--- _id: '6338' abstract: - lang: eng text: Hippocampal activity patterns representing movement trajectories are reactivated in immobility and sleep periods, a process associated with memory recall, consolidation, and decision making. It is thought that only fixed, behaviorally relevant patterns can be reactivated, which are stored across hippocampal synaptic connections. To test whether some generalized rules govern reactivation, we examined trajectory reactivation following non-stereotypical exploration of familiar open-field environments. We found that random trajectories of varying lengths and timescales were reactivated, resembling that of Brownian motion of particles. The animals’ behavioral trajectory did not follow Brownian diffusion demonstrating that the exact behavioral experience is not reactivated. Therefore, hippocampal circuits are able to generate random trajectories of any recently active map by following diffusion dynamics. This ability of hippocampal circuits to generate representations of all behavioral outcome combinations, experienced or not, may underlie a wide variety of hippocampal-dependent cognitive functions such as learning, generalization, and planning. article_processing_charge: No article_type: original author: - first_name: Federico full_name: Stella, Federico id: 39AF1E74-F248-11E8-B48F-1D18A9856A87 last_name: Stella orcid: 0000-0001-9439-3148 - first_name: Peter full_name: Baracskay, Peter id: 361CC00E-F248-11E8-B48F-1D18A9856A87 last_name: Baracskay - first_name: Joseph full_name: O'Neill, Joseph id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - 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: Stella F, Baracskay P, O’Neill J, Csicsvari JL. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 2019;102:450-461. doi:10.1016/j.neuron.2019.01.052 apa: Stella, F., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.052 chicago: Stella, Federico, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.052. ieee: F. Stella, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Hippocampal reactivation of random trajectories resembling Brownian diffusion,” Neuron, vol. 102. Elsevier, pp. 450–461, 2019. ista: Stella F, Baracskay P, O’Neill J, Csicsvari JL. 2019. Hippocampal reactivation of random trajectories resembling Brownian diffusion. Neuron. 102, 450–461. mla: Stella, Federico, et al. “Hippocampal Reactivation of Random Trajectories Resembling Brownian Diffusion.” Neuron, vol. 102, Elsevier, 2019, pp. 450–61, doi:10.1016/j.neuron.2019.01.052. short: F. Stella, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 102 (2019) 450–461. date_created: 2019-04-17T08:28:59Z date_published: 2019-04-17T00:00:00Z date_updated: 2023-08-25T10:13:07Z day: '17' department: - _id: JoCs doi: 10.1016/j.neuron.2019.01.052 ec_funded: 1 external_id: isi: - '000465169700017' pmid: - '30819547' intvolume: ' 102' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2019.01.052 month: '04' oa: 1 oa_version: Published Version page: 450-461 pmid: 1 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 - _id: 2654F984-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03713 name: Interneuro Plasticity During Spatial Learning publication: Neuron publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/memories-of-movement-are-replayed-randomly-during-sleep/ scopus_import: '1' status: public title: Hippocampal reactivation of random trajectories resembling Brownian diffusion type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 102 year: '2019' ... --- _id: '5878' abstract: - lang: eng text: We consider the motion of a droplet bouncing on a vibrating bath of the same fluid in the presence of a central potential. We formulate a rotation symmetry-reduced description of this system, which allows for the straightforward application of dynamical systems theory tools. As an illustration of the utility of the symmetry reduction, we apply it to a model of the pilot-wave system with a central harmonic force. We begin our analysis by identifying local bifurcations and the onset of chaos. We then describe the emergence of chaotic regions and their merging bifurcations, which lead to the formation of a global attractor. In this final regime, the droplet’s angular momentum spontaneously changes its sign as observed in the experiments of Perrard et al. article_number: '013122' article_processing_charge: No article_type: original author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Marc full_name: Fleury, Marc last_name: Fleury citation: ama: 'Budanur NB, Fleury M. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2019;29(1). doi:10.1063/1.5058279' apa: 'Budanur, N. B., & Fleury, M. (2019). State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing. https://doi.org/10.1063/1.5058279' chicago: 'Budanur, Nazmi B, and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science. AIP Publishing, 2019. https://doi.org/10.1063/1.5058279.' ieee: 'N. B. Budanur and M. Fleury, “State space geometry of the chaotic pilot-wave hydrodynamics,” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1. AIP Publishing, 2019.' ista: 'Budanur NB, Fleury M. 2019. State space geometry of the chaotic pilot-wave hydrodynamics. Chaos: An Interdisciplinary Journal of Nonlinear Science. 