[{"department":[{"_id":"ChWo"}],"language":[{"iso":"eng"}],"type":"journal_article","publication":"Computer Graphics Forum","page":"233 - 242","date_created":"2018-12-11T11:51:52Z","has_accepted_license":"1","quality_controlled":"1","volume":35,"pubrep_id":"612","publist_id":"5795","file":[{"relation":"main_file","content_type":"application/pdf","file_size":15873858,"file_id":"5000","checksum":"8e61387ee2e3bd0e776fbe301629bfd9","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:44:53Z","file_name":"IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf","date_created":"2018-12-12T10:13:18Z"}],"author":[{"first_name":"Ryan","last_name":"Goldade","full_name":"Goldade, Ryan"},{"first_name":"Christopher","last_name":"Batty","full_name":"Batty, Christopher"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"}],"project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"day":"27","acknowledgement":"This research was supported by NSERC (RGPIN-04360-2014) and IST Austria. ","title":"A practical method for high-resolution embedded liquid surfaces","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","date_published":"2016-05-27T00:00:00Z","oa_version":"Submitted Version","doi":"10.1111/cgf.12826","publication_status":"published","citation":{"chicago":"Goldade, Ryan, Christopher Batty, and Chris Wojtan. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12826.","ista":"Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242.","mla":"Goldade, Ryan, et al. “A Practical Method for High-Resolution Embedded Liquid Surfaces.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 233–42, doi:10.1111/cgf.12826.","apa":"Goldade, R., Batty, C., & Wojtan, C. (2016). A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12826","short":"R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 233–242.","ieee":"R. Goldade, C. Batty, and C. Wojtan, “A practical method for high-resolution embedded liquid surfaces,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 233–242, 2016.","ama":"Goldade R, Batty C, Wojtan C. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 2016;35(2):233-242. doi:10.1111/cgf.12826"},"intvolume":" 35","ddc":["000"],"file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"_id":"1412","year":"2016","abstract":[{"text":"Combining high-resolution level set surface tracking with lower resolution physics is an inexpensive method for achieving highly detailed liquid animations. Unfortunately, the inherent resolution mismatch introduces several types of disturbing visual artifacts. We identify the primary sources of these artifacts and present simple, efficient, and practical solutions to address them. First, we propose an unconditionally stable filtering method that selectively removes sub-grid surface artifacts not seen by the fluid physics, while preserving fine detail in dynamic splashing regions. It provides comparable results to recent error-correction techniques at lower cost, without substepping, and with better scaling behavior. Second, we show how a modified narrow-band scheme can ensure accurate free surface boundary conditions in the presence of large resolution mismatches. Our scheme preserves the efficiency of the narrow-band methodology, while eliminating objectionable stairstep artifacts observed in prior work. Third, we demonstrate that the use of linear interpolation of velocity during advection of the high-resolution level set surface is responsible for visible grid-aligned kinks; we therefore advocate higher-order velocity interpolation, and show that it dramatically reduces this artifact. While these three contributions are orthogonal, our results demonstrate that taken together they efficiently address the dominant sources of visual artifacts arising with high-resolution embedded liquid surfaces; the proposed approach offers improved visual quality, a straightforward implementation, and substantially greater scalability than competing methods.","lang":"eng"}],"issue":"2","date_updated":"2023-02-21T10:38:30Z","ec_funded":1,"month":"05","oa":1,"status":"public"},{"type":"journal_article","oa_version":"None","department":[{"_id":"ChWo"}],"date_published":"2016-05-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1111/cgf.12812","publication_status":"published","publication":"Computer Graphics Forum","page":"71 - 79","date_created":"2018-12-11T11:51:53Z","quality_controlled":"1","volume":35,"intvolume":" 35","citation":{"chicago":"Jeschke, Stefan. “Generalized Diffusion Curves: An Improved Vector Representation for Smooth-Shaded Images.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12812.","mla":"Jeschke, Stefan. “Generalized Diffusion Curves: An Improved Vector Representation for Smooth-Shaded Images.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 71–79, doi:10.1111/cgf.12812.","apa":"Jeschke, S. (2016). Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12812","ista":"Jeschke S. 2016. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 35(2), 71–79.","ama":"Jeschke S. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 2016;35(2):71-79. doi:10.1111/cgf.12812","ieee":"S. Jeschke, “Generalized diffusion curves: An improved vector representation for smooth-shaded images,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 71–79, 2016.","short":"S. Jeschke, Computer Graphics Forum 35 (2016) 71–79."},"scopus_import":1,"publist_id":"5794","author":[{"first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke","full_name":"Jeschke, Stefan"}],"project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"_id":"1413","abstract":[{"lang":"eng","text":"This paper generalizes the well-known Diffusion Curves Images (DCI), which are composed of a set of Bezier curves with colors specified on either side. These colors are diffused as Laplace functions over the image domain, which results in smooth color gradients interrupted by the Bezier curves. Our new formulation allows for more color control away from the boundary, providing a similar expressive power as recent Bilaplace image models without introducing associated issues and computational costs. The new model is based on a special Laplace function blending and a new edge blur formulation. We demonstrate that given some user-defined boundary curves over an input raster image, fitting colors and edge blur from the image to the new model and subsequent editing and animation is equally convenient as with DCIs. Numerous examples and comparisons to DCIs are presented."}],"issue":"2","date_updated":"2021-01-12T06:50:34Z","year":"2016","day":"01","month":"05","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","status":"public","title":"Generalized diffusion curves: An improved vector representation for smooth-shaded images"},{"type":"journal_article","oa_version":"None","language":[{"iso":"eng"}],"date_published":"2016-05-01T00:00:00Z","department":[{"_id":"BeBi"}],"publication_status":"published","doi":"10.1111/cgf.12840","date_created":"2018-12-11T11:51:53Z","page":"385 - 396","publication":"Computer Graphics Forum","volume":35,"intvolume":" 35","quality_controlled":"1","citation":{"chicago":"Miguel Villalba, Eder, David Miraut, and Miguel Otaduy. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12840.","mla":"Miguel Villalba, Eder, et al. “Modeling and Estimation of Energy-Based Hyperelastic Objects.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 385–96, doi:10.1111/cgf.12840.","apa":"Miguel Villalba, E., Miraut, D., & Otaduy, M. (2016). Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12840","ista":"Miguel Villalba E, Miraut D, Otaduy M. 2016. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 35(2), 385–396.","short":"E. Miguel Villalba, D. Miraut, M. Otaduy, Computer Graphics Forum 35 (2016) 385–396.","ama":"Miguel Villalba E, Miraut D, Otaduy M. Modeling and estimation of energy-based hyperelastic objects. Computer Graphics Forum. 2016;35(2):385-396. doi:10.1111/cgf.12840","ieee":"E. Miguel Villalba, D. Miraut, and M. Otaduy, “Modeling and estimation of energy-based hyperelastic objects,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 385–396, 2016."},"publist_id":"5792","scopus_import":1,"author":[{"first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba","full_name":"Miguel Villalba, Eder"},{"last_name":"Miraut","first_name":"David","full_name":"Miraut, David"},{"full_name":"Otaduy, Miguel","first_name":"Miguel","last_name":"Otaduy"}],"_id":"1414","date_updated":"2021-01-12T06:50:35Z","abstract":[{"text":"In this paper, we present a method to model hyperelasticity that is well suited for representing the nonlinearity of real-world objects, as well as for estimating it from deformation examples. Previous approaches suffer several limitations, such as lack of integrability of elastic forces, failure to enforce energy convexity, lack of robustness of parameter estimation, or difficulty to model cross-modal effects. Our method avoids these problems by relying on a general energy-based definition of elastic properties. The accuracy of the resulting elastic model is maximized by defining an additive model of separable energy terms, which allow progressive parameter estimation. In addition, our method supports efficient modeling of extreme nonlinearities thanks to energy-limiting constraints. We combine our energy-based model with an optimization method to estimate model parameters from force-deformation examples, and we show successful modeling of diverse deformable objects, including cloth, human finger skin, and internal human anatomy in a medical imaging application.","lang":"eng"}],"acknowledgement":"This work was funded in part by grants from the Spanish Ministry of Economy (TIN2012-35840), the European Research Council (ERC Starting Grant no. 280135 Animetrics), and the EU FP7 (project no. 601165 WEARHAP).","issue":"2","day":"01","year":"2016","month":"05","publisher":"Wiley-Blackwell","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Modeling and estimation of energy-based hyperelastic objects"},{"title":"Narrow band FLIP for liquid simulations","publisher":"Wiley-Blackwell","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"984afbe510ed48019025dff1dcc7baad","file_id":"4940","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:44:53Z","file_name":"IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf","date_created":"2018-12-12T10:12:22Z","content_type":"application/pdf","relation":"main_file","file_size":5938324}],"author":[{"full_name":"Ferstl, Florian","last_name":"Ferstl","first_name":"Florian"},{"last_name":"Ando","first_name":"Ryoichi","full_name":"Ando, Ryoichi"},{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J"},{"full_name":"Westermann, Rüdiger","first_name":"Rüdiger","last_name":"Westermann"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"}],"day":"01","quality_controlled":"1","volume":35,"publist_id":"5793","pubrep_id":"611","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"type":"journal_article","page":"225 - 232","date_created":"2018-12-11T11:51:53Z","publication":"Computer Graphics Forum","has_accepted_license":"1","month":"05","oa":1,"status":"public","_id":"1415","year":"2016","date_updated":"2023-02-21T10:38:38Z","abstract":[{"lang":"eng","text":"The Fluid Implicit Particle method (FLIP) for liquid simulations uses particles to reduce numerical dissipation and provide important visual cues for events like complex splashes and small-scale features near the liquid surface. Unfortunately, FLIP simulations can be computationally expensive, because they require a dense sampling of particles to fill the entire liquid volume. Furthermore, the vast majority of these FLIP particles contribute nothing to the fluid's visual appearance, especially for larger volumes of liquid. We present a method that only uses FLIP particles within a narrow band of the liquid surface, while efficiently representing the remaining inner volume on a regular grid. We show that a naïve realization of this idea introduces unstable and uncontrollable energy fluctuations, and we propose a novel coupling scheme between FLIP particles and regular grid which overcomes this problem. Our method drastically reduces the particle count and simulation times while yielding results that are nearly indistinguishable from regular FLIP simulations. Our approach is easy to integrate into any existing FLIP implementation."}],"issue":"2","citation":{"short":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics Forum 35 (2016) 225–232.","ieee":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, and N. Thuerey, “Narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 35, no. 2. Wiley-Blackwell, pp. 225–232, 2016.","ama":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 2016;35(2):225-232. doi:10.1111/cgf.12825","chicago":"Ferstl, Florian, Ryoichi Ando, Chris Wojtan, Rüdiger Westermann, and Nils Thuerey. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley-Blackwell, 2016. https://doi.org/10.1111/cgf.12825.","mla":"Ferstl, Florian, et al. “Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 35, no. 2, Wiley-Blackwell, 2016, pp. 225–32, doi:10.1111/cgf.12825.","apa":"Ferstl, F., Ando, R., Wojtan, C., Westermann, R., & Thuerey, N. (2016). Narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12825","ista":"Ferstl F, Ando R, Wojtan C, Westermann R, Thuerey N. 2016. Narrow band FLIP for liquid simulations. Computer Graphics Forum. 35(2), 225–232."},"intvolume":" 35","ddc":["000"],"file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"date_published":"2016-05-01T00:00:00Z","oa_version":"Submitted Version","publication_status":"published","doi":"10.1111/cgf.12825"},{"oa_version":"Preprint","type":"journal_article","date_published":"2016-05-15T00:00:00Z","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.93.195145","publication_status":"published","publication":"Physical Review B - Condensed Matter and Materials Physics","date_created":"2018-12-11T11:51:54Z","citation":{"chicago":"Van Loon, Erik, Mikhail Katsnelson, Lauriane Chomaz, and Mikhail Lemeshko. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.93.195145.","apa":"Van Loon, E., Katsnelson, M., Chomaz, L., & Lemeshko, M. (2016). Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.93.195145","ista":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. 2016. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 93(19), 195145.","mla":"Van Loon, Erik, et al. “Interaction-Driven Lifshitz Transition with Dipolar Fermions in Optical Lattices.” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19, 195145, American Physical Society, 2016, doi:10.1103/PhysRevB.93.195145.","ama":"Van Loon E, Katsnelson M, Chomaz L, Lemeshko M. Interaction-driven Lifshitz transition with dipolar fermions in optical lattices. Physical Review B - Condensed Matter and Materials Physics. 