C.N. Boccara, F. Stella, P. Schönenberger, J.L. Csicsvari, Science 355 (2017) 184–188. date_created: 2018-12-11T11:50:19Z date_published: 2017-01-13T00:00:00Z date_updated: 2023-09-20T11:30:35Z day: '13' ddc: - '571' department: - _id: JoCs doi: 10.1126/science.aag2787 ec_funded: 1 external_id: isi: - '000391743700044' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:10:22Z date_updated: 2018-12-12T10:10:22Z file_id: '4809' file_name: IST-2018-976-v1+1_2017Preprint_ONeill_Superficial_layers.pdf file_size: 3761201 relation: main_file file_date_updated: 2018-12-12T10:10:22Z has_accepted_license: '1' intvolume: ' 355' isi: 1 issue: '6321' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 184 - 188 project: - _id: 257A4776-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281511' name: Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex publication: Science publication_identifier: issn: - '00368075' publication_status: published publisher: American Association for the Advancement of Science publist_id: '6226' pubrep_id: '976' quality_controlled: '1' scopus_import: '1' status: public title: Superficial layers of the medial entorhinal cortex replay independently of the hippocampus type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 355 year: '2017' ... --- _id: '1120' abstract: - lang: eng text: 'The existence of a self-localization transition in the polaron problem has been under an active debate ever since Landau suggested it 83 years ago. Here we reveal the self-localization transition for the rotational analogue of the polaron -- the angulon quasiparticle. We show that, unlike for the polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of the symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. The predicted effects can potentially be addressed in experiments on cold molecules trapped in superfluid helium droplets and ultracold quantum gases, as well as on electronic excitations in solids and Bose-Einstein condensates. ' article_number: '033608' article_processing_charge: No author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Li X, Seiringer R, Lemeshko M. Angular self-localization of impurities rotating in a bosonic bath. Physical Review A. 2017;95(3). doi:10.1103/PhysRevA.95.033608 apa: Li, X., Seiringer, R., & Lemeshko, M. (2017). Angular self-localization of impurities rotating in a bosonic bath. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.95.033608 chicago: Li, Xiang, Robert Seiringer, and Mikhail Lemeshko. “Angular Self-Localization of Impurities Rotating in a Bosonic Bath.” Physical Review A. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.033608. ieee: X. Li, R. Seiringer, and M. Lemeshko, “Angular self-localization of impurities rotating in a bosonic bath,” Physical Review A, vol. 95, no. 3. American Physical Society, 2017. ista: Li X, Seiringer R, Lemeshko M. 2017. Angular self-localization of impurities rotating in a bosonic bath. Physical Review A. 95(3), 033608. mla: Li, Xiang, et al. “Angular Self-Localization of Impurities Rotating in a Bosonic Bath.” Physical Review A, vol. 95, no. 3, 033608, American Physical Society, 2017, doi:10.1103/PhysRevA.95.033608. short: X. Li, R. Seiringer, M. Lemeshko, Physical Review A 95 (2017). date_created: 2018-12-11T11:50:15Z date_published: 2017-03-06T00:00:00Z date_updated: 2023-09-20T11:30:58Z day: '06' department: - _id: MiLe - _id: RoSe doi: 10.1103/PhysRevA.95.033608 ec_funded: 1 external_id: isi: - '000395981900009' intvolume: ' 95' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.04908 month: '03' oa: 1 oa_version: Published Version project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review A publication_identifier: issn: - '24699926' publication_status: published publisher: American Physical Society publist_id: '6242' quality_controlled: '1' related_material: record: - id: '8958' relation: dissertation_contains status: public scopus_import: '1' status: public title: Angular self-localization of impurities rotating in a bosonic bath type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 95 year: '2017' ... --- _id: '1133' abstract: - lang: eng text: 'It is a common knowledge that an effective interaction of a quantum impurity with an electromagnetic field can be screened by surrounding charge carriers, whether mobile or static. Here we demonstrate that very strong, "anomalous" screening can take place in the presence of a neutral, weakly polarizable environment, due to an exchange of orbital angular momentum between the impurity and the bath. Furthermore, we show that it is possible to generalize all phenomena related to isolated impurities in an external field to the case when a many-body environment is present, by casting the problem in terms of the angulon quasiparticle. As a result, the relevant observables such as the effective Rabi frequency, geometric phase, and impurity spatial alignment are straightforward to evaluate in terms of a single parameter: the angular-momentum-dependent screening factor.' article_number: '085302' article_processing_charge: No author: - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Yakaboylu E, Lemeshko M. Anomalous screening of quantum impurities by a neutral environment. Physical Review Letters. 