29(1), 013122.' mla: 'Budanur, Nazmi B., and Marc Fleury. “State Space Geometry of the Chaotic Pilot-Wave Hydrodynamics.” Chaos: An Interdisciplinary Journal of Nonlinear Science, vol. 29, no. 1, 013122, AIP Publishing, 2019, doi:10.1063/1.5058279.' short: 'N.B. Budanur, M. Fleury, Chaos: An Interdisciplinary Journal of Nonlinear Science 29 (2019).' date_created: 2019-01-23T08:35:09Z date_published: 2019-01-22T00:00:00Z date_updated: 2023-08-25T10:16:11Z day: '22' department: - _id: BjHo doi: 10.1063/1.5058279 external_id: arxiv: - '1812.09011' isi: - '000457409100028' intvolume: ' 29' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1812.09011 month: '01' oa: 1 oa_version: Preprint publication: 'Chaos: An Interdisciplinary Journal of Nonlinear Science' publication_identifier: eissn: - 1089-7682 issn: - 1054-1500 publication_status: published publisher: AIP Publishing quality_controlled: '1' related_material: link: - relation: erratum url: https://aip.scitation.org/doi/abs/10.1063/1.5097157 scopus_import: '1' status: public title: State space geometry of the chaotic pilot-wave hydrodynamics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 29 year: '2019' ... --- _id: '6343' abstract: - lang: eng text: Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA. acknowledgement: The author acknowledges support from IST Austria and the Austrian Science Fund (FWF). article_processing_charge: No article_type: original author: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 2019;58(10):1-9. doi:10.1016/j.sbi.2019.03.018 apa: Schur, F. K. (2019). Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.03.018 chicago: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.03.018. ieee: F. K. Schur, “Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging,” Current Opinion in Structural Biology, vol. 58, no. 10. Elsevier, pp. 1–9, 2019. ista: Schur FK. 2019. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Current Opinion in Structural Biology. 58(10), 1–9. mla: Schur, Florian KM. “Toward High-Resolution in Situ Structural Biology with Cryo-Electron Tomography and Subtomogram Averaging.” Current Opinion in Structural Biology, vol. 58, no. 10, Elsevier, 2019, pp. 1–9, doi:10.1016/j.sbi.2019.03.018. short: F.K. Schur, Current Opinion in Structural Biology 58 (2019) 1–9. date_created: 2019-04-19T11:19:13Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-25T10:13:31Z day: '01' department: - _id: FlSc doi: 10.1016/j.sbi.2019.03.018 external_id: isi: - '000494891800004' intvolume: ' 58' isi: 1 issue: '10' language: - iso: eng month: '10' oa_version: None page: 1-9 publication: Current Opinion in Structural Biology publication_identifier: issn: - 0959-440X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 58 year: '2019' ... --- _id: '6428' abstract: - lang: eng text: 'Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system.' article_processing_charge: No author: - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Alexandre full_name: Donzé, Alexandre last_name: Donzé - first_name: Hisahiro full_name: Ito, Hisahiro last_name: Ito - first_name: James full_name: Kapinski, James last_name: Kapinski citation: ama: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800' apa: 'Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019). Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control (pp. 57–66). Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800' chicago: 'Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, 57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800.' ieee: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.' ista: 'Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.' mla: 'Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.' short: 'T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.' conference: end_date: 2019-04-18 location: Montreal, Canada name: 'HSCC: Hybrid Systems Computation and Control' start_date: 2019-04-16 date_created: 2019-05-13T08:13:46Z date_published: 2019-04-16T00:00:00Z date_updated: 2023-08-25T10:19:23Z day: '16' ddc: - '000' department: - _id: ToHe doi: 10.1145/3302504.3311800 external_id: isi: - '000516713900007' file: - access_level: open_access checksum: b8e967081e051d1c55ca5d18fb187890 content_type: application/pdf creator: dernst date_created: 2020-10-08T17:25:45Z date_updated: 2020-10-08T17:25:45Z file_id: '8633' file_name: 2019_ACM_Ferrere.pdf file_size: 1055421 relation: main_file success: 1 file_date_updated: 2020-10-08T17:25:45Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 57-66 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 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control' publication_identifier: isbn: - '9781450362825' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Interface-aware signal temporal logic type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '6442' abstract: - lang: eng text: This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples. acknowledged_ssus: - _id: ScienComp article_number: '130' article_processing_charge: No author: - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: Christian full_name: Hafner, Christian id: 400429CC-F248-11E8-B48F-1D18A9856A87 last_name: Hafner - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002 apa: Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002 chicago: Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002. ieee: C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019. ista: Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130. mla: Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002. short: C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019). date_created: 