2016;93(19). doi:10.1103/PhysRevB.93.195145","ieee":"E. Van Loon, M. Katsnelson, L. Chomaz, and M. Lemeshko, “Interaction-driven Lifshitz transition with dipolar fermions in optical lattices,” Physical Review B - Condensed Matter and Materials Physics, vol. 93, no. 19. American Physical Society, 2016.","short":"E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 93 (2016)."},"intvolume":" 93","quality_controlled":"1","volume":93,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1603.09358"}],"publist_id":"5791","scopus_import":1,"author":[{"last_name":"Van Loon","first_name":"Erik","full_name":"Van Loon, Erik"},{"full_name":"Katsnelson, Mikhail","first_name":"Mikhail","last_name":"Katsnelson"},{"last_name":"Chomaz","first_name":"Lauriane","full_name":"Chomaz, Lauriane"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802"}],"article_number":"195145","_id":"1416","abstract":[{"lang":"eng","text":"Anisotropic dipole-dipole interactions between ultracold dipolar fermions break the symmetry of the Fermi surface and thereby deform it. Here we demonstrate that such a Fermi surface deformation induces a topological phase transition - the so-called Lifshitz transition - in the regime accessible to present-day experiments. We describe the impact of the Lifshitz transition on observable quantities such as the Fermi surface topology, the density-density correlation function, and the excitation spectrum of the system. The Lifshitz transition in ultracold atoms can be controlled by tuning the dipole orientation and, in contrast to the transition studied in crystalline solids, is completely interaction driven."}],"issue":"19","date_updated":"2021-01-12T06:50:36Z","year":"2016","day":"15","month":"05","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","status":"public","oa":1,"title":"Interaction-driven Lifshitz transition with dipolar fermions in optical lattices"},{"oa_version":"Submitted Version","date_published":"2016-07-01T00:00:00Z","publication_status":"published","doi":"10.1111/nph.14019","intvolume":" 211","citation":{"ieee":"S. Simon et al., “PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis,” New Phytologist, vol. 211, no. 1. Wiley-Blackwell, pp. 65–74, 2016.","ama":"Simon S, Skůpa P, Viaene T, et al. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 2016;211(1):65-74. doi:10.1111/nph.14019","short":"S. Simon, P. Skůpa, T. Viaene, M. Zwiewka, R. Tejos, P. Klíma, M. Čarná, J. Rolčík, R. De Rycke, I. Moreno, P. Dobrev, A. Orellana, E. Zažímalová, J. Friml, New Phytologist 211 (2016) 65–74.","chicago":"Simon, Sibu, Petr Skůpa, Tom Viaene, Marta Zwiewka, Ricardo Tejos, Petr Klíma, Mária Čarná, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14019.","apa":"Simon, S., Skůpa, P., Viaene, T., Zwiewka, M., Tejos, R., Klíma, P., … Friml, J. (2016). PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14019","mla":"Simon, Sibu, et al. “PIN6 Auxin Transporter at Endoplasmic Reticulum and Plasma Membrane Mediates Auxin Homeostasis and Organogenesis in Arabidopsis.” New Phytologist, vol. 211, no. 1, Wiley-Blackwell, 2016, pp. 65–74, doi:10.1111/nph.14019.","ista":"Simon S, Skůpa P, Viaene T, Zwiewka M, Tejos R, Klíma P, Čarná M, Rolčík J, De Rycke R, Moreno I, Dobrev P, Orellana A, Zažímalová E, Friml J. 2016. PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis. New Phytologist. 211(1), 65–74."},"file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"ddc":["581"],"_id":"1417","date_updated":"2021-01-12T06:50:36Z","issue":"1","abstract":[{"text":"Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.","lang":"eng"}],"year":"2016","month":"07","status":"public","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"has_accepted_license":"1","page":"65 - 74","date_created":"2018-12-11T11:51:54Z","publication":"New Phytologist","quality_controlled":"1","volume":211,"publist_id":"5790","pubrep_id":"1004","author":[{"full_name":"Simon, Sibu","orcid":"0000-0002-1998-6741","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","last_name":"Simon"},{"full_name":"Skůpa, Petr","first_name":"Petr","last_name":"Skůpa"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"full_name":"Klíma, Petr","last_name":"Klíma","first_name":"Petr"},{"full_name":"Čarná, Mária","first_name":"Mária","last_name":"Čarná"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"full_name":"Moreno, Ignacio","first_name":"Ignacio","last_name":"Moreno"},{"first_name":"Petre","last_name":"Dobrev","full_name":"Dobrev, Petre"},{"full_name":"Orellana, Ariel","last_name":"Orellana","first_name":"Ariel"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"}],"file":[{"file_size":3828383,"content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"system","file_id":"5016","checksum":"23522ced3508ffe7a4f247c4230e6493","date_created":"2018-12-12T10:13:32Z","date_updated":"2020-07-14T12:44:53Z","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf"}],"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, project CEITEC (CZ.1.05/1.1.00/02.0068) and the Czech Science Foundation GACR (project no. 13-4063 7S to J.F.)","day":"01","publisher":"Wiley-Blackwell","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis"},{"_id":"1419","article_number":"175701","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"author":[{"full_name":"Tomski, Andrzej","last_name":"Tomski","first_name":"Andrzej"},{"first_name":"Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarczyk","full_name":"Kaczmarczyk, Jan"}],"day":"29","year":"2016","date_updated":"2021-01-12T06:50:36Z","issue":"17","abstract":[{"text":"We study the superconducting phase of the Hubbard model using the Gutzwiller variational wave function (GWF) and the recently proposed diagrammatic expansion technique (DE-GWF). The DE-GWF method works on the level of the full GWF and in the thermodynamic limit. Here, we consider a finite-size system to study the accuracy of the results as a function of the system size (which is practically unrestricted). We show that the finite-size scaling used, e.g. in the variational Monte Carlo method can lead to significant, uncontrolled errors. The presented research is the first step towards applying the DE-GWF method in studies of inhomogeneous situations, including systems with impurities, defects, inhomogeneous phases, or disorder.","lang":"eng"}],"ec_funded":1,"month":"03","title":"Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model","publisher":"IOP Publishing Ltd.","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_published":"2016-03-29T00:00:00Z","department":[{"_id":"MiLe"}],"type":"journal_article","oa_version":"None","date_created":"2018-12-11T11:51:55Z","publication":"Journal of Physics: Condensed Matter","publication_status":"published","doi":"10.1088/0953-8984/28/17/175701","intvolume":" 28","citation":{"ama":"Tomski A, Kaczmarczyk J. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 2016;28(17). doi:10.1088/0953-8984/28/17/175701","ieee":"A. Tomski and J. Kaczmarczyk, “Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model,” Journal of Physics: Condensed Matter, vol. 28, no. 17. IOP Publishing Ltd., 2016.","short":"A. Tomski, J. Kaczmarczyk, Journal of Physics: Condensed Matter 28 (2016).","apa":"Tomski, A., & Kaczmarczyk, J. (2016). Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/0953-8984/28/17/175701","mla":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter, vol. 28, no. 17, 175701, IOP Publishing Ltd., 2016, doi:10.1088/0953-8984/28/17/175701.","ista":"Tomski A, Kaczmarczyk J. 2016. Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model. Journal of Physics: Condensed Matter. 28(17), 175701.","chicago":"Tomski, Andrzej, and Jan Kaczmarczyk. “Gutzwiller Wave Function for Finite Systems: Superconductivity in the Hubbard Model.” Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2016. https://doi.org/10.1088/0953-8984/28/17/175701."},"quality_controlled":"1","volume":28,"scopus_import":1,"publist_id":"5788"},{"_id":"1420","date_updated":"2025-05-28T11:42:47Z","abstract":[{"lang":"eng","text":"Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. "}],"issue":"4","arxiv":1,"year":"2016","month":"04","ec_funded":1,"status":"public","oa":1,"oa_version":"Preprint","date_published":"2016-04-06T00:00:00Z","publication_status":"published","doi":"10.1534/genetics.115.184127","citation":{"ama":"Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127","ieee":"K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548.","apa":"Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127","mla":"Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127.","chicago":"Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127."},"intvolume":" 202","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"}],"author":[{"last_name":"Bod'ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarína","full_name":"Bod'ová, Katarína"},{"first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"day":"06","publisher":"Genetics Society of America","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A general approximation for the dynamics of quantitative traits","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"page":"1523 - 1548","date_created":"2018-12-11T11:51:55Z","publication":"Genetics","external_id":{"arxiv":["1510.08344"]},"volume":202,"quality_controlled":"1","publist_id":"5787","article_processing_charge":"No"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","status":"public","title":"Scalable static hybridization methods for analysis of nonlinear systems","month":"04","ec_funded":1,"abstract":[{"text":"Hybridization methods enable the analysis of hybrid automata with complex, nonlinear dynamics through a sound abstraction process. Complex dynamics are converted to simpler ones with added noise, and then analysis is done using a reachability method for the simpler dynamics. Several such recent approaches advocate that only "dynamic" hybridization techniquesi.e., those where the dynamics are abstracted on-The-fly during a reachability computation are effective. In this paper, we demonstrate this is not the case, and create static hybridization methods that are more scalable than earlier approaches. The main insight in our approach is that quick, numeric simulations can be used to guide the process, eliminating the need for an exponential number of hybridization domains. Transitions between domains are generally timetriggered, avoiding accumulated error from geometric intersections. We enhance our static technique by combining time-Triggered transitions with occasional space-Triggered transitions, and demonstrate the benefits of the combined approach in what we call mixed-Triggered hybridization. Finally, error modes are inserted to confirm that the reachable states stay within the hybridized regions. The developed techniques can scale to higher dimensions than previous static approaches, while enabling the parallelization of the main performance bottleneck for many dynamic hybridization approaches: The nonlinear optimization required for sound dynamics abstraction. We implement our method as a model transformation pass in the HYST tool, and perform reachability analysis and evaluation using an unmodified version of SpaceEx on nonlinear models with up to six dimensions.","lang":"eng"}],"date_updated":"2021-01-12T06:50:37Z","year":"2016","day":"11","author":[{"full_name":"Bak, Stanley","first_name":"Stanley","last_name":"Bak"},{"full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","first_name":"Sergiy"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Taylor","last_name":"Johnson","full_name":"Johnson, Taylor"},{"first_name":"Pradyot","last_name":"Prakash","full_name":"Prakash, Pradyot"}],"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"_id":"1421","scopus_import":1,"publist_id":"5786","quality_controlled":"1","citation":{"chicago":"Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, Taylor Johnson, and Pradyot Prakash. “Scalable Static Hybridization Methods for Analysis of Nonlinear Systems,” 155–64. Springer, 2016. https://doi.org/10.1145/2883817.2883837.","apa":"Bak, S., Bogomolov, S., Henzinger, T. A., Johnson, T., & Prakash, P. (2016). Scalable static hybridization methods for analysis of nonlinear systems (pp. 155–164). Presented at the HSCC 2016: International Conference on Hybrid Systems: Computation and Control, Vienna, Austria: Springer. https://doi.org/10.1145/2883817.2883837","mla":"Bak, Stanley, et al. Scalable Static Hybridization Methods for Analysis of Nonlinear Systems. Springer, 2016, pp. 155–64, doi:10.1145/2883817.2883837.","ista":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. 2016. Scalable static hybridization methods for analysis of nonlinear systems. HSCC 2016: International Conference on Hybrid Systems: Computation and Control, 155–164.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, T. Johnson, P. Prakash, in:, Springer, 2016, pp. 155–164.","ama":"Bak S, Bogomolov S, Henzinger TA, Johnson T, Prakash P. Scalable static hybridization methods for analysis of nonlinear systems. In: Springer; 2016:155-164. doi:10.1145/2883817.2883837","ieee":"S. Bak, S. Bogomolov, T. A. Henzinger, T. Johnson, and P. Prakash, “Scalable static hybridization methods for analysis of nonlinear systems,” presented at the HSCC 2016: International Conference on Hybrid Systems: Computation and Control, Vienna, Austria, 2016, pp. 155–164."},"doi":"10.1145/2883817.2883837","conference":{"location":"Vienna, Austria","end_date":"2016-04-14","name":"HSCC 2016: International Conference on Hybrid Systems: Computation and Control","start_date":"2016-04-12"},"publication_status":"published","page":"155 - 164","date_created":"2018-12-11T11:51:55Z","type":"conference","oa_version":"None","department":[{"_id":"ToHe"}],"date_published":"2016-04-11T00:00:00Z","language":[{"iso":"eng"}]},{"publist_id":"5785","article_processing_charge":"Yes (via OA deal)","pubrep_id":"591","quality_controlled":"1","volume":106,"has_accepted_license":"1","page":"913 - 923","date_created":"2018-12-11T11:51:56Z","publication":"Letters in Mathematical Physics","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"author":[{"full_name":"Frank, Rupert","first_name":"Rupert","last_name":"Frank"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"},{"full_name":"Seiringer, Robert","first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"file":[{"date_created":"2018-12-12T10:15:57Z","file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","creator":"system","checksum":"fb404923d8ca9a1faeb949561f26cbea","file_id":"5181","file_size":458968,"content_type":"application/pdf","relation":"main_file"}],"file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"ddc":["510","530"],"citation":{"mla":"Frank, Rupert, et al. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics, vol. 106, no. 7, Springer, 2016, pp. 913–23, doi:10.1007/s11005-016-0847-5.","ista":"Frank R, Hainzl C, Schlein B, Seiringer R. 2016. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 106(7), 913–923.","apa":"Frank, R., Hainzl, C., Schlein, B., & Seiringer, R. (2016). Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0847-5","chicago":"Frank, Rupert, Christian Hainzl, Benjamin Schlein, and Robert Seiringer. “Incompatibility of Time-Dependent Bogoliubov–de-Gennes and Ginzburg–Landau Equations.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0847-5.","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","ama":"Frank R, Hainzl C, Schlein B, Seiringer R. Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations. Letters in Mathematical Physics. 2016;106(7):913-923. doi:10.1007/s11005-016-0847-5","ieee":"R. Frank, C. Hainzl, B. Schlein, and R. Seiringer, “Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations,” Letters in Mathematical Physics, vol. 106, no. 7. Springer, pp. 913–923, 2016."},"intvolume":" 106","publication_status":"published","doi":"10.1007/s11005-016-0847-5","oa_version":"Published Version","date_published":"2016-07-01T00:00:00Z","status":"public","oa":1,"month":"07","date_updated":"2021-01-12T06:50:38Z","abstract":[{"lang":"eng","text":"We study the time-dependent Bogoliubov–de-Gennes equations for generic translation-invariant fermionic many-body systems. For initial states that are close to thermal equilibrium states at temperatures near the critical temperature, we show that the magnitude of the order parameter stays approximately constant in time and, in particular, does not follow a time-dependent Ginzburg–Landau equation, which is often employed as a phenomenological description and predicts a decay of the order parameter in time. The full non-linear structure of the equations is necessary to understand this behavior."}],"issue":"7","year":"2016","_id":"1422"},{"month":"05","oa":1,"status":"public","_id":"1423","article_number":"25676","year":"2016","date_updated":"2021-01-12T06:50:38Z","abstract":[{"text":"Direct reciprocity is a mechanism for the evolution of cooperation based on repeated interactions. When individuals meet repeatedly, they can use conditional strategies to enforce cooperative outcomes that would not be feasible in one-shot social dilemmas. Direct reciprocity requires that individuals keep track of their past interactions and find the right response. However, there are natural bounds on strategic complexity: Humans find it difficult to remember past interactions accurately, especially over long timespans. Given these limitations, it is natural to ask how complex strategies need to be for cooperation to evolve. Here, we study stochastic evolutionary game dynamics in finite populations to systematically compare the evolutionary performance of reactive strategies, which only respond to the co-player's previous move, and memory-one strategies, which take into account the own and the co-player's previous move. In both cases, we compare deterministic strategy and stochastic strategy spaces. For reactive strategies and small costs, we find that stochasticity benefits cooperation, because it allows for generous-tit-for-tat. For memory one strategies and small costs, we find that stochasticity does not increase the propensity for cooperation, because the deterministic rule of win-stay, lose-shift works best. For memory one strategies and large costs, however, stochasticity can augment cooperation.","lang":"eng"}],"intvolume":" 6","citation":{"ama":"Baek S, Jeong H, Hilbe C, Nowak M. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 2016;6. doi:10.1038/srep25676","ieee":"S. Baek, H. Jeong, C. Hilbe, and M. Nowak, “Comparing reactive and memory-one strategies of direct reciprocity,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","chicago":"Baek, Seung, Hyeongchai Jeong, Christian Hilbe, and Martin Nowak. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep25676.","ista":"Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676.","mla":"Baek, Seung, et al. “Comparing Reactive and Memory-One Strategies of Direct Reciprocity.” Scientific Reports, vol. 6, 25676, Nature Publishing Group, 2016, doi:10.1038/srep25676.","apa":"Baek, S., Jeong, H., Hilbe, C., & Nowak, M. (2016). Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep25676"},"ddc":["000"],"file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"date_published":"2016-05-10T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1038/srep25676","title":"Comparing reactive and memory-one strategies of direct reciprocity","publisher":"Nature Publishing Group","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"creator":"system","file_id":"5327","checksum":"ee17c482370d2e1b3add393710d3c696","access_level":"open_access","file_name":"IST-2016-590-v1+1_srep25676.pdf","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:18:08Z","relation":"main_file","content_type":"application/pdf","file_size":1349915}],"author":[{"full_name":"Baek, Seung","first_name":"Seung","last_name":"Baek"},{"last_name":"Jeong","first_name":"Hyeongchai","full_name":"Jeong, Hyeongchai"},{"orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"day":"10","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","quality_controlled":"1","volume":6,"publist_id":"5784","pubrep_id":"590","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"type":"journal_article","date_created":"2018-12-11T11:51:56Z","publication":"Scientific Reports","has_accepted_license":"1"},{"issue":"5","abstract":[{"text":"Brood parasites exploit their host in order to increase their own fitness. Typically, this results in an arms race between parasite trickery and host defence. Thus, it is puzzling to observe hosts that accept parasitism without any resistance. The ‘mafia’ hypothesis suggests that these hosts accept parasitism to avoid retaliation. Retaliation has been shown to evolve when the hosts condition their response to mafia parasites, who use depredation as a targeted response to rejection. However, it is unclear if acceptance would also emerge when ‘farming’ parasites are present in the population. Farming parasites use depredation to synchronize the timing with the host, destroying mature clutches to force the host to re-nest. Herein, we develop an evolutionary model to analyse the interaction between depredatory parasites and their hosts. We show that coevolutionary cycles between farmers and mafia can still induce host acceptance of brood parasites. However, this equilibrium is unstable and in the long-run the dynamics of this host–parasite interaction exhibits strong oscillations: when farmers are the majority, accepters conditional to mafia (the host will reject first and only accept after retaliation by the parasite) have a higher fitness than unconditional accepters (the host always accepts parasitism). This leads to an increase in mafia parasites’ fitness and in turn induce an optimal environment for accepter hosts.","lang":"eng"}],"date_updated":"2021-01-12T06:50:39Z","year":"2016","article_number":"160036","_id":"1426","status":"public","oa":1,"month":"05","doi":"10.1098/rsos.160036","publication_status":"published","oa_version":"Published Version","date_published":"2016-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"ddc":["000"],"citation":{"short":"M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016).","ieee":"M. Chakra, C. Hilbe, and A. Traulsen, “Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites,” Royal Society Open Science, vol. 3, no. 5. Royal Society, The, 2016.","ama":"Chakra M, Hilbe C, Traulsen A. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 2016;3(5). doi:10.1098/rsos.160036","apa":"Chakra, M., Hilbe, C., & Traulsen, A. (2016). Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. Royal Society, The. https://doi.org/10.1098/rsos.160036","mla":"Chakra, Maria, et al. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science, vol. 3, no. 5, 160036, Royal Society, The, 2016, doi:10.1098/rsos.160036.","ista":"Chakra M, Hilbe C, Traulsen A. 2016. Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites. Royal Society Open Science. 3(5), 160036.","chicago":"Chakra, Maria, Christian Hilbe, and Arne Traulsen. “Coevolutionary Interactions between Farmers and Mafia Induce Host Acceptance of Avian Brood Parasites.” Royal Society Open Science. Royal Society, The, 2016. https://doi.org/10.1098/rsos.160036."},"intvolume":" 3","acknowledgement":"C.H. gratefully acknowledges funding by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Chakra","first_name":"Maria","full_name":"Chakra, Maria"},{"last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"},{"last_name":"Traulsen","first_name":"Arne","full_name":"Traulsen, Arne"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":937002,"file_name":"IST-2016-589-v1+1_160036.full.pdf","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:14:49Z","file_id":"5104","checksum":"bf84211b31fe87451e738ba301d729c3","creator":"system","access_level":"open_access"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society, The","title":"Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites","has_accepted_license":"1","publication":"Royal Society Open Science","date_created":"2018-12-11T11:51:57Z","type":"journal_article","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"pubrep_id":"589","publist_id":"5776","quality_controlled":"1","volume":3},{"title":"Epistatic interactions in the arabinose cis-regulatory element","publisher":"Oxford University Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","relation":"main_file","file_size":648115,"file_id":"4751","checksum":"1f456ce1d2aa2f67176a1709f9702ecf","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:44:53Z","file_name":"IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf","date_created":"2018-12-12T10:09:27Z"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"author":[{"full_name":"Lagator, Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"full_name":"Igler, Claudia","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","last_name":"Igler"},{"full_name":"Moreno, Anaisa","first_name":"Anaisa","last_name":"Moreno"},{"full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C"},{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"day":"01","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","volume":33,"publist_id":"5772","pubrep_id":"588","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"JoBo"}],"type":"journal_article","date_created":"2018-12-11T11:51:57Z","page":"761 - 769","publication":"Molecular Biology and Evolution","has_accepted_license":"1","ec_funded":1,"month":"03","oa":1,"status":"public","_id":"1427","year":"2016","date_updated":"2021-01-12T06:50:39Z","abstract":[{"lang":"eng","text":"Changes in gene expression are an important mode of evolution; however, the proximate mechanism of these changes is poorly understood. In particular, little is known about the effects of mutations within cis binding sites for transcription factors, or the nature of epistatic interactions between these mutations. Here, we tested the effects of single and double mutants in two cis binding sites involved in the transcriptional regulation of the Escherichia coli araBAD operon, a component of arabinose metabolism, using a synthetic system. This system decouples transcriptional control from any posttranslational effects on fitness, allowing a precise estimate of the effect of single and double mutations, and hence epistasis, on gene expression. We found that epistatic interactions between mutations in the araBAD cis-regulatory element are common, and that the predominant form of epistasis is negative. The magnitude of the interactions depended on whether the mutations are located in the same or in different operator sites. Importantly, these epistatic interactions were dependent on the presence of arabinose, a native inducer of the araBAD operon in vivo, with some interactions changing in sign (e.g., from negative to positive) in its presence. This study thus reveals that mutations in even relatively simple cis-regulatory elements interact in complex ways such that selection on the level of gene expression in one environment might perturb regulation in the other environment in an unpredictable and uncorrelated manner."}],"issue":"3","intvolume":" 33","citation":{"mla":"Lagator, Mato, et al. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution, vol. 33, no. 3, Oxford University Press, 2016, pp. 761–69, doi:10.1093/molbev/msv269.","ista":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. 2016. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 33(3), 761–769.","apa":"Lagator, M., Igler, C., Moreno, A., Guet, C. C., & Bollback, J. P. (2016). Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msv269","chicago":"Lagator, Mato, Claudia Igler, Anaisa Moreno, Calin C Guet, and Jonathan P Bollback. “Epistatic Interactions in the Arabinose Cis-Regulatory Element.” Molecular Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msv269.","short":"M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769.","ama":"Lagator M, Igler C, Moreno A, Guet CC, Bollback JP. Epistatic interactions in the arabinose cis-regulatory element. Molecular Biology and Evolution. 2016;33(3):761-769. doi:10.1093/molbev/msv269","ieee":"M. Lagator, C. Igler, A. Moreno, C. C. Guet, and J. P. Bollback, “Epistatic interactions in the arabinose cis-regulatory element,” Molecular Biology and Evolution, vol. 33, no. 3. Oxford University Press, pp. 761–769, 2016."},"ddc":["570","576"],"scopus_import":1,"file_date_updated":"2020-07-14T12:44:53Z","date_published":"2016-03-01T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1093/molbev/msv269"},{"doi":"10.1088/1742-6596/691/1/012016","conference":{"start_date":"2015-08-21","name":"24th International Laser Physics Workshop (LPHYS'15)","end_date":"2015-08-25","location":"Shanghai, China"},"publication_status":"published","oa_version":"Published Version","date_published":"2016-03-07T00:00:00Z","file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"ddc":["510","530"],"citation":{"chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” In Journal of Physics: Conference Series, Vol. 691. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1742-6596/691/1/012016.","apa":"Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2016). Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In Journal of Physics: Conference Series (Vol. 691). Shanghai, China: IOP Publishing Ltd. https://doi.org/10.1088/1742-6596/691/1/012016","mla":"Könenberg, Martin, et al. “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential.” Journal of Physics: Conference Series, vol. 691, no. 1, 012016, IOP Publishing Ltd., 2016, doi:10.1088/1742-6596/691/1/012016.","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2016. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. Journal of Physics: Conference Series. 24th International Laser Physics Workshop (LPHYS’15) vol. 691, 012016.