2017;118(8). doi:10.1103/PhysRevLett.118.085302 apa: Yakaboylu, E., & Lemeshko, M. (2017). Anomalous screening of quantum impurities by a neutral environment. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.085302 chicago: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anomalous Screening of Quantum Impurities by a Neutral Environment.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.085302. ieee: E. Yakaboylu and M. Lemeshko, “Anomalous screening of quantum impurities by a neutral environment,” Physical Review Letters, vol. 118, no. 8. American Physical Society, 2017. ista: Yakaboylu E, Lemeshko M. 2017. Anomalous screening of quantum impurities by a neutral environment. Physical Review Letters. 118(8), 085302. mla: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anomalous Screening of Quantum Impurities by a Neutral Environment.” Physical Review Letters, vol. 118, no. 8, 085302, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.085302. short: E. Yakaboylu, M. Lemeshko, Physical Review Letters 118 (2017). date_created: 2018-12-11T11:50:19Z date_published: 2017-02-22T00:00:00Z date_updated: 2023-09-20T11:30:08Z day: '22' department: - _id: MiLe doi: 10.1103/PhysRevLett.118.085302 ec_funded: 1 external_id: isi: - '000394667600003' intvolume: ' 118' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.02820 month: '02' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_identifier: issn: - '00319007' publication_status: published publisher: American Physical Society publist_id: '6225' quality_controlled: '1' scopus_import: '1' status: public title: Anomalous screening of quantum impurities by a neutral environment type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2017' ... --- _id: '1119' abstract: - lang: eng text: Understanding the behavior of molecules interacting with superfluid helium represents a formidable challenge and, in general, requires approaches relying on large-scale numerical simulations. Here we demonstrate that experimental data collected over the last 20 years provide evidence that molecules immersed in superfluid helium form recently-predicted angulon quasiparticles [Phys. Rev. Lett. 114, 203001 (2015)]. Most importantly, casting the many-body problem in terms of angulons amounts to a drastic simplification and yields effective molecular moments of inertia as straightforward analytic solutions of a simple microscopic Hamiltonian. The outcome of the angulon theory is in good agreement with experiment for a broad range of molecular impurities, from heavy to medium-mass to light species. These results pave the way to understanding molecular rotation in liquid and crystalline phases in terms of the angulon quasiparticle. article_number: '095301' article_processing_charge: No author: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Lemeshko M. Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. 2017;118(9). doi:10.1103/PhysRevLett.118.095301 apa: Lemeshko, M. (2017). Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.095301 chicago: Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with Quantum Solvents.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.095301. ieee: M. Lemeshko, “Quasiparticle approach to molecules interacting with quantum solvents,” Physical Review Letters, vol. 118, no. 9. American Physical Society, 2017. ista: Lemeshko M. 2017. Quasiparticle approach to molecules interacting with quantum solvents. Physical Review Letters. 118(9), 095301. mla: Lemeshko, Mikhail. “Quasiparticle Approach to Molecules Interacting with Quantum Solvents.” Physical Review Letters, vol. 118, no. 9, 095301, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.095301. short: M. Lemeshko, Physical Review Letters 118 (2017). date_created: 2018-12-11T11:50:15Z date_published: 2017-02-27T00:00:00Z date_updated: 2023-09-20T11:31:22Z day: '27' department: - _id: MiLe doi: 10.1103/PhysRevLett.118.095301 external_id: isi: - '000404769200006' intvolume: ' 118' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1610.01604 month: '02' oa: 1 oa_version: Submitted Version project: - _id: 25636330-B435-11E9-9278-68D0E5697425 grant_number: 11-NSF-1070 name: ROOTS Genome-wide Analysis of Root Traits publication: Physical Review Letters publication_identifier: issn: - '00319007' publication_status: published publisher: American Physical Society publist_id: '6243' quality_controlled: '1' status: public title: Quasiparticle approach to molecules interacting with quantum solvents type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2017' ... --- _id: '1110' abstract: - lang: eng text: The phytohormone auxin is a major determinant and regulatory component important for plant development. Auxin transport between cells is mediated by a complex system of transporters such as AUX1/LAX, PIN, and ABCB proteins, and their localization and activity is thought to be influenced by phosphatases and kinases. Flavonols have been shown to alter auxin transport activity and changes in flavonol accumulation in the Arabidopsis thaliana rol1-2 mutant cause defects in auxin transport and seedling development. A new mutation in ROOTS CURL IN NPA 1 (RCN1), encoding a regulatory subunit of the phosphatase PP2A, was found to suppress the growth defects of rol1-2 without changing the flavonol content. rol1-2 rcn1-3 double mutants show wild