2019-05-14T07:04:06Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-25T10:18:46Z day: '01' ddc: - '000' - '005' department: - _id: ChWo doi: 10.1145/3306346.3323002 ec_funded: 1 external_id: isi: - '000475740600104' file: - access_level: open_access checksum: 1b737dfe3e051aba8f3f4ab1dceda673 content_type: application/pdf creator: dernst date_created: 2019-05-14T07:03:55Z date_updated: 2020-07-14T12:47:30Z file_id: '6443' file_name: 2019_ACM_Schreck.pdf file_size: 44328918 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: ACM Transactions on Graphics publication_status: published publisher: ACM quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/ scopus_import: '1' status: public title: Fundamental solutions for water wave animation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2019' ... --- _id: '6413' abstract: - lang: eng text: Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase. article_processing_charge: No article_type: original author: - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Carlos full_name: Plana, Carlos last_name: Plana - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Marc full_name: Avila, Marc last_name: Avila citation: ama: Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 2019;117:14-24. doi:10.1016/j.ijmultiphaseflow.2019.04.027 apa: Song, B., Plana, C., Lopez Alonso, J. M., & Avila, M. (2019). Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. Elsevier. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027 chicago: Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow. Elsevier, 2019. https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027. ieee: B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” International Journal of Multiphase Flow, vol. 117. Elsevier, pp. 14–24, 2019. ista: Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24. mla: Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” International Journal of Multiphase Flow, vol. 117, Elsevier, 2019, pp. 14–24, doi:10.1016/j.ijmultiphaseflow.2019.04.027. short: B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24. date_created: 2019-05-13T07:58:35Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-08-25T10:19:55Z day: '01' department: - _id: BjHo doi: 10.1016/j.ijmultiphaseflow.2019.04.027 external_id: arxiv: - '1902.07351' isi: - '000474496000002' intvolume: ' 117' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.07351 month: '08' oa: 1 oa_version: Preprint page: 14-24 publication: International Journal of Multiphase Flow publication_identifier: issn: - '03019322' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Phase-field simulation of core-annular pipe flow type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 117 year: '2019' ... --- _id: '6419' abstract: - lang: eng text: Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible. article_number: e1008079 article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079. ieee: V. Pokusaeva et al., “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS Genetics, vol. 15, no. 4. Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079. mla: Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019). date_created: 2019-05-13T07:58:38Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:37Z day: '10' ddc: - '570' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079 ec_funded: 1 external_id: isi: - '000466866000029' file: - access_level: open_access checksum: cf3889c8a8a16053dacf9c3776cbe217 content_type: application/pdf creator: dernst date_created: 2019-05-14T08:26:08Z date_updated: 2020-07-14T12:47:30Z file_id: '6445' file_name: 2019_PLOSGenetics_Pokusaeva.pdf file_size: 3726017 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '4' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '04' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: PLoS Genetics publication_identifier: eissn: - '15537404' publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '9789' relation: research_data status: public - id: '9790' relation: research_data status: public - id: '9797' relation: research_data status: public scopus_import: '1' status: public title: An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6412' abstract: - lang: eng text: Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates. article_number: '1931' article_processing_charge: No author: - first_name: Hagar F. full_name: Moussa, Hagar F. last_name: Moussa - first_name: Daniel full_name: Bsteh, Daniel last_name: Bsteh - first_name: Ramesh full_name: Yelagandula, Ramesh last_name: Yelagandula - first_name: Carina full_name: Pribitzer, Carina last_name: Pribitzer - first_name: Karin full_name: Stecher, Karin last_name: Stecher - first_name: Katarina full_name: Bartalska, Katarina id: 4D883232-F248-11E8-B48F-1D18A9856A87 last_name: Bartalska - first_name: Luca full_name: Michetti, Luca last_name: Michetti - first_name: Jingkui full_name: Wang, Jingkui last_name: Wang - first_name: Jorge A. full_name: Zepeda-Martinez, Jorge A. last_name: Zepeda-Martinez - first_name: Ulrich full_name: Elling, Ulrich last_name: Elling - first_name: Jacob I. full_name: Stuckey, Jacob I. last_name: Stuckey - first_name: Lindsey I. full_name: James, Lindsey I. last_name: James - first_name: Stephen V. full_name: Frye, Stephen V. last_name: Frye - first_name: Oliver full_name: Bell, Oliver last_name: Bell citation: ama: Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09628-6 