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential. In: Journal of Physics: Conference Series. Vol 691. IOP Publishing Ltd.; 2016. doi:10.1088/1742-6596/691/1/012016","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential,” in Journal of Physics: Conference Series, Shanghai, China, 2016, vol. 691, no. 1.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics: Conference Series, IOP Publishing Ltd., 2016."},"intvolume":" 691","issue":"1","abstract":[{"text":"We report on a mathematically rigorous analysis of the superfluid properties of a Bose- Einstein condensate in the many-body ground state of a one-dimensional model of interacting bosons in a random potential.","lang":"eng"}],"date_updated":"2021-01-12T06:50:40Z","year":"2016","article_number":"012016","_id":"1428","status":"public","oa":1,"month":"03","has_accepted_license":"1","publication":"Journal of Physics: Conference Series","date_created":"2018-12-11T11:51:58Z","type":"conference","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"pubrep_id":"585","publist_id":"5770","quality_controlled":"1","volume":691,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"07","author":[{"full_name":"Könenberg, Martin","last_name":"Könenberg","first_name":"Martin"},{"first_name":"Thomas","last_name":"Moser","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas"},{"first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert"},{"first_name":"Jakob","last_name":"Yngvason","full_name":"Yngvason, Jakob"}],"project":[{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":1434688,"file_id":"4847","creator":"system","checksum":"109db801749072c3f6c8f1a1848700fa","access_level":"open_access","file_name":"IST-2016-585-v1+1_JPCS_691_1_012016.pdf","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:10:55Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"IOP Publishing Ltd.","title":"Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential"},{"publisher":"Nature Publishing Group","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides","author":[{"full_name":"Husko, Chad","last_name":"Husko","first_name":"Chad"},{"first_name":"Matthias","orcid":"0000-0001-6613-1378","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","full_name":"Wulf, Matthias"},{"full_name":"Lefrançois, Simon","first_name":"Simon","last_name":"Lefrançois"},{"last_name":"Combrié","first_name":"Sylvain","full_name":"Combrié, Sylvain"},{"full_name":"Lehoucq, Gaëlle","first_name":"Gaëlle","last_name":"Lehoucq"},{"full_name":"De Rossi, Alfredo","first_name":"Alfredo","last_name":"De Rossi"},{"full_name":"Eggleton, Benjamin","last_name":"Eggleton","first_name":"Benjamin"},{"full_name":"Kuipers, Laurens","last_name":"Kuipers","first_name":"Laurens"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":965176,"checksum":"6484fa81a2e52e4fdd7935e1ae6091d4","creator":"system","file_id":"5177","access_level":"open_access","file_name":"IST-2016-583-v1+1_ncomms11332.pdf","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:15:53Z"}],"acknowledgement":"This research was supported by the Australian Research Council (ARC) Center of Excellence CUDOS (CE110001018), ARC Laureate Fellowship (FL120100029), ARC Discovery Early Career Researcher Award (DECRA DE120102069), the Netherlands Foundation for Fundamental Research on Matter (FOM) and the Netherlands Organization for Scientific Research (NWO). L.K. acknowledges funding from ERC Advanced Investigator Grant (no. 240438-CONSTANS). A.D.R, S.C., and G.L. acknowledge financial support from the ERC-Pharos programme lead by A. P. Mosk.","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"15","quality_controlled":"1","volume":7,"publist_id":"5769","pubrep_id":"583","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"has_accepted_license":"1","date_created":"2018-12-11T11:51:58Z","publication":"Nature Communications","month":"04","status":"public","oa":1,"article_number":"11332 (2016)","_id":"1429","date_updated":"2021-01-12T06:50:40Z","abstract":[{"lang":"eng","text":"Solitons are localized waves formed by a balance of focusing and defocusing effects. These nonlinear waves exist in diverse forms of matter yet exhibit similar properties including stability, periodic recurrence and particle-like trajectories. One important property is soliton fission, a process by which an energetic higher-order soliton breaks apart due to dispersive or nonlinear perturbations. Here we demonstrate through both experiment and theory that nonlinear photocarrier generation can induce soliton fission. Using near-field measurements, we directly observe the nonlinear spatial and temporal evolution of optical pulses in situ in a nanophotonic semiconductor waveguide. We develop an analytic formalism describing the free-carrier dispersion (FCD) perturbation and show the experiment exceeds the minimum threshold by an order of magnitude. We confirm these observations with a numerical nonlinear Schrödinger equation model. These results provide a fundamental explanation and physical scaling of optical pulse evolution in free-carrier media and could enable improved supercontinuum sources in gas based and integrated semiconductor waveguides."}],"year":"2016","citation":{"short":"C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (2016).","ama":"Husko C, Wulf M, Lefrançois S, et al. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 2016;7. doi:10.1038/ncomms11332","ieee":"C. Husko et al., “Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","chicago":"Husko, Chad, Matthias Wulf, Simon Lefrançois, Sylvain Combrié, Gaëlle Lehoucq, Alfredo De Rossi, Benjamin Eggleton, and Laurens Kuipers. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11332.","mla":"Husko, Chad, et al. “Free-Carrier-Induced Soliton Fission Unveiled by in Situ Measurements in Nanophotonic Waveguides.” Nature Communications, vol. 7, 11332 (2016), Nature Publishing Group, 2016, doi:10.1038/ncomms11332.","ista":"Husko C, Wulf M, Lefrançois S, Combrié S, Lehoucq G, De Rossi A, Eggleton B, Kuipers L. 2016. Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. 7, 11332 (2016).","apa":"Husko, C., Wulf, M., Lefrançois, S., Combrié, S., Lehoucq, G., De Rossi, A., … Kuipers, L. (2016). Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11332"},"intvolume":" 7","file_date_updated":"2020-07-14T12:44:53Z","scopus_import":1,"ddc":["530"],"oa_version":"Published Version","date_published":"2016-04-15T00:00:00Z","publication_status":"published","doi":"10.1038/ncomms11332"},{"citation":{"ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” Nature, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 2016;538(7626):533-536. doi:10.1038/nature20110","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","apa":"Huff, J. T., Zilberman, D., & Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. Nature. Springer Nature . https://doi.org/10.1038/nature20110","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” Nature, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:10.1038/nature20110.","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536.","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” Nature. Springer Nature , 2016. https://doi.org/10.1038/nature20110."