type-like auxin transport activity while levels of free auxin are not affected by rcn1-3. In the rol1-2 mutant, PIN2 shows a flavonol-induced basal-to-apical shift in polar localization which is reversed in the rol1-2 rcn1-3 to basal localization. In vivo analysis of PINOID action, a kinase known to influence PIN protein localization in a PP2A-antagonistic manner, revealed a negative impact of flavonols on PINOID activity. Together, these data suggest that flavonols affect auxin transport by modifying the antagonistic kinase/phosphatase equilibrium. acknowledgement: European Research Council (project ERC-2011-StG-20101109-PSDP), European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation (GA13-40637S) [JF]. article_number: '41906' article_processing_charge: No author: - first_name: Benjamin full_name: Kuhn, Benjamin last_name: Kuhn - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Sanae full_name: Errafi, Sanae last_name: Errafi - first_name: Rahel full_name: Bucher, Rahel last_name: Bucher - first_name: Shibu full_name: Gupta, Shibu last_name: Gupta - first_name: Bibek full_name: Aryal, Bibek last_name: Aryal - first_name: Petre full_name: Dobrev, Petre last_name: Dobrev - first_name: Laurent full_name: Bigler, Laurent last_name: Bigler - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Christoph full_name: Ringli, Christoph last_name: Ringli citation: ama: Kuhn B, Nodzyński T, Errafi S, et al. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 2017;7. doi:10.1038/srep41906 apa: Kuhn, B., Nodzyński, T., Errafi, S., Bucher, R., Gupta, S., Aryal, B., … Ringli, C. (2017). Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep41906 chicago: Kuhn, Benjamin, Tomasz Nodzyński, Sanae Errafi, Rahel Bucher, Shibu Gupta, Bibek Aryal, Petre Dobrev, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep41906. ieee: B. Kuhn et al., “Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity,” Scientific Reports, vol. 7. Nature Publishing Group, 2017. ista: Kuhn B, Nodzyński T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler L, Geisler M, Zažímalová E, Friml J, Ringli C. 2017. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports. 7, 41906. mla: Kuhn, Benjamin, et al. “Flavonol-Induced Changes in PIN2 Polarity and Auxin Transport in the Arabidopsis Thaliana Rol1-2 Mutant Require Phosphatase Activity.” Scientific Reports, vol. 7, 41906, Nature Publishing Group, 2017, doi:10.1038/srep41906. short: B. Kuhn, T. Nodzyński, S. Errafi, R. Bucher, S. Gupta, B. Aryal, P. Dobrev, L. Bigler, M. Geisler, E. Zažímalová, J. Friml, C. Ringli, Scientific Reports 7 (2017). date_created: 2018-12-11T11:50:12Z date_published: 2017-02-06T00:00:00Z date_updated: 2023-09-20T11:35:35Z day: '06' ddc: - '581' department: - _id: JiFr doi: 10.1038/srep41906 ec_funded: 1 external_id: isi: - '000393367600001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:18:09Z date_updated: 2018-12-12T10:18:09Z file_id: '5328' file_name: IST-2017-803-v1+1_srep41906.pdf file_size: 1654496 relation: main_file file_date_updated: 2018-12-12T10:18:09Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '02' 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: Scientific Reports publication_identifier: issn: - '20452322' publication_status: published publisher: Nature Publishing Group publist_id: '6258' pubrep_id: '803' quality_controlled: '1' scopus_import: '1' status: public title: Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2017' ... --- _id: '1104' abstract: - lang: eng text: In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems. article_number: '1964' article_processing_charge: No author: - first_name: Stephane full_name: Deny, Stephane last_name: Deny - first_name: Ulisse full_name: Ferrari, Ulisse last_name: Ferrari - first_name: Emilie full_name: Mace, Emilie last_name: Mace - first_name: Pierre full_name: Yger, Pierre last_name: Yger - first_name: Romain full_name: Caplette, Romain last_name: Caplette - first_name: Serge full_name: Picaud, Serge last_name: Picaud - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Olivier full_name: Marre, Olivier last_name: Marre citation: ama: Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-02159-y apa: Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02159-y chicago: Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-02159-y. ieee: S. Deny et al., “Multiplexed computations in retinal ganglion cells of a single type,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017. ista: Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964. mla: Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y. short: S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:10Z date_published: 2017-12-06T00:00:00Z date_updated: 2023-09-20T11:41:19Z day: '06' ddc: - '571' department: - _id: GaTk doi: 10.1038/s41467-017-02159-y ec_funded: 1 external_id: isi: - '000417241200004' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:16:06Z date_updated: 2018-12-12T10:16:06Z file_id: '5191' file_name: IST-2018-921-v1+1_s41467-017-02159-y.pdf file_size: 2872887 relation: main_file file_date_updated: 2018-12-12T10:16:06Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25CD3DD2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '604102' name: Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6266' pubrep_id: '921' quality_controlled: '1' scopus_import: '1' status: public title: Multiplexed computations in retinal ganglion cells of a single type 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '1107' abstract: - lang: eng text: The generation, migration, and differentiation of neurons requires the functional integrity of the microtubule cytoskeleton. Mutations in the tubulin gene family are known to cause various neurological diseases including lissencephaly, ocular motor disorders, polymicrogyria and amyotrophic lateral sclerosis. We have previously reported that mutations in TUBB5 cause microcephaly that is accompanied by severe intellectual impairment and motor delay. Here we present the characterization of a Tubb5 mouse model that allows for the conditional expression of the pathogenic E401K mutation. Homozygous knockin animals exhibit a severe reduction in brain size and in body weight. These animals do not show any significant impairment in general activity, anxiety, or in the acoustic startle response, however, present with notable defects in motor coordination. When assessed on the static rod apparatus mice took longer to orient and often lost their balance completely. Interestingly, mutant animals also showed defects in prepulse inhibition, a phenotype associated with sensorimotor gating and considered an endophenotype for schizophrenia. This study provides insight into the behavioral consequences of tubulin gene mutations. acknowledgement: Austrian Science Fund (FWF) for funding this research [I914,P21092] article_processing_charge: No author: - first_name: Martin full_name: Breuss, Martin last_name: Breuss - first_name: Andi H full_name: Hansen, Andi H id: 38853E16-F248-11E8-B48F-1D18A9856A87 last_name: Hansen - first_name: Lukas full_name: Landler, Lukas last_name: Landler - first_name: David full_name: Keays, David last_name: Keays citation: ama: Breuss M, Hansen AH, Landler L, Keays D. Brain specific knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition. Behavioural Brain Research. 2017;323:47-55. doi:10.1016/j.bbr.2017.01.029 apa: Breuss, M., Hansen, A. H., Landler, L., & Keays, D. (2017). Brain specific knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition. Behavioural Brain Research. Elsevier. https://doi.org/10.1016/j.bbr.2017.01.029 chicago: Breuss, Martin, Andi H Hansen, Lukas Landler, and David Keays. “Brain Specific Knockin of the Pathogenic Tubb5 E401K Allele Causes Defects in Motor Coordination and Prepulse Inhibition.” Behavioural Brain Research. Elsevier, 2017. https://doi.org/10.1016/j.bbr.2017.01.029. ieee: M. Breuss, A. H. Hansen, L. Landler, and D. Keays, “Brain specific knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition,” Behavioural Brain Research, vol. 323. Elsevier, pp. 47–55, 2017. ista: Breuss M, Hansen AH, Landler L, Keays D. 2017. Brain specific knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition. Behavioural Brain Research. 323, 47–55. mla: Breuss, Martin, et al. “Brain Specific Knockin of the Pathogenic Tubb5 E401K Allele Causes Defects in Motor Coordination and Prepulse Inhibition.” Behavioural Brain Research, vol. 323, Elsevier, 2017, pp. 47–55, doi:10.1016/j.bbr.2017.01.029. short: M. Breuss, A.H. Hansen, L. Landler, D. Keays, Behavioural Brain Research 323 (2017) 47–55. date_created: 2018-12-11T11:50:11Z date_published: 2017-04-14T00:00:00Z date_updated: 2023-09-20T11:37:25Z day: '14' ddc: - '570' - '571' doi: 10.1016/j.bbr.2017.01.029 extern: '1' external_id: isi: - '000397369100007' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:12:03Z date_updated: 2018-12-12T10:12:03Z file_id: '4921' file_name: IST-2017-868-v1+1_1-s2.0-S0166432816309160-main.pdf file_size: 2291511 relation: main_file file_date_updated: 2018-12-12T10:12:03Z has_accepted_license: '1' intvolume: ' 323' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '04' oa: 1 oa_version: Published Version page: 47 - 55 publication: Behavioural Brain Research publication_identifier: issn: - '01664328' publication_status: published publisher: Elsevier publist_id: '6262' pubrep_id: '868' quality_controlled: '1' status: public title: Brain specific knockin of the pathogenic Tubb5 E401K allele causes defects in motor coordination and prepulse inhibition 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 323 year: '2017' ... --- _id: '1114' abstract: - lang: eng text: Nonequilibrium phase transitions exist in damped-driven open quantum systems when the continuous tuning of an external parameter leads to a transition between two robust steady states. In second-order transitions this change is abrupt at a critical point, whereas in first-order transitions the two phases can coexist in a critical hysteresis domain. Here, we report the observation of a first-order dissipative quantum phase transition in a driven circuit quantum electrodynamics system. It takes place when the photon blockade of the driven cavity-atom system is broken by increasing the drive power. The observed experimental signature is a bimodal phase space distribution with varying weights controlled by the drive strength. Our measurements show an improved stabilization of the classical attractors up to the millisecond range when the size of the quantum system is increased from one to three