apa: Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09628-6 chicago: Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09628-6. ieee: H. F. Moussa et al., “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019. ista: Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931. mla: Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” Nature Communications, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:10.1038/s41467-019-09628-6. short: H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019). date_created: 2019-05-13T07:58:35Z date_published: 2019-04-29T00:00:00Z date_updated: 2023-08-25T10:31:56Z day: '29' ddc: - '570' department: - _id: SaSi doi: 10.1038/s41467-019-09628-6 external_id: isi: - '000466118700002' file: - access_level: open_access checksum: 6550a328335396c856db4cbdda7d2994 content_type: application/pdf creator: dernst date_created: 2019-05-14T08:45:51Z date_updated: 2020-07-14T12:47:29Z file_id: '6448' file_name: 2019_NatureComm_Moussa.pdf file_size: 1223647 relation: main_file file_date_updated: 2020-07-14T12:47:29Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6415' abstract: - lang: eng text: Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Cremer S. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011 apa: Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011 chicago: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011. ieee: S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019. ista: Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68. mla: Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011. short: S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68. date_created: 2019-05-13T07:58:36Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-25T10:31:31Z day: '01' department: - _id: SyCr doi: 10.1016/j.cois.2019.03.011 external_id: isi: - '000477666000012' intvolume: ' 33' isi: 1 language: - iso: eng month: '06' oa_version: None page: 63-68 publication: Current Opinion in Insect Science publication_identifier: eissn: - '22145753' issn: - '22145745' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Pathogens and disease defense of invasive ants type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 33 year: '2019' ... --- _id: '9790' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011. ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011. mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T08:50:15Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s011 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: A statistical summary of segment libraries and sequencing results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9797' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A Statistical Summary of Segment Libraries and Sequencing Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011. ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and sequencing results.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing results, Public Library of Science, 10.1371/journal.pgen.1008079.s011. mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T11:08:20Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s011 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: A statistical summary of segment libraries and sequencing results type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9789' article_processing_charge: No author: - first_name: Victoria full_name: Pokusaeva, Victoria id: 3184041C-F248-11E8-B48F-1D18A9856A87 last_name: Pokusaeva orcid: 0000-0001-7660-444X - first_name: Dinara R. full_name: Usmanova, Dinara R. last_name: Usmanova - first_name: Ekaterina V. full_name: Putintseva, Ekaterina V. last_name: Putintseva - first_name: Lorena full_name: Espinar, Lorena last_name: Espinar - first_name: Karen full_name: Sarkisyan, Karen id: 39A7BF80-F248-11E8-B48F-1D18A9856A87 last_name: Sarkisyan orcid: 0000-0002-5375-6341 - first_name: Alexander S. full_name: Mishin, Alexander S. last_name: Mishin - first_name: Natalya S. full_name: Bogatyreva, Natalya S. last_name: Bogatyreva - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Inna S. full_name: Povolotskaya, Inna S. last_name: Povolotskaya - first_name: Guillaume J. full_name: Filion, Guillaume J. last_name: Filion - first_name: Lucas B. full_name: Carey, Lucas B. last_name: Carey - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3 orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010 apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010 chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010. ieee: V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public Library of Science, 2019. ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library of Science, 10.1371/journal.pgen.1008079.s010. mla: Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010. short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, (2019). date_created: 2021-08-06T08:38:50Z date_published: 2019-04-10T00:00:00Z date_updated: 2023-08-25T10:30:36Z day: '10' department: - _id: FyKo doi: 10.1371/journal.pgen.1008079.s010 month: '04' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '6419' relation: used_in_publication status: public status: public title: Multiple alignment of His3 orthologues type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6462' abstract: - lang: eng text: A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive synthesis. First, we abstract the plant by building a stochastic model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles. 