},"intvolume":" 538","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/"}],"scopus_import":"1","date_published":"2016-10-27T00:00:00Z","oa_version":"Submitted Version","publication_status":"published","doi":"10.1038/nature20110","month":"10","oa":1,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"status":"public","_id":"9456","year":"2016","date_updated":"2021-12-14T07:55:30Z","issue":"7626","abstract":[{"text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution.","lang":"eng"}],"external_id":{"pmid":["27760113"]},"volume":538,"quality_controlled":"1","article_processing_charge":"No","article_type":"letter_note","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"type":"journal_article","date_created":"2021-06-04T11:34:55Z","page":"533-536","publication":"Nature","title":"Mechanism for DNA transposons to generate introns on genomic scales","publisher":"Springer Nature ","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel"},{"first_name":"Scott W.","last_name":"Roy","full_name":"Roy, Scott W."}],"day":"27","extern":"1","pmid":1},{"article_processing_charge":"No","article_type":"original","quality_controlled":"1","volume":113,"external_id":{"pmid":["27956643"]},"publication":"Proceedings of the National Academy of Sciences","date_created":"2021-06-07T06:21:39Z","page":"15132-15137","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"language":[{"iso":"eng"}],"type":"journal_article","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","extern":"1","day":"27","pmid":1,"author":[{"first_name":"Ping-Hung","last_name":"Hsieh","full_name":"Hsieh, Ping-Hung"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"full_name":"Buttress, Toby","first_name":"Toby","last_name":"Buttress"},{"full_name":"Gao, Hongbo","first_name":"Hongbo","last_name":"Gao"},{"first_name":"Matthew","last_name":"Couchman","full_name":"Couchman, Matthew"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel"},{"full_name":"Feng, Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619074114"}],"scopus_import":"1","citation":{"ieee":"P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” Proceedings of the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:10.1073/pnas.1619074114.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619074114."},"intvolume":" 113","doi":"10.1073/pnas.1619074114","publication_status":"published","date_published":"2016-12-27T00:00:00Z","oa_version":"Published Version","oa":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","month":"12","year":"2016","abstract":[{"text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.","lang":"eng"}],"issue":"52","date_updated":"2023-05-08T11:00:40Z","_id":"9473"},{"year":"2016","abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"issue":"52","date_updated":"2023-05-08T11:00:07Z","_id":"9477","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"oa":1,"status":"public","month":"12","doi":"10.1073/pnas.1619047114","publication_status":"published","date_published":"2016-12-27T00:00:00Z","oa_version":"Published Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1619047114"}],"citation":{"ieee":"K. Park et al., “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” Proceedings of the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 2016;113(52):15138-15143. doi:10.1073/pnas.1619047114","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619047114","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114."},"intvolume":" 113","extern":"1","day":"27","pmid":1,"author":[{"first_name":"Kyunghyuk","last_name":"Park","full_name":"Park, Kyunghyuk"},{"full_name":"Kim, M. Yvonne","first_name":"M. Yvonne","last_name":"Kim"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"first_name":"Jin-Sup","last_name":"Park","full_name":"Park, Jin-Sup"},{"first_name":"Youbong","last_name":"Hyun","full_name":"Hyun, Youbong"},{"last_name":"Okamoto","first_name":"Takashi","full_name":"Okamoto, Takashi"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi"},{"first_name":"Yeonhee","last_name":"Choi","full_name":"Choi, Yeonhee"},{"full_name":"Scholten, Stefan","first_name":"Stefan","last_name":"Scholten"}],"title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","page":"15138-15143","date_created":"2021-06-07T07:10:59Z","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","article_type":"original","keyword":["Multidisciplinary"],"quality_controlled":"1","volume":113,"external_id":{"pmid":["27956642"]}},{"quality_controlled":"1","volume":29,"publist_id":"6469","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"date_created":"2018-12-11T11:49:21Z","page":"4285 - 4293","alternative_title":["Advances in Neural Information Processing Systems"],"publisher":"Neural Information Processing Systems","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"author":[{"last_name":"Monk","first_name":"Travis","full_name":"Monk, Travis"},{"full_name":"Savin, Cristina","first_name":"Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lücke, Jörg","first_name":"Jörg","last_name":"Lücke"}],"acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","day":"01","intvolume":" 29","citation":{"ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems; 2016:4285-4293.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.","mla":"Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics. Vol. 29, Neural Information Processing Systems, 2016, pp. 4285–93.","apa":"Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems."},"main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}],"scopus_import":1,"oa_version":"None","date_published":"2016-01-01T00:00:00Z","publication_status":"published","conference":{"end_date":"2016-12-10","location":"Barcelona, Spaine","start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems"},"month":"01","ec_funded":1,"status":"public","_id":"948","date_updated":"2021-01-12T08:22:08Z","abstract":[{"text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations.","lang":"eng"}],"year":"2016"},{"date_updated":"2021-01-12T06:47:37Z","abstract":[{"lang":"eng","text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways."}],"acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","issue":"10","day":"05","year":"2016","author":[{"first_name":"Robert","last_name":"Gnügge","full_name":"Gnügge, Robert"},{"last_name":"Dharmarajan","first_name":"Lekshmi","full_name":"Dharmarajan, Lekshmi"},{"last_name":"Lang","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","full_name":"Lang, Moritz"},{"full_name":"Stelling, Jörg","first_name":"Jörg","last_name":"Stelling"}],"_id":"1008","status":"public","publisher":"American Chemical Society","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","month":"05","publication_status":"published","doi":"10.1021/acssynbio.6b00013","page":"1098 - 1107","date_created":"2018-12-11T11:49:40Z","publication":"ACS Synthetic Biology","type":"journal_article","oa_version":"None","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"date_published":"2016-05-05T00:00:00Z","publist_id":"6390","intvolume":" 5","quality_controlled":"1","volume":5,"citation":{"ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 2016;5(10):1098-1107. doi:10.1021/acssynbio.6b00013","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” ACS Synthetic Biology, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016.","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS Synthetic Biology. American Chemical Society, 2016. https://doi.org/10.1021/acssynbio.6b00013.","ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","apa":"Gnügge, R., Dharmarajan, L., Lang, M., & Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00013","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” ACS Synthetic Biology, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:10.1021/acssynbio.6b00013."}}]