--- _id: '807' abstract: - lang: eng text: 'On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.' author: - first_name: Magdalena full_name: Andrae, Magdalena last_name: Andrae - first_name: Márton full_name: Villányi, Márton id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87 last_name: Villányi orcid: 0000-0001-8126-0426 citation: ama: Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898 apa: Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898 chicago: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1898. ieee: M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB, pp. 274–280, 2017. ista: Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280. mla: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898. short: M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280. date_created: 2018-12-11T11:48:36Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:16:45Z day: '01' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v70i2.1898 file: - access_level: open_access checksum: 558c18bcf5580d87dd371ec626d52075 content_type: application/pdf creator: dernst date_created: 2019-01-18T13:39:26Z date_updated: 2020-07-14T12:48:09Z file_id: '5851' file_name: 2017_VOEB_Andrae.pdf file_size: 125065 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' intvolume: ' 70' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '08' oa: 1 oa_version: Published Version page: 274 - 280 popular_science: '1' publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare publication_identifier: issn: - '10222588' publication_status: published publisher: VÖB publist_id: '6843' scopus_import: 1 status: public title: Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2017' ... --- _id: '825' abstract: - lang: eng text: What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep. author: - first_name: Barbara full_name: Petritsch, Barbara id: 406048EC-F248-11E8-B48F-1D18A9856A87 last_name: Petritsch orcid: 0000-0003-2724-4614 citation: ama: Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207. doi:10.31263/voebm.v70i2.1678 apa: Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1678 chicago: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1678. ieee: B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017. ista: Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207. mla: Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678. short: B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 70 (2017) 200–207. date_created: 2018-12-11T11:48:42Z date_published: 2017-08-01T00:00:00Z date_updated: 2021-01-12T08:17:44Z day: '01' ddc: - '020' department: - _id: E-Lib doi: 10.31263/voebm.v70i2.1678 file: - access_level: open_access checksum: 7c4544d07efa2c2add8612b489abb4e2 content_type: application/pdf creator: dernst date_created: 2019-01-18T13:32:17Z date_updated: 2020-07-14T12:48:11Z file_id: '5850' file_name: 2017_VOEB_Petritsch.pdf file_size: 7843975 relation: main_file file_date_updated: 2020-07-14T12:48:11Z has_accepted_license: '1' intvolume: ' 70' issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 200 - 207 publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare publication_identifier: issn: - '10222588' publication_status: published publisher: VÖB publist_id: '6823' scopus_import: 1 status: public title: Metadata for research data in practice tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2017' ... --- _id: '9445' abstract: - lang: eng text: Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation. article_number: e30674 article_processing_charge: No article_type: original author: - first_name: David B full_name: Lyons, David B last_name: Lyons - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674 apa: Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674 chicago: Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674. ieee: D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017. ista: Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674. mla: Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674. short: D.B. Lyons, D. Zilberman, ELife 6 (2017). date_created: 2021-06-02T14:28:58Z date_published: 2017-11-15T00:00:00Z date_updated: 2021-12-14T07:54:36Z day: '15' ddc: - '570' department: - _id: DaZi doi: 10.7554/elife.30674 extern: '1' external_id: pmid: - '29140247' file: - access_level: open_access checksum: 4cfcdd67511ae4aed3d993550e46e146 content_type: application/pdf creator: cziletti date_created: 2021-06-02T14:33:36Z date_updated: 2021-06-02T14:33:36Z file_id: '9446' file_name: 2017_eLife_Lyons.pdf file_size: 1603102 relation: main_file success: 1 file_date_updated: 2021-06-02T14:33:36Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 6 year: '2017' ... --- _id: '957' abstract: - lang: eng text: Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors. alternative_title: - Methods in Molecular Biology author: - first_name: Ben full_name: Clifton, Ben last_name: Clifton - first_name: Jason full_name: Whitfield, Jason last_name: Whitfield - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Colin full_name: Jackson, Colin last_name: Jackson citation: ama: 'Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5' apa: Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5 chicago: Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5. ieee: B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87. ista: 'Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.' mla: Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5. short: B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87. date_created: 2018-12-11T11:49:24Z date_published: 2017-03-15T00:00:00Z date_updated: 2021-01-12T08:22:13Z day: '15' department: - _id: HaJa doi: 10.1007/978-1-4939-6940-1_5 editor: - first_name: Viktor full_name: Stein, Viktor last_name: Stein intvolume: ' 1596' language: - iso: eng month: '03' oa_version: None page: 71 - 87 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) publication: Synthetic Protein Switches publication_identifier: issn: - '10643745' publication_status: published publisher: Springer publist_id: '6451' quality_controlled: '1' scopus_import: 1 series_title: Synthetic Protein Switches status: public title: Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1596 year: '2017' ... --- _id: '963' abstract: - lang: eng text: 'Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ' alternative_title: - LIPIcs article_number: '37' author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Shibashis full_name: Guha, Shibashis last_name: Guha - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37' apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37' chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37. ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.' ista: 'Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.' mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37. short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-08-25 location: Aalborg, Denmark name: 'MFCS: Mathematical Foundations of Computer Science (SG)' start_date: 2017-08-21 date_created: 2018-12-11T11:49:26Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-23T12:35:50Z day: '01' ddc: - '004' department: - _id: ToHe doi: 10.4230/LIPIcs.MFCS.2017.37 file: - access_level: open_access checksum: f55eaf7f3c36ea07801112acfedd17d5 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:10Z date_updated: 2020-07-14T12:48:18Z file_id: '5059' file_name: IST-2017-829-v1+1_mfcs-cr.pdf file_size: 369730 relation: main_file file_date_updated: 2020-07-14T12:48:18Z has_accepted_license: '1' intvolume: ' 83' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6438' pubrep_id: '829' quality_controlled: '1' related_material: record: - id: '6005' relation: later_version status: public scopus_import: 1 status: public title: Timed network games with clocks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 83 year: '2017' ... --- _id: '9709' abstract: - lang: eng text: Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina. article_processing_charge: No author: - first_name: Jason full_name: Prentice, Jason last_name: Prentice - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Mark full_name: Ioffe, Mark last_name: Ioffe - first_name: Adrianna full_name: Loback, Adrianna last_name: Loback - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc' apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc' chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.' ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.' ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.' mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.' short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017). date_created: 2021-07-23T11:34:34Z date_published: 2017-10-18T00:00:00Z date_updated: 2023-02-21T16:34:41Z day: '18' department: - _id: GaTk doi: 10.5061/dryad.1f1rc main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.1f1rc month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '1197' relation: used_in_publication status: public status: public title: 'Data from: Error-robust modes of the retinal population code' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '541' abstract: - lang: eng text: 'While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed.' article_number: e1007122 author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Frank full_name: Schreiber, Frank last_name: Schreiber - first_name: Alma full_name: Dal Co, Alma last_name: Dal Co - first_name: Daniel full_name: Kiviet, Daniel last_name: Kiviet - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Sten full_name: Littmann, Sten last_name: Littmann - first_name: Marcel full_name: Kuypers, Marcel last_name: Kuypers - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann citation: ama: Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12). doi:10.1371/journal.pgen.1007122 apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122 chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122. ieee: N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12. Public Library of Science, 2017. ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122. mla: Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122. short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017). date_created: 2018-12-11T11:47:04Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-02-23T14:10:34Z day: '18' ddc: - '576' - '579' department: - _id: CaGu doi: 10.1371/journal.pgen.1007122 ec_funded: 1 file: - access_level: open_access checksum: 22426d9382f21554bad5fa5967afcfd0 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:35Z date_updated: 2020-07-14T12:46:46Z file_id: '5088' file_name: IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf file_size: 1308475 relation: main_file file_date_updated: 2020-07-14T12:46:46Z has_accepted_license: '1' intvolume: ' 13' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PLoS Genetics publication_identifier: issn: - '15537390' publication_status: published publisher: Public Library of Science publist_id: '7275' pubrep_id: '959' quality_controlled: '1' related_material: record: - id: '9844' relation: research_data status: public - id: '9845' relation: research_data status: public - id: '9846' relation: research_data status: public scopus_import: 1 status: public title: Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '9847' abstract: - lang: eng text: information on culture conditions, phage mutagenesis, verification and lysate preparation; Raw data article_processing_charge: No author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Pleska M, Guet CC. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. 2017. doi:10.6084/m9.figshare.5633917.v1 apa: Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1 chicago: Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1. ieee: M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification.” The Royal Society, 2017. ista: Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification, The Royal Society, 10.6084/m9.figshare.5633917.v1. mla: Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1. short: M. Pleska, C.C. Guet, (2017). date_created: 2021-08-09T13:54:38Z date_published: 2017-11-27T00:00:00Z date_updated: 2023-02-23T12:29:44Z day: '27' department: - _id: CaGu doi: 10.6084/m9.figshare.5633917.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.5633917.v1 month: '11' oa: 1 oa_version: Published Version publisher: The Royal Society related_material: record: - id: '561' relation: used_in_publication status: public status: public title: Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9845' abstract: - lang: eng text: "Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured\tin single cells" article_processing_charge: No author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Frank full_name: Schreiber, Frank last_name: Schreiber - first_name: Alma full_name: Dal Co, Alma last_name: Dal Co - first_name: Daniel full_name: Kiviet, Daniel last_name: Kiviet - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Sten full_name: Littmann, Sten last_name: Littmann - first_name: Marcel full_name: Kuypers, Marcel last_name: Kuypers - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann citation: ama: Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017 apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017 chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017. ieee: N. Nikolic et al., “Mathematical model.” Public Library of Science, 2017. ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017. mla: Nikolic, Nela, et al. Mathematical Model. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s017. short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017). date_created: 2021-08-09T13:31:51Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-02-23T12:25:04Z day: '18' department: - _id: CaGu doi: 10.1371/journal.pgen.1007122.s017 month: '12' oa_version: None publisher: Public Library of Science related_material: record: - id: '541' relation: used_in_publication status: public status: public title: Mathematical model type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9849' abstract: - lang: eng text: This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set. article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:10.1371/journal.pcbi.1005609.s001 apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001 chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001. ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017. ista: Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, 10.1371/journal.pcbi.1005609.s001. mla: Lukacisinova, Marta, et al. Modelling and Simulation Details. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001. short: M. Lukacisinova, S. Novak, T. Paixao, (2017). date_created: 2021-08-09T14:02:34Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-02-23T12:55:39Z day: '18' department: - _id: ToBo - _id: NiBa - _id: CaGu doi: 10.1371/journal.pcbi.1005609.s001 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '696' relation: used_in_publication status: public status: public title: Modelling and simulation details type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9850' abstract: - lang: eng text: In this text, we discuss how a cost of resistance and the possibility of lethal mutations impact our model. article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002 apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002 chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002. ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017. ista: Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, 10.1371/journal.pcbi.1005609.s002. mla: Lukacisinova, Marta, et al. Extensions of the Model. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002. short: M. Lukacisinova, S. Novak, T. Paixao, (2017). date_created: 2021-08-09T14:05:24Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-02-23T12:55:39Z day: '18' department: - _id: ToBo - _id: CaGu - _id: NiBa doi: 10.1371/journal.pcbi.1005609.s002 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '696' relation: used_in_publication status: public status: public title: Extensions of the model type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9846' article_processing_charge: No author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Frank full_name: Schreiber, Frank last_name: Schreiber - first_name: Alma full_name: Dal Co, Alma last_name: Dal Co - first_name: Daniel full_name: Kiviet, Daniel last_name: Kiviet - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Sten full_name: Littmann, Sten last_name: Littmann - first_name: Marcel full_name: Kuypers, Marcel last_name: Kuypers - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann citation: ama: Nikolic N, Schreiber F, Dal Co A, et al. Supplementary methods. 2017. doi:10.1371/journal.pgen.1007122.s016 apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Supplementary methods. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s016 chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s016. ieee: N. Nikolic et al., “Supplementary methods.” Public Library of Science, 2017. ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Supplementary methods, Public Library of Science, 10.1371/journal.pgen.1007122.s016. mla: Nikolic, Nela, et al. Supplementary Methods. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s016. short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017). date_created: 2021-08-09T13:35:17Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-02-23T12:25:04Z day: '18' department: - _id: CaGu doi: 10.1371/journal.pgen.1007122.s016 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '541' relation: used_in_publication status: public status: public title: Supplementary methods type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '680' abstract: - lang: eng text: In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics. article_number: e1005582 author: - first_name: Matthew J full_name: Chalk, Matthew J id: 2BAAC544-F248-11E8-B48F-1D18A9856A87 last_name: Chalk orcid: 0000-0001-7782-4436 - first_name: Paul full_name: Masset, Paul last_name: Masset - first_name: Boris full_name: Gutkin, Boris last_name: Gutkin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 2017;13(6). doi:10.1371/journal.pcbi.1005582 apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582 chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582. ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts divisive reshaping of receptive fields,” PLoS Computational Biology, vol. 13, no. 6. Public Library of Science, 2017. ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582. mla: Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational Biology, vol. 13, no. 6, e1005582, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582. short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017). date_created: 2018-12-11T11:47:53Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-23T14:10:54Z day: '01' ddc: - '571' department: - _id: GaTk doi: 10.1371/journal.pcbi.1005582 file: - access_level: open_access checksum: 796a1026076af6f4405a47d985bc7b68 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:47Z date_updated: 2020-07-14T12:47:40Z file_id: '4645' file_name: IST-2017-898-v1+1_journal.pcbi.1005582.pdf file_size: 14555676 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 13' issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS Computational Biology publication_identifier: issn: - 1553734X publication_status: published publisher: Public Library of Science publist_id: '7035' pubrep_id: '898' quality_controlled: '1' related_material: record: - id: '9855' relation: research_data status: public scopus_import: 1 status: public title: Sensory noise predicts divisive reshaping of receptive fields tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '9851' abstract: - lang: eng text: Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations. article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003 apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003 chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003. ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017. ista: Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003. mla: Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003. short: M. Lukacisinova, S. Novak, T. Paixao, (2017). date_created: 2021-08-09T14:08:14Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-02-23T12:55:39Z day: '18' department: - _id: ToBo - _id: CaGu - _id: NiBa doi: 10.1371/journal.pcbi.1005609.s003 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '696' relation: used_in_publication status: public status: public title: Heuristic prediction for multiple stresses type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9852' abstract: - lang: eng text: We show how different combination strategies affect the fraction of individuals that are multi-resistant. article_processing_charge: No author: - first_name: Marta full_name: Lukacisinova, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisinova orcid: 0000-0002-2519-8004 - first_name: Sebastian full_name: Novak, Sebastian id: 461468AE-F248-11E8-B48F-1D18A9856A87 last_name: Novak - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 citation: ama: Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004 apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004 chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004. ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017. ista: Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004. mla: Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004. short: M. Lukacisinova, S. Novak, T. Paixao, (2017). date_created: 2021-08-09T14:11:40Z date_published: 2017-07-18T00:00:00Z date_updated: 2023-02-23T12:55:39Z day: '18' department: - _id: ToBo - _id: CaGu - _id: NiBa doi: 10.1371/journal.pcbi.1005609.s004 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '696' relation: used_in_publication status: public status: public title: Resistance frequencies for different combination strategies type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9855' abstract: - lang: eng text: Includes derivation of optimal estimation algorithm, generalisation to non-poisson noise statistics, correlated input noise, and implementation of in a multi-layer neural network. article_processing_charge: No author: - first_name: Matthew J full_name: Chalk, Matthew J id: 2BAAC544-F248-11E8-B48F-1D18A9856A87 last_name: Chalk orcid: 0000-0001-7782-4436 - first_name: Paul full_name: Masset, Paul last_name: Masset - first_name: Boris full_name: Gutkin, Boris last_name: Gutkin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001 apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Supplementary appendix. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582.s001 chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001. ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017. ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public Library of Science, 10.1371/journal.pcbi.1005582.s001. mla: Chalk, Matthew J., et al. Supplementary Appendix. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582.s001. short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017). date_created: 2021-08-10T07:05:10Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-02-23T12:52:17Z day: '01' department: - _id: GaTk doi: 10.1371/journal.pcbi.1005582.s001 month: '06' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '680' relation: used_in_publication status: public status: public title: Supplementary appendix type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '941' abstract: - lang: eng text: 'Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ ' author: - first_name: Xuan full_name: Le, Xuan last_name: Le - first_name: Duc Hiep full_name: Chu, Duc Hiep id: 3598E630-F248-11E8-B48F-1D18A9856A87 last_name: Chu - first_name: David full_name: Lo, David last_name: Lo - first_name: Claire full_name: Le Goues, Claire last_name: Le Goues - first_name: Willem full_name: Visser, Willem last_name: Visser citation: ama: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. In: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ACM; 2017:376-379. doi:10.1145/3092703.3098225' apa: 'Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis (pp. 376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225' chicago: 'Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic  PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.' ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic  PathFinder,” in Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa Barbara, CA, United States, 2017, pp. 376–379.' ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic  PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379.' mla: 'Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic  PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.' short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379. conference: end_date: 2017-07-14 location: Santa Barbara, CA, United States name: 'ISSTA: International Symposium on Software Testing and Analysis' start_date: 2017-07-10 date_created: 2018-12-11T11:49:19Z date_published: 2017-07-10T00:00:00Z date_updated: 2021-01-12T08:22:05Z day: '10' department: - _id: ToHe doi: 10.1145/3092703.3098225 language: - iso: eng month: '07' oa_version: None page: '376 - 379 ' project: - _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: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis publication_status: published publisher: ACM publist_id: '6478' quality_controlled: '1' scopus_import: 1 status: public title: 'JFIX: Semantics-based repair of Java programs via symbolic PathFinder' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '9506' abstract: - lang: eng text: Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation. article_number: '87' article_processing_charge: No author: - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2 apa: Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2 chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2. ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017. ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87. mla: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature, 2017, doi:10.1186/s13059-017-1230-2. short: D. Zilberman, Genome Biology 18 (2017). date_created: 2021-06-07T12:27:39Z date_published: 2017-05-09T00:00:00Z date_updated: 2021-12-14T07:55:02Z day: '09' ddc: - '570' department: - _id: DaZi doi: 10.1186/s13059-017-1230-2 extern: '1' external_id: pmid: - '28486944' file: - access_level: open_access checksum: 5a455ad914e7d225b1baa4ab07fd925e content_type: application/pdf creator: asandaue date_created: 2021-06-07T12:31:36Z date_updated: 2021-06-07T12:31:36Z file_id: '9507' file_name: 2017_GenomeBiology_Zilberman.pdf file_size: 278183 relation: main_file success: 1 file_date_updated: 2021-06-07T12:31:36Z has_accepted_license: '1' intvolume: ' 18' issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: eissn: - 1465-6906 issn: - 1474-760X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: An evolutionary case for functional gene body methylation in plants and animals tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 18 year: '2017' ... --- _id: '958' abstract: - lang: eng text: Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors. alternative_title: - Methods in Molecular Biology author: - first_name: Joshua full_name: Mitchell, Joshua last_name: Mitchell - first_name: William full_name: Zhang, William last_name: Zhang - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Megan full_name: O'Mara, Megan last_name: O'Mara - first_name: Colin full_name: Jackson, Colin last_name: Jackson citation: ama: 'Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6' apa: Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer. https://doi.org/10.1007/978-1-4939-6940-1_6 chicago: Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6. ieee: J. Mitchell et al., “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99. ista: 'Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99.' mla: Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6. short: J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99. date_created: 2018-12-11T11:49:24Z date_published: 2017-05-15T00:00:00Z date_updated: 2021-01-12T08:22:13Z day: '15' department: - _id: HaJa doi: 10.1007/978-1-4939-6940-1_6 editor: - first_name: Viktor full_name: Stein, Viktor last_name: Stein intvolume: ' 1596' language: - iso: eng month: '05' oa_version: None page: 89 - 99 publication: Synthetic Protein Switches publication_identifier: issn: - '10643745' publication_status: published publisher: Springer publist_id: '6450' quality_controlled: '1' scopus_import: 1 series_title: Synthetic Protein Switches status: public title: Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 1596 year: '2017' ... --- _id: '9707' abstract: - lang: eng text: Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis. article_processing_charge: No author: - first_name: Paul full_name: Riccio, Paul last_name: Riccio - first_name: Christina full_name: Cebrián, Christina last_name: Cebrián - first_name: Hui full_name: Zong, Hui last_name: Zong - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Frank full_name: Costantini, Frank last_name: Costantini citation: ama: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:10.5061/dryad.pk16b' apa: 'Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b' chicago: 'Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b.' ieee: 'P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.' ista: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, 10.5061/dryad.pk16b.' mla: 'Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.' short: P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017). date_created: 2021-07-23T09:39:34Z date_published: 2017-01-14T00:00:00Z date_updated: 2022-08-25T13:34:55Z day: '14' department: - _id: SiHi doi: 10.5061/dryad.pk16b main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.pk16b month: '01' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9702' relation: used_in_publication status: deleted status: public title: 'Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '9844' article_processing_charge: No author: - first_name: Nela full_name: Nikolic, Nela id: 42D9CABC-F248-11E8-B48F-1D18A9856A87 last_name: Nikolic orcid: 0000-0001-9068-6090 - first_name: Frank full_name: Schreiber, Frank last_name: Schreiber - first_name: Alma full_name: Dal Co, Alma last_name: Dal Co - first_name: Daniel full_name: Kiviet, Daniel last_name: Kiviet - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Sten full_name: Littmann, Sten last_name: Littmann - first_name: Marcel full_name: Kuypers, Marcel last_name: Kuypers - first_name: Martin full_name: Ackermann, Martin last_name: Ackermann citation: ama: Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:10.1371/journal.pgen.1007122.s018 apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s018 chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s018. ieee: N. Nikolic et al., “Source data for figures and tables.” Public Library of Science, 2017. ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science, 10.1371/journal.pgen.1007122.s018. mla: Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s018. short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017). date_created: 2021-08-09T13:27:16Z date_published: 2017-12-18T00:00:00Z date_updated: 2023-02-23T12:25:04Z day: '18' department: - _id: CaGu doi: 10.1371/journal.pgen.1007122.s018 month: '12' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '541' relation: used_in_publication status: public status: public title: Source data for figures and tables type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '12905' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Janos full_name: Kiss, Janos id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87 last_name: Kiss citation: ama: 'Schlögl A, Kiss J. Scientific Computing at IST Austria. In: AHPC17 – Austrian HPC Meeting 2017. FSP Scientific Computing; 2017:28.' apa: 'Schlögl, A., & Kiss, J. (2017). Scientific Computing at IST Austria. In AHPC17 – Austrian HPC Meeting 2017 (p. 28). Grundlsee, Austria: FSP Scientific Computing.' chicago: Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In AHPC17 – Austrian HPC Meeting 2017, 28. FSP Scientific Computing, 2017. ieee: A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in AHPC17 – Austrian HPC Meeting 2017, Grundlsee, Austria, 2017, p. 28. ista: 'Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.' mla: Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28. short: A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28. conference: end_date: 2017-03-03 location: Grundlsee, Austria name: 'AHPC: Austrian HPC Meeting' start_date: 2017-03-01 date_created: 2023-05-05T12:58:53Z date_published: 2017-03-03T00:00:00Z date_updated: 2023-05-16T07:22:23Z day: '03' ddc: - '000' department: - _id: ScienComp file: - access_level: open_access checksum: 7bcc499479d4f4c5ce6c0071c24ca6c6 content_type: application/pdf creator: dernst date_created: 2023-05-16T07:20:50Z date_updated: 2023-05-16T07:20:50Z file_id: '12969' file_name: 2017_AHPC_Schloegl.pdf file_size: 1005486 relation: main_file success: 1 file_date_updated: 2023-05-16T07:20:50Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf month: '03' oa: 1 oa_version: Published Version page: '28' publication: AHPC17 – Austrian HPC Meeting 2017 publication_status: published publisher: FSP Scientific Computing status: public title: Scientific Computing at IST Austria type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '13160' abstract: - lang: eng text: "Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae." acknowledgement: This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 - first_name: Clara full_name: Waldmann, Clara last_name: Waldmann - first_name: Maximilian full_name: Weininger, Maximilian last_name: Weininger citation: ama: 'Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 10205. Springer; 2017:443-460. doi:10.1007/978-3-662-54577-5_26' apa: 'Kretinsky, J., Meggendorfer, T., Waldmann, C., & Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_26' chicago: Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In Tools and Algorithms for the Construction and Analysis of Systems, 10205:443–60. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_26. ieee: J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460. ista: 'Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.' mla: Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 10205, Springer, 2017, pp. 443–60, doi:10.1007/978-3-662-54577-5_26. short: J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460. 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: 2023-06-21T13:21:14Z date_published: 2017-03-31T00:00:00Z date_updated: 2023-06-21T13:29:46Z day: '31' department: - _id: KrCh doi: 10.1007/978-3-662-54577-5_26 external_id: arxiv: - '1701.05738' intvolume: ' 10205' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1701.05738 month: '03' oa: 1 oa_version: Preprint page: 443-460 publication: Tools and Algorithms for the Construction and Analysis of Systems publication_identifier: eisbn: - '9783662545775' eissn: - 1611-3349 isbn: - '9783662545768' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' status: public title: Index appearance record for transforming Rabin automata into parity automata type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10205 year: '2017' ... --- _id: '950' abstract: - lang: eng text: "Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n" alternative_title: - LIPIcs article_number: '17' author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - 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: Ventsislav K full_name: Chonev, Ventsislav K id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87 last_name: Chonev citation: ama: 'Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21' apa: 'Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21' chicago: Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21. ieee: 'G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.' ista: 'Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.' mla: Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21. short: G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-09-07 location: Berlin, Germany name: 'CONCUR: Concurrency Theory' start_date: 2017-09-05 date_created: 2018-12-11T11:49:22Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-08-29T07:02:13Z day: '01' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.4230/LIPIcs.CONCUR.2017.21 external_id: arxiv: - '1705.01433' file: - access_level: open_access checksum: 6d5cccf755207b91ccbef95d8275b013 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:00Z date_updated: 2020-07-14T12:48:16Z file_id: '5318' file_name: IST-2017-844-v1+1_concur-cr.pdf file_size: 335170 relation: main_file file_date_updated: 2020-07-14T12:48:16Z has_accepted_license: '1' intvolume: ' 85' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '6466' pubrep_id: '844' quality_controlled: '1' related_material: record: - id: '6752' relation: later_version status: public scopus_import: 1 status: public title: Infinite-duration bidding games tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 85 year: '2017' ... --- _id: '683' abstract: - lang: eng text: 'Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.' alternative_title: - LIPIcs article_number: '49' author: - first_name: Anna full_name: Lubiw, Anna last_name: Lubiw - first_name: Zuzana full_name: Masárová, Zuzana id: 45CFE238-F248-11E8-B48F-1D18A9856A87 last_name: Masárová orcid: 0000-0002-6660-1322 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.SoCG.2017.49' apa: 'Lubiw, A., Masárová, Z., & Wagner, U. (2017). A proof of the orbit conjecture for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.49' chicago: Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.49. ieee: 'A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia, 2017, vol. 77.' ista: 'Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 77, 49.' mla: Lubiw, Anna, et al. A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.SoCG.2017.49. short: A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. conference: end_date: 2017-07-07 location: Brisbane, Australia name: 'SoCG: Symposium on Computational Geometry' start_date: 2017-07-04 date_created: 2018-12-11T11:47:54Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-05T15:01:43Z day: '01' ddc: - '514' - '516' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2017.49 file: - access_level: open_access checksum: 24fdde981cc513352a78dcf9b0660ae9 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:12Z date_updated: 2020-07-14T12:47:41Z file_id: '5265' file_name: IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf file_size: 710007 relation: main_file file_date_updated: 2020-07-14T12:47:41Z has_accepted_license: '1' intvolume: ' 77' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7033' pubrep_id: '896' quality_controlled: '1' related_material: record: - id: '5986' relation: later_version status: public scopus_import: 1 status: public title: A proof of the orbit conjecture for flipping edge labelled triangulations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 77 year: '2017' ... --- _id: '1155' abstract: - lang: eng text: This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results. acknowledgement: ' First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Przemyslaw full_name: Daca, Przemyslaw id: 49351290-F248-11E8-B48F-1D18A9856A87 last_name: Daca citation: ama: Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730 apa: Daca, P. (2017). Statistical and logical methods for property checking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_730 chicago: Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:TH_730. ieee: P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017. ista: Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria. mla: Daca, Przemyslaw. Statistical and Logical Methods for Property Checking. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730. short: P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:50:27Z date_published: 2017-01-02T00:00:00Z date_updated: 2023-09-07T11:58:34Z day: '02' ddc: - '004' - '005' degree_awarded: PhD department: - _id: ToHe doi: 10.15479/AT:ISTA:TH_730 ec_funded: 1 file: - access_level: open_access checksum: 1406a681cb737508234fde34766be2c2 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:26Z date_updated: 2020-07-14T12:44:34Z file_id: '4880' file_name: IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf file_size: 1028586 relation: main_file file_date_updated: 2020-07-14T12:44:34Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '163' project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6203' pubrep_id: '730' related_material: record: - id: '1093' relation: part_of_dissertation status: public - id: '1230' relation: part_of_dissertation status: public - id: '1234' relation: part_of_dissertation status: public - id: '1391' relation: part_of_dissertation status: public - id: '1501' relation: part_of_dissertation status: public - id: '1502' relation: part_of_dissertation status: public - id: '2063' relation: part_of_dissertation status: public - id: '2167' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 title: Statistical and logical methods for property checking type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '6291' abstract: - lang: eng text: Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pavel full_name: Payne, Pavel id: 35F78294-F248-11E8-B48F-1D18A9856A87 last_name: Payne orcid: 0000-0002-2711-9453 citation: ama: Payne P. Bacterial herd and social immunity to phages. 2017. apa: Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria. chicago: Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017. ieee: P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017. ista: Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria. mla: Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017. short: P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017. date_created: 2019-04-09T15:16:45Z date_published: 2017-02-01T00:00:00Z date_updated: 2023-09-07T12:00:00Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: NiBa - _id: JoBo file: - access_level: closed checksum: a0fc5c26a89c0ea759947ffba87d0d8f content_type: application/pdf creator: dernst date_created: 2019-04-09T15:15:32Z date_updated: 2020-07-14T12:47:27Z file_id: '6292' file_name: thesis_pavel_payne_final_w_signature_page.pdf file_size: 3025175 relation: main_file - access_level: open_access checksum: af531e921a7f64a9e0af4cd8783b2226 content_type: application/pdf creator: dernst date_created: 2021-02-22T13:45:59Z date_updated: 2021-02-22T13:45:59Z file_id: '9187' file_name: 2017_Payne_Thesis.pdf file_size: 3111536 relation: main_file success: 1 file_date_updated: 2021-02-22T13:45:59Z has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '83' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Bacterial herd and social immunity to phages type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '561' abstract: - lang: eng text: Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape. acknowledgement: This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria. article_number: '20170646' article_processing_charge: No article_type: original author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646 apa: Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0646 chicago: Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646. ieee: M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017. ista: Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646. mla: Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646. short: M. Pleska, C.C. Guet, Biology Letters 13 (2017). date_created: 2018-12-11T11:47:11Z date_published: 2017-12-01T00:00:00Z date_updated: 2023-09-07T11:59:32Z day: '01' department: - _id: CaGu doi: 10.1098/rsbl.2017.0646 external_id: pmid: - '29237814' intvolume: ' 13' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rsbl.2017.0646 month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 251BCBEC-B435-11E9-9278-68D0E5697425 grant_number: RGY0079/2011 name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant) - _id: 251D65D8-B435-11E9-9278-68D0E5697425 grant_number: '24210' name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship) publication: Biology Letters publication_identifier: issn: - 1744-9561 publication_status: published publisher: The Royal Society publist_id: '7253' quality_controlled: '1' related_material: record: - id: '9847' relation: research_data status: public - id: '202' relation: dissertation_contains status: public scopus_import: '1' status: public title: Effects of mutations in phage restriction sites during escape from restriction–modification type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2017' ... --- _id: '818' abstract: - lang: eng text: 'Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ' acknowledgement: 'First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch citation: ama: Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862 apa: Mitosch, K. (2017). Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862 chicago: Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862. ieee: K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017. ista: Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. mla: Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862. short: K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:40Z date_published: 2017-09-27T00:00:00Z date_updated: 2023-09-07T12:00:26Z day: '27' ddc: - '571' - '579' degree_awarded: PhD department: - _id: ToBo doi: 10.15479/AT:ISTA:th_862 file: - access_level: closed checksum: da3993c5f90f59a8e8623cc31ad501dd content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:48:51Z date_updated: 2020-07-14T12:48:09Z file_id: '6210' file_name: Thesis_KarinMitosch.docx file_size: 6331071 relation: source_file - access_level: open_access checksum: 24c3d9e51992f1b721f3df55aa13fcb8 content_type: application/pdf creator: dernst date_created: 2019-04-05T08:48:51Z date_updated: 2020-07-14T12:48:09Z file_id: '6211' file_name: Thesis_KarinMitosch.pdf file_size: 9289852 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '113' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6831' pubrep_id: '862' related_material: record: - id: '2001' relation: part_of_dissertation status: public - id: '666' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X title: Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '666' abstract: - lang: eng text: Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors. article_processing_charge: Yes (in subscription journal) author: - first_name: Karin full_name: Mitosch, Karin id: 39B66846-F248-11E8-B48F-1D18A9856A87 last_name: Mitosch - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001 apa: Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001 chicago: Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001. ieee: K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017. ista: Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403. mla: Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001. short: K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403. date_created: 2018-12-11T11:47:48Z date_published: 2017-04-26T00:00:00Z date_updated: 2023-09-07T12:00:25Z day: '26' ddc: - '576' - '610' department: - _id: ToBo - _id: GaTk doi: 10.1016/j.cels.2017.03.001 ec_funded: 1 file: - access_level: open_access checksum: 04ff20011c3d9a601c514aa999a5fe1a content_type: application/pdf creator: system date_created: 2018-12-12T10:13:54Z date_updated: 2020-07-14T12:47:35Z file_id: '5041' file_name: IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf file_size: 2438660 relation: main_file file_date_updated: 2020-07-14T12:47:35Z has_accepted_license: '1' intvolume: ' 4' issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '04' oa: 1 oa_version: Published Version page: 393 - 403 project: - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth publication: Cell Systems publication_identifier: issn: - '24054712' publication_status: published publisher: Cell Press publist_id: '7061' pubrep_id: '901' quality_controlled: '1' related_material: record: - id: '818' relation: dissertation_contains status: public scopus_import: 1 status: public title: Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2017' ... --- _id: '821' abstract: - lang: eng text: "This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games." acknowledgement: "First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, \ Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 citation: ama: Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854 apa: Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854 chicago: Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854. ieee: A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017. ista: Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. mla: Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854. short: A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:41Z date_published: 2017-08-09T00:00:00Z date_updated: 2023-09-07T12:01:59Z day: '09' ddc: - '000' degree_awarded: PhD department: - _id: KrCh doi: 10.15479/AT:ISTA:th_854 ec_funded: 1 file: - access_level: open_access checksum: 3a3ec003f6ee73f41f82a544d63dfc77 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:44Z date_updated: 2020-07-14T12:48:10Z file_id: '4900' file_name: IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf file_size: 4103115 relation: main_file - access_level: closed checksum: bd2facc45ff8a2e20c5ed313c2ccaa83 content_type: application/zip creator: dernst date_created: 2019-04-05T07:59:31Z date_updated: 2020-07-14T12:48:10Z file_id: '6201' file_name: 2017_thesis_Pavlogiannis.zip file_size: 14744374 relation: source_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nd/4.0/ month: '08' oa: 1 oa_version: Published Version page: '418' project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6828' pubrep_id: '854' related_material: record: - id: '1071' relation: part_of_dissertation status: public - id: '1437' relation: part_of_dissertation status: public - id: '1602' relation: part_of_dissertation status: public - id: '1604' relation: part_of_dissertation status: public - id: '1607' relation: part_of_dissertation status: public - id: '1714' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: Algorithmic advances in program analysis and their applications tmp: image: /image/cc_by_nd.png legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) short: CC BY-ND (4.0) type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '820' abstract: - lang: eng text: "The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background." acknowledgement: "ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Fabienne full_name: Jesse, Fabienne id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87 last_name: Jesse citation: ama: Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857 apa: Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857 chicago: Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857. ieee: F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017. ista: Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria. mla: Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857. short: F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:41Z date_published: 2017-08-25T00:00:00Z date_updated: 2023-09-07T12:01:21Z day: '25' ddc: - '576' - '577' - '579' degree_awarded: PhD department: - _id: JoBo doi: 10.15479/AT:ISTA:th_857 ec_funded: 1 file: - access_level: open_access checksum: c62257a7bff0c5f39e1abffc6bfcca5c content_type: application/pdf creator: system date_created: 2018-12-12T10:17:00Z date_updated: 2020-07-14T12:48:10Z file_id: '5252' file_name: IST-2017-857-v1+1_thesis_fabienne.pdf file_size: 3417773 relation: main_file - access_level: closed checksum: fc87d7d72fce52824a3ae7dcad0413a8 content_type: application/x-tex creator: dernst date_created: 2019-04-05T08:51:59Z date_updated: 2020-07-14T12:48:10Z file_id: '6212' file_name: 2017_thesis_Jesse_source.tex file_size: 215899 relation: source_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '87' project: - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6829' pubrep_id: '857' status: public supervisor: - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 title: The lac operon in the wild 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '838' abstract: - lang: eng text: 'In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: ama: Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828 apa: Rybar, M. (2017). (The exact security of) Message authentication codes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828 chicago: Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828. ieee: M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017. ista: Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria. mla: Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828. short: M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:46Z date_published: 2017-06-26T00:00:00Z date_updated: 2023-09-07T12:02:28Z day: '26' ddc: - '000' degree_awarded: PhD department: - _id: KrPi doi: 10.15479/AT:ISTA:th_828 file: - access_level: open_access checksum: ff8639ec4bded6186f44c7bd3ee26804 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:13Z date_updated: 2020-07-14T12:48:12Z file_id: '4799' file_name: IST-2017-828-v1+3_2017_Rybar_thesis.pdf file_size: 847400 relation: main_file - access_level: closed checksum: 3462101745ce8ad199c2d0f75dae4a7e content_type: application/zip creator: dernst date_created: 2019-04-05T08:24:11Z date_updated: 2020-07-14T12:48:12Z file_id: '6202' file_name: 2017_Thesis_Rybar_source.zip file_size: 26054879 relation: source_file file_date_updated: 2020-07-14T12:48:12Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '86' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6810' pubrep_id: '828' related_material: record: - id: '2082' relation: part_of_dissertation status: public - id: '6196' relation: part_of_dissertation status: public status: public title: (The exact security of) Message authentication codes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '6196' abstract: - lang: eng text: PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem. author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: ama: Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161 apa: Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC. IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161 chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum, 2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161. ieee: P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017. ista: Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 145–161. mla: Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161. short: P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 145–161. date_created: 2019-04-04T13:48:23Z date_published: 2017-02-03T00:00:00Z date_updated: 2023-09-07T12:02:27Z day: '03' ddc: - '000' department: - _id: KrPi doi: 10.13154/TOSC.V2016.I2.145-161 ec_funded: 1 file: - access_level: open_access checksum: f23161d685dd957ae8d7274132999684 content_type: application/pdf creator: dernst date_created: 2019-04-04T13:53:58Z date_updated: 2020-07-14T12:47:24Z file_id: '6197' file_name: 2017_IACR_Gazi.pdf file_size: 597335 relation: main_file file_date_updated: 2020-07-14T12:47:24Z has_accepted_license: '1' intvolume: ' 2016' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 145-161 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: IACR Transactions on Symmetric Cryptology publication_identifier: eissn: - 2519-173X publication_status: published publisher: Ruhr University Bochum quality_controlled: '1' related_material: record: - id: '838' relation: dissertation_contains status: public status: public title: The exact security of PMAC tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016 year: '2017' ... --- _id: '837' abstract: - lang: eng text: 'The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ' acknowledgement: 'I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Haibing full_name: Xu, Haibing id: 310349D0-F248-11E8-B48F-1D18A9856A87 last_name: Xu citation: ama: Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858 apa: Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858 chicago: Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858. ieee: H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017. ista: Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. mla: Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858. short: H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:48:46Z date_published: 2017-08-23T00:00:00Z date_updated: 2023-09-07T12:06:38Z day: '23' ddc: - '571' degree_awarded: PhD department: - _id: JoCs doi: 10.15479/AT:ISTA:th_858 file: - access_level: closed checksum: f11925fbbce31e495124b6bc4f10573c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:59:51Z date_updated: 2020-07-14T12:48:12Z file_id: '6213' file_name: 2017_Xu_Haibing_Thesis_Source.docx file_size: 3589490 relation: source_file - access_level: open_access checksum: ffb10749a537d615fab1ef0937ccb157 content_type: application/pdf creator: dernst date_created: 2019-04-05T08:59:51Z date_updated: 2020-07-14T12:48:12Z file_id: '6214' file_name: 2017_Xu_Thesis_IST.pdf file_size: 11668613 relation: main_file file_date_updated: 2020-07-14T12:48:12Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '93' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6811' pubrep_id: '858' related_material: record: - id: '5828' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Reactivation of the hippocampal cognitive map in goal-directed spatial tasks 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '938' abstract: - lang: eng text: The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Maciek full_name: Adamowski, Maciek id: 45F536D2-F248-11E8-B48F-1D18A9856A87 last_name: Adamowski orcid: 0000-0001-6463-5257 citation: ama: Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842 apa: Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842 chicago: Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842. ieee: M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017. ista: Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. mla: Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842. short: M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:49:18Z date_published: 2017-06-02T00:00:00Z date_updated: 2023-09-07T12:06:09Z day: '02' ddc: - '581' - '583' - '580' degree_awarded: PhD department: - _id: JiFr doi: 10.15479/AT:ISTA:th_842 file: - access_level: closed checksum: 193425764d9aaaed3ac57062a867b315 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T09:03:20Z date_updated: 2020-07-14T12:48:15Z file_id: '6215' file_name: 2017_Adamowski-Thesis_Source.docx file_size: 46903863 relation: source_file - access_level: open_access checksum: df5ab01be81f821e1b958596a1ec8d21 content_type: application/pdf creator: dernst date_created: 2019-04-05T09:03:19Z date_updated: 2020-07-14T12:48:15Z file_id: '6216' file_name: 2017_Adamowski-Thesis.pdf file_size: 8698888 relation: main_file file_date_updated: 2020-07-14T12:48:15Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '117' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6483' pubrep_id: '842' related_material: record: - id: '1591' 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: 'Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '992' abstract: - lang: eng text: "An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of\r\nvariables, a finite domain of labels, and a set of constraints, each constraint acting on\r\na subset of the variables. The goal is to find an assignment of labels to its variables\r\nthat satisfies all constraints (or decide whether one exists). If we allow more general\r\n“soft” constraints, which come with (possibly infinite) costs of particular assignments,\r\nwe obtain instances from a richer class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal is to find an assignment with minimum total cost.\r\nIn this thesis, we focus (assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage, that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe complexity classification modulo (missing pieces of) complexity classification for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’ perfect\r\nmatching algorithm. This generalization contributes to complexity classfications in two\r\nways. First, it gives a new (largest known) polynomial-time solvable class of Boolean\r\nCSPs in which every variable may appear in at most two constraints and second, it\r\nsettles full classification of Boolean CSPs with planar drawing (again parametrized by a\r\nconstraint language)." acknowledgement: FP7/2007-2013/ERC grant agreement no 616160 alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815 apa: Rolinek, M. (2017). Complexity of constraint satisfaction. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815 chicago: Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815. ieee: M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017. ista: Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria. mla: Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815. short: M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:49:35Z date_published: 2017-05-01T00:00:00Z date_updated: 2023-09-07T12:05:41Z day: '01' ddc: - '004' degree_awarded: PhD department: - _id: VlKo doi: 10.15479/AT:ISTA:th_815 ec_funded: 1 file: - access_level: open_access checksum: 81761fb939acb7585c36629f765b4373 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:55Z date_updated: 2020-07-14T12:48:18Z file_id: '4654' file_name: IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf file_size: 786145 relation: main_file - access_level: closed checksum: 2b2d7e1d6c1c79a9795a7aa0f860baf3 content_type: application/zip creator: dernst date_created: 2019-04-05T08:43:24Z date_updated: 2020-07-14T12:48:18Z file_id: '6208' file_name: 2017_Thesis_Rolinek_source.zip file_size: 5936337 relation: source_file file_date_updated: 2020-07-14T12:48:18Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '97' project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6407' pubrep_id: '815' status: public supervisor: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov title: Complexity of constraint satisfaction type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '718' abstract: - lang: eng text: Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 - first_name: Matthias full_name: Reitzner, Matthias last_name: Reitzner citation: ama: Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 2017;49(3):745-767. doi:10.1017/apr.2017.20 apa: Edelsbrunner, H., Nikitenko, A., & Reitzner, M. (2017). Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. Cambridge University Press. https://doi.org/10.1017/apr.2017.20 chicago: Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability. Cambridge University Press, 2017. https://doi.org/10.1017/apr.2017.20. ieee: H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson Delaunay mosaics and their discrete Morse functions,” Advances in Applied Probability, vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017. ista: Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3), 745–767. mla: Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability, vol. 49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:10.1017/apr.2017.20. short: H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767. date_created: 2018-12-11T11:48:07Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-07T12:07:12Z day: '01' department: - _id: HeEd doi: 10.1017/apr.2017.20 ec_funded: 1 external_id: arxiv: - '1607.05915' intvolume: ' 49' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.05915 month: '09' oa: 1 oa_version: Preprint page: 745 - 767 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Advances in Applied Probability publication_identifier: issn: - '00018678' publication_status: published publisher: Cambridge University Press publist_id: '6962' quality_controlled: '1' related_material: record: - id: '6287' relation: dissertation_contains status: public scopus_import: 1 status: public title: Expected sizes of poisson Delaunay mosaics and their discrete Morse functions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2017' ... --- _id: '559' abstract: - lang: eng text: 'Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2).' alternative_title: - LNCS author: - first_name: Hamza M full_name: Abusalah, Hamza M id: 40297222-F248-11E8-B48F-1D18A9856A87 last_name: Abusalah - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Bram full_name: Cohen, Bram last_name: Cohen - first_name: Danylo full_name: Khilko, Danylo last_name: Khilko - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Leonid full_name: Reyzin, Leonid last_name: Reyzin citation: ama: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer; 2017:357-379. doi:10.1007/978-3-319-70697-9_13' apa: 'Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., & Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China: Springer. https://doi.org/10.1007/978-3-319-70697-9_13' chicago: Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space,” 10625:357–79. Springer, 2017. https://doi.org/10.1007/978-3-319-70697-9_13. ieee: 'H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L. Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.' ista: 'Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT: Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625, 357–379.' mla: Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13. short: H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379. conference: end_date: 2017-12-07 location: Hong Kong, China name: 'ASIACRYPT: Theory and Applications of Cryptology and Information Security' start_date: 2017-12-03 date_created: 2018-12-11T11:47:10Z date_published: 2017-11-18T00:00:00Z date_updated: 2023-09-07T12:30:22Z day: '18' department: - _id: KrPi doi: 10.1007/978-3-319-70697-9_13 ec_funded: 1 intvolume: ' 10625' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/893.pdf month: '11' oa: 1 oa_version: Submitted Version page: 357 - 379 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331970696-2 publication_status: published publisher: Springer publist_id: '7257' quality_controlled: '1' related_material: record: - id: '83' relation: dissertation_contains status: public scopus_import: 1 status: public title: Beyond Hellman’s time-memory trade-offs with applications to proofs of space type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10625 year: '2017' ... --- _id: '550' abstract: - lang: eng text: For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities. article_number: '63' author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt citation: ama: Alt J. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 2017;22. doi:10.1214/17-ECP97 apa: Alt, J. (2017). Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-ECP97 chicago: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-ECP97. ieee: J. Alt, “Singularities of the density of states of random Gram matrices,” Electronic Communications in Probability, vol. 22. Institute of Mathematical Statistics, 2017. ista: Alt J. 2017. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 22, 63. mla: Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability, vol. 22, 63, Institute of Mathematical Statistics, 2017, doi:10.1214/17-ECP97. short: J. Alt, Electronic Communications in Probability 22 (2017). date_created: 2018-12-11T11:47:07Z date_published: 2017-11-21T00:00:00Z date_updated: 2023-09-07T12:38:08Z day: '21' ddc: - '539' department: - _id: LaEr doi: 10.1214/17-ECP97 ec_funded: 1 file: - access_level: open_access checksum: 0ec05303a0de190de145654237984c79 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:04Z date_updated: 2020-07-14T12:47:00Z file_id: '4663' file_name: IST-2018-926-v1+1_euclid.ecp.1511233247.pdf file_size: 470876 relation: main_file file_date_updated: 2020-07-14T12:47:00Z has_accepted_license: '1' intvolume: ' 22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Communications in Probability publication_identifier: issn: - 1083589X publication_status: published publisher: Institute of Mathematical Statistics publist_id: '7265' pubrep_id: '926' quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: 1 status: public title: Singularities of the density of states of random Gram 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2017' ... --- _id: '647' abstract: - lang: eng text: Despite researchers’ efforts in the last couple of decades, reachability analysis is still a challenging problem even for linear hybrid systems. Among the existing approaches, the most practical ones are mainly based on bounded-time reachable set over-approximations. For the purpose of unbounded-time analysis, one important strategy is to abstract the original system and find an invariant for the abstraction. In this paper, we propose an approach to constructing a new kind of abstraction called conic abstraction for affine hybrid systems, and to computing reachable sets based on this abstraction. The essential feature of a conic abstraction is that it partitions the state space of a system into a set of convex polyhedral cones which is derived from a uniform conic partition of the derivative space. Such a set of polyhedral cones is able to cut all trajectories of the system into almost straight segments so that every segment of a reach pipe in a polyhedral cone tends to be straight as well, and hence can be over-approximated tightly by polyhedra using similar techniques as HyTech or PHAVer. In particular, for diagonalizable affine systems, our approach can guarantee to find an invariant for unbounded reachable sets, which is beyond the capability of bounded-time reachability analysis tools. We implemented the approach in a tool and experiments on benchmarks show that our approach is more powerful than SpaceEx and PHAVer in dealing with diagonalizable systems. alternative_title: - LNCS author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - 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: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 citation: ama: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid systems. In: Vol 10419. Springer; 2017:116-132. doi:10.1007/978-3-319-65765-3_7' apa: 'Bogomolov, S., Giacobbe, M., Henzinger, T. A., & Kong, H. (2017). Conic abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_7' chicago: Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_7. ieee: 'S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.' ista: 'Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 116–132.' mla: Bogomolov, Sergiy, et al. Conic Abstractions for Hybrid Systems. Vol. 10419, Springer, 2017, pp. 116–32, doi:10.1007/978-3-319-65765-3_7. short: S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017, pp. 116–132. conference: end_date: 2017-09-07 location: Berlin, Germany name: 'FORMATS: Formal Modelling and Analysis of Timed Systems' start_date: 2017-09-05 date_created: 2018-12-11T11:47:41Z date_published: 2017-09-01T00:00:00Z date_updated: 2023-09-07T12:53:00Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-319-65765-3_7 file: - access_level: open_access checksum: faf546914ba29bcf9974ee36b6b16750 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:38Z date_updated: 2020-07-14T12:47:31Z file_id: '4956' file_name: IST-2017-831-v1+1_main.pdf file_size: 3806864 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 116 - 132 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-331965764-6 publication_status: published publisher: Springer publist_id: '7129' pubrep_id: '831' quality_controlled: '1' related_material: record: - id: '6894' relation: dissertation_contains status: public scopus_import: 1 status: public title: Conic abstractions for hybrid systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: '10419 ' year: '2017' ... --- _id: '631' abstract: - lang: eng text: Template polyhedra generalize intervals and octagons to polyhedra whose facets are orthogonal to a given set of arbitrary directions. They have been employed in the abstract interpretation of programs and, with particular success, in the reachability analysis of hybrid automata. While previously, the choice of directions has been left to the user or a heuristic, we present a method for the automatic discovery of directions that generalize and eliminate spurious counterexamples. We show that for the class of convex hybrid automata, i.e., hybrid automata with (possibly nonlinear) convex constraints on derivatives, such directions always exist and can be found using convex optimization. We embed our method inside a CEGAR loop, thus enabling the time-unbounded reachability analysis of an important and richer class of hybrid automata than was previously possible. We evaluate our method on several benchmarks, demonstrating also its superior efficiency for the special case of linear hybrid automata. acknowledgement: This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), by the European Commission under grant 643921 (UnCoVerCPS), and by the ARC project DP140104219 (Robust AI Planning for Hybrid Systems). alternative_title: - LNCS author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. Counterexample guided refinement of template polyhedra. In: Vol 10205. Springer; 2017:589-606. doi:10.1007/978-3-662-54577-5_34' apa: 'Bogomolov, S., Frehse, G., Giacobbe, M., & Henzinger, T. A. (2017). Counterexample guided refinement of template polyhedra (Vol. 10205, pp. 589–606). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_34' chicago: Bogomolov, Sergiy, Goran Frehse, Mirco Giacobbe, and Thomas A Henzinger. “Counterexample Guided Refinement of Template Polyhedra,” 10205:589–606. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_34. ieee: 'S. Bogomolov, G. Frehse, M. Giacobbe, and T. A. Henzinger, “Counterexample guided refinement of template polyhedra,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 589–606.' ista: 'Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. 2017. Counterexample guided refinement of template polyhedra. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 589–606.' mla: Bogomolov, Sergiy, et al. Counterexample Guided Refinement of Template Polyhedra. Vol. 10205, Springer, 2017, pp. 589–606, doi:10.1007/978-3-662-54577-5_34. short: S. Bogomolov, G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2017, pp. 589–606. 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: 2018-12-11T11:47:36Z date_published: 2017-03-31T00:00:00Z date_updated: 2023-09-07T12:53:00Z day: '31' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-662-54577-5_34 file: - access_level: open_access checksum: f395d0d20102b89aeaad8b4ef4f18f4f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:41Z date_updated: 2020-07-14T12:47:27Z file_id: '4897' file_name: IST-2017-741-v1+1_main.pdf file_size: 569863 relation: main_file - access_level: open_access checksum: f416ee1ae4497b23ecdf28b1f18bb8df content_type: application/pdf creator: system date_created: 2018-12-12T10:11:42Z date_updated: 2020-07-14T12:47:27Z file_id: '4898' file_name: IST-2018-741-v2+2_main.pdf file_size: 563276 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' intvolume: ' 10205' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 589 - 606 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-366254576-8 publication_status: published publisher: Springer publist_id: '7162' pubrep_id: '966' quality_controlled: '1' related_material: record: - id: '6894' relation: dissertation_contains status: public scopus_import: 1 status: public title: Counterexample guided refinement of template polyhedra type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10205 year: '2017' ... --- _id: '1144' abstract: - lang: eng text: We show that matrix elements of functions of N × N Wigner matrices fluctuate on a scale of order N−1/2 and we identify the limiting fluctuation. Our result holds for any function f of the matrix that has bounded variation thus considerably relaxing the regularity requirement imposed in [7, 11]. acknowledgement: Partially supported by the IST Austria Excellence Scholarship. article_number: '86' author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Erdös L, Schröder DJ. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 2017;21. doi:10.1214/16-ECP38 apa: Erdös, L., & Schröder, D. J. (2017). Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-ECP38 chicago: Erdös, László, and Dominik J Schröder. “Fluctuations of Functions of Wigner Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-ECP38. ieee: L. Erdös and D. J. Schröder, “Fluctuations of functions of Wigner matrices,” Electronic Communications in Probability, vol. 21. Institute of Mathematical Statistics, 2017. ista: Erdös L, Schröder DJ. 2017. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 21, 86. mla: Erdös, László, and Dominik J. Schröder. “Fluctuations of Functions of Wigner Matrices.” Electronic Communications in Probability, vol. 21, 86, Institute of Mathematical Statistics, 2017, doi:10.1214/16-ECP38. short: L. Erdös, D.J. Schröder, Electronic Communications in Probability 21 (2017). date_created: 2018-12-11T11:50:23Z date_published: 2017-01-02T00:00:00Z date_updated: 2023-09-07T12:54:12Z day: '02' ddc: - '510' department: - _id: LaEr doi: 10.1214/16-ECP38 ec_funded: 1 file: - access_level: open_access content_type: application/pdf creator: system date_created: 2018-12-12T10:18:10Z date_updated: 2018-12-12T10:18:10Z file_id: '5329' file_name: IST-2017-747-v1+1_euclid.ecp.1483347665.pdf file_size: 440770 relation: main_file file_date_updated: 2018-12-12T10:18:10Z has_accepted_license: '1' intvolume: ' 21' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: Electronic Communications in Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '6214' pubrep_id: '747' quality_controlled: '1' related_material: record: - id: '6179' relation: dissertation_contains status: public scopus_import: 1 status: public title: Fluctuations of functions of Wigner 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2017' ... --- _id: '486' abstract: - lang: eng text: Color texture reproduction in 3D printing commonly ignores volumetric light transport (cross-talk) between surface points on a 3D print. Such light diffusion leads to significant blur of details and color bleeding, and is particularly severe for highly translucent resin-based print materials. Given their widely varying scattering properties, this cross-talk between surface points strongly depends on the internal structure of the volume surrounding each surface point. Existing scattering-aware methods use simplified models for light diffusion, and often accept the visual blur as an immutable property of the print medium. In contrast, our work counteracts heterogeneous scattering to obtain the impression of a crisp albedo texture on top of the 3D print, by optimizing for a fully volumetric material distribution that preserves the target appearance. Our method employs an efficient numerical optimizer on top of a general Monte-Carlo simulation of heterogeneous scattering, supported by a practical calibration procedure to obtain scattering parameters from a given set of printer materials. Despite the inherent translucency of the medium, we reproduce detailed surface textures on 3D prints. We evaluate our system using a commercial, five-tone 3D print process and compare against the printer’s native color texturing mode, demonstrating that our method preserves high-frequency features well without having to compromise on color gamut. article_number: '241' article_processing_charge: No article_type: original author: - first_name: Oskar full_name: Elek, Oskar last_name: Elek - first_name: Denis full_name: Sumin, Denis last_name: Sumin - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Alexander full_name: Wilkie, Alexander last_name: Wilkie - first_name: Jaroslav full_name: Krivanek, Jaroslav last_name: Krivanek citation: ama: Elek O, Sumin D, Zhang R, et al. Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 2017;36(6). doi:10.1145/3130800.3130890 apa: Elek, O., Sumin, D., Zhang, R., Weyrich, T., Myszkowski, K., Bickel, B., … Krivanek, J. (2017). Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3130800.3130890 chicago: Elek, Oskar, Denis Sumin, Ran Zhang, Tim Weyrich, Karol Myszkowski, Bernd Bickel, Alexander Wilkie, and Jaroslav Krivanek. “Scattering-Aware Texture Reproduction for 3D Printing.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3130800.3130890. ieee: O. Elek et al., “Scattering-aware texture reproduction for 3D printing,” ACM Transactions on Graphics, vol. 36, no. 6. ACM, 2017. ista: Elek O, Sumin D, Zhang R, Weyrich T, Myszkowski K, Bickel B, Wilkie A, Krivanek J. 2017. Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 36(6), 241. mla: Elek, Oskar, et al. “Scattering-Aware Texture Reproduction for 3D Printing.” ACM Transactions on Graphics, vol. 36, no. 6, 241, ACM, 2017, doi:10.1145/3130800.3130890. short: O. Elek, D. Sumin, R. Zhang, T. Weyrich, K. Myszkowski, B. Bickel, A. Wilkie, J. Krivanek, ACM Transactions on Graphics 36 (2017). date_created: 2018-12-11T11:46:44Z date_published: 2017-11-20T00:00:00Z date_updated: 2023-09-07T13:11:15Z day: '20' ddc: - '003' - '000' - '005' department: - _id: BeBi doi: 10.1145/3130800.3130890 ec_funded: 1 file: - access_level: open_access checksum: 48386fa6956c3645fc89594dc898b147 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:46Z date_updated: 2020-07-14T12:46:35Z file_id: '4836' file_name: IST-2018-1052-v1+1_ElekSumin2017SGA.pdf file_size: 107349827 relation: main_file - access_level: open_access checksum: 21c89c28fb8d70f6602f752bf997aa0f content_type: application/pdf creator: bbickel date_created: 2019-12-16T14:48:57Z date_updated: 2020-07-14T12:46:35Z file_id: '7189' file_name: ElekSumin2017SGA_reduced_file_size.pdf file_size: 4683145 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 36' issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ACM Transactions on Graphics publication_identifier: issn: - '07300301' publication_status: published publisher: ACM publist_id: '7334' pubrep_id: '1052' quality_controlled: '1' related_material: record: - id: '8386' relation: dissertation_contains status: public scopus_import: 1 status: public title: Scattering-aware texture reproduction for 3D printing type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2017' ... --- _id: '637' abstract: - lang: eng text: For many cryptographic primitives, it is relatively easy to achieve selective security (where the adversary commits a-priori to some of the choices to be made later in the attack) but appears difficult to achieve the more natural notion of adaptive security (where the adversary can make all choices on the go as the attack progresses). A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption (Panjwani, TCC ’07 and Fuchsbauer et al., CRYPTO ’15), constrained PRFs (Fuchsbauer et al., ASIACRYPT ’14), and Yao garbled circuits (Jafargholi and Wichs, TCC ’16b). Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework that connects all of these works and allows us to present them in a unified and simplified fashion. Moreover, we use the framework to derive a new result for adaptively secure secret sharing over access structures defined via monotone circuits. We envision that further applications will follow in the future. Underlying our framework is the following simple idea. It is well known that selective security, where the adversary commits to n-bits of information about his future choices, automatically implies adaptive security at the cost of amplifying the adversary’s advantage by a factor of up to 2n. However, in some cases the proof of selective security proceeds via a sequence of hybrids, where each pair of adjacent hybrids locally only requires some smaller partial information consisting of m ≪ n bits. The partial information needed might be completely different between different pairs of hybrids, and if we look across all the hybrids we might rely on the entire n-bit commitment. Nevertheless, the above is sufficient to prove adaptive security, at the cost of amplifying the adversary’s advantage by a factor of only 2m ≪ 2n. In all of our examples using the above framework, the different hybrids are captured by some sort of a graph pebbling game and the amount of information that the adversary needs to commit to in each pair of hybrids is bounded by the maximum number of pebbles in play at any point in time. Therefore, coming up with better strategies for proving adaptive security translates to various pebbling strategies for different types of graphs. alternative_title: - LNCS author: - first_name: Zahra full_name: Jafargholi, Zahra last_name: Jafargholi - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Ilan full_name: Komargodski, Ilan last_name: Komargodski - 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: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs D. Be adaptive avoid overcommitting. In: Katz J, Shacham H, eds. Vol 10401. Springer; 2017:133-163. doi:10.1007/978-3-319-63688-7_5' apa: 'Jafargholi, Z., Kamath Hosdurg, C., Klein, K., Komargodski, I., Pietrzak, K. Z., & Wichs, D. (2017). Be adaptive avoid overcommitting. In J. Katz & H. Shacham (Eds.) (Vol. 10401, pp. 133–163). Presented at the CRYPTO: Cryptology, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-319-63688-7_5' chicago: Jafargholi, Zahra, Chethan Kamath Hosdurg, Karen Klein, Ilan Komargodski, Krzysztof Z Pietrzak, and Daniel Wichs. “Be Adaptive Avoid Overcommitting.” edited by Jonathan Katz and Hovav Shacham, 10401:133–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63688-7_5. ieee: 'Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K. Z. Pietrzak, and D. Wichs, “Be adaptive avoid overcommitting,” presented at the CRYPTO: Cryptology, Santa Barbara, CA, United States, 2017, vol. 10401, pp. 133–163.' ista: 'Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs D. 2017. Be adaptive avoid overcommitting. CRYPTO: Cryptology, LNCS, vol. 10401, 133–163.' mla: Jafargholi, Zahra, et al. Be Adaptive Avoid Overcommitting. Edited by Jonathan Katz and Hovav Shacham, vol. 10401, Springer, 2017, pp. 133–63, doi:10.1007/978-3-319-63688-7_5. short: Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K.Z. Pietrzak, D. Wichs, in:, J. Katz, H. Shacham (Eds.), Springer, 2017, pp. 133–163. conference: end_date: 2017-07-24 location: Santa Barbara, CA, United States name: 'CRYPTO: Cryptology' start_date: 2017-07-20 date_created: 2018-12-11T11:47:38Z date_published: 2017-01-01T00:00:00Z date_updated: 2023-09-07T13:32:11Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-63688-7_5 ec_funded: 1 editor: - first_name: Jonathan full_name: Katz, Jonathan last_name: Katz - first_name: Hovav full_name: Shacham, Hovav last_name: Shacham intvolume: ' 10401' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/515 month: '01' oa: 1 oa_version: Submitted Version page: 133 - 163 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: isbn: - 978-331963687-0 publication_status: published publisher: Springer publist_id: '7151' quality_controlled: '1' related_material: record: - id: '10035' relation: dissertation_contains status: public scopus_import: 1 status: public title: Be adaptive avoid overcommitting type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 10401 year: '2017' ... --- _id: '9842' abstract: - lang: eng text: Mathematica notebooks used to generate figures. article_processing_charge: No author: - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge - 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: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:10.17632/nw68fxzjpm.1' apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1' chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.' ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.' ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.' mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.' short: A. Etheridge, N.H. Barton, (2017). date_created: 2021-08-09T13:18:55Z date_published: 2017-12-29T00:00:00Z date_updated: 2023-09-11T13:41:21Z day: '29' department: - _id: NiBa doi: 10.17632/nw68fxzjpm.1 main_file_link: - open_access: '1' url: https://doi.org/10.17632/nw68fxzjpm.1 month: '12' oa: 1 oa_version: Published Version publisher: Mendeley Data related_material: record: - id: '564' relation: used_in_publication status: public status: public title: 'Data for: Establishment in a new habitat by polygenic adaptation' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2017' ... --- _id: '14206' abstract: - lang: eng text: Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings. article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Michael full_name: Tschannen, Michael last_name: Tschannen - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Martin full_name: Jaggi, Martin last_name: Jaggi citation: ama: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: Advances in Neural Information Processing Systems. ; 2017.' apa: Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In Advances in Neural Information Processing Systems. Long Beach, CA, United States. chicago: Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In Advances in Neural Information Processing Systems, 2017. ieee: F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in Advances in Neural Information Processing Systems, Long Beach, CA, United States, 2017. ista: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.' mla: Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” Advances in Neural Information Processing Systems, 2017. short: F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017. conference: end_date: 2017-12-09 location: Long Beach, CA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2017-12-04 date_created: 2023-08-22T14:17:38Z date_published: 2017-05-31T00:00:00Z date_updated: 2023-09-13T08:32:23Z day: '31' department: - _id: FrLo extern: '1' external_id: arxiv: - '1705.11041' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.11041 month: '05' oa: 1 oa_version: Preprint publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781510860964' publication_status: published quality_controlled: '1' status: public title: Greedy algorithms for cone constrained optimization with convergence guarantees type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2017' ... --- _id: '14205' abstract: - lang: eng text: Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions. article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Rajiv full_name: Khanna, Rajiv last_name: Khanna - first_name: Michael full_name: Tschannen, Michael last_name: Tschannen - first_name: Martin full_name: Jaggi, Martin last_name: Jaggi citation: ama: 'Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. Vol 54. ML Research Press; 2017:860-868.' apa: 'Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.' chicago: Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 54:860–68. ML Research Press, 2017. ieee: F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868. ista: 'Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.' mla: Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017, pp. 860–68. short: F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868. conference: end_date: 2017-04-22 location: Fort Lauderdale, FL, United States name: 'AISTATS: Conference on Artificial Intelligence and Statistics' start_date: 2017-04-20 date_created: 2023-08-22T14:17:19Z date_published: 2017-02-21T00:00:00Z date_updated: 2023-09-13T09:49:10Z day: '21' department: - _id: FrLo extern: '1' external_id: arxiv: - '1702.06457' intvolume: ' 54' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1702.06457 month: '02' oa: 1 oa_version: Preprint page: 860-868 publication: Proceedings of the 20th International Conference on Artificial Intelligence and Statistics publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: A unified optimization view on generalized matching pursuit and Frank-Wolfe type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 54 year: '2017' ... --- _id: '202' abstract: - lang: eng text: 'Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.' acknowledgement: "During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 citation: ama: Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:10.15479/AT:ISTA:th_916 apa: Pleska, M. (2017). Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916 chicago: Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916. ieee: M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017. ista: Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. mla: Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916. short: M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017. date_created: 2018-12-11T11:45:10Z date_published: 2017-10-01T00:00:00Z date_updated: 2023-09-15T12:04:56Z day: '01' ddc: - '576' - '579' degree_awarded: PhD department: - _id: CaGu doi: 10.15479/AT:ISTA:th_916 file: - access_level: open_access checksum: 33cfb59674e91f82e3738396d3fb3776 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:48Z date_updated: 2020-07-14T12:45:24Z file_id: '4710' file_name: IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf file_size: 18569590 relation: main_file - access_level: closed checksum: dcc239968decb233e7f98cf1083d8c26 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T08:33:14Z date_updated: 2020-07-14T12:45:24Z file_id: '6204' file_name: 2017_Pleska_Maros_Thesis.docx file_size: 2801649 relation: source_file file_date_updated: 2020-07-14T12:45:24Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '126' project: - _id: 251D65D8-B435-11E9-9278-68D0E5697425 grant_number: '24210' name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship) publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7711' pubrep_id: '916' related_material: record: - id: '1243' relation: part_of_dissertation status: public - id: '561' relation: part_of_dissertation status: public - id: '457' relation: part_of_dissertation status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: Biology of restriction-modification systems at the single-cell and population level 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _id: '6287' abstract: - lang: eng text: The main objects considered in the present work are simplicial and CW-complexes with vertices forming a random point cloud. In particular, we consider a Poisson point process in R^n and study Delaunay and Voronoi complexes of the first and higher orders and weighted Delaunay complexes obtained as sections of Delaunay complexes, as well as the Čech complex. Further, we examine theDelaunay complex of a Poisson point process on the sphere S^n, as well as of a uniform point cloud, which is equivalent to the convex hull, providing a connection to the theory of random polytopes. Each of the complexes in question can be endowed with a radius function, which maps its cells to the radii of appropriately chosen circumspheres, called the radius of the cell. Applying and developing discrete Morse theory for these functions, joining it together with probabilistic and sometimes analytic machinery, and developing several integral geometric tools, we aim at getting the distributions of circumradii of typical cells. For all considered complexes, we are able to generalize and obtain up to constants the distribution of radii of typical intervals of all types. In low dimensions the constants can be computed explicitly, thus providing the explicit expressions for the expected numbers of cells. In particular, it allows to find the expected density of simplices of every dimension for a Poisson point process in R^4, whereas the result for R^3 was known already in 1970's. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:10.15479/AT:ISTA:th_873 apa: Nikitenko, A. (2017). Discrete Morse theory for random complexes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_873 chicago: Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_873. ieee: A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of Science and Technology Austria, 2017. ista: Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria. mla: Nikitenko, Anton. Discrete Morse Theory for Random Complexes . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_873. short: A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science and Technology Austria, 2017. date_created: 2019-04-09T15:04:32Z date_published: 2017-10-27T00:00:00Z date_updated: 2023-09-15T12:10:34Z day: '27' ddc: - '514' - '516' - '519' degree_awarded: PhD department: - _id: HeEd doi: 10.15479/AT:ISTA:th_873 file: - access_level: open_access checksum: ece7e598a2f060b263c2febf7f3fe7f9 content_type: application/pdf creator: dernst date_created: 2019-04-09T14:54:51Z date_updated: 2020-07-14T12:47:26Z file_id: '6289' file_name: 2017_Thesis_Nikitenko.pdf file_size: 2324870 relation: main_file - access_level: closed checksum: 99b7ad76e317efd447af60f91e29b49b content_type: application/zip creator: dernst date_created: 2019-04-09T14:54:51Z date_updated: 2020-07-14T12:47:26Z file_id: '6290' file_name: 2017_Thesis_Nikitenko_source.zip file_size: 2863219 relation: source_file file_date_updated: 2020-07-14T12:47:26Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '86' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria pubrep_id: '873' related_material: record: - id: '718' relation: part_of_dissertation status: public - id: '5678' relation: part_of_dissertation status: public - id: '87' relation: part_of_dissertation status: public status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: 'Discrete Morse theory for random complexes ' 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2017' ... --- _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: '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: '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' ... --- _id: '1084' abstract: - lang: eng text: 'BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities.' article_processing_charge: No author: - first_name: Chong full_name: Fang, Chong last_name: Fang - first_name: Anna A full_name: Nagy-Staron, Anna A id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87 last_name: Nagy-Staron orcid: 0000-0002-1391-8377 - first_name: Martin full_name: Grafe, Martin last_name: Grafe - first_name: Ralf full_name: Heermann, Ralf last_name: Heermann - first_name: Kirsten full_name: Jung, Kirsten last_name: Jung - first_name: Susanne full_name: Gebhard, Susanne last_name: Gebhard - first_name: Thorsten full_name: Mascher, Thorsten last_name: Mascher citation: ama: Fang C, Nagy-Staron AA, Grafe M, et al. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 2017;104(1):16-31. doi:10.1111/mmi.13597 apa: Fang, C., Nagy-Staron, A. A., Grafe, M., Heermann, R., Jung, K., Gebhard, S., & Mascher, T. (2017). Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.13597 chicago: Fang, Chong, Anna A Nagy-Staron, Martin Grafe, Ralf Heermann, Kirsten Jung, Susanne Gebhard, and Thorsten Mascher. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology. Wiley-Blackwell, 2017. https://doi.org/10.1111/mmi.13597. ieee: C. Fang et al., “Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis,” Molecular Microbiology, vol. 104, no. 1. Wiley-Blackwell, pp. 16–31, 2017. ista: Fang C, Nagy-Staron AA, Grafe M, Heermann R, Jung K, Gebhard S, Mascher T. 2017. Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis. Molecular Microbiology. 104(1), 16–31. mla: Fang, Chong, et al. “Insulation and Wiring Specificity of BceR like Response Regulators and Their Target Promoters in Bacillus Subtilis.” Molecular Microbiology, vol. 104, no. 1, Wiley-Blackwell, 2017, pp. 16–31, doi:10.1111/mmi.13597. short: C. Fang, A.A. Nagy-Staron, M. Grafe, R. Heermann, K. Jung, S. Gebhard, T. Mascher, Molecular Microbiology 104 (2017) 16–31. date_created: 2018-12-11T11:50:03Z date_published: 2017-04-01T00:00:00Z date_updated: 2023-09-20T11:48:43Z day: '01' department: - _id: CaGu doi: 10.1111/mmi.13597 external_id: isi: - '000398059200002' intvolume: ' 104' isi: 1 issue: '1' language: - iso: eng month: '04' oa_version: None page: 16 - 31 publication: Molecular Microbiology publication_identifier: issn: - ' 0950382X' publication_status: published publisher: Wiley-Blackwell publist_id: '6294' quality_controlled: '1' scopus_import: '1' status: public title: Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 104 year: '2017' ... --- _id: '1079' abstract: - lang: eng text: We study the ionization problem in the Thomas-Fermi-Dirac-von Weizsäcker theory for atoms and molecules. We prove the nonexistence of minimizers for the energy functional when the number of electrons is large and the total nuclear charge is small. This nonexistence result also applies to external potentials decaying faster than the Coulomb potential. In the case of arbitrary nuclear charges, we obtain the nonexistence of stable minimizers and radial minimizers. article_number: '6' article_processing_charge: No author: - first_name: Phan full_name: Nam, Phan id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Nam - first_name: Hanne full_name: Van Den Bosch, Hanne last_name: Van Den Bosch citation: ama: Nam P, Van Den Bosch H. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 2017;20(2). doi:10.1007/s11040-017-9238-0 apa: Nam, P., & Van Den Bosch, H. (2017). Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-017-9238-0 chicago: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry. Springer, 2017. https://doi.org/10.1007/s11040-017-9238-0. ieee: P. Nam and H. Van Den Bosch, “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges,” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2. Springer, 2017. ista: Nam P, Van Den Bosch H. 2017. Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges. Mathematical Physics, Analysis and Geometry. 20(2), 6. mla: Nam, Phan, and Hanne Van Den Bosch. “Nonexistence in Thomas Fermi-Dirac-von Weizsäcker Theory with Small Nuclear Charges.” Mathematical Physics, Analysis and Geometry, vol. 20, no. 2, 6, Springer, 2017, doi:10.1007/s11040-017-9238-0. short: P. Nam, H. Van Den Bosch, Mathematical Physics, Analysis and Geometry 20 (2017). date_created: 2018-12-11T11:50:02Z date_published: 2017-06-01T00:00:00Z date_updated: 2023-09-20T11:53:35Z day: '01' department: - _id: RoSe doi: 10.1007/s11040-017-9238-0 external_id: isi: - '000401270000004' intvolume: ' 20' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1603.07368 month: '06' oa: 1 oa_version: Submitted Version 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 publication: Mathematical Physics, Analysis and Geometry publication_identifier: issn: - '13850172' publication_status: published publisher: Springer publist_id: '6300' quality_controlled: '1' scopus_import: '1' status: public title: Nonexistence in Thomas Fermi-Dirac-von Weizsäcker theory with small nuclear charges type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 20 year: '2017' ...