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: Roderick full_name: Bloem, Roderick last_name: Bloem - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Bettina full_name: Konighofer, Bettina last_name: Konighofer - first_name: Stefan full_name: Pranger, Stefan last_name: Pranger citation: ama: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649. doi:10.1007/978-3-030-25540-4_36' apa: 'Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., & Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36' chicago: Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In 31st International Conference on Computer-Aided Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36. ieee: G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in 31st International Conference on Computer-Aided Verification, New York, NY, United States, 2019, vol. 11561, pp. 630–649. ista: 'Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.' mla: Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36. short: G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649. conference: end_date: 2019-07-18 location: New York, NY, United States name: 'CAV: Computer Aided Verification' start_date: 2019-07-13 date_created: 2019-05-16T11:22:30Z date_published: 2019-07-12T00:00:00Z date_updated: 2023-08-25T10:33:27Z day: '12' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-030-25540-4_36 external_id: isi: - '000491468000036' file: - access_level: open_access checksum: c231579f2485c6fd4df17c9443a4d80b content_type: application/pdf creator: dernst date_created: 2019-08-14T09:35:24Z date_updated: 2020-07-14T12:47:31Z file_id: '6816' file_name: 2019_CAV_Avni.pdf file_size: 659766 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' intvolume: ' 11561' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 630-649 project: - _id: 264B3912-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02369 name: Formal Methods meets Algorithmic Game Theory - _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: 31st International Conference on Computer-Aided Verification publication_identifier: isbn: - '9783030255398' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Run-time optimization for learned controllers through quantitative 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11561 year: '2019' ... --- _id: '6477' abstract: - lang: eng text: 'Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions.' article_number: '021001' article_processing_charge: No article_type: original author: - first_name: Dmitry A. full_name: Abanin, Dmitry A. last_name: Abanin - first_name: Ehud full_name: Altman, Ehud last_name: Altman - first_name: Immanuel full_name: Bloch, Immanuel last_name: Bloch - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 citation: ama: 'Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2). doi:10.1103/revmodphys.91.021001' apa: 'Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001' chicago: 'Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001.' ieee: 'D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” Reviews of Modern Physics, vol. 91, no. 2. American Physical Society, 2019.' ista: 'Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.' mla: 'Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:10.1103/revmodphys.91.021001.' short: D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019). date_created: 2019-05-23T07:38:43Z date_published: 2019-05-22T00:00:00Z date_updated: 2023-08-25T10:37:56Z day: '22' ddc: - '530' department: - _id: MaSe doi: 10.1103/revmodphys.91.021001 external_id: arxiv: - '1804.11065' isi: - '000469046900001' file: - access_level: open_access checksum: 4aec0e6662b09f6e0f828cd30ff2c3a6 content_type: application/pdf creator: mserbyn date_created: 2019-05-23T07:39:05Z date_updated: 2020-07-14T12:47:31Z file_id: '6478' file_name: RevModPhys.91.021001.pdf file_size: 1695677 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' intvolume: ' 91' isi: 1 issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Reviews of Modern Physics publication_identifier: eissn: - 0034-6861 issn: - 1539-0756 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Colloquium: Many-body localization, thermalization, and entanglement' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 91 year: '2019' ... --- _id: '6466' abstract: - lang: eng text: "One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates." article_processing_charge: No author: - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 citation: ama: Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048 apa: Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048 chicago: Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048. ieee: D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019. ista: Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581. mla: Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048. short: D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581. date_created: 2019-05-19T21:59:15Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-08-25T10:37:30Z day: '01' ddc: - '580' - '576' department: - _id: NiBa doi: 10.1111/mec.15048 external_id: isi: - '000474808300001' file: - access_level: open_access checksum: 521e3aff3e9263ddf2ffbfe0b6157715 content_type: application/pdf creator: dernst date_created: 2019-05-20T11:49:06Z date_updated: 2020-07-14T12:47:31Z file_id: '6472' file_name: 2019_MolecularEcology_Field.pdf file_size: 