artificial atoms. The formation of such robust pointer states could be used for new quantum measurement schemes or to investigate multiphoton phases of finite-size, nonlinear, open quantum systems. article_number: '011012' article_processing_charge: Yes author: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: András full_name: Dombi, András last_name: Dombi - first_name: András full_name: Vukics, András last_name: Vukics - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff - first_name: Peter full_name: Domokos, Peter last_name: Domokos citation: ama: Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. Observation of the photon blockade breakdown phase transition. Physical Review X. 2017;7(1). doi:10.1103/PhysRevX.7.011012 apa: Fink, J. M., Dombi, A., Vukics, A., Wallraff, A., & Domokos, P. (2017). Observation of the photon blockade breakdown phase transition. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.7.011012 chicago: Fink, Johannes M, András Dombi, András Vukics, Andreas Wallraff, and Peter Domokos. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical Review X. American Physical Society, 2017. https://doi.org/10.1103/PhysRevX.7.011012. ieee: J. M. Fink, A. Dombi, A. Vukics, A. Wallraff, and P. Domokos, “Observation of the photon blockade breakdown phase transition,” Physical Review X, vol. 7, no. 1. American Physical Society, 2017. ista: Fink JM, Dombi A, Vukics A, Wallraff A, Domokos P. 2017. Observation of the photon blockade breakdown phase transition. Physical Review X. 7(1), 011012. mla: Fink, Johannes M., et al. “Observation of the Photon Blockade Breakdown Phase Transition.” Physical Review X, vol. 7, no. 1, 011012, American Physical Society, 2017, doi:10.1103/PhysRevX.7.011012. short: J.M. Fink, A. Dombi, A. Vukics, A. Wallraff, P. Domokos, Physical Review X 7 (2017). date_created: 2018-12-11T11:50:13Z date_published: 2017-01-31T00:00:00Z date_updated: 2023-09-20T11:33:07Z day: '31' ddc: - '539' department: - _id: JoFi doi: 10.1103/PhysRevX.7.011012 external_id: isi: - '000397450500001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:12:52Z date_updated: 2018-12-12T10:12:52Z file_id: '4972' file_name: IST-2017-753-v1+1_PhysRevX.7.011012.pdf file_size: 1172926 relation: main_file file_date_updated: 2018-12-12T10:12:52Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Physical Review X publication_identifier: issn: - '21603308' publication_status: published publisher: American Physical Society publist_id: '6252' pubrep_id: '753' quality_controlled: '1' scopus_import: '1' status: public title: Observation of the photon blockade breakdown phase transition 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2017' ... --- _id: '1111' abstract: - lang: eng text: Adaptation depends critically on the effects of new mutations and their dependency on the genetic background in which they occur. These two factors can be summarized by the fitness landscape. However, it would require testing all mutations in all backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible. Instead of postulating a particular fitness landscape, we address this problem by considering general classes of landscapes and calculating an upper limit for the time it takes for a population to reach a fitness peak, circumventing the need to have full knowledge about the fitness landscape. We analyze populations in the weak-mutation regime and characterize the conditions that enable them to quickly reach the fitness peak as a function of the number of sites under selection. We show that for additive landscapes there is a critical selection strength enabling populations to reach high-fitness genotypes, regardless of the distribution of effects. This threshold scales with the number of sites under selection, effectively setting a limit to adaptation, and results from the inevitable increase in deleterious mutational pressure as the population adapts in a space of discrete genotypes. Furthermore, we show that for the class of all unimodal landscapes this condition is sufficient but not necessary for rapid adaptation, as in some highly epistatic landscapes the critical strength does not depend on the number of sites under selection; effectively removing this barrier to adaptation. article_processing_charge: No article_type: original author: - 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 - first_name: Dirk full_name: Sudholt, Dirk last_name: Sudholt - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340 apa: Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection limits to adaptive walks on correlated landscapes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.189340 chicago: Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.189340. ieee: J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics Society of America, pp. 803–825, 2017. ista: Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825. mla: Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25, doi:10.1534/genetics.116.189340. short: J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825. date_created: 2018-12-11T11:50:12Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-20T11:35:03Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.116.189340 ec_funded: 1 external_id: isi: - '000394144900025' pmid: - '27881471' intvolume: ' 205' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1534/genetics.116.189340 month: '02' oa: 1 oa_version: Published Version page: 803 - 825 pmid: 1 project: - _id: 25B1EC9E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618091' name: Speed of Adaptation in Population Genetics and Evolutionary Computation publication: Genetics publication_identifier: issn: - '00166731' publication_status: published publisher: Genetics Society of America publist_id: '6256' quality_controlled: '1' scopus_import: '1' status: public title: Selection limits to adaptive walks on correlated landscapes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 205 year: '2017' ... --- _id: '1109' abstract: - lang: eng text: 'Rotation of molecules embedded in He nanodroplets is explored by a combination of fs laser-induced alignment experiments and angulon quasiparticle theory. We demonstrate that at low fluence of the fs alignment pulse, the molecule and its solvation shell can be set into coherent collective rotation lasting long enough to form revivals. With increasing fluence, however, the revivals disappear -- instead, rotational dynamics as rapid as for an isolated molecule is observed during the first few picoseconds. Classical calculations trace this phenomenon to transient decoupling of the molecule from its He shell. Our results open novel opportunities for studying non-equilibrium solute-solvent dynamics and quantum thermalization. ' article_number: '203203' article_processing_charge: No author: - first_name: Benjamin full_name: Shepperson, Benjamin last_name: Shepperson - first_name: Anders full_name: Søndergaard, Anders last_name: Søndergaard - first_name: Lars full_name: Christiansen, Lars last_name: Christiansen - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Robert full_name: Zillich, Robert last_name: Zillich - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Henrik full_name: Stapelfeldt, Henrik last_name: Stapelfeldt citation: ama: 'Shepperson B, Søndergaard A, Christiansen L, et al. Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. 2017;118(20). doi:10.1103/PhysRevLett.118.203203' apa: 'Shepperson, B., Søndergaard, A., Christiansen, L., Kaczmarczyk, J., Zillich, R., Lemeshko, M., & Stapelfeldt, H. (2017). Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.203203' chicago: 'Shepperson, Benjamin, Anders Søndergaard, Lars Christiansen, Jan Kaczmarczyk, Robert Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Laser-Induced Rotation of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.203203.' ieee: 'B. Shepperson et al., “Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free,” Physical Review Letters, vol. 118, no. 20. American Physical Society, 2017.' ista: 'Shepperson B, Søndergaard A, Christiansen L, Kaczmarczyk J, Zillich R, Lemeshko M, Stapelfeldt H. 2017. Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free. Physical Review Letters. 118(20), 203203.' mla: 'Shepperson, Benjamin, et al. “Laser-Induced Rotation of Iodine Molecules in Helium Nanodroplets: Revivals and Breaking-Free.” Physical Review Letters, vol. 118, no. 20, 203203, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.203203.' short: B. Shepperson, A. Søndergaard, L. Christiansen, J. Kaczmarczyk, R. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 118 (2017). date_created: 2018-12-11T11:50:12Z date_published: 2017-05-19T00:00:00Z date_updated: 2023-09-20T11:36:17Z day: '19' department: - _id: MiLe doi: 10.1103/PhysRevLett.118.203203 external_id: isi: - '000401664000005' intvolume: ' 118' isi: 1 issue: '20' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.01977 month: '05' oa: 1 oa_version: Preprint project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6260' quality_controlled: '1' scopus_import: '1' status: public title: 'Laser-induced rotation of iodine molecules in helium nanodroplets: Revivals and breaking-free' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 118 year: '2017' ... --- _id: '1087' abstract: - lang: eng text: Using extensive direct numerical simulations, the dynamics of laminar-turbulent fronts in pipe flow is investigated for Reynolds numbers between and 5500. We here investigate the physical distinction between the fronts of weak and strong slugs both by analysing the turbulent kinetic energy budget and by comparing the downstream front motion to the advection speed of bulk turbulent structures. Our study shows that weak downstream fronts travel slower than turbulent structures in the bulk and correspond to decaying turbulence at the front. At the downstream front speed becomes faster than the advection speed, marking the onset of strong fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts by feeding on the downstream laminar flow. Our study also suggests that temporal fluctuations of production and dissipation at the downstream laminar-turbulent front drive the dynamical switches between the two types of front observed up to. acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Dwight full_name: Barkley, Dwight last_name: Barkley - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 2017;813:1045-1059. doi:10.1017/jfm.2017.14 apa: Song, B., Barkley, D., Hof, B., & Avila, M. (2017). Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.14 chicago: Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2017. https://doi.org/10.1017/jfm.2017.14. ieee: B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent fronts in pipe flow,” Journal of Fluid Mechanics, vol. 813. Cambridge University Press, pp. 1045–1059, 2017. ista: Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059. mla: Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.” Journal of Fluid Mechanics, vol. 813, Cambridge University Press, 2017, pp. 1045–59, doi:10.1017/jfm.2017.14. short: B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017) 1045–1059. date_created: 2018-12-11T11:50:04Z date_published: 2017-02-25T00:00:00Z date_updated: 2023-09-20T11:47:22Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2017.14 ec_funded: 1 external_id: isi: - '000394376400044' intvolume: ' 813' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1603.04077 month: '02' oa: 1 oa_version: Submitted Version page: 1045 - 1059 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluid Mechanics publication_identifier: issn: - '00221120' publication_status: published publisher: Cambridge University Press publist_id: '6290' quality_controlled: '1' scopus_import: '1' status: public title: Speed and structure of turbulent fronts in pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 813 year: '2017' ... --- _id: '1089' abstract: - lang: eng text: We discuss properties of distributions that are multivariate totally positive of order two (MTP2) related to conditional independence. In particular, we show that any independence model generated by an MTP2 distribution is a compositional semigraphoid which is upward-stable and singleton-transitive. In addition, we prove that any MTP2 distribution satisfying an appropriate support condition is faithful to its concentration graph. Finally, we analyze factorization properties of MTP2 distributions and discuss ways of constructing MTP2 distributions; in particular we give conditions on the log-linear parameters of a discrete distribution which ensure MTP2 and characterize conditional Gaussian distributions which satisfy MTP2. article_processing_charge: No author: - first_name: Shaun full_name: Fallat, Shaun last_name: Fallat - first_name: Steffen full_name: Lauritzen, Steffen last_name: Lauritzen - first_name: Kayvan full_name: Sadeghi, Kayvan last_name: Sadeghi - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Nanny full_name: Wermuth, Nanny last_name: Wermuth - first_name: Piotr full_name: Zwiernik, Piotr last_name: Zwiernik citation: ama: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. Total positivity in Markov structures. Annals of Statistics. 2017;45(3):1152-1184. doi:10.1214/16-AOS1478 apa: Fallat, S., Lauritzen, S., Sadeghi, K., Uhler, C., Wermuth, N., & Zwiernik, P. (2017). Total positivity in Markov structures. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AOS1478 chicago: Fallat, Shaun, Steffen Lauritzen, Kayvan Sadeghi, Caroline Uhler, Nanny Wermuth, and Piotr Zwiernik. “Total Positivity in Markov Structures.” Annals of Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AOS1478. ieee: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, and P. Zwiernik, “Total positivity in Markov structures,” Annals of Statistics, vol. 45, no. 3. Institute of Mathematical Statistics, pp. 1152–1184, 2017. ista: Fallat S, Lauritzen S, Sadeghi K, Uhler C, Wermuth N, Zwiernik P. 2017. Total positivity in Markov structures. Annals of Statistics. 45(3), 1152–1184. mla: Fallat, Shaun, et al. “Total Positivity in Markov Structures.” Annals of Statistics, vol. 45, no. 3, Institute of Mathematical Statistics, 2017, pp. 1152–84, doi:10.1214/16-AOS1478. short: S. Fallat, S. Lauritzen, K. Sadeghi, C. Uhler, N. Wermuth, P. Zwiernik, Annals of Statistics 45 (2017) 1152–1184. date_created: 2018-12-11T11:50:05Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T11:46:53Z day: '01' department: - _id: CaUh doi: 10.1214/16-AOS1478 external_id: isi: - '000404395900008' intvolume: ' 45' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.01290 month: '06' oa: 1 oa_version: Submitted Version page: 1152 - 1184 project: - _id: 2530CA10-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 903-N35 name: 'Gaussian Graphical Models: Theory and Applications' publication: Annals of Statistics publication_identifier: issn: - '00905364' publication_status: published publisher: Institute of Mathematical Statistics publist_id: '6288' quality_controlled: '1' scopus_import: '1' status: public title: Total positivity in Markov structures type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 45 year: '2017' ... --- _id: '1080' abstract: - lang: eng text: Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumour samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. Here we develop a tool, called Treeomics, to reconstruct the phylogeny of metastases and map subclones to their anatomic locations. Treeomics infers comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguates true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumour heterogeneity among distinct samples. In silico benchmarking on simulated tumour phylogenies across a wide range of sample purities (15–95%) and sequencing depths (25-800 × ) demonstrates the accuracy of Treeomics compared with existing methods. article_number: '14114' article_processing_charge: No author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Alvin full_name: Makohon Moore, Alvin last_name: Makohon Moore - first_name: Jeffrey full_name: Gerold, Jeffrey last_name: Gerold - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Christine full_name: Iacobuzio Donahue, Christine last_name: Iacobuzio Donahue - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Reiter J, Makohon Moore A, Gerold J, et al. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 2017;8. doi:10.1038/ncomms14114 apa: Reiter, J., Makohon Moore, A., Gerold, J., Božić, I., Chatterjee, K., Iacobuzio Donahue, C., … Nowak, M. (2017). Reconstructing metastatic seeding patterns of human cancers. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14114 chicago: Reiter, Johannes, Alvin Makohon Moore, Jeffrey Gerold, Ivana Božić, Krishnendu Chatterjee, Christine Iacobuzio Donahue, Bert Vogelstein, and Martin Nowak. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14114. ieee: J. Reiter et al., “Reconstructing metastatic seeding patterns of human cancers,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Reiter J, Makohon Moore A, Gerold J, Božić I, Chatterjee K, Iacobuzio Donahue C, Vogelstein B, Nowak M. 2017. Reconstructing metastatic seeding patterns of human cancers. Nature Communications. 8, 14114. mla: Reiter, Johannes, et al. “Reconstructing Metastatic Seeding Patterns of Human Cancers.” Nature Communications, vol. 8, 14114, Nature Publishing Group, 2017, doi:10.1038/ncomms14114. short: J. Reiter, A. Makohon Moore, J. Gerold, I. Božić, K. Chatterjee, C. Iacobuzio Donahue, B. Vogelstein, M. Nowak, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:02Z date_published: 2017-01-31T00:00:00Z date_updated: 2023-09-20T11:55:31Z day: '31' ddc: - '004' - '006' department: - _id: KrCh doi: 10.1038/ncomms14114 ec_funded: 1 external_id: isi: - '000393096600001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:15:15Z date_updated: 2018-12-12T10:15:15Z file_id: '5133' file_name: IST-2017-786-v1+1_ncomms14114.pdf file_size: 897050 relation: main_file file_date_updated: 2018-12-12T10:15:15Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '01' 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: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6301' pubrep_id: '786' quality_controlled: '1' scopus_import: '1' status: public title: Reconstructing metastatic seeding patterns of human cancers 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ... --- _id: '1085' abstract: - lang: eng text: Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution. article_number: '14251' article_processing_charge: No author: - first_name: Alison full_name: Wright, Alison last_name: Wright - first_name: Iulia full_name: Darolti, Iulia last_name: Darolti - first_name: Natasha full_name: Bloch, Natasha last_name: Bloch - first_name: Vicencio full_name: Oostra, Vicencio last_name: Oostra - first_name: Benjamin full_name: Sandkam, Benjamin last_name: Sandkam - first_name: Séverine full_name: Buechel, Séverine last_name: Buechel - first_name: Niclas full_name: Kolm, Niclas last_name: Kolm - first_name: Felix full_name: Breden, Felix last_name: Breden - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Judith full_name: Mank, Judith last_name: Mank citation: ama: Wright A, Darolti I, Bloch N, et al. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 2017;8. doi:10.1038/ncomms14251 apa: Wright, A., Darolti, I., Bloch, N., Oostra, V., Sandkam, B., Buechel, S., … Mank, J. (2017). Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14251 chicago: Wright, Alison, Iulia Darolti, Natasha Bloch, Vicencio Oostra, Benjamin Sandkam, Séverine Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith Mank. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14251. ieee: A. Wright et al., “Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation,” Nature Communications, vol. 8. Nature Publishing Group, 2017. ista: Wright A, Darolti I, Bloch N, Oostra V, Sandkam B, Buechel S, Kolm N, Breden F, Vicoso B, Mank J. 2017. Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation. Nature Communications. 8, 14251. mla: Wright, Alison, et al. “Convergent Recombination Suppression Suggests Role of Sexual Selection in Guppy Sex Chromosome Formation.” Nature Communications, vol. 8, 14251, Nature Publishing Group, 2017, doi:10.1038/ncomms14251. short: A. Wright, I. Darolti, N. Bloch, V. Oostra, B. Sandkam, S. Buechel, N. Kolm, F. Breden, B. Vicoso, J. Mank, Nature Communications 8 (2017). date_created: 2018-12-11T11:50:04Z date_published: 2017-01-31T00:00:00Z date_updated: 2023-09-20T11:48:16Z day: '31' ddc: - '570' - '576' department: - _id: BeVi doi: 10.1038/ncomms14251 external_id: isi: - '000392953700001' file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:15:22Z date_updated: 2018-12-12T10:15:22Z file_id: '5141' file_name: IST-2017-791-v1+1_ncomms14251.pdf file_size: 955256 relation: main_file file_date_updated: 2018-12-12T10:15:22Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - '20411723' publication_status: published publisher: Nature Publishing Group publist_id: '6292' pubrep_id: '791' quality_controlled: '1' scopus_import: '1' status: public title: Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2017' ...