367711 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' intvolume: ' 28' isi: 1 issue: '7' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1579-1581 publication: Molecular ecology publication_identifier: eissn: - 1365294X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Breaking down barriers in morning glories 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 28 year: '2019' ... --- _id: '6465' abstract: - lang: eng text: Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells. article_number: '2013' article_processing_charge: No author: - first_name: Hélène full_name: Chassin, Hélène last_name: Chassin - first_name: Marius full_name: Müller, Marius last_name: Müller - first_name: Marcel full_name: Tigges, Marcel last_name: Tigges - first_name: Leo full_name: Scheller, Leo last_name: Scheller - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Martin full_name: Fussenegger, Martin last_name: Fussenegger citation: ama: Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-09974-5 apa: Chassin, H., Müller, M., Tigges, M., Scheller, L., Lang, M., & Fussenegger, M. (2019). A modular degron library for synthetic circuits in mammalian cells. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09974-5 chicago: Chassin, Hélène, Marius Müller, Marcel Tigges, Leo Scheller, Moritz Lang, and Martin Fussenegger. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09974-5. ieee: H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, and M. Fussenegger, “A modular degron library for synthetic circuits in mammalian cells,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019. ista: Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. 2019. A modular degron library for synthetic circuits in mammalian cells. Nature Communications. 10(1), 2013. mla: Chassin, Hélène, et al. “A Modular Degron Library for Synthetic Circuits in Mammalian Cells.” Nature Communications, vol. 10, no. 1, 2013, Springer Nature, 2019, doi:10.1038/s41467-019-09974-5. short: H. Chassin, M. Müller, M. Tigges, L. Scheller, M. Lang, M. Fussenegger, Nature Communications 10 (2019). date_created: 2019-05-19T21:59:14Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-08-25T10:33:51Z day: '01' ddc: - '570' department: - _id: CaGu doi: 10.1038/s41467-019-09974-5 external_id: isi: - '000466338600006' file: - access_level: open_access checksum: e214d3e4f8c81e35981583c4569b51b8 content_type: application/pdf creator: dernst date_created: 2019-05-20T07:33:54Z date_updated: 2020-07-14T12:47:31Z file_id: '6471' file_name: 2019_NatureComm_Chassin.pdf file_size: 1191827 relation: main_file file_date_updated: 2020-07-14T12:47:31Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-023-36111-0 scopus_import: '1' status: public title: A modular degron library for synthetic circuits in mammalian cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6467' abstract: - lang: eng text: Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. article_number: '0881' article_processing_charge: No article_type: original author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: John J. full_name: Welch, John J. last_name: Welch citation: ama: Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881 apa: Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881 chicago: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881. ieee: C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019. ista: Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881. mla: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881. short: C. Fraisse, J.J. Welch, Biology Letters 15 (2019). date_created: 2019-05-19T21:59:15Z date_published: 2019-04-03T00:00:00Z date_updated: 2023-08-25T10:34:41Z day: '03' department: - _id: BeVi - _id: NiBa doi: 10.1098/rsbl.2018.0881 ec_funded: 1 external_id: isi: - '000465405300010' pmid: - '31014191' intvolume: ' 15' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1098/rsbl.2018.0881 month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Biology Letters publication_identifier: eissn: - 1744957X issn: - '17449561' publication_status: published publisher: Royal Society of London quality_controlled: '1' related_material: link: - relation: supplementary_material url: https://dx.doi.org/10.6084/m9.figshare.c.4461008 record: - id: '9798' relation: research_data status: public - id: '9799' relation: research_data status: public scopus_import: '1' status: public title: The distribution of epistasis on simple fitness landscapes type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 15 year: '2019' ... --- _id: '6470' abstract: - lang: eng text: 'Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. ' article_processing_charge: No article_type: original author: - first_name: Tímea full_name: Éltes, Tímea last_name: Éltes - first_name: Miklos full_name: Szoboszlay, Miklos last_name: Szoboszlay - first_name: Margit Katalin full_name: Szigeti, Margit Katalin id: 44F4BDC0-F248-11E8-B48F-1D18A9856A87 last_name: Szigeti orcid: 0000-0001-9500-8758 - first_name: Zoltan full_name: Nusser, Zoltan last_name: Nusser citation: ama: Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681 apa: Éltes, T., Szoboszlay, M., Szigeti, M. K., & Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. Wiley. https://doi.org/10.1113/JP277681 chicago: Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681. ieee: T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019. ista: Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947. mla: Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681. short: T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947. date_created: 2019-05-19T21:59:17Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-08-25T10:34:15Z day: '01' department: - _id: GaNo doi: 10.1113/JP277681 external_id: isi: - '000470780400013' pmid: - '31006863' intvolume: ' 597' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1113/JP277681 month: '06' oa: 1 oa_version: Published Version page: 2925–2947 pmid: 1 publication: Journal of Physiology publication_identifier: eissn: - '14697793' issn: - '00223751' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 597 year: '2019' ... --- _id: '6493' abstract: - lang: eng text: We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements. alternative_title: - LNCS article_processing_charge: No author: - first_name: Miriam full_name: Garcia Soto, Miriam id: 4B3207F6-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Soto orcid: 0000−0003−2936−5719 - 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: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Luka full_name: Zeleznik, Luka id: 3ADCA2E4-F248-11E8-B48F-1D18A9856A87 last_name: Zeleznik citation: ama: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16' apa: 'Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16' chicago: Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16. ieee: M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314. ista: 'Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314.' mla: Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16. short: M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314. conference: end_date: 2019-07-18 location: New York City, NY, USA name: 'CAV: Computer-Aided Verification' start_date: 2019-07-15 date_created: 2019-05-27T07:09:53Z date_published: 2019-07-12T00:00:00Z date_updated: 2023-08-25T10:40:41Z day: '12' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-25540-4_16 ec_funded: 1 external_id: isi: - '000491468000016' file: - access_level: open_access checksum: 1f1d61b83a151031745ef70a501da3d6 content_type: application/pdf creator: dernst date_created: 2019-08-14T11:05:30Z date_updated: 2020-07-14T12:47:32Z file_id: '6817' file_name: 2019_CAV_GarciaSoto.pdf file_size: 674795 relation: main_file file_date_updated: 2020-07-14T12:47:32Z has_accepted_license: '1' intvolume: ' 11561' isi: 1 keyword: - Synthesis - Linear hybrid automaton - Membership language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 297-314 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _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: 31st International Conference on Computer-Aided Verification publication_identifier: isbn: - '9783030255398' issn: - 0302-9743 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Membership-based synthesis of linear hybrid automata tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11561 year: '2019' ... --- _id: '6485' abstract: - lang: eng text: Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous channelis the common abstraction for communication between several processes, where senders and receivers perform a rendezvous handshake as a part of their protocol (senders wait for receivers and vice versa). Additionally to this, channels support the select expression. In this work, we present the first efficient lock-free channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations. article_processing_charge: No author: - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Roman full_name: Elizarov, Roman last_name: Elizarov citation: ama: Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via Communicating Sequential Processes. ACM Press; 2019:417-418. doi:10.1145/3293883.3297000 apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels for programming via communicating sequential processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming (pp. 417–418). Washington, NY, United States: ACM Press. https://doi.org/10.1145/3293883.3297000' chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels for Programming via Communicating Sequential Processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming. ACM Press, 2019. https://doi.org/10.1145/3293883.3297000. ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming via communicating sequential processes. ACM Press, 2019, pp. 417–418. ista: Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM Press,p. mla: Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming, ACM Press, 2019, pp. 417–18, doi:10.1145/3293883.3297000. short: N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM Press, 2019. conference: end_date: 2019-02-20 location: Washington, NY, United States name: 'PPoPP: Principles and Practice of Parallel Programming' start_date: 2019-02-16 date_created: 2019-05-24T10:09:12Z date_published: 2019-02-01T00:00:00Z date_updated: 2023-08-25T10:41:20Z day: '01' department: - _id: DaAl doi: 10.1145/3293883.3297000 external_id: isi: - '000587604600044' isi: 1 language: - iso: eng month: '02' oa_version: None page: 417-418 publication: Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming publication_identifier: isbn: - '9781450362252' publication_status: published publisher: ACM Press quality_controlled: '1' status: public title: Lock-free channels for programming via communicating sequential processes type: conference_poster user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ...