[{"abstract":[{"text":"In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Preprint","title":"The dual of the space of interactions in neural network models","status":"public","intvolume":" 27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1260","day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2016-06-01T00:00:00Z","article_type":"original","publication":"International Journal of Modern Physics C","citation":{"ieee":"D. De Martino, “The dual of the space of interactions in neural network models,” International Journal of Modern Physics C, vol. 27, no. 6. World Scientific Publishing, 2016.","apa":"De Martino, D. (2016). The dual of the space of interactions in neural network models. International Journal of Modern Physics C. World Scientific Publishing. https://doi.org/10.1142/S0129183116500674","ista":"De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.","ama":"De Martino D. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674","chicago":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C. World Scientific Publishing, 2016. https://doi.org/10.1142/S0129183116500674.","short":"D. De Martino, International Journal of Modern Physics C 27 (2016).","mla":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C, vol. 27, no. 6, 1650067, World Scientific Publishing, 2016, doi:10.1142/S0129183116500674."},"publist_id":"6065","article_number":"1650067","date_updated":"2021-01-12T06:49:28Z","date_created":"2018-12-11T11:51:00Z","volume":27,"author":[{"orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele","full_name":"De Martino, Daniele"}],"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"World Scientific Publishing","year":"2016","month":"06","language":[{"iso":"eng"}],"doi":"10.1142/S0129183116500674","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.02963"}],"external_id":{"arxiv":["1505.02963"]},"oa":1},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1261","intvolume":" 29","title":"Long-time behavior of a finite volume discretization for a fourth order diffusion equation","status":"public","oa_version":"Preprint","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"We consider a non-standard finite-volume discretization of a strongly non-linear fourth order diffusion equation on the d-dimensional cube, for arbitrary . The scheme preserves two important structural properties of the equation: the first is the interpretation as a gradient flow in a mass transportation metric, and the second is an intimate relation to a linear Fokker-Planck equation. Thanks to these structural properties, the scheme possesses two discrete Lyapunov functionals. These functionals approximate the entropy and the Fisher information, respectively, and their dissipation rates converge to the optimal ones in the discrete-to-continuous limit. Using the dissipation, we derive estimates on the long-time asymptotics of the discrete solutions. Finally, we present results from numerical experiments which indicate that our discretization is able to capture significant features of the complex original dynamics, even with a rather coarse spatial resolution."}],"citation":{"ama":"Maas J, Matthes D. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 2016;29(7):1992-2023. doi:10.1088/0951-7715/29/7/1992","apa":"Maas, J., & Matthes, D. (2016). Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. IOP Publishing Ltd. https://doi.org/10.1088/0951-7715/29/7/1992","ieee":"J. Maas and D. Matthes, “Long-time behavior of a finite volume discretization for a fourth order diffusion equation,” Nonlinearity, vol. 29, no. 7. IOP Publishing Ltd., pp. 1992–2023, 2016.","ista":"Maas J, Matthes D. 2016. Long-time behavior of a finite volume discretization for a fourth order diffusion equation. Nonlinearity. 29(7), 1992–2023.","short":"J. Maas, D. Matthes, Nonlinearity 29 (2016) 1992–2023.","mla":"Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” Nonlinearity, vol. 29, no. 7, IOP Publishing Ltd., 2016, pp. 1992–2023, doi:10.1088/0951-7715/29/7/1992.","chicago":"Maas, Jan, and Daniel Matthes. “Long-Time Behavior of a Finite Volume Discretization for a Fourth Order Diffusion Equation.” Nonlinearity. IOP Publishing Ltd., 2016. https://doi.org/10.1088/0951-7715/29/7/1992."},"publication":"Nonlinearity","page":"1992 - 2023","date_published":"2016-06-10T00:00:00Z","scopus_import":1,"day":"10","acknowledgement":"This research was supported by the DFG Collaborative Research Centers TRR 109, ‘ Discretization in Geometry and Dynamics ’ and 1060 ‘ The Mathematics of Emergent Effects ’ .","year":"2016","department":[{"_id":"JaMa"}],"publisher":"IOP Publishing Ltd.","publication_status":"published","author":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan"},{"full_name":"Matthes, Daniel","first_name":"Daniel","last_name":"Matthes"}],"volume":29,"date_created":"2018-12-11T11:51:00Z","date_updated":"2021-01-12T06:49:28Z","publist_id":"6062","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.03178"}],"quality_controlled":"1","doi":"10.1088/0951-7715/29/7/1992","language":[{"iso":"eng"}],"month":"06"},{"page":"1965 - 1982","citation":{"ama":"Sancho Andrés G, Soriano Ortega E, Gao C, et al. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 2016;171(3):1965-1982. doi:10.1104/pp.16.00373","ista":"Sancho Andrés G, Soriano Ortega E, Gao C, Bernabé Orts J, Narasimhan M, Müller A, Tejos R, Jiang L, Friml J, Aniento F, Marcote M. 2016. Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. 171(3), 1965–1982.","apa":"Sancho Andrés, G., Soriano Ortega, E., Gao, C., Bernabé Orts, J., Narasimhan, M., Müller, A., … Marcote, M. (2016). Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00373","ieee":"G. Sancho Andrés et al., “Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier,” Plant Physiology, vol. 171, no. 3. American Society of Plant Biologists, pp. 1965–1982, 2016.","mla":"Sancho Andrés, Gloria, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology, vol. 171, no. 3, American Society of Plant Biologists, 2016, pp. 1965–82, doi:10.1104/pp.16.00373.","short":"G. Sancho Andrés, E. Soriano Ortega, C. Gao, J. Bernabé Orts, M. Narasimhan, A. Müller, R. Tejos, L. Jiang, J. Friml, F. Aniento, M. Marcote, Plant Physiology 171 (2016) 1965–1982.","chicago":"Sancho Andrés, Gloria, Esther Soriano Ortega, Caiji Gao, Joan Bernabé Orts, Madhumitha Narasimhan, Anna Müller, Ricardo Tejos, et al. “Sorting Motifs Involved in the Trafficking and Localization of the PIN1 Auxin Efflux Carrier.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00373."},"publication":"Plant Physiology","date_published":"2016-07-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 171","status":"public","title":"Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier","_id":"1264","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively."}],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4936568/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1104/pp.16.00373","month":"07","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publisher":"American Society of Plant Biologists","publication_status":"published","year":"2016","acknowledgement":"We thank Dr. R. Offringa (Leiden University) for providing the GST-\r\nPIN-CL construct; Sandra Richter and Gerd Jurgens (University of Tübin-\r\ngen) for providing the estradiol-inducible PIN1-RFP construct and the\r\ngnl1 mutant expressing BFA-sensitive GNL1; F.J. Santonja (University of Valencia)\r\nfor help with the statistical analysis; Jurgen Kleine-Vehn, Elke Barbez, and\r\nEva Benkova for helpful discussions; the Salk Institute Genomic Analysis\r\nLaboratory for providing the sequence-indexed Arabidopsis T-DNA in-\r\nsertion mutants; and the greenhouse section and the microscopy section\r\nof SCSIE (University of Valencia) and Pilar Selvi for excellent technical\r\nassistance.","volume":171,"date_created":"2018-12-11T11:51:01Z","date_updated":"2021-01-12T06:49:29Z","author":[{"last_name":"Sancho Andrés","first_name":"Gloria","full_name":"Sancho Andrés, Gloria"},{"first_name":"Esther","last_name":"Soriano Ortega","full_name":"Soriano Ortega, Esther"},{"first_name":"Caiji","last_name":"Gao","full_name":"Gao, Caiji"},{"last_name":"Bernabé Orts","first_name":"Joan","full_name":"Bernabé Orts, Joan"},{"full_name":"Narasimhan, Madhumitha","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8600-0671","first_name":"Madhumitha","last_name":"Narasimhan"},{"last_name":"Müller","first_name":"Anna","id":"420AB15A-F248-11E8-B48F-1D18A9856A87","full_name":"Müller, Anna"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"first_name":"Liwen","last_name":"Jiang","full_name":"Jiang, Liwen"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aniento, Fernando","first_name":"Fernando","last_name":"Aniento"},{"first_name":"Maria","last_name":"Marcote","full_name":"Marcote, Maria"}],"ec_funded":1,"publist_id":"6059"},{"_id":"1265","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","publisher":"American Association for the Advancement of Science","department":[{"_id":"EvBe"}],"intvolume":" 9","title":"Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging","status":"public","publication_status":"published","author":[{"first_name":"Kareem","last_name":"Elsayad","full_name":"Elsayad, Kareem"},{"last_name":"Werner","first_name":"Stephanie","full_name":"Werner, Stephanie"},{"full_name":"Gallemi Rovira, Marcal","first_name":"Marcal","last_name":"Gallemi Rovira","id":"460C6802-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jixiang","last_name":"Kong","full_name":"Kong, Jixiang"},{"first_name":"Edmundo","last_name":"Guajardo","full_name":"Guajardo, Edmundo"},{"full_name":"Zhang, Lijuan","last_name":"Zhang","first_name":"Lijuan"},{"last_name":"Jaillais","first_name":"Yvon","full_name":"Jaillais, Yvon"},{"full_name":"Greb, Thomas","last_name":"Greb","first_name":"Thomas"},{"first_name":"Youssef","last_name":"Belkhadir","full_name":"Belkhadir, Youssef"}],"volume":9,"oa_version":"None","date_updated":"2021-01-12T06:49:29Z","date_created":"2018-12-11T11:51:02Z","type":"journal_article","article_number":"rs5","issue":"435","publist_id":"6057","abstract":[{"text":"Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical propertiesare modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patternedin hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology.","lang":"eng"}],"citation":{"ama":"Elsayad K, Werner S, Gallemi M, et al. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 2016;9(435). doi:10.1126/scisignal.aaf6326","ieee":"K. Elsayad et al., “Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging,” Science Signaling, vol. 9, no. 435. American Association for the Advancement of Science, 2016.","apa":"Elsayad, K., Werner, S., Gallemi, M., Kong, J., Guajardo, E., Zhang, L., … Belkhadir, Y. (2016). Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. American Association for the Advancement of Science. https://doi.org/10.1126/scisignal.aaf6326","ista":"Elsayad K, Werner S, Gallemi M, Kong J, Guajardo E, Zhang L, Jaillais Y, Greb T, Belkhadir Y. 2016. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging. Science Signaling. 9(435), rs5.","short":"K. Elsayad, S. Werner, M. Gallemi, J. Kong, E. Guajardo, L. Zhang, Y. Jaillais, T. Greb, Y. Belkhadir, Science Signaling 9 (2016).","mla":"Elsayad, Kareem, et al. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling, vol. 9, no. 435, rs5, American Association for the Advancement of Science, 2016, doi:10.1126/scisignal.aaf6326.","chicago":"Elsayad, Kareem, Stephanie Werner, Marçal Gallemi, Jixiang Kong, Edmundo Guajardo, Lijuan Zhang, Yvon Jaillais, Thomas Greb, and Youssef Belkhadir. “Mapping the Subcellular Mechanical Properties of Live Cells in Tissues with Fluorescence Emission-Brillouin Imaging.” Science Signaling. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/scisignal.aaf6326."},"publication":"Science Signaling","quality_controlled":"1","doi":"10.1126/scisignal.aaf6326","date_published":"2016-07-05T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"05","month":"07"},{"type":"journal_article","issue":"2016JULY","abstract":[{"text":"Cortical networks exhibit ‘global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ‘prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1266","intvolume":" 5","title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays","status":"public","ddc":["571"],"pubrep_id":"700","file":[{"checksum":"dc52d967dc76174477bb258d84be2899","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:11:20Z","relation":"main_file","file_id":"4874","file_size":2819055,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-700-v1+1_e13824-download.pdf"}],"oa_version":"Published Version","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ista":"Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.","apa":"Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.13824","ieee":"M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” eLife, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.","ama":"Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 2016;5(2016JULY). doi:10.7554/eLife.13824","chicago":"Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.13824.","mla":"Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824.","short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016)."},"publication":"eLife","date_published":"2016-07-01T00:00:00Z","article_number":"e13824","publist_id":"6056","file_date_updated":"2020-07-14T12:44:42Z","year":"2016","acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","publisher":"eLife Sciences Publications","department":[{"_id":"GaTk"}],"publication_status":"published","author":[{"first_name":"Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J"},{"full_name":"Gutkin, Boris","first_name":"Boris","last_name":"Gutkin"},{"last_name":"Denève","first_name":"Sophie","full_name":"Denève, Sophie"}],"volume":5,"date_created":"2018-12-11T11:51:02Z","date_updated":"2021-01-12T06:49:30Z","month":"07","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.7554/eLife.13824","language":[{"iso":"eng"}]},{"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"chicago":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology. Springer, 2016. https://doi.org/10.1007/s11103-016-0501-8.","short":"E. Benková, Plant Molecular Biology 91 (2016) 597.","mla":"Benková, Eva. “Plant Hormones in Interactions with the Environment.” Plant Molecular Biology, vol. 91, no. 6, Springer, 2016, p. 597, doi:10.1007/s11103-016-0501-8.","apa":"Benková, E. (2016). Plant hormones in interactions with the environment. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-016-0501-8","ieee":"E. Benková, “Plant hormones in interactions with the environment,” Plant Molecular Biology, vol. 91, no. 6. Springer, p. 597, 2016.","ista":"Benková E. 2016. Plant hormones in interactions with the environment. Plant Molecular Biology. 91(6), 597.","ama":"Benková E. Plant hormones in interactions with the environment. Plant Molecular Biology. 2016;91(6):597. doi:10.1007/s11103-016-0501-8"},"publication":"Plant Molecular Biology","page":"597","date_published":"2016-08-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Plants are continuously exposed to a myriad of external signals such as fluctuating nutrients availability, drought, heat, cold, high salinity, or pathogen/pest attacks that can severely affect their development, growth, and fertility. As sessile organisms, plants must therefore be able to sense and rapidly react to these external inputs, activate efficient responses, and adjust development to changing conditions. In recent years, significant progress has been made towards understanding the molecular mechanisms underlying the intricate and complex communication between plants and the environment. It is now becoming increasingly evident that hormones have an important regulatory role in plant adaptation and defense mechanisms."}],"_id":"1269","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 91","status":"public","title":"Plant hormones in interactions with the environment","ddc":["581"],"pubrep_id":"697","file":[{"access_level":"open_access","file_name":"IST-2016-697-v1+1_s11103-016-0501-8.pdf","creator":"system","content_type":"application/pdf","file_size":297282,"file_id":"5349","relation":"main_file","checksum":"0ffb7a15c5336b3a55248cc67021a825","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:18:28Z"}],"oa_version":"Published Version","month":"08","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1007/s11103-016-0501-8","language":[{"iso":"eng"}],"publist_id":"6052","file_date_updated":"2020-07-14T12:44:42Z","year":"2016","publisher":"Springer","department":[{"_id":"EvBe"}],"publication_status":"published","author":[{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"volume":91,"date_updated":"2021-01-12T06:49:31Z","date_created":"2018-12-11T11:51:03Z"},{"month":"08","doi":"10.1007/s11005-016-0860-8","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","publist_id":"6054","file_date_updated":"2020-07-14T12:44:42Z","author":[{"last_name":"Frank","first_name":"Rupert","full_name":"Frank, Rupert"},{"full_name":"Killip, Rowan","first_name":"Rowan","last_name":"Killip"},{"full_name":"Nam, Phan","first_name":"Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"}],"volume":106,"date_created":"2018-12-11T11:51:02Z","date_updated":"2021-01-12T06:49:30Z","acknowledgement":"Open access funding provided by Institute of Science and Technology Austria.\r\n","year":"2016","department":[{"_id":"RoSe"}],"publisher":"Springer","publication_status":"published","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-08-01T00:00:00Z","citation":{"chicago":"Frank, Rupert, Rowan Killip, and Phan Nam. “Nonexistence of Large Nuclei in the Liquid Drop Model.” Letters in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s11005-016-0860-8.","short":"R. Frank, R. Killip, P. Nam, Letters in Mathematical Physics 106 (2016) 1033–1036.","mla":"Frank, Rupert, et al. “Nonexistence of Large Nuclei in the Liquid Drop Model.” Letters in Mathematical Physics, vol. 106, no. 8, Springer, 2016, pp. 1033–36, doi:10.1007/s11005-016-0860-8.","apa":"Frank, R., Killip, R., & Nam, P. (2016). Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0860-8","ieee":"R. Frank, R. Killip, and P. Nam, “Nonexistence of large nuclei in the liquid drop model,” Letters in Mathematical Physics, vol. 106, no. 8. Springer, pp. 1033–1036, 2016.","ista":"Frank R, Killip R, Nam P. 2016. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 106(8), 1033–1036.","ama":"Frank R, Killip R, Nam P. Nonexistence of large nuclei in the liquid drop model. Letters in Mathematical Physics. 2016;106(8):1033-1036. doi:10.1007/s11005-016-0860-8"},"publication":"Letters in Mathematical Physics","page":"1033 - 1036","issue":"8","abstract":[{"lang":"eng","text":"We give a simplified proof of the nonexistence of large nuclei in the liquid drop model and provide an explicit bound. Our bound is within a factor of 2.3 of the conjectured value and seems to be the first quantitative result."}],"type":"journal_article","pubrep_id":"698","oa_version":"Published Version","file":[{"file_name":"IST-2016-698-v1+1_s11005-016-0860-8.pdf","access_level":"open_access","content_type":"application/pdf","file_size":349464,"creator":"system","relation":"main_file","file_id":"4863","date_created":"2018-12-12T10:11:09Z","date_updated":"2020-07-14T12:44:42Z","checksum":"d740a6a226e0f5f864f40e3e269d3cc0"}],"_id":"1267","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 106","status":"public","ddc":["510","539"],"title":"Nonexistence of large nuclei in the liquid drop model"},{"publication":"Seminars in Immunology","citation":{"apa":"Milutinovic, B., & Kurtz, J. (2016). Immune memory in invertebrates. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2016.05.004","ieee":"B. Milutinovic and J. Kurtz, “Immune memory in invertebrates,” Seminars in Immunology, vol. 28, no. 4. Academic Press, pp. 328–342, 2016.","ista":"Milutinovic B, Kurtz J. 2016. Immune memory in invertebrates. Seminars in Immunology. 28(4), 328–342.","ama":"Milutinovic B, Kurtz J. Immune memory in invertebrates. Seminars in Immunology. 2016;28(4):328-342. doi:10.1016/j.smim.2016.05.004","chicago":"Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.” Seminars in Immunology. Academic Press, 2016. https://doi.org/10.1016/j.smim.2016.05.004.","short":"B. Milutinovic, J. Kurtz, Seminars in Immunology 28 (2016) 328–342.","mla":"Milutinovic, Barbara, and Joachim Kurtz. “Immune Memory in Invertebrates.” Seminars in Immunology, vol. 28, no. 4, Academic Press, 2016, pp. 328–42, doi:10.1016/j.smim.2016.05.004."},"quality_controlled":"1","page":"328 - 342","doi":"10.1016/j.smim.2016.05.004","date_published":"2016-08-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"month":"08","day":"01","acknowledgement":"We would like to thank Mihai Netea for inviting us to contribute to this Theme Issue.","_id":"1268","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","title":"Immune memory in invertebrates","publication_status":"published","status":"public","department":[{"_id":"SyCr"}],"publisher":"Academic Press","intvolume":" 28","author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","first_name":"Barbara","last_name":"Milutinovic","full_name":"Milutinovic, Barbara"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"}],"date_created":"2018-12-11T11:51:03Z","date_updated":"2021-01-12T06:49:30Z","volume":28,"oa_version":"None","type":"journal_article","publist_id":"6053","issue":"4"},{"has_accepted_license":"1","day":"02","scopus_import":1,"date_published":"2016-09-02T00:00:00Z","citation":{"mla":"Diz Muñoz, Alba, et al. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology, vol. 14, no. 1, 74, BioMed Central, 2016, doi:10.1186/s12915-016-0294-x.","short":"A. Diz Muñoz, P. Romanczuk, W. Yu, M. Bergert, K. Ivanovitch, G. Salbreux, C.-P.J. Heisenberg, E. Paluch, BMC Biology 14 (2016).","chicago":"Diz Muñoz, Alba, Pawel Romanczuk, Weimiao Yu, Martin Bergert, Kenzo Ivanovitch, Guillame Salbreux, Carl-Philipp J Heisenberg, and Ewa Paluch. “Steering Cell Migration by Alternating Blebs and Actin-Rich Protrusions.” BMC Biology. BioMed Central, 2016. https://doi.org/10.1186/s12915-016-0294-x.","ama":"Diz Muñoz A, Romanczuk P, Yu W, et al. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 2016;14(1). doi:10.1186/s12915-016-0294-x","ista":"Diz Muñoz A, Romanczuk P, Yu W, Bergert M, Ivanovitch K, Salbreux G, Heisenberg C-PJ, Paluch E. 2016. Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. 14(1), 74.","apa":"Diz Muñoz, A., Romanczuk, P., Yu, W., Bergert, M., Ivanovitch, K., Salbreux, G., … Paluch, E. (2016). Steering cell migration by alternating blebs and actin-rich protrusions. BMC Biology. BioMed Central. https://doi.org/10.1186/s12915-016-0294-x","ieee":"A. Diz Muñoz et al., “Steering cell migration by alternating blebs and actin-rich protrusions,” BMC Biology, vol. 14, no. 1. BioMed Central, 2016."},"publication":"BMC Biology","issue":"1","abstract":[{"text":"Background: High directional persistence is often assumed to enhance the efficiency of chemotactic migration. Yet, cells in vivo usually display meandering trajectories with relatively low directional persistence, and the control and function of directional persistence during cell migration in three-dimensional environments are poorly understood. Results: Here, we use mesendoderm progenitors migrating during zebrafish gastrulation as a model system to investigate the control of directional persistence during migration in vivo. We show that progenitor cells alternate persistent run phases with tumble phases that result in cell reorientation. Runs are characterized by the formation of directed actin-rich protrusions and tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions or blebs leads to longer or shorter run phases, respectively. Importantly, both reducing and increasing run phases result in larger spatial dispersion of the cells, indicative of reduced migration precision. A physical model quantitatively recapitulating the migratory behavior of mesendoderm progenitors indicates that the ratio of tumbling to run times, and thus the specific degree of directional persistence of migration, are critical for optimizing migration precision. Conclusions: Together, our experiments and model provide mechanistic insight into the control of migration directionality for cells moving in three-dimensional environments that combine different protrusion types, whereby the proportion of blebs to actin-rich protrusions determines the directional persistence and precision of movement by regulating the ratio of tumbling to run times.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"5002","relation":"main_file","date_created":"2018-12-12T10:13:20Z","date_updated":"2020-07-14T12:44:42Z","checksum":"0bfa484ac69a0a560fb9a4589aeda7f6","file_name":"IST-2016-695-v1+1_s12915-016-0294-x.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1875695}],"oa_version":"Published Version","pubrep_id":"695","intvolume":" 14","ddc":["572","576"],"status":"public","title":"Steering cell migration by alternating blebs and actin-rich protrusions","_id":"1271","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"09","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"doi":"10.1186/s12915-016-0294-x","project":[{"grant_number":"HE_3231/6-1","_id":"252064B8-B435-11E9-9278-68D0E5697425","name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publist_id":"6049","file_date_updated":"2020-07-14T12:44:42Z","article_number":"74","volume":14,"date_updated":"2021-01-12T06:49:32Z","date_created":"2018-12-11T11:51:04Z","author":[{"full_name":"Diz Muñoz, Alba","last_name":"Diz Muñoz","first_name":"Alba"},{"first_name":"Pawel","last_name":"Romanczuk","full_name":"Romanczuk, Pawel"},{"first_name":"Weimiao","last_name":"Yu","full_name":"Yu, Weimiao"},{"full_name":"Bergert, Martin","last_name":"Bergert","first_name":"Martin"},{"full_name":"Ivanovitch, Kenzo","last_name":"Ivanovitch","first_name":"Kenzo"},{"first_name":"Guillame","last_name":"Salbreux","full_name":"Salbreux, Guillame"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"last_name":"Paluch","first_name":"Ewa","full_name":"Paluch, Ewa"}],"department":[{"_id":"CaHe"}],"publisher":"BioMed Central","publication_status":"published","acknowledgement":"We thank K. Lee, C. Norden, A. Webb, and the members of the Paluch lab for\r\ncomments on the manuscript. We are grateful to P. Rørth and Peter Dieterich\r\nfor discussions, S. Ares, Y. Arboleda-Estudillo and S. Schneider for technical help,\r\nM. Biro for help with programming, and the BIOTEC/MPI-CBG and IST zebrafish\r\nand imaging facilities for help and advice at various stages of this project. This work was supported by the Max Planck Society, the Medical Research Council UK (core funding to the MRC LMCB), and by grants from the Polish Ministry of Science and Higher Education (454/N-MPG/2009/0) to EKP, the Deutsche Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EKP, a A*Star JCO career development award (12302FG010) to WY and a Damon Runyon fellowship award to ADM (DRG 2157-12). This work was also supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001317), the UK Medical Research Council (FC001317), and the Wellcome Trust (FC001317) to GS.","year":"2016"},{"publist_id":"6044","author":[{"full_name":"Porco, Silvana","last_name":"Porco","first_name":"Silvana"},{"full_name":"Larrieu, Antoine","first_name":"Antoine","last_name":"Larrieu"},{"last_name":"Du","first_name":"Yujuan","full_name":"Du, Yujuan"},{"last_name":"Gaudinier","first_name":"Allison","full_name":"Gaudinier, Allison"},{"first_name":"Tatsuaki","last_name":"Goh","full_name":"Goh, Tatsuaki"},{"full_name":"Swarup, Kamal","last_name":"Swarup","first_name":"Kamal"},{"first_name":"Ranjan","last_name":"Swarup","full_name":"Swarup, Ranjan"},{"last_name":"Kuempers","first_name":"Britta","full_name":"Kuempers, Britta"},{"full_name":"Bishopp, Anthony","first_name":"Anthony","last_name":"Bishopp"},{"first_name":"Julien","last_name":"Lavenus","full_name":"Lavenus, Julien"},{"full_name":"Casimiro, Ilda","first_name":"Ilda","last_name":"Casimiro"},{"full_name":"Hill, Kristine","last_name":"Hill","first_name":"Kristine"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"first_name":"Hidehiro","last_name":"Fukaki","full_name":"Fukaki, Hidehiro"},{"full_name":"Brady, Siobhan","first_name":"Siobhan","last_name":"Brady"},{"first_name":"Ben","last_name":"Scheres","full_name":"Scheres, Ben"},{"last_name":"Peéet","first_name":"Benjamin","full_name":"Peéet, Benjamin"},{"last_name":"Bennett","first_name":"Malcolm","full_name":"Bennett, Malcolm"}],"volume":143,"date_updated":"2021-01-12T06:49:32Z","date_created":"2018-12-11T11:51:04Z","year":"2016","acknowledgement":"We acknowledge the support of glasshouse technicians at the University of\r\nNottingham for help with plant growth and the Nottingham\r\nArabidopsis\r\nStock Centre\r\n(NASC) for providing\r\nArabidopsis\r\nlines. This research was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (to A.B. and M.J.B.); the European Research Council (ERC) Advanced Grant SysArc (to B.S.) and FUTUREROOTS (to M.J.B.); The Royal Society for University and Wolfson Research Fellowship awards (to A.B. and M.J.B.); a Federation of European Biochemical Societies (FEBS) Long-Term Fellowship (to B.P.); an Intra-European Fellowship for Career Development under the 7th framework of the European Commission [IEF-2008-220506 to B.P.]; a European Molecular Biology Organization (EMBO) Long-Term Fellowship (to B.P.); and a European Reintegration Grant under the 7th framework of the European Commission [ERG-2010-276662 to B.P.]; Interuniversity Attraction Poles Programme [initiated by the Belgian Science Policy Office (Federaal Wetenschapsbeleid)] (to M.J.B.); The Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan: Grants-in-Aid for Scientific Research on Innovative Areas [25110330 to H.F.] and a JSPS Research Fellowship for Young Scientists [12J02079 to T.G.]; funds for research performed by S.M.B. and A.G. were provided by University of California, Davis startup funds.","department":[{"_id":"EvBe"}],"publisher":"Company of Biologists","publication_status":"published","month":"09","doi":"10.1242/dev.136283","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01595056/"}],"quality_controlled":"1","issue":"18","abstract":[{"lang":"eng","text":"Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence."}],"type":"journal_article","oa_version":"Preprint","_id":"1273","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 143","title":"Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3","status":"public","day":"13","scopus_import":1,"date_published":"2016-09-13T00:00:00Z","citation":{"short":"S. Porco, A. Larrieu, Y. Du, A. Gaudinier, T. Goh, K. Swarup, R. Swarup, B. Kuempers, A. Bishopp, J. Lavenus, I. Casimiro, K. Hill, E. Benková, H. Fukaki, S. Brady, B. Scheres, B. Peéet, M. Bennett, Development 143 (2016) 3340–3349.","mla":"Porco, Silvana, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development, vol. 143, no. 18, Company of Biologists, 2016, pp. 3340–49, doi:10.1242/dev.136283.","chicago":"Porco, Silvana, Antoine Larrieu, Yujuan Du, Allison Gaudinier, Tatsuaki Goh, Kamal Swarup, Ranjan Swarup, et al. “Lateral Root Emergence in Arabidopsis Is Dependent on Transcription Factor LBD29 Regulation of Auxin Influx Carrier LAX3.” Development. Company of Biologists, 2016. https://doi.org/10.1242/dev.136283.","ama":"Porco S, Larrieu A, Du Y, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 2016;143(18):3340-3349. doi:10.1242/dev.136283","apa":"Porco, S., Larrieu, A., Du, Y., Gaudinier, A., Goh, T., Swarup, K., … Bennett, M. (2016). Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. Company of Biologists. https://doi.org/10.1242/dev.136283","ieee":"S. Porco et al., “Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3,” Development, vol. 143, no. 18. Company of Biologists, pp. 3340–3349, 2016.","ista":"Porco S, Larrieu A, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady S, Scheres B, Peéet B, Bennett M. 2016. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development. 143(18), 3340–3349."},"publication":"Development","page":"3340 - 3349"},{"scopus_import":1,"day":"02","has_accepted_license":"1","page":"712 - 721","publication":"Computer-Aided Design and Applications","citation":{"chicago":"Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications. Taylor and Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718.","short":"M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721.","mla":"Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications, vol. 13, no. 5, Taylor and Francis, 2016, pp. 712–21, doi:10.1080/16864360.2016.1150718.","apa":"Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. Taylor and Francis. https://doi.org/10.1080/16864360.2016.1150718","ieee":"M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” Computer-Aided Design and Applications, vol. 13, no. 5. Taylor and Francis, pp. 712–721, 2016.","ista":"Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.","ama":"Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721. doi:10.1080/16864360.2016.1150718"},"date_published":"2016-09-02T00:00:00Z","type":"journal_article","abstract":[{"text":"We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams.","lang":"eng"}],"issue":"5","ddc":["004","516"],"status":"public","title":"Generalized offsetting of planar structures using skeletons","intvolume":" 13","_id":"1272","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":1678369,"access_level":"open_access","file_name":"IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf","checksum":"c746f3a48edb62b588d92ea5d0fd2c0e","date_created":"2018-12-12T10:16:20Z","date_updated":"2020-07-14T12:44:42Z","file_id":"5206","relation":"main_file"}],"pubrep_id":"694","month":"09","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"doi":"10.1080/16864360.2016.1150718","file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6048","publication_status":"published","publisher":"Taylor and Francis","department":[{"_id":"HeEd"}],"year":"2016","acknowledgement":"This work was supported by Austrian Science Fund (FWF): P25816-N15.","date_updated":"2021-01-12T06:49:32Z","date_created":"2018-12-11T11:51:04Z","volume":13,"author":[{"full_name":"Held, Martin","first_name":"Martin","last_name":"Held"},{"full_name":"Huber, Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber"},{"full_name":"Palfrader, Peter","last_name":"Palfrader","first_name":"Peter"}]},{"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7"}],"doi":"10.1371/journal.pone.0164675","language":[{"iso":"eng"}],"article_number":"e0164675","file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6037","ec_funded":1,"acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734] via the IST FELLOWSHIP awarded to Dr. Krisztián A. Kovács and the European Research Council starting grant (acronym: HIPECMEM Project reference: 281511) awarded to Dr. Jozsef Csicsvari. We thank Lauri Viljanto for technical help in building the ripple detector.","year":"2016","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"JoCs"}],"author":[{"id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","first_name":"Krisztián","last_name":"Kovács","full_name":"Kovács, Krisztián"},{"full_name":"O'Neill, Joseph","first_name":"Joseph","last_name":"O'Neill","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Philipp","last_name":"Schönenberger","id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp"},{"first_name":"Markku","last_name":"Penttonen","full_name":"Penttonen, Markku"},{"id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8602-4374","first_name":"Dámaris K","last_name":"Rangel Guerrero","full_name":"Rangel Guerrero, Dámaris K"},{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"date_updated":"2021-01-12T06:49:35Z","date_created":"2018-12-11T11:51:06Z","volume":11,"scopus_import":1,"day":"19","has_accepted_license":"1","publication":"PLoS One","citation":{"mla":"Kovács, Krisztián, et al. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” PLoS One, vol. 11, no. 10, e0164675, Public Library of Science, 2016, doi:10.1371/journal.pone.0164675.","short":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D.K. Rangel Guerrero, J.L. Csicsvari, PLoS One 11 (2016).","chicago":"Kovács, Krisztián, Joseph O’Neill, Philipp Schönenberger, Markku Penttonen, Dámaris K Rangel Guerrero, and Jozsef L Csicsvari. “Optogenetically Blocking Sharp Wave Ripple Events in Sleep Does Not Interfere with the Formation of Stable Spatial Representation in the CA1 Area of the Hippocampus.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164675.","ama":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164675","ista":"Kovács K, O’Neill J, Schönenberger P, Penttonen M, Rangel Guerrero DK, Csicsvari JL. 2016. Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. 11(10), e0164675.","apa":"Kovács, K., O’Neill, J., Schönenberger, P., Penttonen, M., Rangel Guerrero, D. K., & Csicsvari, J. L. (2016). Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0164675","ieee":"K. Kovács, J. O’Neill, P. Schönenberger, M. Penttonen, D. K. Rangel Guerrero, and J. L. Csicsvari, “Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016."},"date_published":"2016-10-19T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory inputdriven neuronal firing patterns are replayed. Such replay is thought to be important for plasticity- related processes and consolidation of memory traces. It has previously been shown that the electrical stimulation-induced disruption of SWR events interferes with learning in rodents in different experimental paradigms. On the other hand, the cognitive map theory posits that the plastic changes of the firing of hippocampal place cells constitute the electrophysiological counterpart of the spatial learning, observable at the behavioral level. Therefore, we tested whether intact SWR events occurring during the sleep/rest session after the first exploration of a novel environment are needed for the stabilization of the CA1 code, which process requires plasticity. We found that the newly-formed representation in the CA1 has the same level of stability with optogenetic SWR blockade as with a control manipulation that delivered the same amount of light into the brain. Therefore our results suggest that at least in the case of passive exploratory behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles."}],"issue":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1279","ddc":["570","571"],"status":"public","title":"Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus","intvolume":" 11","pubrep_id":"690","oa_version":"Published Version","file":[{"checksum":"395895ecb2216e9c39135abaa56b28b3","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:13:26Z","relation":"main_file","file_id":"5009","file_size":4353592,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-690-v1+1_journal.pone.0164675.PDF"}]},{"month":"10","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pone.0164037","language":[{"iso":"eng"}],"article_number":"e0164037","publist_id":"6038","file_date_updated":"2020-07-14T12:44:42Z","year":"2016","acknowledgement":"This work was supported by RIKEN [to SN]; Grant-in-Aid from the Japan Society for the Promotion of Science, https://www.jsps.go.jp/english/e-grants/ [22300112 to SN].","department":[{"_id":"RySh"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"last_name":"Matsuno","first_name":"Hitomi","full_name":"Matsuno, Hitomi"},{"last_name":"Kudoh","first_name":"Moeko","full_name":"Kudoh, Moeko"},{"full_name":"Watakabe, Akiya","first_name":"Akiya","last_name":"Watakabe"},{"full_name":"Yamamori, Tetsuo","last_name":"Yamamori","first_name":"Tetsuo"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"last_name":"Nagao","first_name":"Soichi","full_name":"Nagao, Soichi"}],"volume":11,"date_updated":"2021-01-12T06:49:34Z","date_created":"2018-12-11T11:51:06Z","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"06","citation":{"ama":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 2016;11(10). doi:10.1371/journal.pone.0164037","ista":"Matsuno H, Kudoh M, Watakabe A, Yamamori T, Shigemoto R, Nagao S. 2016. Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. 11(10), e0164037.","ieee":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, and S. Nagao, “Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies,” PLoS One, vol. 11, no. 10. Public Library of Science, 2016.","apa":"Matsuno, H., Kudoh, M., Watakabe, A., Yamamori, T., Shigemoto, R., & Nagao, S. (2016). Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0164037","mla":"Matsuno, Hitomi, et al. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One, vol. 11, no. 10, e0164037, Public Library of Science, 2016, doi:10.1371/journal.pone.0164037.","short":"H. Matsuno, M. Kudoh, A. Watakabe, T. Yamamori, R. Shigemoto, S. Nagao, PLoS One 11 (2016).","chicago":"Matsuno, Hitomi, Moeko Kudoh, Akiya Watakabe, Tetsuo Yamamori, Ryuichi Shigemoto, and Soichi Nagao. “Distribution and Structure of Synapses on Medial Vestibular Nuclear Neurons Targeted by Cerebellar Flocculus Purkinje Cells and Vestibular Nerve in Mice: Light and Electron Microscopy Studies.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0164037."},"publication":"PLoS One","article_type":"original","date_published":"2016-10-06T00:00:00Z","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Adaptations of vestibulo-ocular and optokinetic response eye movements have been studied as an experimental model of cerebellum-dependent motor learning. Several previous physiological and pharmacological studies have consistently suggested that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively maintain the memory traces of short- and long-term adaptation. To study the basic structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy (EM), we injected green florescence protein (GFP)-expressing lentivirus into FL to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal boutons were distributed in the magnocellular MVN and in the border region of parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the FL-P cell axons mainly terminated on somata and proximal dendrites. On the other hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly terminated on the relatively small-diameter (< 1 μm) distal dendrites of MVN neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH neurons were determined to be glutamatergic by immunocytochemistry and in-situ hybridization of GFP expressing transgenic mice. To further examine the spatial relationship between the synapses of FL P-cells and those of vestibular nerve on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated dextran amine into the semicircular canal and anterogradely labeled vestibular nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic boutons often closely apposed vestibular nerve synaptic boutons in both LM and EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with those of vestibular nerve axons in the distal dendrites of MVN neurons suggests that inhibitory synapses of FL P-cells may influence the function of neighboring excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons."}],"_id":"1278","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 11","title":"Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies","ddc":["570","571"],"status":"public","pubrep_id":"689","file":[{"checksum":"7c0ba0ca6d79844059158059d2a38d25","date_created":"2018-12-12T10:17:16Z","date_updated":"2020-07-14T12:44:42Z","file_id":"5269","relation":"main_file","creator":"system","file_size":3657084,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-689-v1+1_journal.pone.0164037.PDF"}],"oa_version":"Published Version"},{"abstract":[{"lang":"eng","text":"The cytochrome (cyt) bc 1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated semiquinone-a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q i-site."}],"type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-691-v1+1_srep33607.pdf","creator":"system","content_type":"application/pdf","file_size":1960563,"file_id":"5261","relation":"main_file","checksum":"07c591c1250ebef266333cbc3228b4dd","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:17:09Z"}],"pubrep_id":"691","intvolume":" 6","title":"Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex","status":"public","ddc":["576"],"_id":"1276","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"26","scopus_import":1,"date_published":"2016-09-26T00:00:00Z","citation":{"ama":"Postila P, Kaszuba K, Kuleta P, et al. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 2016;6. doi:10.1038/srep33607","ieee":"P. Postila et al., “Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.","apa":"Postila, P., Kaszuba, K., Kuleta, P., Vattulainen, I., Sarewicz, M., Osyczka, A., & Róg, T. (2016). Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep33607","ista":"Postila P, Kaszuba K, Kuleta P, Vattulainen I, Sarewicz M, Osyczka A, Róg T. 2016. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex. Scientific Reports. 6, 33607.","short":"P. Postila, K. Kaszuba, P. Kuleta, I. Vattulainen, M. Sarewicz, A. Osyczka, T. Róg, Scientific Reports 6 (2016).","mla":"Postila, Pekka, et al. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports, vol. 6, 33607, Nature Publishing Group, 2016, doi:10.1038/srep33607.","chicago":"Postila, Pekka, Karol Kaszuba, Patryk Kuleta, Ilpo Vattulainen, Marcin Sarewicz, Artur Osyczka, and Tomasz Róg. “Atomistic Determinants of Co-Enzyme Q Reduction at the Qi-Site of the Cytochrome Bc1 Complex.” Scientific Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep33607."},"publication":"Scientific Reports","publist_id":"6040","file_date_updated":"2020-07-14T12:44:42Z","article_number":"33607","volume":6,"date_updated":"2021-01-12T06:49:34Z","date_created":"2018-12-11T11:51:05Z","author":[{"full_name":"Postila, Pekka","last_name":"Postila","first_name":"Pekka"},{"full_name":"Kaszuba, Karol","first_name":"Karol","last_name":"Kaszuba","id":"3FDF9472-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Patryk","last_name":"Kuleta","full_name":"Kuleta, Patryk"},{"full_name":"Vattulainen, Ilpo","last_name":"Vattulainen","first_name":"Ilpo"},{"first_name":"Marcin","last_name":"Sarewicz","full_name":"Sarewicz, Marcin"},{"first_name":"Artur","last_name":"Osyczka","full_name":"Osyczka, Artur"},{"full_name":"Róg, Tomasz","last_name":"Róg","first_name":"Tomasz"}],"publisher":"Nature Publishing Group","department":[{"_id":"LeSa"}],"publication_status":"published","acknowledgement":"We wish to thank CSC – IT Centre for Science (Espoo, Finland) for computational resources. For financial support, we wish to thank the Academy of Finland (TR, IV and PAP; Center of Excellence in Biomembrane Research (IV, TR)), the Finnish Doctoral Programme in Computational Sciences (KK), the Sigrid Juselius Foundation (IV), the Paulo Foundation (PAP), and the European Research Council (IV, TR; Advanced Grant project CROWDED-PRO-LIPIDS). AO acknowledges The Wellcome Trust International Senior Research Fellowship.","year":"2016","month":"09","language":[{"iso":"eng"}],"doi":"10.1038/srep33607","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"citation":{"ieee":"F. Ortiz Morea et al., “Danger-associated peptide signaling in Arabidopsis requires clathrin,” PNAS, vol. 113, no. 39. National Academy of Sciences, pp. 11028–11033, 2016.","apa":"Ortiz Morea, F., Savatin, D., Dejonghe, W., Kumar, R., Luo, Y., Adamowski, M., … Russinova, E. (2016). Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1605588113","ista":"Ortiz Morea F, Savatin D, Dejonghe W, Kumar R, Luo Y, Adamowski M, Van Begin J, Dressano K, De Oliveira G, Zhao X, Lu Q, Madder A, Friml J, De Moura D, Russinova E. 2016. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 113(39), 11028–11033.","ama":"Ortiz Morea F, Savatin D, Dejonghe W, et al. Danger-associated peptide signaling in Arabidopsis requires clathrin. PNAS. 2016;113(39):11028-11033. doi:10.1073/pnas.1605588113","chicago":"Ortiz Morea, Fausto, Daniel Savatin, Wim Dejonghe, Rahul Kumar, Yu Luo, Maciek Adamowski, Jos Van Begin, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1605588113.","short":"F. Ortiz Morea, D. Savatin, W. Dejonghe, R. Kumar, Y. Luo, M. Adamowski, J. Van Begin, K. Dressano, G. De Oliveira, X. Zhao, Q. Lu, A. Madder, J. Friml, D. De Moura, E. Russinova, PNAS 113 (2016) 11028–11033.","mla":"Ortiz Morea, Fausto, et al. “Danger-Associated Peptide Signaling in Arabidopsis Requires Clathrin.” PNAS, vol. 113, no. 39, National Academy of Sciences, 2016, pp. 11028–33, doi:10.1073/pnas.1605588113."},"publication":"PNAS","page":"11028 - 11033","date_published":"2016-09-27T00:00:00Z","scopus_import":1,"day":"27","_id":"1277","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 113","status":"public","title":"Danger-associated peptide signaling in Arabidopsis requires clathrin","oa_version":"Preprint","type":"journal_article","issue":"39","abstract":[{"lang":"eng","text":"The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.\r\n"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047203/"}],"quality_controlled":"1","doi":"10.1073/pnas.1605588113","language":[{"iso":"eng"}],"month":"09","year":"2016","acknowledgement":"F.A.O.-M. was supported by special\r\nresearch funding from the Flemish Government for a joint doctorate fellowship\r\nat Ghent University, and funding from the Student Program\r\n–\r\nGraduate Studies\r\nPlan Program from the Coordination for the Improvement of Higher Educa-\r\ntion Personnel, Brazil, for a doctorate fellowship at the University of São Paulo.\r\nX.Z. and Q.L. are indebted to the China Science Council and G.P.d.O. to the\r\n“\r\nCiência sem Fronteiras\r\n”\r\nfor predoctoral fellowships. R.K. and Y.L. have re-\r\nceived postdoctoral fellowships from the Belgian Science Policy Office. This\r\nresearch was supported by Flanders Research Foundation Grant G008416N\r\n(to E.R.) and by the São Paulo Research Foundation and the National Council\r\nfor Scientific and Technological Development (CNPq) (D.S.d.M.). D.S.d.M. is a\r\nresearch fellow of CNPq.\r\nWe thank D. Van Damme, E. Mylle, M. Castro Silva-Filho,\r\nand J. Goeman for providing usefu\r\nl advice and technical assistance;\r\nI. Hara-Nishimura, J. Lin, G. Jürgens, M. A. Johnson, and P. Bozhkov for sharing\r\npublished materials; and M. Nowack and M. Fendrych for kindly donating the\r\npUBQ10::ATG8-YFP\r\n-expressing marker line.","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"last_name":"Ortiz Morea","first_name":"Fausto","full_name":"Ortiz Morea, Fausto"},{"first_name":"Daniel","last_name":"Savatin","full_name":"Savatin, Daniel"},{"first_name":"Wim","last_name":"Dejonghe","full_name":"Dejonghe, Wim"},{"full_name":"Kumar, Rahul","last_name":"Kumar","first_name":"Rahul"},{"first_name":"Yu","last_name":"Luo","full_name":"Luo, Yu"},{"full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257"},{"full_name":"Van Begin, Jos","last_name":"Van Begin","first_name":"Jos"},{"full_name":"Dressano, Keini","last_name":"Dressano","first_name":"Keini"},{"full_name":"De Oliveira, Guilherme","first_name":"Guilherme","last_name":"De Oliveira"},{"full_name":"Zhao, Xiuyang","first_name":"Xiuyang","last_name":"Zhao"},{"full_name":"Lu, Qing","first_name":"Qing","last_name":"Lu"},{"last_name":"Madder","first_name":"Annemieke","full_name":"Madder, Annemieke"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"De Moura, Daniel","last_name":"De Moura","first_name":"Daniel"},{"full_name":"Russinova, Eugenia","first_name":"Eugenia","last_name":"Russinova"}],"volume":113,"date_updated":"2021-01-12T06:49:34Z","date_created":"2018-12-11T11:51:06Z","publist_id":"6039"},{"department":[{"_id":"EvBe"}],"publisher":"American Society of Plant Biologists","publication_status":"published","acknowledgement":"This work was supported by the Agropolis Foundation (RHIZOPOLIS project to A.G. and P.N., and RTRA 2009-2011 project to F.P.-W.), the Knowledge Biobase Economy European project (KBBE-005-002 Root enhancement for crop improvement to M.P. and P.N.), and the European EURoot project (FP7-KBBE-2011-5 to J.R., A.G., and P.N.). We thank Carine Alcon for the help with analysis of confocal images, Xavier\r\nDumont for assistance with Arabidopsis transformations, staff members of the\r\nInstitut de Biologie Intégrative des Plantes for technical assistance with biological\r\nmaterial culture, and students and trainees for assistance with laboratory work.\r\nConfocal observations were made at the Montpellier RIO Imaging facility.","year":"2016","volume":172,"date_updated":"2021-01-12T06:49:36Z","date_created":"2018-12-11T11:51:07Z","author":[{"last_name":"Bouguyon","first_name":"Eléonore","full_name":"Bouguyon, Eléonore"},{"full_name":"Perrine Walker, Francine","last_name":"Perrine Walker","first_name":"Francine"},{"first_name":"Marjorie","last_name":"Pervent","full_name":"Pervent, Marjorie"},{"last_name":"Rochette","first_name":"Juliette","full_name":"Rochette, Juliette"},{"full_name":"Cuesta, Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1923-2410","first_name":"Candela","last_name":"Cuesta"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva"},{"full_name":"Martinière, Alexandre","last_name":"Martinière","first_name":"Alexandre"},{"full_name":"Bach, Lien","last_name":"Bach","first_name":"Lien"},{"first_name":"Gabriel","last_name":"Krouk","full_name":"Krouk, Gabriel"},{"full_name":"Gojon, Alain","last_name":"Gojon","first_name":"Alain"},{"full_name":"Nacry, Philippe","first_name":"Philippe","last_name":"Nacry"}],"publist_id":"6035","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047109/"}],"language":[{"iso":"eng"}],"doi":"10.1104/pp.16.01047","month":"10","intvolume":" 172","title":"Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1281","oa_version":"Preprint","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue."}],"page":"1237 - 1248","citation":{"chicago":"Bouguyon, Eléonore, Francine Perrine Walker, Marjorie Pervent, Juliette Rochette, Candela Cuesta, Eva Benková, Alexandre Martinière, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.01047.","short":"E. Bouguyon, F. Perrine Walker, M. Pervent, J. Rochette, C. Cuesta, E. Benková, A. Martinière, L. Bach, G. Krouk, A. Gojon, P. Nacry, Plant Physiology 172 (2016) 1237–1248.","mla":"Bouguyon, Eléonore, et al. “Nitrate Controls Root Development through Posttranscriptional Regulation of the NRT1.1/NPF6.3 Transporter Sensor.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1237–48, doi:10.1104/pp.16.01047.","ieee":"E. Bouguyon et al., “Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1237–1248, 2016.","apa":"Bouguyon, E., Perrine Walker, F., Pervent, M., Rochette, J., Cuesta, C., Benková, E., … Nacry, P. (2016). Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01047","ista":"Bouguyon E, Perrine Walker F, Pervent M, Rochette J, Cuesta C, Benková E, Martinière A, Bach L, Krouk G, Gojon A, Nacry P. 2016. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 172(2), 1237–1248.","ama":"Bouguyon E, Perrine Walker F, Pervent M, et al. Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor. Plant Physiology. 2016;172(2):1237-1248. doi:10.1104/pp.16.01047"},"publication":"Plant Physiology","date_published":"2016-10-01T00:00:00Z","scopus_import":1,"day":"01"},{"author":[{"full_name":"Gundert, Anna","first_name":"Anna","last_name":"Gundert"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"date_updated":"2021-01-12T06:49:36Z","date_created":"2018-12-11T11:51:07Z","oa_version":"Preprint","volume":216,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1282","year":"2016","status":"public","title":"On eigenvalues of random complexes","publication_status":"published","department":[{"_id":"UlWa"}],"intvolume":" 216","publisher":"Springer","abstract":[{"lang":"eng","text":"We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k."}],"publist_id":"6034","issue":"2","type":"journal_article","date_published":"2016-10-01T00:00:00Z","doi":"10.1007/s11856-016-1419-1","language":[{"iso":"eng"}],"publication":"Israel Journal of Mathematics","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1411.4906"}],"citation":{"mla":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 545–82, doi:10.1007/s11856-016-1419-1.","short":"A. Gundert, U. Wagner, Israel Journal of Mathematics 216 (2016) 545–582.","chicago":"Gundert, Anna, and Uli Wagner. “On Eigenvalues of Random Complexes.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1419-1.","ama":"Gundert A, Wagner U. On eigenvalues of random complexes. Israel Journal of Mathematics. 2016;216(2):545-582. doi:10.1007/s11856-016-1419-1","ista":"Gundert A, Wagner U. 2016. On eigenvalues of random complexes. Israel Journal of Mathematics. 216(2), 545–582.","ieee":"A. Gundert and U. Wagner, “On eigenvalues of random complexes,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 545–582, 2016.","apa":"Gundert, A., & Wagner, U. (2016). On eigenvalues of random complexes. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1419-1"},"quality_controlled":"1","page":"545 - 582","month":"10","day":"01","scopus_import":1},{"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21624","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1407.5606"}],"month":"10","volume":69,"date_created":"2018-12-11T11:51:07Z","date_updated":"2021-01-12T06:49:35Z","author":[{"full_name":"Bourgade, Paul","first_name":"Paul","last_name":"Bourgade"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"},{"full_name":"Yau, Horngtzer","last_name":"Yau","first_name":"Horngtzer"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"publisher":"Wiley-Blackwell","department":[{"_id":"LaEr"}],"publication_status":"published","acknowledgement":"The work of P.B. was partially supported by National Sci-\r\nence Foundation Grant DMS-1208859. The work of L.E. was partially supported\r\nby ERC Advanced Grant RANMAT 338804. The work of H.-T. Y. was partially\r\nsupported by National Science Foundation Grant DMS-1307444 and a Simons In-\r\nvestigator award. The work of J.Y. was partially supported by National Science\r\nFoundation Grant DMS-1207961. The major part of this research was conducted\r\nwhen all authors were visiting IAS and were also supported by National Science\r\nFoundation Grant DMS-1128255.","year":"2016","publist_id":"6036","ec_funded":1,"date_published":"2016-10-01T00:00:00Z","page":"1815 - 1881","citation":{"chicago":"Bourgade, Paul, László Erdös, Horngtzer Yau, and Jun Yin. “Fixed Energy Universality for Generalized Wigner Matrices.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2016. https://doi.org/10.1002/cpa.21624.","mla":"Bourgade, Paul, et al. “Fixed Energy Universality for Generalized Wigner Matrices.” Communications on Pure and Applied Mathematics, vol. 69, no. 10, Wiley-Blackwell, 2016, pp. 1815–81, doi:10.1002/cpa.21624.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Communications on Pure and Applied Mathematics 69 (2016) 1815–1881.","ista":"Bourgade P, Erdös L, Yau H, Yin J. 2016. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 69(10), 1815–1881.","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Fixed energy universality for generalized wigner matrices,” Communications on Pure and Applied Mathematics, vol. 69, no. 10. Wiley-Blackwell, pp. 1815–1881, 2016.","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2016). Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21624","ama":"Bourgade P, Erdös L, Yau H, Yin J. Fixed energy universality for generalized wigner matrices. Communications on Pure and Applied Mathematics. 2016;69(10):1815-1881. doi:10.1002/cpa.21624"},"publication":"Communications on Pure and Applied Mathematics","day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 69","title":"Fixed energy universality for generalized wigner matrices","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1280","issue":"10","abstract":[{"lang":"eng","text":"We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous results concerning the universality of random matrices either require an averaging in the energy parameter or they hold only for Hermitian matrices if the energy parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion and show that microscopic universality follows from mesoscopic statistics."}],"type":"journal_article"},{"scopus_import":1,"day":"22","month":"09","publication":"Physical Review Letters","citation":{"chicago":"Callan Jones, Andrew, Verena Ruprecht, Stefan Wieser, Carl-Philipp J Heisenberg, and Raphaël Voituriez. “Callan-Jones et Al. Reply.” Physical Review Letters. American Physical Society, 2016. https://doi.org/10.1103/PhysRevLett.117.139802.","short":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P.J. Heisenberg, R. Voituriez, Physical Review Letters 117 (2016).","mla":"Callan Jones, Andrew, et al. “Callan-Jones et Al. Reply.” Physical Review Letters, vol. 117, no. 13, 139802, American Physical Society, 2016, doi:10.1103/PhysRevLett.117.139802.","apa":"Callan Jones, A., Ruprecht, V., Wieser, S., Heisenberg, C.-P. J., & Voituriez, R. (2016). Callan-Jones et al. Reply. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.117.139802","ieee":"A. Callan Jones, V. Ruprecht, S. Wieser, C.-P. J. Heisenberg, and R. Voituriez, “Callan-Jones et al. Reply,” Physical Review Letters, vol. 117, no. 13. American Physical Society, 2016.","ista":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. 2016. Callan-Jones et al. Reply. Physical Review Letters. 117(13), 139802.","ama":"Callan Jones A, Ruprecht V, Wieser S, Heisenberg C-PJ, Voituriez R. Callan-Jones et al. Reply. Physical Review Letters. 2016;117(13). doi:10.1103/PhysRevLett.117.139802"},"quality_controlled":"1","doi":"10.1103/PhysRevLett.117.139802","date_published":"2016-09-22T00:00:00Z","language":[{"iso":"eng"}],"article_number":"139802","type":"journal_article","publist_id":"6041","issue":"13","_id":"1275","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","status":"public","title":"Callan-Jones et al. Reply","publication_status":"published","intvolume":" 117","publisher":"American Physical Society","department":[{"_id":"CaHe"}],"author":[{"full_name":"Callan Jones, Andrew","first_name":"Andrew","last_name":"Callan Jones"},{"first_name":"Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena"},{"last_name":"Wieser","first_name":"Stefan","orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Voituriez, Raphaël","last_name":"Voituriez","first_name":"Raphaël"}],"date_created":"2018-12-11T11:51:05Z","date_updated":"2021-01-12T06:49:33Z","volume":117,"oa_version":"None"},{"issue":"10","abstract":[{"lang":"eng","text":"The impact of the plant hormone ethylene on seedling development has long been recognized; however, its ecophysiological relevance is unexplored. Three recent studies demonstrate that ethylene is a critical endogenous integrator of various environmental signals including mechanical stress, light, and oxygen availability during seedling germination and growth through the soil."}],"type":"journal_article","oa_version":"Submitted Version","file":[{"file_name":"IST-2018-1018-v1+1_Zhu_and_Benkova_TIPS_2016.pdf","access_level":"local","file_size":229094,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4679","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:08:19Z","checksum":"4d569977fad7a7f22b7e3424003d2ab1"}],"pubrep_id":"1018","intvolume":" 21","ddc":["575"],"status":"public","title":"Seedlings’ strategy to overcome a soil barrier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1283","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-10-01T00:00:00Z","page":"809 - 811","article_type":"original","citation":{"short":"Q. Zhu, E. Benková, Trends in Plant Science 21 (2016) 809–811.","mla":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” Trends in Plant Science, vol. 21, no. 10, Cell Press, 2016, pp. 809–11, doi:10.1016/j.tplants.2016.08.003.","chicago":"Zhu, Qiang, and Eva Benková. “Seedlings’ Strategy to Overcome a Soil Barrier.” Trends in Plant Science. Cell Press, 2016. https://doi.org/10.1016/j.tplants.2016.08.003.","ama":"Zhu Q, Benková E. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 2016;21(10):809-811. doi:10.1016/j.tplants.2016.08.003","apa":"Zhu, Q., & Benková, E. (2016). Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2016.08.003","ieee":"Q. Zhu and E. Benková, “Seedlings’ strategy to overcome a soil barrier,” Trends in Plant Science, vol. 21, no. 10. Cell Press, pp. 809–811, 2016.","ista":"Zhu Q, Benková E. 2016. Seedlings’ strategy to overcome a soil barrier. Trends in Plant Science. 21(10), 809–811."},"publication":"Trends in Plant Science","publist_id":"6033","file_date_updated":"2020-07-14T12:44:42Z","volume":21,"date_updated":"2021-01-12T06:49:36Z","date_created":"2018-12-11T11:51:08Z","author":[{"full_name":"Zhu, Qiang","id":"40A4B9E6-F248-11E8-B48F-1D18A9856A87","first_name":"Qiang","last_name":"Zhu"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"department":[{"_id":"EvBe"}],"publisher":"Cell Press","publication_status":"published","acknowledgement":"This work was supported by the Austrian Science Fund (FWF01_I1774S) to E.B., the Natural Science Foundation of Fujian Province (2016J01099), and the Fujian–Taiwan Joint Innovative Center for Germplasm Resources and Cultivation of Crops (FJ 2011 Program, No 2015-75) to Q.Z. The\r\nauthors\r\nthank\r\nIsrael\r\nAusin\r\nand\r\nXu\r\nChen\r\nfor\r\ncritical\r\nreading\r\nof\r\nthe\r\nmanuscript.","year":"2016","month":"10","language":[{"iso":"eng"}],"doi":"10.1016/j.tplants.2016.08.003","project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","call_identifier":"FWF","grant_number":"I 1774-B16","_id":"2542D156-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"}},{"day":"13","scopus_import":1,"date_published":"2016-10-13T00:00:00Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","citation":{"apa":"Midya, B., Tomza, M., Schmidt, R., & Lemeshko, M. (2016). Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.94.041601","ieee":"B. Midya, M. Tomza, R. Schmidt, and M. Lemeshko, “Rotation of cold molecular ions inside a Bose-Einstein condensate,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 94, no. 4. American Physical Society, 2016.","ista":"Midya B, Tomza M, Schmidt R, Lemeshko M. 2016. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 94(4), 041601.","ama":"Midya B, Tomza M, Schmidt R, Lemeshko M. Rotation of cold molecular ions inside a Bose-Einstein condensate. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;94(4). doi:10.1103/PhysRevA.94.041601","chicago":"Midya, Bikashkali, Michał Tomza, Richard Schmidt, and Mikhail Lemeshko. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.94.041601.","short":"B. Midya, M. Tomza, R. Schmidt, M. Lemeshko, Physical Review A - Atomic, Molecular, and Optical Physics 94 (2016).","mla":"Midya, Bikashkali, et al. “Rotation of Cold Molecular Ions inside a Bose-Einstein Condensate.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 94, no. 4, 041601, American Physical Society, 2016, doi:10.1103/PhysRevA.94.041601."},"abstract":[{"text":"We use recently developed angulon theory [R. Schmidt and M. Lemeshko, Phys. Rev. Lett. 114, 203001 (2015)PRLTAO0031-900710.1103/PhysRevLett.114.203001] to study the rotational spectrum of a cyanide molecular anion immersed into Bose-Einstein condensates of rubidium and strontium. Based on ab initio potential energy surfaces, we provide a detailed study of the rotational Lamb shift and many-body-induced fine structure which arise due to dressing of molecular rotation by a field of phonon excitations. We demonstrate that the magnitude of these effects is large enough in order to be observed in modern experiments on cold molecular ions. Furthermore, we introduce a novel method to construct pseudopotentials starting from the ab initio potential energy surfaces, which provides a means to obtain effective coupling constants for low-energy polaron models.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Preprint","status":"public","title":"Rotation of cold molecular ions inside a Bose-Einstein condensate","intvolume":" 94","_id":"1286","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"10","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.94.041601","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.06092"}],"oa":1,"publist_id":"6030","ec_funded":1,"article_number":"041601","date_updated":"2021-01-12T06:49:37Z","date_created":"2018-12-11T11:51:09Z","volume":94,"author":[{"full_name":"Midya, Bikashkali","last_name":"Midya","first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tomza","first_name":"Michał","full_name":"Tomza, Michał"},{"full_name":"Schmidt, Richard","last_name":"Schmidt","first_name":"Richard"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","year":"2016","acknowledgement":"The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and the Smithsonian Astrophysical Observatory. B.M. acknowledges financial support received from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. 291734. M.T. acknowledges support from the EU Marie Curie COFUND action (ICFOnest), the EU Grants ERC AdG OSYRIS, FP7 SIQS and EQuaM, FETPROACT QUIC, the Spanish Ministry Grants FOQUS (FIS2013-46768-P) and Severo Ochoa (SEV-2015-0522), Generalitat de Catalunya (SGR 874), Fundacio Cellex, the National Science Centre (2015/19/D/ST4/02173), and the PL-Grid Infrastructure."},{"quality_controlled":"1","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7"},{"name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"page":"469 - 490","publication":"Annual Review of Cell and Developmental Biology","citation":{"ama":"Paluch E, Aspalter I, Sixt MK. Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. 2016;32:469-490. doi:10.1146/annurev-cellbio-111315-125341","ieee":"E. Paluch, I. Aspalter, and M. K. Sixt, “Focal adhesion-independent cell migration,” Annual Review of Cell and Developmental Biology, vol. 32. Annual Reviews, pp. 469–490, 2016.","apa":"Paluch, E., Aspalter, I., & Sixt, M. K. (2016). Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. Annual Reviews. https://doi.org/10.1146/annurev-cellbio-111315-125341","ista":"Paluch E, Aspalter I, Sixt MK. 2016. Focal adhesion-independent cell migration. Annual Review of Cell and Developmental Biology. 32, 469–490.","short":"E. Paluch, I. Aspalter, M.K. Sixt, Annual Review of Cell and Developmental Biology 32 (2016) 469–490.","mla":"Paluch, Ewa, et al. “Focal Adhesion-Independent Cell Migration.” Annual Review of Cell and Developmental Biology, vol. 32, Annual Reviews, 2016, pp. 469–90, doi:10.1146/annurev-cellbio-111315-125341.","chicago":"Paluch, Ewa, Irene Aspalter, and Michael K Sixt. “Focal Adhesion-Independent Cell Migration.” Annual Review of Cell and Developmental Biology. Annual Reviews, 2016. https://doi.org/10.1146/annurev-cellbio-111315-125341."},"language":[{"iso":"eng"}],"date_published":"2016-10-06T00:00:00Z","doi":"10.1146/annurev-cellbio-111315-125341","scopus_import":1,"day":"06","month":"10","title":"Focal adhesion-independent cell migration","publication_status":"published","status":"public","department":[{"_id":"MiSi"}],"publisher":"Annual Reviews","intvolume":" 32","acknowledgement":"We would like to thank Dani Bodor for critical comments on the manuscript and Guillaume Salbreux for discussions. The authors are supported by the United Kingdom's Medical Research Council (MRC) (E.K.P. and I.M.A.; core funding to the MRC Laboratory for Molecular Cell Biology), by the European Research Council [ERC GA 311637 (E.K.P.) and ERC GA 281556 (M.S.)], and by a START award from the Austrian Science Foundation (M.S.).","_id":"1285","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:51:08Z","date_updated":"2021-01-12T06:49:37Z","oa_version":"None","volume":32,"author":[{"first_name":"Ewa","last_name":"Paluch","full_name":"Paluch, Ewa"},{"full_name":"Aspalter, Irene","last_name":"Aspalter","first_name":"Irene"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"type":"journal_article","abstract":[{"text":"Cell migration is central to a multitude of physiological processes, including embryonic development, immune surveillance, and wound healing, and deregulated migration is key to cancer dissemination. Decades of investigations have uncovered many of the molecular and physical mechanisms underlying cell migration. Together with protrusion extension and cell body retraction, adhesion to the substrate via specific focal adhesion points has long been considered an essential step in cell migration. Although this is true for cells moving on two-dimensional substrates, recent studies have demonstrated that focal adhesions are not required for cells moving in three dimensions, in which confinement is sufficient to maintain a cell in contact with its substrate. Here, we review the investigations that have led to challenging the requirement of specific adhesions for migration, discuss the physical mechanisms proposed for cell body translocation during focal adhesion-independent migration, and highlight the remaining open questions for the future.","lang":"eng"}],"publist_id":"6031","ec_funded":1},{"date_published":"2016-11-01T00:00:00Z","doi":"10.1016/j.bbabio.2016.08.008","language":[{"iso":"eng"}],"citation":{"ista":"Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. 2016. Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(11), 1777–1785.","apa":"Holt, P., Efremov, R., Nakamaru Ogiso, E., & Sazanov, L. A. (2016). Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2016.08.008","ieee":"P. Holt, R. Efremov, E. Nakamaru Ogiso, and L. A. Sazanov, “Reversible FMN dissociation from Escherichia coli respiratory complex I,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no. 11. Elsevier, pp. 1777–1785, 2016.","ama":"Holt P, Efremov R, Nakamaru Ogiso E, Sazanov LA. Reversible FMN dissociation from Escherichia coli respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 2016;1857(11):1777-1785. doi:10.1016/j.bbabio.2016.08.008","chicago":"Holt, Peter, Rouslan Efremov, Eiko Nakamaru Ogiso, and Leonid A Sazanov. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2016. https://doi.org/10.1016/j.bbabio.2016.08.008.","mla":"Holt, Peter, et al. “Reversible FMN Dissociation from Escherichia Coli Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no. 11, Elsevier, 2016, pp. 1777–85, doi:10.1016/j.bbabio.2016.08.008.","short":"P. Holt, R. Efremov, E. Nakamaru Ogiso, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1857 (2016) 1777–1785."},"publication":"Biochimica et Biophysica Acta - Bioenergetics","page":"1777 - 1785","quality_controlled":"1","day":"01","month":"11","scopus_import":1,"author":[{"last_name":"Holt","first_name":"Peter","full_name":"Holt, Peter"},{"full_name":"Efremov, Rouslan","last_name":"Efremov","first_name":"Rouslan"},{"full_name":"Nakamaru Ogiso, Eiko","first_name":"Eiko","last_name":"Nakamaru Ogiso"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}],"oa_version":"None","volume":1857,"date_created":"2018-12-11T11:51:09Z","date_updated":"2021-01-12T06:49:38Z","_id":"1288","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","acknowledgement":"This work was funded by the UK Medical Research Council.","department":[{"_id":"LeSa"}],"publisher":"Elsevier","intvolume":" 1857","title":"Reversible FMN dissociation from Escherichia coli respiratory complex I","status":"public","publication_status":"published","issue":"11","publist_id":"6028","abstract":[{"text":"Respiratory complex I transfers electrons from NADH to quinone, utilizing the reaction energy to translocate protons across the membrane. It is a key enzyme of the respiratory chain of many prokaryotic and most eukaryotic organisms. The reversible NADH oxidation reaction is facilitated in complex I by non-covalently bound flavin mononucleotide (FMN). Here we report that the catalytic activity of E. coli complex I with artificial electron acceptors potassium ferricyanide (FeCy) and hexaamineruthenium (HAR) is significantly inhibited in the enzyme pre-reduced by NADH. Further, we demonstrate that the inhibition is caused by reversible dissociation of FMN. The binding constant (Kd) for FMN increases from the femto- or picomolar range in oxidized complex I to the nanomolar range in the NADH reduced enzyme, with an FMN dissociation time constant of ~ 5 s. The oxidation state of complex I, rather than that of FMN, proved critical to the dissociation. Such dissociation is not observed with the T. thermophilus enzyme and our analysis suggests that the difference may be due to the unusually high redox potential of Fe-S cluster N1a in E. coli. It is possible that the enzyme attenuates ROS production in vivo by releasing FMN under highly reducing conditions.","lang":"eng"}],"type":"journal_article"},{"doi":"10.1007/s00220-016-2665-0","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"quality_controlled":"1","month":"11","author":[{"first_name":"Alessandro","last_name":"Giuliani","full_name":"Giuliani, Alessandro"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"volume":347,"date_created":"2018-12-11T11:51:11Z","date_updated":"2021-01-12T06:49:40Z","year":"2016","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The\r\nresearch leading to these results has received funding from the European Research Council under the European\r\nUnion’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694), from\r\nthe Italian PRIN National Grant Geometric and analytic theory of Hamiltonian systems in finite and infinite\r\ndimensions, and the Austrian Science Fund (FWF), project Nr. P 27533-N27. Part of this work was completed\r\nduring a stay at the Erwin Schrödinger Institute for Mathematical Physics in Vienna (ESI program 2015\r\n“Quantum many-body systems, random matrices, and disorder”), whose hospitality and financial support is\r\ngratefully acknowledged.","department":[{"_id":"RoSe"}],"publisher":"Springer","publication_status":"published","publist_id":"6025","file_date_updated":"2020-07-14T12:44:42Z","date_published":"2016-11-01T00:00:00Z","citation":{"short":"A. Giuliani, R. Seiringer, Communications in Mathematical Physics 347 (2016) 983–1007.","mla":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” Communications in Mathematical Physics, vol. 347, no. 3, Springer, 2016, pp. 983–1007, doi:10.1007/s00220-016-2665-0.","chicago":"Giuliani, Alessandro, and Robert Seiringer. “Periodic Striped Ground States in Ising Models with Competing Interactions.” Communications in Mathematical Physics. Springer, 2016. https://doi.org/10.1007/s00220-016-2665-0.","ama":"Giuliani A, Seiringer R. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 2016;347(3):983-1007. doi:10.1007/s00220-016-2665-0","apa":"Giuliani, A., & Seiringer, R. (2016). Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2665-0","ieee":"A. Giuliani and R. Seiringer, “Periodic striped ground states in Ising models with competing interactions,” Communications in Mathematical Physics, vol. 347, no. 3. Springer, pp. 983–1007, 2016.","ista":"Giuliani A, Seiringer R. 2016. Periodic striped ground states in Ising models with competing interactions. Communications in Mathematical Physics. 347(3), 983–1007."},"publication":"Communications in Mathematical Physics","page":"983 - 1007","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"688","oa_version":"Published Version","file":[{"creator":"system","file_size":794983,"content_type":"application/pdf","file_name":"IST-2016-688-v1+1_s00220-016-2665-0.pdf","access_level":"open_access","date_created":"2018-12-12T10:09:02Z","date_updated":"2020-07-14T12:44:42Z","checksum":"3c6e08c048fc462e312788be72874bb1","file_id":"4725","relation":"main_file"}],"_id":"1291","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 347","status":"public","ddc":["510","530"],"title":"Periodic striped ground states in Ising models with competing interactions","issue":"3","abstract":[{"lang":"eng","text":"We consider Ising models in two and three dimensions, with short range ferromagnetic and long range, power-law decaying, antiferromagnetic interactions. We let J be the ratio between the strength of the ferromagnetic to antiferromagnetic interactions. The competition between these two kinds of interactions induces the system to form domains of minus spins in a background of plus spins, or vice versa. If the decay exponent p of the long range interaction is larger than d + 1, with d the space dimension, this happens for all values of J smaller than a critical value Jc(p), beyond which the ground state is homogeneous. In this paper, we give a characterization of the infinite volume ground states of the system, for p > 2d and J in a left neighborhood of Jc(p). In particular, we prove that the quasi-one-dimensional states consisting of infinite stripes (d = 2) or slabs (d = 3), all of the same optimal width and orientation, and alternating magnetization, are infinite volume ground states. Our proof is based on localization bounds combined with reflection positivity."}],"type":"journal_article"},{"publist_id":"6024","volume":509,"date_updated":"2021-01-12T06:49:40Z","date_created":"2018-12-11T11:51:11Z","author":[{"full_name":"Solus, Liam T","first_name":"Liam T","last_name":"Solus","id":"2AADA620-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline","full_name":"Uhler, Caroline"},{"full_name":"Yoshida, Ruriko","last_name":"Yoshida","first_name":"Ruriko"}],"publisher":"Elsevier","department":[{"_id":"CaUh"}],"publication_status":"published","year":"2016","acknowledgement":"We wish to thank Alexander Engström and Bernd Sturmfels for various valuable discussions and insights. We also thank the two anonymous referees for their thoughtful feedback on the paper. CU was partially supported by the Austrian Science Fund (FWF) Y 903-N35.","month":"11","language":[{"iso":"eng"}],"doi":"10.1016/j.laa.2016.07.026","project":[{"name":"Gaussian Graphical Models: Theory and Applications","call_identifier":"FWF","grant_number":"Y 903-N35","_id":"2530CA10-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1506.06702.pdf"}],"oa":1,"abstract":[{"text":"For a graph G with p vertices the closed convex cone S⪰0(G) consists of all real positive semidefinite p×p matrices whose sparsity pattern is given by G, that is, those matrices with zeros in the off-diagonal entries corresponding to nonedges of G. The extremal rays of this cone and their associated ranks have applications to matrix completion problems, maximum likelihood estimation in Gaussian graphical models in statistics, and Gauss elimination for sparse matrices. While the maximum rank of an extremal ray in S⪰0(G), known as the sparsity order of G, has been characterized for different classes of graphs, we here study all possible extremal ranks of S⪰0(G). We investigate when the geometry of the (±1)-cut polytope of G yields a polyhedral characterization of the set of extremal ranks of S⪰0(G). For a graph G without K5 minors, we show that appropriately chosen normal vectors to the facets of the (±1)-cut polytope of G specify the off-diagonal entries of extremal matrices in S⪰0(G). We also prove that for appropriately chosen scalars the constant term of the linear equation of each facet-supporting hyperplane is the rank of its corresponding extremal matrix in S⪰0(G). Furthermore, we show that if G is series-parallel then this gives a complete characterization of all possible extremal ranks of S⪰0(G). Consequently, the sparsity order problem for series-parallel graphs can be solved in terms of polyhedral geometry.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 509","title":"Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors","status":"public","_id":"1293","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"15","scopus_import":1,"date_published":"2016-11-15T00:00:00Z","page":"247 - 275","citation":{"chicago":"Solus, Liam T, Caroline Uhler, and Ruriko Yoshida. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” Linear Algebra and Its Applications. Elsevier, 2016. https://doi.org/10.1016/j.laa.2016.07.026.","mla":"Solus, Liam T., et al. “Extremal Positive Semidefinite Matrices Whose Sparsity Pattern Is given by Graphs without K5 Minors.” Linear Algebra and Its Applications, vol. 509, Elsevier, 2016, pp. 247–75, doi:10.1016/j.laa.2016.07.026.","short":"L.T. Solus, C. Uhler, R. Yoshida, Linear Algebra and Its Applications 509 (2016) 247–275.","ista":"Solus LT, Uhler C, Yoshida R. 2016. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 509, 247–275.","ieee":"L. T. Solus, C. Uhler, and R. Yoshida, “Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors,” Linear Algebra and Its Applications, vol. 509. Elsevier, pp. 247–275, 2016.","apa":"Solus, L. T., Uhler, C., & Yoshida, R. (2016). Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2016.07.026","ama":"Solus LT, Uhler C, Yoshida R. Extremal positive semidefinite matrices whose sparsity pattern is given by graphs without K5 minors. Linear Algebra and Its Applications. 2016;509:247-275. doi:10.1016/j.laa.2016.07.026"},"publication":"Linear Algebra and Its Applications"},{"issue":"11","abstract":[{"text":"We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 12","title":"Compounds that select against the tetracycline-resistance efflux pump","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1290","day":"01","scopus_import":1,"date_published":"2016-11-01T00:00:00Z","page":"902 - 904","citation":{"ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.","apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176","ieee":"L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” Nature Chemical Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.","ama":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 2016;12(11):902-904. doi:10.1038/nchembio.2176","chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176.","mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176.","short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904."},"publication":"Nature Chemical Biology","publist_id":"6026","volume":12,"date_created":"2018-12-11T11:51:10Z","date_updated":"2021-01-12T06:49:39Z","author":[{"full_name":"Stone, Laura","first_name":"Laura","last_name":"Stone"},{"last_name":"Baym","first_name":"Michael","full_name":"Baym, Michael"},{"last_name":"Lieberman","first_name":"Tami","full_name":"Lieberman, Tami"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","first_name":"Remy P","last_name":"Chait","full_name":"Chait, Remy P"},{"full_name":"Clardy, Jon","last_name":"Clardy","first_name":"Jon"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"Nature Publishing Group","publication_status":"published","year":"2016","acknowledgement":"This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n","month":"11","language":[{"iso":"eng"}],"doi":"10.1038/nchembio.2176","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"oa":1},{"month":"10","day":"01","scopus_import":1,"doi":"10.1016/j.endm.2016.09.030","date_published":"2016-10-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"short":"H. Edelsbrunner, M. Iglesias Ham, Electronic Notes in Discrete Mathematics 54 (2016) 169–174.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” Electronic Notes in Discrete Mathematics, vol. 54, Elsevier, 2016, pp. 169–74, doi:10.1016/j.endm.2016.09.030.","chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls II: Weighted Averages.” Electronic Notes in Discrete Mathematics. Elsevier, 2016. https://doi.org/10.1016/j.endm.2016.09.030.","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. 2016;54:169-174. doi:10.1016/j.endm.2016.09.030","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls II: Weighted averages,” Electronic Notes in Discrete Mathematics, vol. 54. Elsevier, pp. 169–174, 2016.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2016). Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2016.09.030","ista":"Edelsbrunner H, Iglesias Ham M. 2016. Multiple covers with balls II: Weighted averages. Electronic Notes in Discrete Mathematics. 54, 169–174."},"publication":"Electronic Notes in Discrete Mathematics","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"page":"169 - 174","quality_controlled":"1","ec_funded":1,"publist_id":"5976","abstract":[{"text":"Voronoi diagrams and Delaunay triangulations have been extensively used to represent and compute geometric features of point configurations. We introduce a generalization to poset diagrams and poset complexes, which contain order-k and degree-k Voronoi diagrams and their duals as special cases. Extending a result of Aurenhammer from 1990, we show how to construct poset diagrams as weighted Voronoi diagrams of average balls.","lang":"eng"}],"type":"journal_article","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"Mabel","last_name":"Iglesias Ham","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","full_name":"Iglesias Ham, Mabel"}],"volume":54,"oa_version":"None","date_created":"2018-12-11T11:51:12Z","date_updated":"2021-01-12T06:49:41Z","_id":"1295","year":"2016","acknowledgement":"This work is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"publisher":"Elsevier","intvolume":" 54","publication_status":"published","title":"Multiple covers with balls II: Weighted averages","status":"public"},{"author":[{"last_name":"Durst","first_name":"Sebastian","full_name":"Durst, Sebastian"},{"full_name":"Kegel, Marc","last_name":"Kegel","first_name":"Marc"},{"full_name":"Klukas, Mirko D","id":"34927512-F248-11E8-B48F-1D18A9856A87","first_name":"Mirko D","last_name":"Klukas"}],"date_updated":"2021-01-12T06:49:40Z","date_created":"2018-12-11T11:51:11Z","volume":150,"acknowledgement":"The authors are veryg rateful to Hansj ̈org Geiges \r\nfor fruitful discussions and advice and Christian Evers for helpful remarks on a draft version.","year":"2016","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer","publist_id":"6023","doi":"10.1007/s10474-016-0648-4","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.00794"}],"quality_controlled":"1","month":"12","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1292","status":"public","title":"Computing the Thurston–Bennequin invariant in open books","intvolume":" 150","abstract":[{"text":"We give explicit formulas and algorithms for the computation of the Thurston–Bennequin invariant of a nullhomologous Legendrian knot on a page of a contact open book and on Heegaard surfaces in convex position. Furthermore, we extend the results to rationally nullhomologous knots in arbitrary 3-manifolds.","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2016-12-01T00:00:00Z","publication":"Acta Mathematica Hungarica","citation":{"ieee":"S. Durst, M. Kegel, and M. D. Klukas, “Computing the Thurston–Bennequin invariant in open books,” Acta Mathematica Hungarica, vol. 150, no. 2. Springer, pp. 441–455, 2016.","apa":"Durst, S., Kegel, M., & Klukas, M. D. (2016). Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. Springer. https://doi.org/10.1007/s10474-016-0648-4","ista":"Durst S, Kegel M, Klukas MD. 2016. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 150(2), 441–455.","ama":"Durst S, Kegel M, Klukas MD. Computing the Thurston–Bennequin invariant in open books. Acta Mathematica Hungarica. 2016;150(2):441-455. doi:10.1007/s10474-016-0648-4","chicago":"Durst, Sebastian, Marc Kegel, and Mirko D Klukas. “Computing the Thurston–Bennequin Invariant in Open Books.” Acta Mathematica Hungarica. Springer, 2016. https://doi.org/10.1007/s10474-016-0648-4.","short":"S. Durst, M. Kegel, M.D. Klukas, Acta Mathematica Hungarica 150 (2016) 441–455.","mla":"Durst, Sebastian, et al. “Computing the Thurston–Bennequin Invariant in Open Books.” Acta Mathematica Hungarica, vol. 150, no. 2, Springer, 2016, pp. 441–55, doi:10.1007/s10474-016-0648-4."},"page":"441 - 455","day":"01","scopus_import":1},{"scopus_import":1,"day":"07","month":"05","citation":{"mla":"Bächer, Moritz, et al. DefSense: Computational Design of Customized Deformable Input Devices. ACM, 2016, pp. 3806–16, doi:10.1145/2858036.2858354.","short":"M. Bächer, B. Hepp, F. Pece, P. Kry, B. Bickel, B. Thomaszewski, O. Hilliges, in:, ACM, 2016, pp. 3806–3816.","chicago":"Bächer, Moritz, Benjamin Hepp, Fabrizio Pece, Paul Kry, Bernd Bickel, Bernhard Thomaszewski, and Otmar Hilliges. “DefSense: Computational Design of Customized Deformable Input Devices,” 3806–16. ACM, 2016. https://doi.org/10.1145/2858036.2858354.","ama":"Bächer M, Hepp B, Pece F, et al. DefSense: computational design of customized deformable input devices. In: ACM; 2016:3806-3816. doi:10.1145/2858036.2858354","ista":"Bächer M, Hepp B, Pece F, Kry P, Bickel B, Thomaszewski B, Hilliges O. 2016. DefSense: computational design of customized deformable input devices. CHI: Conference on Human Factors in Computing Systems, 3806–3816.","apa":"Bächer, M., Hepp, B., Pece, F., Kry, P., Bickel, B., Thomaszewski, B., & Hilliges, O. (2016). DefSense: computational design of customized deformable input devices (pp. 3806–3816). Presented at the CHI: Conference on Human Factors in Computing Systems, San Jose, California, USA: ACM. https://doi.org/10.1145/2858036.2858354","ieee":"M. Bächer et al., “DefSense: computational design of customized deformable input devices,” presented at the CHI: Conference on Human Factors in Computing Systems, San Jose, California, USA, 2016, pp. 3806–3816."},"page":"3806 - 3816","quality_controlled":"1","date_published":"2016-05-07T00:00:00Z","doi":"10.1145/2858036.2858354","conference":{"location":"San Jose, California, USA","start_date":"2016-05-07","end_date":"2016-05-12","name":"CHI: Conference on Human Factors in Computing Systems"},"language":[{"iso":"eng"}],"type":"conference","publist_id":"5951","abstract":[{"lang":"eng","text":"We present a novel optimization-based algorithm for the design and fabrication of customized, deformable input devices, capable of continuously sensing their deformation. We propose to embed piezoresistive sensing elements into flexible 3D printed objects. These sensing elements are then utilized to recover rich and natural user interactions at runtime. Designing such objects is a challenging and hard problem if attempted manually for all but the simplest geometries and deformations. Our method simultaneously optimizes the internal routing of the sensing elements and computes a mapping from low-level sensor readings to user-specified outputs in order to minimize reconstruction error. We demonstrate the power and flexibility of the approach by designing and fabricating a set of flexible input devices. Our results indicate that the optimization-based design greatly outperforms manual routings in terms of reconstruction accuracy and thus interaction fidelity."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1319","acknowledgement":"We thank Damian Karrer, Rocco Ghielmini and Jemin\r\nHwangbo for their help in our initial explorations. We would\r\nlike to thank Christian Schumacher for creating the video and\r\nC\r\n ́\r\necile Edwards-Rietmann for providing the voiceover. Mau-\r\nrizio Nitti helped us in designing our 3D characters. We thank\r\nChiara Daraio for insightful discussions on material proper-\r\nties and 3D printing. We also thank the CHI reviewers for\r\ntheir feedback and guidance. Fabrizio Pece was supported by\r\nan ETH/Marie Curie fellowship (FEL-3314-1).","year":"2016","publisher":"ACM","department":[{"_id":"BeBi"}],"title":"DefSense: computational design of customized deformable input devices","status":"public","publication_status":"published","author":[{"full_name":"Bächer, Moritz","first_name":"Moritz","last_name":"Bächer"},{"full_name":"Hepp, Benjamin","last_name":"Hepp","first_name":"Benjamin"},{"last_name":"Pece","first_name":"Fabrizio","full_name":"Pece, Fabrizio"},{"last_name":"Kry","first_name":"Paul","full_name":"Kry, Paul"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Thomaszewski, Bernhard","last_name":"Thomaszewski","first_name":"Bernhard"},{"full_name":"Hilliges, Otmar","last_name":"Hilliges","first_name":"Otmar"}],"oa_version":"None","date_created":"2018-12-11T11:51:21Z","date_updated":"2021-01-12T06:49:51Z"},{"scopus_import":1,"has_accepted_license":"1","day":"25","citation":{"mla":"Vyleta, Nicholas, et al. “Plasticity-Dependent, Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” ELife, vol. 5, e17977, eLife Sciences Publications, 2016, doi:10.7554/eLife.17977.","short":"N. Vyleta, C. Borges Merjane, P.M. Jonas, ELife 5 (2016).","chicago":"Vyleta, Nicholas, Carolina Borges Merjane, and Peter M Jonas. “Plasticity-Dependent, Full Detonation at Hippocampal Mossy Fiber–CA3 Pyramidal Neuron Synapses.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.17977.","ama":"Vyleta N, Borges Merjane C, Jonas PM. Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 2016;5. doi:10.7554/eLife.17977","ista":"Vyleta N, Borges Merjane C, Jonas PM. 2016. Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. eLife. 5, e17977.","apa":"Vyleta, N., Borges Merjane, C., & Jonas, P. M. (2016). Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.17977","ieee":"N. Vyleta, C. Borges Merjane, and P. M. Jonas, “Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses,” eLife, vol. 5. eLife Sciences Publications, 2016."},"publication":"eLife","date_published":"2016-10-25T00:00:00Z","type":"journal_article","abstract":[{"text":"Mossy fiber synapses on CA3 pyramidal cells are 'conditional detonators' that reliably discharge postsynaptic targets. The 'conditional' nature implies that burst activity in dentate gyrus granule cells is required for detonation. Whether single unitary excitatory postsynaptic potentials (EPSPs) trigger spikes in CA3 neurons remains unknown. Mossy fiber synapses exhibit both pronounced short-term facilitation and uniquely large post-tetanic potentiation (PTP). We tested whether PTP could convert mossy fiber synapses from subdetonator into detonator mode, using a recently developed method to selectively and noninvasively stimulate individual presynaptic terminals in rat brain slices. Unitary EPSPs failed to initiate a spike in CA3 neurons under control conditions, but reliably discharged them after induction of presynaptic short-term plasticity. Remarkably, PTP switched mossy fiber synapses into full detonators for tens of seconds. Plasticity-dependent detonation may be critical for efficient coding, storage, and recall of information in the granule cell–CA3 cell network.","lang":"eng"}],"_id":"1323","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 5","title":"Plasticity-dependent, full detonation at hippocampal mossy fiber–CA3 pyramidal neuron synapses","ddc":["571","572"],"status":"public","pubrep_id":"715","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5257","checksum":"a7201280c571bed88ebd459ce5ce6a47","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:17:05Z","access_level":"open_access","file_name":"IST-2016-715-v1+1_e17977-download.pdf","content_type":"application/pdf","file_size":1477891,"creator":"system"}],"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548"},{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"}],"quality_controlled":"1","doi":"10.7554/eLife.17977","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"}],"article_number":"e17977","ec_funded":1,"publist_id":"5947","file_date_updated":"2020-07-14T12:44:44Z","year":"2016","publisher":"eLife Sciences Publications","department":[{"_id":"PeJo"}],"publication_status":"published","author":[{"full_name":"Vyleta, Nicholas","last_name":"Vyleta","first_name":"Nicholas","id":"36C4978E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Borges Merjane, Carolina","orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina"},{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"volume":5,"date_updated":"2023-02-21T10:34:24Z","date_created":"2018-12-11T11:51:22Z"},{"_id":"1325","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Stability in graphs and games","ddc":["004"],"intvolume":" 59","pubrep_id":"665","file":[{"content_type":"application/pdf","file_size":553648,"creator":"system","file_name":"IST-2016-665-v1+1_Forejt_et_al__Stability_in_graphs_and_games.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:16:40Z","checksum":"3c2dc6ab0358f8aa8f7aa7d6c1293159","relation":"main_file","file_id":"5229"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"text":"We study graphs and two-player games in which rewards are assigned to states, and the goal of the players is to satisfy or dissatisfy certain property of the generated outcome, given as a mean payoff property. Since the notion of mean-payoff does not reflect possible fluctuations from the mean-payoff along a run, we propose definitions and algorithms for capturing the stability of the system, and give algorithms for deciding if a given mean payoff and stability objective can be ensured in the system.","lang":"eng"}],"citation":{"ama":"Brázdil T, Forejt V, Kučera A, Novotný P. Stability in graphs and games. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.10","apa":"Brázdil, T., Forejt, V., Kučera, A., & Novotný, P. (2016). Stability in graphs and games (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.10","ieee":"T. Brázdil, V. Forejt, A. Kučera, and P. Novotný, “Stability in graphs and games,” presented at the CONCUR: Concurrency Theory, Quebec City, Canada, 2016, vol. 59.","ista":"Brázdil T, Forejt V, Kučera A, Novotný P. 2016. Stability in graphs and games. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 10.","short":"T. Brázdil, V. Forejt, A. Kučera, P. Novotný, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Brázdil, Tomáš, et al. Stability in Graphs and Games. Vol. 59, 10, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.10.","chicago":"Brázdil, Tomáš, Vojtěch Forejt, Antonín Kučera, and Petr Novotný. “Stability in Graphs and Games,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.10."},"date_published":"2016-08-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","acknowledgement":"The work has been supported by the Czech Science Foundation, grant No. 15-17564S, by EPSRC grant\r\nEP/M023656/1, and by the People Programme (Marie Curie Actions) of the European Union’s Seventh\r\nFramework Programme (FP7/2007-2013) under REA grant agreement no [291734]","year":"2016","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"last_name":"Forejt","first_name":"Vojtěch","full_name":"Forejt, Vojtěch"},{"last_name":"Kučera","first_name":"Antonín","full_name":"Kučera, Antonín"},{"full_name":"Novotny, Petr","last_name":"Novotny","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:49:53Z","date_created":"2018-12-11T11:51:23Z","volume":59,"article_number":"10","file_date_updated":"2020-07-14T12:44:44Z","ec_funded":1,"publist_id":"5944","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"conference":{"location":"Quebec City, Canada","start_date":"2016-08-23","end_date":"2016-08-26","name":"CONCUR: Concurrency Theory"},"doi":"10.4230/LIPIcs.CONCUR.2016.10","language":[{"iso":"eng"}],"month":"08"},{"scopus_import":1,"has_accepted_license":"1","day":"28","citation":{"short":"M. Lang, E. Sontag, in:, IEEE, 2016.","mla":"Lang, Moritz, and Eduardo Sontag. Scale-Invariant Systems Realize Nonlinear Differential Operators. Vol. 2016–July, 7526722, IEEE, 2016, doi:10.1109/ACC.2016.7526722.","chicago":"Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722.","ama":"Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722","apa":"Lang, M., & Sontag, E. (2016). Scale-invariant systems realize nonlinear differential operators (Vol. 2016–July). Presented at the ACC: American Control Conference, Boston, MA, USA: IEEE. https://doi.org/10.1109/ACC.2016.7526722","ieee":"M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.","ista":"Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722."},"date_published":"2016-07-28T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"In recent years, several biomolecular systems have been shown to be scale-invariant (SI), i.e. to show the same output dynamics when exposed to geometrically scaled input signals (u → pu, p > 0) after pre-adaptation to accordingly scaled constant inputs. In this article, we show that SI systems-as well as systems invariant with respect to other input transformations-can realize nonlinear differential operators: when excited by inputs obeying functional forms characteristic for a given class of invariant systems, the systems' outputs converge to constant values directly quantifying the speed of the input."}],"title":"Scale-invariant systems realize nonlinear differential operators","ddc":["003","621"],"status":"public","_id":"1320","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"5203","relation":"main_file","checksum":"7219432b43defc62a0d45f48d4ce6a19","date_updated":"2020-07-14T12:44:43Z","date_created":"2018-12-12T10:16:17Z","access_level":"local","file_name":"IST-2017-810-v1+1_root.pdf","creator":"system","content_type":"application/pdf","file_size":539166}],"oa_version":"Preprint","pubrep_id":"810","month":"07","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1109/ACC.2016.7526722","conference":{"name":"ACC: American Control Conference","location":"Boston, MA, USA","start_date":"2016-07-06","end_date":"2016-07-08"},"article_number":"7526722","ec_funded":1,"publist_id":"5950","file_date_updated":"2020-07-14T12:44:43Z","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publisher":"IEEE","publication_status":"published","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734]. Work supported in part by grants AFOSR FA9550-14-1-0060 and NIH 1R01GM100473.","year":"2016","volume":"2016-July","date_created":"2018-12-11T11:51:21Z","date_updated":"2021-01-12T06:49:51Z","author":[{"full_name":"Lang, Moritz","last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sontag, Eduardo","last_name":"Sontag","first_name":"Eduardo"}]},{"scopus_import":1,"day":"01","month":"01","citation":{"chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability in Goal-DEC-POMDPs.” In Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, 2016–January:88–96. AAAI Press, 2016.","short":"K. Chatterjee, M. Chmelik, in:, Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, AAAI Press, 2016, pp. 88–96.","mla":"Chatterjee, Krishnendu, and Martin Chmelik. “Indefinite-Horizon Reachability in Goal-DEC-POMDPs.” Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, vol. 2016–January, AAAI Press, 2016, pp. 88–96.","ieee":"K. Chatterjee and M. Chmelik, “Indefinite-horizon reachability in Goal-DEC-POMDPs,” in Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling, London, United Kingdom, 2016, vol. 2016–January, pp. 88–96.","apa":"Chatterjee, K., & Chmelik, M. (2016). Indefinite-horizon reachability in Goal-DEC-POMDPs. In Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling (Vol. 2016–January, pp. 88–96). London, United Kingdom: AAAI Press.","ista":"Chatterjee K, Chmelik M. 2016. Indefinite-horizon reachability in Goal-DEC-POMDPs. Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling. ICAPS: International Conference on Automated Planning and Scheduling vol. 2016–January, 88–96.","ama":"Chatterjee K, Chmelik M. Indefinite-horizon reachability in Goal-DEC-POMDPs. In: Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling. Vol 2016-January. AAAI Press; 2016:88-96."},"main_file_link":[{"url":"http://www.aaai.org/ocs/index.php/ICAPS/ICAPS16/paper/view/12999"}],"publication":"Proceedings of the Twenty-Sixth International Conference on International Conference on Automated Planning and Scheduling","page":"88 - 96","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"quality_controlled":"1","date_published":"2016-01-01T00:00:00Z","conference":{"location":"London, United Kingdom","start_date":"2016-06-12","end_date":"2016-06-17","name":"ICAPS: International Conference on Automated Planning and Scheduling"},"language":[{"iso":"eng"}],"type":"conference","ec_funded":1,"publist_id":"5946","abstract":[{"text":"DEC-POMDPs extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. DEC-POMDPs have been studied with finite-horizon and infinite-horizon discounted-sum objectives, and there exist solvers both for exact and approximate solutions. In this work we consider Goal-DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the RTDP-Bel approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. Copyright ","lang":"eng"}],"year":"2016","_id":"1324","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"AAAI Press","department":[{"_id":"KrCh"}],"title":"Indefinite-horizon reachability in Goal-DEC-POMDPs","status":"public","publication_status":"published","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"}],"oa_version":"None","volume":"2016-January","date_created":"2018-12-11T11:51:22Z","date_updated":"2021-01-12T06:49:53Z"},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-10-01T00:00:00Z","citation":{"ama":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 2016;8(10):3120-3139. doi:10.1093/gbe/evw221","apa":"Huylmans, A. K., López Ezquerra, A., Parsch, J., & Cordellier, M. (2016). De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evw221","ieee":"A. K. Huylmans, A. López Ezquerra, J. Parsch, and M. Cordellier, “De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata,” Genome Biology and Evolution, vol. 8, no. 10. Oxford University Press, pp. 3120–3139, 2016.","ista":"Huylmans AK, López Ezquerra A, Parsch J, Cordellier M. 2016. De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata. Genome Biology and Evolution. 8(10), 3120–3139.","short":"A.K. Huylmans, A. López Ezquerra, J. Parsch, M. Cordellier, Genome Biology and Evolution 8 (2016) 3120–3139.","mla":"Huylmans, Ann K., et al. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution, vol. 8, no. 10, Oxford University Press, 2016, pp. 3120–39, doi:10.1093/gbe/evw221.","chicago":"Huylmans, Ann K, Alberto López Ezquerra, John Parsch, and Mathilde Cordellier. “De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia Galeata.” Genome Biology and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/gbe/evw221."},"publication":"Genome Biology and Evolution","page":"3120 - 3139","issue":"10","abstract":[{"lang":"eng","text":"Daphnia species have become models for ecological genomics and exhibit interesting features, such as high phenotypic plasticity and a densely packed genome with many lineage-specific genes. They are also cyclic parthenogenetic, with alternating asexual and sexual cycles and environmental sex determination. Here, we present a de novo transcriptome assembly of over 32,000 D. galeata genes and use it to investigate gene expression in females and spontaneously produced males of two clonal lines derived from lakes in Germany and the Czech Republic. We find that only a low percentage (18%) of genes shows sex-biased expression and that there are many more female-biased gene (FBG) than male-biased gene (MBG). Furthermore, FBGs tend to be more conserved between species than MBGs in both sequence and expression. These patterns may be a consequence of cyclic parthenogenesis leading to a relaxation of purifying selection on MBGs. The two clonal lines show considerable differences in both number and identity of sex-biased genes, suggesting that they may have reproductive strategies differing in their investment in sexual reproduction. Orthologs of key genes in the sex determination and juvenile hormone pathways, which are thought to be important for the transition from asexual to sexual reproduction, are present in D. galeata and highly conserved among Daphnia species."}],"type":"journal_article","pubrep_id":"663","file":[{"access_level":"open_access","file_name":"IST-2016-663-v1+1_Genome_Biol_Evol-2016-Huylmans-3120-39.pdf","file_size":1406265,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4924","checksum":"25c7adcb452d39d3b6343ff4b57a652d","date_created":"2018-12-12T10:12:06Z","date_updated":"2020-07-14T12:44:44Z"}],"oa_version":"Published Version","_id":"1329","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 8","ddc":["576"],"title":"De novo transcriptome assembly and sex-biased gene expression in the cyclical parthenogenetic Daphnia galeata","status":"public","month":"10","doi":"10.1093/gbe/evw221","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","publist_id":"5940","file_date_updated":"2020-07-14T12:44:44Z","author":[{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K"},{"first_name":"Alberto","last_name":"López Ezquerra","full_name":"López Ezquerra, Alberto"},{"last_name":"Parsch","first_name":"John","full_name":"Parsch, John"},{"first_name":"Mathilde","last_name":"Cordellier","full_name":"Cordellier, Mathilde"}],"volume":8,"date_updated":"2021-01-12T06:49:55Z","date_created":"2018-12-11T11:51:24Z","acknowledgement":"This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). The authors would like to thank I. Schrank, L. Theodosiou, M. Kredler, C. Laforsch, J. Wolinska, J. Griebel, R. Jaenichen, and K. Otte for providing the necessary resources and help for maintaining Daphnia cultures in the laboratory. H. Lainer supported us for the molecular laboratory work. D. Gilbert and J. K. Colbourne contributed ideas for the bioinformatics analysis, and L. Hardulak did the orthology mapping including more insect species. This study was financially supported by individual grants from the Volkswagen Stiftung (to M.C.), the Deutsche Forschungsgemeinschaft (grant PA 903/6 to J.P.) and the DAAD (to A.K.H.). This work benefits from and contributes to the Daphnia Genomics Consortium.","year":"2016","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"publication_status":"published"},{"author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gupta, Anchit","first_name":"Anchit","last_name":"Gupta"},{"last_name":"Novotny","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotny, Petr"}],"oa_version":"Preprint","date_created":"2018-12-11T11:51:23Z","date_updated":"2021-01-12T06:49:54Z","_id":"1327","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","department":[{"_id":"KrCh"}],"publisher":"ACM","status":"public","title":"Stochastic shortest path with energy constraints in POMDPs","publication_status":"published","ec_funded":1,"publist_id":"5942","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize the expected total cost until the target set is reached. We extend the traditional framework of POMDPs to model energy consumption, which represents a hard constraint. The energy levels may increase and decrease with transitions, and the hard constraint requires that the energy level must remain positive in all steps till the target is reached. First, we present a novel algorithm for solving POMDPs with energy levels, developing on existing POMDP solvers and using RTDP as its main method. Our second contribution is related to policy representation. For larger POMDP instances the policies computed by existing solvers are too large to be understandable. We present an automated procedure based on machine learning techniques that automatically extracts important decisions of the policy allowing us to compute succinct human readable policies. Finally, we show experimentally that our algorithm performs well and computes succinct policies on a number of POMDP instances from the literature that were naturally enhanced with energy levels. "}],"type":"conference","date_published":"2016-01-01T00:00:00Z","conference":{"end_date":"2016-05-13","start_date":"2016-05-09","location":"Singapore","name":"AAMAS: Autonomous Agents & Multiagent Systems"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1602.07565"}],"citation":{"mla":"Brázdil, Tomáš, et al. “Stochastic Shortest Path with Energy Constraints in POMDPs.” Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–66.","short":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, P. Novotný, in:, Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, ACM, 2016, pp. 1465–1466.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Anchit Gupta, and Petr Novotný. “Stochastic Shortest Path with Energy Constraints in POMDPs.” In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, 1465–66. ACM, 2016.","ama":"Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. Stochastic shortest path with energy constraints in POMDPs. In: Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. ACM; 2016:1465-1466.","ista":"Brázdil T, Chatterjee K, Chmelik M, Gupta A, Novotný P. 2016. Stochastic shortest path with energy constraints in POMDPs. Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems. AAMAS: Autonomous Agents & Multiagent Systems, 1465–1466.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Gupta, A., & Novotný, P. (2016). Stochastic shortest path with energy constraints in POMDPs. In Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems (pp. 1465–1466). Singapore: ACM.","ieee":"T. Brázdil, K. Chatterjee, M. Chmelik, A. Gupta, and P. Novotný, “Stochastic shortest path with energy constraints in POMDPs,” in Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems, Singapore, 2016, pp. 1465–1466."},"oa":1,"publication":"Proceedings of the 15th International Conference on Autonomous Agents and Multiagent Systems","page":"1465 - 1466","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","day":"01","month":"01","scopus_import":1},{"author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr","full_name":"Novotny, Petr"}],"volume":9938,"date_created":"2018-12-11T11:51:23Z","date_updated":"2021-01-12T06:49:53Z","acknowledgement":"The research was funded by the Czech Science Foundation Grant No. P202/12/G061 and by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].","year":"2016","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","publist_id":"5943","ec_funded":1,"doi":"10.1007/978-3-319-46520-3_3","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2016-10-20","location":"Chiba, Japan","start_date":"2016-10-17"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1607.00678","open_access":"1"}],"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","month":"09","oa_version":"Preprint","_id":"1326","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 9938","title":"Optimizing the expected mean payoff in Energy Markov Decision Processes","status":"public","abstract":[{"lang":"eng","text":"Energy Markov Decision Processes (EMDPs) are finite-state Markov decision processes where each transition is assigned an integer counter update and a rational payoff. An EMDP configuration is a pair s(n), where s is a control state and n is the current counter value. The configurations are changed by performing transitions in the standard way. We consider the problem of computing a safe strategy (i.e., a strategy that keeps the counter non-negative) which maximizes the expected mean payoff. "}],"type":"conference","alternative_title":["LNCS"],"date_published":"2016-09-22T00:00:00Z","citation":{"short":"T. Brázdil, A. Kučera, P. Novotný, in:, Springer, 2016, pp. 32–49.","mla":"Brázdil, Tomáš, et al. Optimizing the Expected Mean Payoff in Energy Markov Decision Processes. Vol. 9938, Springer, 2016, pp. 32–49, doi:10.1007/978-3-319-46520-3_3.","chicago":"Brázdil, Tomáš, Antonín Kučera, and Petr Novotný. “Optimizing the Expected Mean Payoff in Energy Markov Decision Processes,” 9938:32–49. Springer, 2016. https://doi.org/10.1007/978-3-319-46520-3_3.","ama":"Brázdil T, Kučera A, Novotný P. Optimizing the expected mean payoff in Energy Markov Decision Processes. In: Vol 9938. Springer; 2016:32-49. doi:10.1007/978-3-319-46520-3_3","ieee":"T. Brázdil, A. Kučera, and P. Novotný, “Optimizing the expected mean payoff in Energy Markov Decision Processes,” presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan, 2016, vol. 9938, pp. 32–49.","apa":"Brázdil, T., Kučera, A., & Novotný, P. (2016). Optimizing the expected mean payoff in Energy Markov Decision Processes (Vol. 9938, pp. 32–49). Presented at the ATVA: Automated Technology for Verification and Analysis, Chiba, Japan: Springer. https://doi.org/10.1007/978-3-319-46520-3_3","ista":"Brázdil T, Kučera A, Novotný P. 2016. Optimizing the expected mean payoff in Energy Markov Decision Processes. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 9938, 32–49."},"page":"32 - 49","day":"22","scopus_import":1},{"day":"15","scopus_import":1,"date_published":"2016-10-15T00:00:00Z","page":"833 - 845","citation":{"ama":"Akopyan A, Balitskiy A. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 2016;216(2):833-845. doi:10.1007/s11856-016-1429-z","ista":"Akopyan A, Balitskiy A. 2016. Billiards in convex bodies with acute angles. Israel Journal of Mathematics. 216(2), 833–845.","ieee":"A. Akopyan and A. Balitskiy, “Billiards in convex bodies with acute angles,” Israel Journal of Mathematics, vol. 216, no. 2. Springer, pp. 833–845, 2016.","apa":"Akopyan, A., & Balitskiy, A. (2016). Billiards in convex bodies with acute angles. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-016-1429-z","mla":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics, vol. 216, no. 2, Springer, 2016, pp. 833–45, doi:10.1007/s11856-016-1429-z.","short":"A. Akopyan, A. Balitskiy, Israel Journal of Mathematics 216 (2016) 833–845.","chicago":"Akopyan, Arseniy, and Alexey Balitskiy. “Billiards in Convex Bodies with Acute Angles.” Israel Journal of Mathematics. Springer, 2016. https://doi.org/10.1007/s11856-016-1429-z."},"publication":"Israel Journal of Mathematics","issue":"2","abstract":[{"text":"In this paper we investigate the existence of closed billiard trajectories in not necessarily smooth convex bodies. In particular, we show that if a body K ⊂ Rd has the property that the tangent cone of every non-smooth point q ∉ ∂K is acute (in a certain sense), then there is a closed billiard trajectory in K.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 216","status":"public","title":"Billiards in convex bodies with acute angles","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1330","month":"10","language":[{"iso":"eng"}],"doi":"10.1007/s11856-016-1429-z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1506.06014"}],"publist_id":"5938","ec_funded":1,"volume":216,"date_updated":"2021-01-12T06:49:56Z","date_created":"2018-12-11T11:51:24Z","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy"},{"last_name":"Balitskiy","first_name":"Alexey","full_name":"Balitskiy, Alexey"}],"publisher":"Springer","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2016","acknowledgement":"Supported by People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n°[291734]. Supported by the Russian Foundation for Basic Research grant 15-31-20403 (mol a ved), by the Russian Foundation for Basic Research grant 15-01-99563 A, in part by the Moebius Contest Foundation for Young Scientists, and in part by the Simons Foundation."},{"scopus_import":1,"has_accepted_license":"1","day":"10","citation":{"apa":"Schönenberger, P., O’Neill, J., & Csicsvari, J. L. (2016). Activity dependent plasticity of hippocampal place maps. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms11824","ieee":"P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Activity dependent plasticity of hippocampal place maps,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","ista":"Schönenberger P, O’Neill J, Csicsvari JL. 2016. Activity dependent plasticity of hippocampal place maps. Nature Communications. 7, 11824.","ama":"Schönenberger P, O’Neill J, Csicsvari JL. Activity dependent plasticity of hippocampal place maps. Nature Communications. 2016;7. doi:10.1038/ncomms11824","chicago":"Schönenberger, Philipp, Joseph O’Neill, and Jozsef L Csicsvari. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms11824.","short":"P. Schönenberger, J. O’Neill, J.L. Csicsvari, Nature Communications 7 (2016).","mla":"Schönenberger, Philipp, et al. “Activity Dependent Plasticity of Hippocampal Place Maps.” Nature Communications, vol. 7, 11824, Nature Publishing Group, 2016, doi:10.1038/ncomms11824."},"publication":"Nature Communications","date_published":"2016-06-10T00:00:00Z","type":"journal_article","abstract":[{"text":"Hippocampal neurons encode a cognitive map of space. These maps are thought to be updated during learning and in response to changes in the environment through activity-dependent synaptic plasticity. Here we examine how changes in activity influence spatial coding in rats using halorhodopsin-mediated, spatially selective optogenetic silencing. Halorhoposin stimulation leads to light-induced suppression in many place cells and interneurons; some place cells increase their firing through disinhibition, whereas some show no effect. We find that place fields of the unaffected subpopulation remain stable. On the other hand, place fields of suppressed place cells were unstable, showing remapping across sessions before and after optogenetic inhibition. Disinhibited place cells had stable maps but sustained an elevated firing rate. These findings suggest that place representation in the hippocampus is constantly governed by activity-dependent processes, and that disinhibition may provide a mechanism for rate remapping.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1334","intvolume":" 7","ddc":["570"],"status":"public","title":"Activity dependent plasticity of hippocampal place maps","pubrep_id":"660","oa_version":"Published Version","file":[{"checksum":"e43307754abe65b840a21939fe163618","date_created":"2018-12-12T10:16:10Z","date_updated":"2020-07-14T12:44:44Z","relation":"main_file","file_id":"5196","file_size":1793846,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-660-v1+1_ncomms11824.pdf"}],"month":"06","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"name":"Interneuron plasticity during spatial learning","call_identifier":"FWF","_id":"257D4372-B435-11E9-9278-68D0E5697425","grant_number":"I2072-B27"}],"quality_controlled":"1","doi":"10.1038/ncomms11824","language":[{"iso":"eng"}],"article_number":"11824","publist_id":"5934","ec_funded":1,"file_date_updated":"2020-07-14T12:44:44Z","year":"2016","department":[{"_id":"JoCs"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","last_name":"Schönenberger","first_name":"Philipp","full_name":"Schönenberger, Philipp"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"volume":7,"date_updated":"2021-01-12T06:49:57Z","date_created":"2018-12-11T11:51:26Z"},{"volume":172,"date_created":"2018-12-11T11:51:25Z","date_updated":"2022-05-24T09:26:03Z","author":[{"full_name":"Zwack, Paul","first_name":"Paul","last_name":"Zwack"},{"full_name":"De Clercq, Inge","first_name":"Inge","last_name":"De Clercq"},{"first_name":"Timothy","last_name":"Howton","full_name":"Howton, Timothy"},{"last_name":"Hallmark","first_name":"H Tucker","full_name":"Hallmark, H Tucker"},{"full_name":"Hurny, Andrej","first_name":"Andrej","last_name":"Hurny","id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Keshishian","first_name":"Erika","full_name":"Keshishian, Erika"},{"full_name":"Parish, Alyssa","last_name":"Parish","first_name":"Alyssa"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Benková, Eva"},{"last_name":"Mukhtar","first_name":"M Shahid","full_name":"Mukhtar, M Shahid"},{"full_name":"Van Breusegem, Frank","first_name":"Frank","last_name":"Van Breusegem"},{"full_name":"Rashotte, Aaron","first_name":"Aaron","last_name":"Rashotte"}],"publisher":"American Society of Plant Biologists","department":[{"_id":"EvBe"}],"publication_status":"published","year":"2016","acknowledgement":"This work was financially supported by the following: The Alabama Agricultural Experiment Station HATCH grants 370222-310010-2055 and 370225-310006-2055 for funding to P.J.Z., E.A.K, A.M.P., and A.M.R. P.J.Z. and E.A.K were supported by an Auburn University Cellular and Molecular Biosciences Research Fellowship. I.D.C. is a postdoctoral fellow of the Research Foundation Flanders (FWO) (FWO/PDO14/043) and is also supported by FWO travel\r\ngrant 12N2415N. F.V.B. was supported by grants from the Interuniversity Attraction Poles Programme (IUAP P7/29 MARS) initiated by the Belgian Science Policy Office and Ghent University (Multidisciplinary Research Partnership Biotechnology for a Sustainable Economy, grant 01MRB510W).","publist_id":"5937","language":[{"iso":"eng"}],"doi":"10.1104/pp.16.00415","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1104/pp.16.00415","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"month":"10","oa_version":"Published Version","intvolume":" 172","status":"public","title":"Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress","_id":"1331","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","abstract":[{"lang":"eng","text":"Cytokinin is a phytohormone that is well known for its roles in numerous plant growth and developmental processes, yet it has also been linked to abiotic stress response in a less defined manner. Arabidopsis (Arabidopsis thaliana) Cytokinin Response Factor 6 (CRF6) is a cytokinin-responsive AP2/ERF-family transcription factor that, through the cytokinin signaling pathway, plays a key role in the inhibition of dark-induced senescence. CRF6 expression is also induced by oxidative stress, and here we show a novel function for CRF6 in relation to oxidative stress and identify downstream transcriptional targets of CRF6 that are repressed in response to oxidative stress. Analysis of transcriptomic changes in wild-type and crf6 mutant plants treated with H2O2 identified CRF6-dependent differentially expressed transcripts, many of which were repressed rather than induced. Moreover, many repressed genes also show decreased expression in 35S:CRF6 overexpressing plants. Together, these findings suggest that CRF6 functions largely as a transcriptional repressor. Interestingly, among the H2O2 repressed CRF6-dependent transcripts was a set of five genes associated with cytokinin processes: (signaling) ARR6, ARR9, ARR11, (biosynthesis) LOG7, and (transport) ABCG14. We have examined mutants of these cytokinin-associated target genes to reveal novel connections to oxidative stress. Further examination of CRF6-DNA interactions indicated that CRF6 may regulate its targets both directly and indirectly. Together, this shows that CRF6 functions during oxidative stress as a negative regulator to control this cytokinin-associated module of CRF6- dependent genes and establishes a novel connection between cytokinin and oxidative stress response."}],"type":"journal_article","date_published":"2016-10-02T00:00:00Z","page":"1249 - 1258","article_type":"original","citation":{"short":"P. Zwack, I. De Clercq, T. Howton, H.T. Hallmark, A. Hurny, E. Keshishian, A. Parish, E. Benková, M.S. Mukhtar, F. Van Breusegem, A. Rashotte, Plant Physiology 172 (2016) 1249–1258.","mla":"Zwack, Paul, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology, vol. 172, no. 2, American Society of Plant Biologists, 2016, pp. 1249–58, doi:10.1104/pp.16.00415.","chicago":"Zwack, Paul, Inge De Clercq, Timothy Howton, H Tucker Hallmark, Andrej Hurny, Erika Keshishian, Alyssa Parish, et al. “Cytokinin Response Factor 6 Represses Cytokinin-Associated Genes during Oxidative Stress.” Plant Physiology. American Society of Plant Biologists, 2016. https://doi.org/10.1104/pp.16.00415.","ama":"Zwack P, De Clercq I, Howton T, et al. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 2016;172(2):1249-1258. doi:10.1104/pp.16.00415","ieee":"P. Zwack et al., “Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress,” Plant Physiology, vol. 172, no. 2. American Society of Plant Biologists, pp. 1249–1258, 2016.","apa":"Zwack, P., De Clercq, I., Howton, T., Hallmark, H. T., Hurny, A., Keshishian, E., … Rashotte, A. (2016). Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00415","ista":"Zwack P, De Clercq I, Howton T, Hallmark HT, Hurny A, Keshishian E, Parish A, Benková E, Mukhtar MS, Van Breusegem F, Rashotte A. 2016. Cytokinin response factor 6 represses cytokinin-associated genes during oxidative stress. Plant Physiology. 172(2), 1249–1258."},"publication":"Plant Physiology","article_processing_charge":"No","day":"02","scopus_import":"1"},{"pubrep_id":"661","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4834","checksum":"9ea0d7ce59a555a1cb8353d5559407cb","date_created":"2018-12-12T10:10:44Z","date_updated":"2020-07-14T12:44:44Z","access_level":"open_access","file_name":"IST-2016-661-v1+1_ncomms10915.pdf","content_type":"application/pdf","file_size":1432577,"creator":"system"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1333","intvolume":" 7","ddc":["519","530","599"],"status":"public","title":"Humans choose representatives who enforce cooperation in social dilemmas through extortion","abstract":[{"lang":"eng","text":"Social dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the "representatives" treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most."}],"type":"journal_article","date_published":"2016-03-07T00:00:00Z","citation":{"ama":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 2016;7. doi:10.1038/ncomms10915","ista":"Milinski M, Hilbe C, Semmann D, Sommerfeld R, Marotzke J. 2016. Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. 7, 10915.","ieee":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, and J. Marotzke, “Humans choose representatives who enforce cooperation in social dilemmas through extortion,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","apa":"Milinski, M., Hilbe, C., Semmann, D., Sommerfeld, R., & Marotzke, J. (2016). Humans choose representatives who enforce cooperation in social dilemmas through extortion. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10915","mla":"Milinski, Manfred, et al. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications, vol. 7, 10915, Nature Publishing Group, 2016, doi:10.1038/ncomms10915.","short":"M. Milinski, C. Hilbe, D. Semmann, R. Sommerfeld, J. Marotzke, Nature Communications 7 (2016).","chicago":"Milinski, Manfred, Christian Hilbe, Dirk Semmann, Ralf Sommerfeld, and Jochem Marotzke. “Humans Choose Representatives Who Enforce Cooperation in Social Dilemmas through Extortion.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10915."},"publication":"Nature Communications","has_accepted_license":"1","day":"07","scopus_import":1,"author":[{"full_name":"Milinski, Manfred","last_name":"Milinski","first_name":"Manfred"},{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"full_name":"Semmann, Dirk","first_name":"Dirk","last_name":"Semmann"},{"last_name":"Sommerfeld","first_name":"Ralf","full_name":"Sommerfeld, Ralf"},{"first_name":"Jochem","last_name":"Marotzke","full_name":"Marotzke, Jochem"}],"volume":7,"date_updated":"2021-01-12T06:49:57Z","date_created":"2018-12-11T11:51:25Z","acknowledgement":"We thank the students for participation; H.-J. Krambeck for writing the software for the game; H. Arndt, T. Bakker, L. Becks, H. Brendelberger, S. Dobler and T. Reusch for support; and the Max Planck Society for the Advancement of Science for funding.","year":"2016","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","publist_id":"5935","file_date_updated":"2020-07-14T12:44:44Z","article_number":"10915","doi":"10.1038/ncomms10915","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"03"},{"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms10333","month":"01","publisher":"Nature Publishing Group","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publication_status":"published","year":"2016","acknowledgement":"This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891.","volume":7,"date_created":"2018-12-11T11:51:25Z","date_updated":"2021-01-12T06:49:57Z","author":[{"first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P"},{"full_name":"Palmer, Adam","first_name":"Adam","last_name":"Palmer"},{"full_name":"Yelin, Idan","first_name":"Idan","last_name":"Yelin"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"}],"article_number":"10333","publist_id":"5936","file_date_updated":"2020-07-14T12:44:44Z","citation":{"mla":"Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications, vol. 7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333.","short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).","chicago":"Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333.","ama":"Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 2016;7. doi:10.1038/ncomms10333","ista":"Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333.","apa":"Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333","ieee":"R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016."},"publication":"Nature Communications","date_published":"2016-01-20T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"20","intvolume":" 7","status":"public","ddc":["570","579"],"title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1332","file":[{"access_level":"open_access","file_name":"IST-2016-662-v1+1_ncomms10333.pdf","creator":"system","content_type":"application/pdf","file_size":1844107,"file_id":"5039","relation":"main_file","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d","date_created":"2018-12-12T10:13:52Z","date_updated":"2020-07-14T12:44:44Z"}],"oa_version":"Published Version","pubrep_id":"662","type":"journal_article","abstract":[{"text":"Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance.","lang":"eng"}]},{"citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative monitor automata. SAS: Static Analysis Symposium, LNCS, vol. 9837, 23–38.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Quantitative monitor automata (Vol. 9837, pp. 23–38). Presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53413-7_2","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative monitor automata,” presented at the SAS: Static Analysis Symposium, Edinburgh, United Kingdom, 2016, vol. 9837, pp. 23–38.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative monitor automata. In: Vol 9837. Springer; 2016:23-38. doi:10.1007/978-3-662-53413-7_2","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Monitor Automata,” 9837:23–38. Springer, 2016. https://doi.org/10.1007/978-3-662-53413-7_2.","mla":"Chatterjee, Krishnendu, et al. Quantitative Monitor Automata. Vol. 9837, Springer, 2016, pp. 23–38, doi:10.1007/978-3-662-53413-7_2.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Springer, 2016, pp. 23–38."},"page":"23 - 38","date_published":"2016-08-31T00:00:00Z","scopus_import":1,"day":"31","_id":"1335","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 9837","title":"Quantitative monitor automata","status":"public","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"In this paper we review various automata-theoretic formalisms for expressing quantitative properties. We start with finite-state Boolean automata that express the traditional regular properties. We then consider weighted ω-automata that can measure the average density of events, which finite-state Boolean automata cannot. However, even weighted ω-automata cannot express basic performance properties like average response time. We finally consider two formalisms of weighted ω-automata with monitors, where the monitors are either (a) counters or (b) weighted automata themselves. We present a translation result to establish that these two formalisms are equivalent. Weighted ω-automata with monitors generalize weighted ω-automata, and can express average response time property. They present a natural, robust, and expressive framework for quantitative specifications, with important decidable properties."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"oa":1,"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","doi":"10.1007/978-3-662-53413-7_2","conference":{"start_date":"2016-09-08","location":"Edinburgh, United Kingdom","end_date":"2016-09-10","name":"SAS: Static Analysis Symposium"},"language":[{"iso":"eng"}],"month":"08","year":"2016","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan"}],"volume":9837,"date_updated":"2021-01-12T06:49:58Z","date_created":"2018-12-11T11:51:26Z","publist_id":"5932","ec_funded":1},{"language":[{"iso":"eng"}],"doi":"10.7554/eLife.19048","quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"09","date_created":"2018-12-11T11:51:29Z","date_updated":"2021-01-12T06:50:01Z","volume":5,"author":[{"id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych","full_name":"Fendrych, Matyas"},{"first_name":"Jeffrey","last_name":"Leung","full_name":"Leung, Jeffrey"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"JiFr"}],"year":"2016","acknowledgement":"The authors express their gratitude to Veronika Bierbaum, Robert Hauschild for help with MATLAB,\r\nDaniel von Wangenheim for the gravitropism assay. We are thankful to Bill Gray, Mark Estelle,\r\nMichael Prigge, Ottoline Leyser, Claudia Oecking for sharing the seeds with us. We thank Katelyn\r\nSageman-Furnas and the members of the Friml lab for critical reading of the manuscript. The\r\nresearch leading to these results has received funding from the People Programme (Marie Curie\r\nActions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant\r\nagreement n° 291734. This work was also supported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP).","file_date_updated":"2020-07-14T12:44:45Z","publist_id":"5908","ec_funded":1,"article_number":"e19048","date_published":"2016-09-14T00:00:00Z","publication":"eLife","citation":{"chicago":"Fendrych, Matyas, Jeffrey Leung, and Jiří Friml. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.19048.","mla":"Fendrych, Matyas, et al. “TIR1 AFB Aux IAA Auxin Perception Mediates Rapid Cell Wall Acidification and Growth of Arabidopsis Hypocotyls.” ELife, vol. 5, e19048, eLife Sciences Publications, 2016, doi:10.7554/eLife.19048.","short":"M. Fendrych, J. Leung, J. Friml, ELife 5 (2016).","ista":"Fendrych M, Leung J, Friml J. 2016. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 5, e19048.","apa":"Fendrych, M., Leung, J., & Friml, J. (2016). TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.19048","ieee":"M. Fendrych, J. Leung, and J. Friml, “TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls,” eLife, vol. 5. eLife Sciences Publications, 2016.","ama":"Fendrych M, Leung J, Friml J. TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. eLife. 2016;5. doi:10.7554/eLife.19048"},"day":"14","has_accepted_license":"1","scopus_import":1,"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4748","checksum":"9209541fbba00f24daad21a5d568540d","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:09:24Z","access_level":"open_access","file_name":"IST-2016-693-v1+1_e19048-download.pdf","file_size":5666343,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"654","title":"TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls","ddc":["581"],"status":"public","intvolume":" 5","_id":"1344","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms.","lang":"eng"}],"type":"journal_article"},{"day":"22","has_accepted_license":"1","scopus_import":1,"date_published":"2016-09-22T00:00:00Z","publication":"New Journal of Physics","citation":{"ama":"Kaczmarczyk J, Weimer H, Lemeshko M. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 2016;18(9). doi:10.1088/1367-2630/18/9/093042","ista":"Kaczmarczyk J, Weimer H, Lemeshko M. 2016. Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. 18(9), 093042.","apa":"Kaczmarczyk, J., Weimer, H., & Lemeshko, M. (2016). Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/18/9/093042","ieee":"J. Kaczmarczyk, H. Weimer, and M. Lemeshko, “Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model,” New Journal of Physics, vol. 18, no. 9. IOP Publishing Ltd., 2016.","mla":"Kaczmarczyk, Jan, et al. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics, vol. 18, no. 9, 093042, IOP Publishing Ltd., 2016, doi:10.1088/1367-2630/18/9/093042.","short":"J. Kaczmarczyk, H. Weimer, M. Lemeshko, New Journal of Physics 18 (2016).","chicago":"Kaczmarczyk, Jan, Hendrik Weimer, and Mikhail Lemeshko. “Dissipative Preparation of Antiferromagnetic Order in the Fermi-Hubbard Model.” New Journal of Physics. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1367-2630/18/9/093042."},"abstract":[{"lang":"eng","text":"The Fermi-Hubbard model is one of the key models of condensed matter physics, which holds a\r\n\r\npotential for explaining the mystery of high-temperature superconductivity. Recent progress in\r\n\r\nultracold atoms in optical lattices has paved the way to studying the model’s phase diagram using\r\n\r\nthe tools of quantum simulation, which emerged as a promising alternative to the numerical\r\n\r\ncalculations plagued by the infamous sign problem. However, the temperatures achieved using\r\n\r\nelaborate laser cooling protocols so far have been too high to show the appearance of\r\n\r\nantiferromagnetic (AF) and superconducting quantum phases directly. In this work, we demonstrate\r\n\r\nthat using the machinery of dissipative quantum state engineering, one can observe the emergence of\r\n\r\nthe AF order in the Fermi-Hubbard model with fermions in optical lattices. The core of the approach\r\n\r\nis to add incoherent laser scattering in such a way that the AF state emerges as the dark state of\r\n\r\nthe driven-dissipative dynamics. The proposed controlled dissipation channels described in this work\r\n\r\nare straightforward to add to already existing experimental setups."}],"issue":"9","type":"journal_article","pubrep_id":"655","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-655-v1+1_njp_18_9_093042.pdf","file_size":1076029,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5309","checksum":"2a43e235222755e31ffbd369882c61de","date_created":"2018-12-12T10:17:52Z","date_updated":"2020-07-14T12:44:45Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1343","title":"Dissipative preparation of antiferromagnetic order in the Fermi-Hubbard model","status":"public","ddc":["530"],"intvolume":" 18","month":"09","doi":"10.1088/1367-2630/18/9/093042","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"file_date_updated":"2020-07-14T12:44:45Z","publist_id":"5909","ec_funded":1,"article_number":"093042","author":[{"full_name":"Kaczmarczyk, Jan","first_name":"Jan","last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1629-3675"},{"full_name":"Weimer, Hendrik","last_name":"Weimer","first_name":"Hendrik"},{"full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802"}],"date_updated":"2021-01-12T06:50:01Z","date_created":"2018-12-11T11:51:29Z","volume":18,"acknowledgement":"We acknowledge stimulating discussions with Ken Brown, Tommaso Calarco, Andrew Daley, Suzanne\r\nMcEndoo, Tobias Osborne, Cindy Regal, Luis Santos, Micha\r\nł\r\nTomza, and Martin Zwierlein. The work was supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. [291734], by the Volkswagen Foundation, and by DFG within SFB 1227 (DQ-mat).","year":"2016","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"IOP Publishing Ltd."},{"abstract":[{"text":"We study repeated games with absorbing states, a type of two-player, zero-sum concurrent mean-payoff games with the prototypical example being the Big Match of Gillete (1957). These games may not allow optimal strategies but they always have ε-optimal strategies. In this paper we design ε-optimal strategies for Player 1 in these games that use only O(log log T) space. Furthermore, we construct strategies for Player 1 that use space s(T), for an arbitrary small unbounded non-decreasing function s, and which guarantee an ε-optimal value for Player 1 in the limit superior sense. The previously known strategies use space Ω(log T) and it was known that no strategy can use constant space if it is ε-optimal even in the limit superior sense. We also give a complementary lower bound. Furthermore, we also show that no Markov strategy, even extended with finite memory, can ensure value greater than 0 in the Big Match, answering a question posed by Neyman [11].","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","title":"The big match in small space","status":"public","intvolume":" 9928","_id":"1340","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":1,"date_published":"2016-09-01T00:00:00Z","page":"64 - 76","citation":{"short":"K. Hansen, R. Ibsen-Jensen, M. Koucký, in:, Springer, 2016, pp. 64–76.","mla":"Hansen, Kristoffer, et al. The Big Match in Small Space. Vol. 9928, Springer, 2016, pp. 64–76, doi:10.1007/978-3-662-53354-3_6.","chicago":"Hansen, Kristoffer, Rasmus Ibsen-Jensen, and Michal Koucký. “The Big Match in Small Space,” 9928:64–76. Springer, 2016. https://doi.org/10.1007/978-3-662-53354-3_6.","ama":"Hansen K, Ibsen-Jensen R, Koucký M. The big match in small space. In: Vol 9928. Springer; 2016:64-76. doi:10.1007/978-3-662-53354-3_6","apa":"Hansen, K., Ibsen-Jensen, R., & Koucký, M. (2016). The big match in small space (Vol. 9928, pp. 64–76). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-53354-3_6","ieee":"K. Hansen, R. Ibsen-Jensen, and M. Koucký, “The big match in small space,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 64–76.","ista":"Hansen K, Ibsen-Jensen R, Koucký M. 2016. The big match in small space. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 64–76."},"publist_id":"5927","ec_funded":1,"date_created":"2018-12-11T11:51:28Z","date_updated":"2021-01-12T06:50:00Z","volume":9928,"author":[{"last_name":"Hansen","first_name":"Kristoffer","full_name":"Hansen, Kristoffer"},{"full_name":"Ibsen-Jensen, Rasmus","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus"},{"first_name":"Michal","last_name":"Koucký","full_name":"Koucký, Michal"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2016","month":"09","language":[{"iso":"eng"}],"conference":{"end_date":"2016-09-21","start_date":"2016-09-19","location":"Liverpool, United Kingdom","name":"SAGT: Symposium on Algorithmic Game Theory"},"doi":"10.1007/978-3-662-53354-3_6","quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.07634"}]},{"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/nplants.2016.102","month":"07","publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Nature Publishing Group","year":"2016","date_created":"2018-12-11T11:51:30Z","date_updated":"2021-01-12T06:50:02Z","volume":2,"author":[{"last_name":"Molnar","first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Molnar, Gergely"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699","first_name":"Matyas","last_name":"Fendrych"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"article_number":"16102","file_date_updated":"2020-07-14T12:44:45Z","publist_id":"5907","publication":"Nature Plants","citation":{"chicago":"Molnar, Gergely, Matyas Fendrych, and Jiří Friml. “Plasma Membrane: Negative Attraction.” Nature Plants. Nature Publishing Group, 2016. https://doi.org/10.1038/nplants.2016.102.","mla":"Molnar, Gergely, et al. “Plasma Membrane: Negative Attraction.” Nature Plants, vol. 2, 16102, Nature Publishing Group, 2016, doi:10.1038/nplants.2016.102.","short":"G. Molnar, M. Fendrych, J. Friml, Nature Plants 2 (2016).","ista":"Molnar G, Fendrych M, Friml J. 2016. Plasma membrane: Negative attraction. Nature Plants. 2, 16102.","ieee":"G. Molnar, M. Fendrych, and J. Friml, “Plasma membrane: Negative attraction,” Nature Plants, vol. 2. Nature Publishing Group, 2016.","apa":"Molnar, G., Fendrych, M., & Friml, J. (2016). Plasma membrane: Negative attraction. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2016.102","ama":"Molnar G, Fendrych M, Friml J. Plasma membrane: Negative attraction. Nature Plants. 2016;2. doi:10.1038/nplants.2016.102"},"date_published":"2016-07-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","ddc":["581"],"status":"public","title":"Plasma membrane: Negative attraction","intvolume":" 2","_id":"1345","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"IST-2018-1007-v1+1_Molnar_NatPlants_2016.pdf","creator":"system","content_type":"application/pdf","file_size":127781,"file_id":"4954","relation":"main_file","checksum":"9ba65f558563b287f875f48fa9f30fb2","date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:12:36Z"},{"creator":"system","content_type":"application/pdf","file_size":430556,"access_level":"open_access","file_name":"IST-2018-1007-v1+2_Molnar_NatPlants_2016_editor_statement.pdf","checksum":"550d252be808d8ca2b43e83dddb4212f","date_created":"2018-12-12T10:12:37Z","date_updated":"2020-07-14T12:44:45Z","file_id":"4955","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"1007","type":"journal_article","abstract":[{"lang":"eng","text":"The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components."}]},{"publist_id":"5911","issue":"6304","abstract":[{"lang":"eng","text":"A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics."}],"type":"journal_article","oa_version":"Preprint","volume":353,"date_created":"2018-12-11T11:51:29Z","date_updated":"2021-01-12T06:50:01Z","author":[{"last_name":"Baym","first_name":"Michael","full_name":"Baym, Michael"},{"first_name":"Tami","last_name":"Lieberman","full_name":"Lieberman, Tami"},{"full_name":"Kelsic, Eric","last_name":"Kelsic","first_name":"Eric"},{"full_name":"Chait, Remy P","last_name":"Chait","first_name":"Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gross","first_name":"Rotem","full_name":"Gross, Rotem"},{"full_name":"Yelin, Idan","first_name":"Idan","last_name":"Yelin"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"intvolume":" 353","publication_status":"published","title":"Spatiotemporal microbial evolution on antibiotic landscapes","status":"public","year":"2016","_id":"1342","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"09","day":"09","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2016-09-09T00:00:00Z","doi":"10.1126/science.aag0822","page":"1147 - 1151","quality_controlled":"1","citation":{"apa":"Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., & Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag0822","ieee":"M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016.","ista":"Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151.","ama":"Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016;353(6304):1147-1151. doi:10.1126/science.aag0822","chicago":"Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aag0822.","short":"M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151.","mla":"Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:10.1126/science.aag0822."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/"}],"publication":"Science"},{"scopus_import":1,"day":"04","month":"10","publication":"Applied Physics Letter","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.04406"}],"citation":{"ista":"Verbiest G, Xu D, Goldsche M, Khodkov T, Barzanjeh S, Von Den Driesch N, Buca D, Stampfer C. 2016. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 109, 143507.","ieee":"G. Verbiest et al., “Tunable mechanical coupling between driven microelectromechanical resonators,” Applied Physics Letter, vol. 109. American Institute of Physics, 2016.","apa":"Verbiest, G., Xu, D., Goldsche, M., Khodkov, T., Barzanjeh, S., Von Den Driesch, N., … Stampfer, C. (2016). Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. American Institute of Physics. https://doi.org/10.1063/1.4964122","ama":"Verbiest G, Xu D, Goldsche M, et al. Tunable mechanical coupling between driven microelectromechanical resonators. Applied Physics Letter. 2016;109. doi:10.1063/1.4964122","chicago":"Verbiest, Gerard, Duo Xu, Matthias Goldsche, Timofiy Khodkov, Shabir Barzanjeh, Nils Von Den Driesch, Dan Buca, and Christoph Stampfer. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter. American Institute of Physics, 2016. https://doi.org/10.1063/1.4964122.","mla":"Verbiest, Gerard, et al. “Tunable Mechanical Coupling between Driven Microelectromechanical Resonators.” Applied Physics Letter, vol. 109, 143507, American Institute of Physics, 2016, doi:10.1063/1.4964122.","short":"G. Verbiest, D. Xu, M. Goldsche, T. Khodkov, S. Barzanjeh, N. Von Den Driesch, D. Buca, C. Stampfer, Applied Physics Letter 109 (2016)."},"quality_controlled":"1","doi":"10.1063/1.4964122","date_published":"2016-10-04T00:00:00Z","language":[{"iso":"eng"}],"article_number":"143507","type":"journal_article","abstract":[{"lang":"eng","text":"We present a microelectromechanical system, in which a silicon beam is attached to a comb-drive\r\nactuator, which is used to tune the tension in the silicon beam and thus its resonance frequency. By\r\nmeasuring the resonance frequencies of the system, we show that the comb-drive actuator and the\r\nsilicon beam behave as two strongly coupled resonators. Interestingly, the effective coupling rate\r\n(1.5 MHz) is tunable with the comb-drive actuator (10%) as well as with a side-gate (10%)\r\nplaced close to the silicon beam. In contrast, the effective spring constant of the system is insensitive\r\nto either of them and changes only by 60.5%. Finally, we show that the comb-drive actuator\r\ncan be used to switch between different coupling rates with a frequency of at least 10 kHz.\r\n"}],"publist_id":"5928","_id":"1339","acknowledgement":"We acknowledge the support from the Helmholtz Nanoelectronic Facility (HNF) and funding from the ERC (GA-Nr. 280140).","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2016","status":"public","title":"Tunable mechanical coupling between driven microelectromechanical resonators","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"American Institute of Physics","intvolume":" 109","author":[{"full_name":"Verbiest, Gerard","first_name":"Gerard","last_name":"Verbiest"},{"full_name":"Xu, Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","first_name":"Duo","last_name":"Xu"},{"full_name":"Goldsche, Matthias","last_name":"Goldsche","first_name":"Matthias"},{"last_name":"Khodkov","first_name":"Timofiy","full_name":"Khodkov, Timofiy"},{"full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0415-1423"},{"last_name":"Von Den Driesch","first_name":"Nils","full_name":"Von Den Driesch, Nils"},{"first_name":"Dan","last_name":"Buca","full_name":"Buca, Dan"},{"last_name":"Stampfer","first_name":"Christoph","full_name":"Stampfer, Christoph"}],"date_updated":"2023-02-21T10:35:06Z","date_created":"2018-12-11T11:51:28Z","volume":109,"oa_version":"Preprint"},{"ec_funded":1,"publist_id":"5900","file_date_updated":"2020-07-14T12:44:45Z","date_updated":"2021-01-12T06:50:03Z","date_created":"2018-12-11T11:51:31Z","author":[{"first_name":"Pietro","last_name":"Oliveto","full_name":"Oliveto, Pietro"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"last_name":"Heredia","first_name":"Jorge","full_name":"Heredia, Jorge"},{"full_name":"Sudholt, Dirk","first_name":"Dirk","last_name":"Sudholt"},{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"}],"publisher":"ACM","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","year":"2016","month":"07","language":[{"iso":"eng"}],"doi":"10.1145/2908812.2908909","conference":{"end_date":"2016-07-24","start_date":"2016-07-20","location":"Denver, CO, USA","name":"GECCO: Genetic and evolutionary computation conference"},"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"abstract":[{"lang":"eng","text":"Crossing fitness valleys is one of the major obstacles to function optimization. In this paper we investigate how the structure of the fitness valley, namely its depth d and length ℓ, influence the runtime of different strategies for crossing these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis algorithm. While the (1+1) EA has to jump across the valley to a point of higher fitness because it does not accept decreasing moves, the non-elitist algorithms may cross the valley by accepting worsening moves. We show that while the runtime of the (1+1) EA algorithm depends critically on the length of the valley, the runtimes of the non-elitist algorithms depend crucially only on the depth of the valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of small length. Moreover, we show that both SSWM and Metropolis can also efficiently optimize a rugged function consisting of consecutive valleys."}],"type":"conference","file":[{"creator":"system","file_size":979026,"content_type":"application/pdf","file_name":"IST-2016-650-v1+1_p1163-oliveto.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:27Z","date_updated":"2020-07-14T12:44:45Z","checksum":"a1896e39e4113f2711e46b435d5f3e69","file_id":"5214","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"650","ddc":["576"],"title":"When non-elitism outperforms elitism for crossing fitness valleys","status":"public","_id":"1349","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"20","scopus_import":1,"date_published":"2016-07-20T00:00:00Z","page":"1163 - 1170","citation":{"mla":"Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909.","short":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.","chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.” In Proceedings of the Genetic and Evolutionary Computation Conference 2016 , 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.","ama":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909","ista":"Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation conference, 1163–1170.","apa":"Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016). When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170). Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909","ieee":"P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp. 1163–1170."},"publication":"Proceedings of the Genetic and Evolutionary Computation Conference 2016 "},{"type":"journal_article","issue":"6304","abstract":[{"lang":"eng","text":"The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion. However, the\r\nsynaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient\r\nmemory storage and retrieval in hippocampal networks."}],"intvolume":" 353","status":"public","ddc":["570"],"title":"Synaptic mechanisms of pattern completion in the hippocampal CA3 network","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1350","file":[{"creator":"system","file_size":19408143,"content_type":"application/pdf","file_name":"IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:12:27Z","checksum":"89caefa4e181424cbf0aecc835fcc5ec","file_id":"4945","relation":"main_file"}],"oa_version":"Preprint","pubrep_id":"823","scopus_import":1,"has_accepted_license":"1","day":"09","page":"1117 - 1123","citation":{"chicago":"Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aaf1836.","short":"J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123.","mla":"Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1117–23, doi:10.1126/science.aaf1836.","apa":"Guzmán, J., Schlögl, A., Frotscher, M., & Jonas, P. M. (2016). Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aaf1836","ieee":"J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms of pattern completion in the hippocampal CA3 network,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1117–1123, 2016.","ista":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123.","ama":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 2016;353(6304):1117-1123. doi:10.1126/science.aaf1836"},"publication":"Science","date_published":"2016-09-09T00:00:00Z","publist_id":"5899","ec_funded":1,"file_date_updated":"2020-07-14T12:44:46Z","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2016","volume":353,"date_updated":"2021-01-12T06:50:04Z","date_created":"2018-12-11T11:51:31Z","author":[{"full_name":"Guzmán, José","first_name":"José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Frotscher, Michael","first_name":"Michael","last_name":"Frotscher"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"}],"month":"09","project":[{"call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548"},{"grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Mechanisms of transmitter release at GABAergic synapses"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1126/science.aaf1836"},{"_id":"1347","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["530"],"title":"Deformation of a quantum many-particle system by a rotating impurity","intvolume":" 6","pubrep_id":"652","file":[{"date_updated":"2020-07-14T12:44:45Z","date_created":"2018-12-12T10:15:59Z","checksum":"6757a164d3c38905e05b2b5a188cb8ff","file_id":"5183","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":1165869,"file_name":"IST-2016-652-v1+1_PhysRevX.6.011012.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"During the past 70 years, the quantum theory of angular momentum has been successfully applied to describing the properties of nuclei, atoms, and molecules, and their interactions with each other as well as with external fields. Because of the properties of quantum rotations, the angular-momentum algebra can be of tremendous complexity even for a few interacting particles, such as valence electrons of an atom, not to mention larger many-particle systems. In this work, we study an example of the latter: A rotating quantum impurity coupled to a many-body bosonic bath. In the regime of strong impurity-bath couplings, the problem involves the addition of an infinite number of angular momenta, which renders it intractable using currently available techniques. Here, we introduce a novel canonical transformation that allows us to eliminate the complex angular-momentum algebra from such a class of many-body problems. In addition, the transformation exposes the problem's constants of motion, and renders it solvable exactly in the limit of a slowly rotating impurity. We exemplify the technique by showing that there exists a critical rotational speed at which the impurity suddenly acquires one quantum of angular momentum from the many-particle bath. Such an instability is accompanied by the deformation of the phonon density in the frame rotating along with the impurity.","lang":"eng"}],"issue":"1","publication":"Physical Review X","citation":{"ama":"Schmidt R, Lemeshko M. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 2016;6(1). doi:10.1103/PhysRevX.6.011012","ista":"Schmidt R, Lemeshko M. 2016. Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. 6(1), 011012.","ieee":"R. Schmidt and M. Lemeshko, “Deformation of a quantum many-particle system by a rotating impurity,” Physical Review X, vol. 6, no. 1. American Physical Society, 2016.","apa":"Schmidt, R., & Lemeshko, M. (2016). Deformation of a quantum many-particle system by a rotating impurity. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.6.011012","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X, vol. 6, no. 1, 011012, American Physical Society, 2016, doi:10.1103/PhysRevX.6.011012.","short":"R. Schmidt, M. Lemeshko, Physical Review X 6 (2016).","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Deformation of a Quantum Many-Particle System by a Rotating Impurity.” Physical Review X. American Physical Society, 2016. https://doi.org/10.1103/PhysRevX.6.011012."},"date_published":"2016-01-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","acknowledgement":"We are grateful to Eugene Demler, Jan Kaczmarczyk, Laleh Safari, and Hendrik Weimer for insightful discussions. The work was supported by the NSF through a grant for the Institute for Theoretical Atomic, Molecular, and Optical Physics at Harvard University and Smithsonian Astrophysical Observatory.","year":"2016","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"author":[{"last_name":"Schmidt","first_name":"Richard","full_name":"Schmidt, Richard"},{"orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","full_name":"Lemeshko, Mikhail"}],"date_created":"2018-12-11T11:51:30Z","date_updated":"2021-01-12T06:50:03Z","volume":6,"article_number":"011012","file_date_updated":"2020-07-14T12:44:45Z","publist_id":"5902","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1103/PhysRevX.6.011012","language":[{"iso":"eng"}],"month":"01"},{"scopus_import":1,"day":"09","citation":{"chicago":"Fulek, Radoslav. “Bounded Embeddings of Graphs in the Plane,” 9843:31–42. Springer, 2016. https://doi.org/10.1007/978-3-319-44543-4_3.","mla":"Fulek, Radoslav. Bounded Embeddings of Graphs in the Plane. Vol. 9843, Springer, 2016, pp. 31–42, doi:10.1007/978-3-319-44543-4_3.","short":"R. Fulek, in:, Springer, 2016, pp. 31–42.","ista":"Fulek R. 2016. Bounded embeddings of graphs in the plane. IWOCA: International Workshop on Combinatorial Algorithms, LNCS, vol. 9843, 31–42.","apa":"Fulek, R. (2016). Bounded embeddings of graphs in the plane (Vol. 9843, pp. 31–42). Presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-319-44543-4_3","ieee":"R. Fulek, “Bounded embeddings of graphs in the plane,” presented at the IWOCA: International Workshop on Combinatorial Algorithms, Helsinki, Finland, 2016, vol. 9843, pp. 31–42.","ama":"Fulek R. Bounded embeddings of graphs in the plane. In: Vol 9843. Springer; 2016:31-42. doi:10.1007/978-3-319-44543-4_3"},"page":"31 - 42","date_published":"2016-08-09T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"A drawing in the plane (ℝ2) of a graph G = (V,E) equipped with a function γ : V → ℕ is x-bounded if (i) x(u) < x(v) whenever γ(u) < γ(v) and (ii) γ(u) ≤ γ(w) ≤ γ(v), where uv ∈ E and γ(u) ≤ γ(v), whenever x(w) ∈ x(uv), where x(.) denotes the projection to the xaxis.We prove a characterization of isotopy classes of embeddings of connected graphs equipped with γ in the plane containing an x-bounded embedding.Then we present an efficient algorithm, which relies on our result, for testing the existence of an x-bounded embedding if the given graph is a forest.This partially answers a question raised recently by Angelini et al.and Chang et al., and proves that c-planarity testing of flat clustered graphs with three clusters is tractable when the underlying abstract graph is a forest."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1348","status":"public","title":"Bounded embeddings of graphs in the plane","intvolume":" 9843","oa_version":"Preprint","month":"08","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1610.07144","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"conference":{"name":"IWOCA: International Workshop on Combinatorial Algorithms","end_date":"2018-08-19","location":"Helsinki, Finland","start_date":"2016-08-17"},"doi":"10.1007/978-3-319-44543-4_3","language":[{"iso":"eng"}],"publist_id":"5901","ec_funded":1,"year":"2016","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"author":[{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","first_name":"Radoslav","full_name":"Fulek, Radoslav"}],"date_created":"2018-12-11T11:51:31Z","date_updated":"2021-01-12T06:50:03Z","volume":9843},{"date_published":"2016-08-03T00:00:00Z","publication":"Nature Communications","citation":{"chicago":"Fink, Johannes M, Mahmoud Kalaee, Alessandro Pitanti, Richard Norte, Lukas Heinzle, Marcelo Davanço, Kartik Srinivasan, and Oskar Painter. “Quantum Electromechanics on Silicon Nitride Nanomembranes.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12396.","mla":"Fink, Johannes M., et al. “Quantum Electromechanics on Silicon Nitride Nanomembranes.” Nature Communications, vol. 7, 12396, Nature Publishing Group, 2016, doi:10.1038/ncomms12396.","short":"J.M. Fink, M. Kalaee, A. Pitanti, R. Norte, L. Heinzle, M. Davanço, K. Srinivasan, O. Painter, Nature Communications 7 (2016).","ista":"Fink JM, Kalaee M, Pitanti A, Norte R, Heinzle L, Davanço M, Srinivasan K, Painter O. 2016. Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. 7, 12396.","apa":"Fink, J. M., Kalaee, M., Pitanti, A., Norte, R., Heinzle, L., Davanço, M., … Painter, O. (2016). Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12396","ieee":"J. M. Fink et al., “Quantum electromechanics on silicon nitride nanomembranes,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","ama":"Fink JM, Kalaee M, Pitanti A, et al. Quantum electromechanics on silicon nitride nanomembranes. Nature Communications. 2016;7. doi:10.1038/ncomms12396"},"day":"03","has_accepted_license":"1","scopus_import":1,"pubrep_id":"629","file":[{"file_name":"IST-2016-629-v1+1_ncomms12396.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2139802,"creator":"system","relation":"main_file","file_id":"5014","date_created":"2018-12-12T10:13:30Z","date_updated":"2020-07-14T12:44:46Z","checksum":"25513bd59d5bda495efa8f5920e91b22"}],"oa_version":"Published Version","_id":"1355","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Quantum electromechanics on silicon nitride nanomembranes","status":"public","ddc":["530"],"intvolume":" 7","abstract":[{"text":"Radiation pressure has recently been used to effectively couple the quantum motion of mechanical elements to the fields of optical or microwave light. Integration of all three degrees of freedom—mechanical, optical and microwave—would enable a quantum interconnect between microwave and optical quantum systems. We present a platform based on silicon nitride nanomembranes for integrating superconducting microwave circuits with planar acoustic and optical devices such as phononic and photonic crystals. Using planar capacitors with vacuum gaps of 60 nm and spiral inductor coils of micron pitch we realize microwave resonant circuits with large electromechanical coupling to planar acoustic structures of nanoscale dimensions and femtoFarad motional capacitance. Using this enhanced coupling, we demonstrate microwave backaction cooling of the 4.48 MHz mechanical resonance of a nanobeam to an occupancy as low as 0.32. These results indicate the viability of silicon nitride nanomembranes as an all-in-one substrate for quantum electro-opto-mechanical experiments.","lang":"eng"}],"type":"journal_article","doi":"10.1038/ncomms12396","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","month":"08","author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M"},{"full_name":"Kalaee, Mahmoud","last_name":"Kalaee","first_name":"Mahmoud"},{"full_name":"Pitanti, Alessandro","last_name":"Pitanti","first_name":"Alessandro"},{"first_name":"Richard","last_name":"Norte","full_name":"Norte, Richard"},{"last_name":"Heinzle","first_name":"Lukas","full_name":"Heinzle, Lukas"},{"last_name":"Davanço","first_name":"Marcelo","full_name":"Davanço, Marcelo"},{"full_name":"Srinivasan, Kartik","first_name":"Kartik","last_name":"Srinivasan"},{"first_name":"Oskar","last_name":"Painter","full_name":"Painter, Oskar"}],"date_updated":"2021-01-12T06:50:06Z","date_created":"2018-12-11T11:51:33Z","volume":7,"year":"2016","acknowledgement":"This work was supported by the DARPA MESO programme, the Institute for Quantum Information and Matter, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore Foundation, and the Kavli Nanoscience Institute at Caltech. A.P. was supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme, NEMO (GA 298861). Certain commercial equipment and software are identified in this documentation to describe the subject adequately. Such identification does not imply recommendation or endorsement by the NIST, nor does it imply that the equipment identified is necessarily the best available for the purpose.","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"JoFi"}],"file_date_updated":"2020-07-14T12:44:46Z","publist_id":"5891","article_number":"12396"},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/","open_access":"1"}],"external_id":{"pmid":["27044080"]},"oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"},{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1073/pnas.1518830113","language":[{"iso":"eng"}],"month":"04","pmid":1,"year":"2016","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"National Academy of Sciences","publication_status":"published","author":[{"full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"volume":113,"date_updated":"2021-01-12T06:50:08Z","date_created":"2018-12-11T11:51:34Z","ec_funded":1,"publist_id":"5886","citation":{"chicago":"Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1518830113.","short":"T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.","mla":"Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.","ieee":"T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences, pp. 4422–4427, 2016.","apa":"Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on the long-term response to selection. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1518830113","ista":"Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term response to selection. PNAS. 113(16), 4422–4427.","ama":"Paixao T, Barton NH. The effect of gene interactions on the long-term response to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113"},"publication":"PNAS","page":"4422 - 4427","article_type":"original","date_published":"2016-04-19T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1359","intvolume":" 113","title":"The effect of gene interactions on the long-term response to selection","status":"public","oa_version":"Published Version","type":"journal_article","issue":"16","abstract":[{"text":"The role of gene interactions in the evolutionary process has long\r\nbeen controversial. Although some argue that they are not of\r\nimportance, because most variation is additive, others claim that\r\ntheir effect in the long term can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions under directional\r\nselection assuming no mutation or dominance, and that epistasis is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can be increased by selection and analyze two extreme\r\nregimes, in which either drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios, epistatic interactions affect\r\nthe long-term response to selection by modulating the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument to show that, for any form of epistasis, the total response\r\nof a haploid population is proportional to the initial total genotypic\r\nvariance. In contrast, the total response of a diploid population is\r\nincreased by epistasis, for a given initial genotypic variance. When\r\nselection dominates, we show that the total selection response can\r\nonly be increased by epistasis when s\r\nome initially deleterious alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple approximation for this effect and show that, in this regime, it is\r\nthe structure of the genotype - phenotype map that matters and not\r\nthe variance components of the population.","lang":"eng"}]},{"acknowledgement":"The authors are grateful to Florian Gebhard and Mikhail Lemeshko for discussions and critical reading of the manuscript. The work was supported by the Ministry of Science and Higher Education in Poland through the Iuventus Plus Grant No. IP2012 017172, as well as by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. 291734. J.K. acknowledges hospitality of the Leibniz Universität in Hannover where a large part of the work was performed.","year":"2016","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarczyk","first_name":"Jan"},{"full_name":"Schickling, Tobias","last_name":"Schickling","first_name":"Tobias"},{"full_name":"Bünemann, Jörg","last_name":"Bünemann","first_name":"Jörg"}],"date_created":"2018-12-11T11:51:32Z","date_updated":"2021-01-12T06:50:05Z","volume":94,"article_number":"085152","publist_id":"5897","ec_funded":1,"main_file_link":[{"url":"http://arxiv.org/abs/1512.06688","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"doi":"10.1103/PhysRevB.94.085152","language":[{"iso":"eng"}],"month":"08","_id":"1352","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Coexistence of nematic order and superconductivity in the Hubbard model","status":"public","intvolume":" 94","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We study the interplay of nematic and superconducting order in the two-dimensional Hubbard model and show that they can coexist, especially when superconductivity is not the energetically dominant phase. Due to a breaking of the C4 symmetry, the coexisting phase inherently contains admixture of the s-wave pairing components. As a result, the superconducting gap exhibits nonstandard features including changed nodal directions. Our results also show that in the optimally doped regime the pure superconducting phase is typically unstable towards developing nematicity (breaking of the C4 symmetry). This has implications for the cuprate high-Tc superconductors, for which in this regime the so-called intertwined orders have recently been observed. Namely, the coexisting phase may be viewed as a precursor to such more involved patterns of symmetry breaking.","lang":"eng"}],"issue":"8","publication":"Physical Review B - Condensed Matter and Materials Physics","citation":{"apa":"Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2016). Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.085152","ieee":"J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Coexistence of nematic order and superconductivity in the Hubbard model,” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 8. American Physical Society, 2016.","ista":"Kaczmarczyk J, Schickling T, Bünemann J. 2016. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 94(8), 085152.","ama":"Kaczmarczyk J, Schickling T, Bünemann J. Coexistence of nematic order and superconductivity in the Hubbard model. Physical Review B - Condensed Matter and Materials Physics. 2016;94(8). doi:10.1103/PhysRevB.94.085152","chicago":"Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.94.085152.","short":"J. Kaczmarczyk, T. Schickling, J. Bünemann, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","mla":"Kaczmarczyk, Jan, et al. “Coexistence of Nematic Order and Superconductivity in the Hubbard Model.” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 8, 085152, American Physical Society, 2016, doi:10.1103/PhysRevB.94.085152."},"date_published":"2016-08-30T00:00:00Z","scopus_import":1,"day":"30"},{"author":[{"full_name":"Dieterle, Paul","first_name":"Paul","last_name":"Dieterle"},{"first_name":"Mahmoud","last_name":"Kalaee","full_name":"Kalaee, Mahmoud"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"},{"full_name":"Painter, Oskar","last_name":"Painter","first_name":"Oskar"}],"oa_version":"Preprint","volume":6,"date_updated":"2021-01-12T06:50:06Z","date_created":"2018-12-11T11:51:32Z","year":"2016","_id":"1354","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","title":"Superconducting cavity electromechanics on a silicon-on-insulator platform","publication_status":"published","status":"public","issue":"1","publist_id":"5892","abstract":[{"text":"Fabrication processes involving anhydrous hydrofluoric vapor etching are developed to create high-Q aluminum superconducting microwave resonators on free-standing silicon membranes formed from a silicon-on-insulator wafer. Using this fabrication process, a high-impedance 8.9-GHz coil resonator is coupled capacitively with a large participation ratio to a 9.7-MHz micromechanical resonator. Two-tone microwave spectroscopy and radiation pressure backaction are used to characterize the coupled system in a dilution refrigerator down to temperatures of Tf=11 mK, yielding a measured electromechanical vacuum coupling rate of g0/2π=24.6 Hz and a mechanical resonator Q factor of Qm=1.7×107. Microwave backaction cooling of the mechanical resonator is also studied, with a minimum phonon occupancy of nm≈16 phonons being realized at an elevated fridge temperature of Tf=211 mK.","lang":"eng"}],"type":"journal_article","article_number":"014013","date_published":"2016-07-22T00:00:00Z","doi":"10.1103/PhysRevApplied.6.014013","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1601.04019","open_access":"1"}],"citation":{"short":"P. Dieterle, M. Kalaee, J.M. Fink, O. Painter, Physical Review Applied 6 (2016).","mla":"Dieterle, Paul, et al. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review Applied, vol. 6, no. 1, 014013, American Physical Society, 2016, doi:10.1103/PhysRevApplied.6.014013.","chicago":"Dieterle, Paul, Mahmoud Kalaee, Johannes M Fink, and Oskar Painter. “Superconducting Cavity Electromechanics on a Silicon-on-Insulator Platform.” Physical Review Applied. American Physical Society, 2016. https://doi.org/10.1103/PhysRevApplied.6.014013.","ama":"Dieterle P, Kalaee M, Fink JM, Painter O. Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 2016;6(1). doi:10.1103/PhysRevApplied.6.014013","apa":"Dieterle, P., Kalaee, M., Fink, J. M., & Painter, O. (2016). Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. American Physical Society. https://doi.org/10.1103/PhysRevApplied.6.014013","ieee":"P. Dieterle, M. Kalaee, J. M. Fink, and O. Painter, “Superconducting cavity electromechanics on a silicon-on-insulator platform,” Physical Review Applied, vol. 6, no. 1. American Physical Society, 2016.","ista":"Dieterle P, Kalaee M, Fink JM, Painter O. 2016. Superconducting cavity electromechanics on a silicon-on-insulator platform. Physical Review Applied. 6(1), 014013."},"publication":"Physical Review Applied","quality_controlled":"1","day":"22","month":"07","scopus_import":1},{"language":[{"iso":"eng"}],"doi":"10.1534/genetics.115.184796","quality_controlled":"1","oa":1,"month":"01","volume":202,"date_updated":"2021-01-12T06:50:07Z","date_created":"2018-12-11T11:51:33Z","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","year":"2016","publist_id":"5889","file_date_updated":"2020-07-14T12:44:46Z","date_published":"2016-01-05T00:00:00Z","page":"3 - 4","citation":{"chicago":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184796.","mla":"Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796.","short":"N.H. Barton, Genetics 202 (2016) 3–4.","ista":"Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”. Genetics. 202(1), 3–4.","ieee":"N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the ‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America, pp. 3–4, 2016.","apa":"Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796","ama":"Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796"},"publication":"Genetics","has_accepted_license":"1","day":"05","scopus_import":1,"file":[{"access_level":"open_access","file_name":"IST-2017-769-v1+1_SewallWright1931.pdf","file_size":112674,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4687","checksum":"3562b89c821a4be84edf2b6ebd870cf5","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:08:26Z"}],"oa_version":"Submitted Version","pubrep_id":"769","intvolume":" 202","ddc":["570"],"status":"public","title":"Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1356","issue":"1","type":"journal_article"},{"date_published":"2016-03-01T00:00:00Z","citation":{"apa":"Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542","ieee":"N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,” Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.","ista":"Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 202(3), 865–866.","ama":"Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics. 2016;202(3):865-866. doi:10.1534/genetics.116.187542","chicago":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542.","short":"N.H. Barton, Genetics 202 (2016) 865–866.","mla":"Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.” Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66, doi:10.1534/genetics.116.187542."},"publication":"Genetics","page":"865 - 866","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"768","oa_version":"Submitted Version","file":[{"relation":"main_file","file_id":"5127","date_created":"2018-12-12T10:15:09Z","date_updated":"2020-07-14T12:44:46Z","checksum":"b2174bab2de1d1142900062a150f35c9","file_name":"IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf","access_level":"open_access","file_size":130779,"content_type":"application/pdf","creator":"system"}],"_id":"1357","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 202","title":"Richard Hudson and Norman Kaplan on the coalescent process","status":"public","ddc":["576"],"issue":"3","type":"journal_article","doi":"10.1534/genetics.116.187542","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"03","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"volume":202,"date_created":"2018-12-11T11:51:33Z","date_updated":"2021-01-12T06:50:07Z","year":"2016","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","publist_id":"5888","file_date_updated":"2020-07-14T12:44:46Z"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1353","intvolume":" 26","title":"Deciding absorption","status":"public","oa_version":"Preprint","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"We characterize absorption in finite idempotent algebras by means of Jónsson absorption and cube term blockers. As an application we show that it is decidable whether a given subset is an absorbing subuniverse of an algebra given by the tables of its basic operations."}],"citation":{"ama":"Barto L, Kazda A. Deciding absorption. International Journal of Algebra and Computation. 2016;26(5):1033-1060. doi:10.1142/S0218196716500430","ista":"Barto L, Kazda A. 2016. Deciding absorption. International Journal of Algebra and Computation. 26(5), 1033–1060.","ieee":"L. Barto and A. Kazda, “Deciding absorption,” International Journal of Algebra and Computation, vol. 26, no. 5. World Scientific Publishing, pp. 1033–1060, 2016.","apa":"Barto, L., & Kazda, A. (2016). Deciding absorption. International Journal of Algebra and Computation. World Scientific Publishing. https://doi.org/10.1142/S0218196716500430","mla":"Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal of Algebra and Computation, vol. 26, no. 5, World Scientific Publishing, 2016, pp. 1033–60, doi:10.1142/S0218196716500430.","short":"L. Barto, A. Kazda, International Journal of Algebra and Computation 26 (2016) 1033–1060.","chicago":"Barto, Libor, and Alexandr Kazda. “Deciding Absorption.” International Journal of Algebra and Computation. World Scientific Publishing, 2016. https://doi.org/10.1142/S0218196716500430."},"publication":"International Journal of Algebra and Computation","page":"1033 - 1060","date_published":"2016-07-20T00:00:00Z","scopus_import":1,"day":"20","year":"2016","acknowledgement":"Libor Barto and Alexandr Kazda were supported by the the Grant Agency of the Czech Republic, grant GACR 13-01832S. ","publisher":"World Scientific Publishing","department":[{"_id":"VlKo"}],"publication_status":"published","author":[{"last_name":"Barto","first_name":"Libor","full_name":"Barto, Libor"},{"full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr","last_name":"Kazda"}],"volume":26,"date_created":"2018-12-11T11:51:32Z","date_updated":"2021-01-12T06:50:06Z","publist_id":"5893","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1512.07009"}],"quality_controlled":"1","doi":"10.1142/S0218196716500430","language":[{"iso":"eng"}],"month":"07"},{"file_date_updated":"2020-07-14T12:44:47Z","ec_funded":1,"publist_id":"5879","article_number":"96","date_created":"2018-12-11T11:51:35Z","date_updated":"2023-02-21T10:36:12Z","volume":35,"author":[{"full_name":"Bojsen-Hansen, Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224","first_name":"Morten","last_name":"Bojsen-Hansen"},{"full_name":"Wojtan, Christopher J","last_name":"Wojtan","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"acknowledgement":"We thank the IST Austria Visual Computing group for helpful feedback throughout the project. ","year":"2016","month":"07","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"conference":{"name":"ACM SIGGRAPH","end_date":"2016-07-28","start_date":"2016-07-24","location":"Anaheim, CA, USA"},"doi":"10.1145/2897824.2925963","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"text":"When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special "non-reflecting" boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation.","lang":"eng"}],"issue":"4","alternative_title":["ACM Transactions on Graphics"],"type":"conference","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:44:47Z","date_created":"2018-12-12T10:13:00Z","checksum":"140b5532f0a2a006a0149cab7c73c17c","file_id":"4981","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":12422760,"file_name":"IST-2016-631-v1+2_a96-bojsen-hansen.pdf","access_level":"open_access"}],"pubrep_id":"631","title":"Generalized non-reflecting boundaries for fluid re-simulation","ddc":["000"],"status":"public","intvolume":" 35","_id":"1363","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","day":"11","has_accepted_license":"1","date_published":"2016-07-11T00:00:00Z","citation":{"short":"M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. Generalized Non-Reflecting Boundaries for Fluid Re-Simulation. Vol. 35, no. 4, 96, ACM, 2016, doi:10.1145/2897824.2925963.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries for Fluid Re-Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925963.","ama":"Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid re-simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925963","ieee":"M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","apa":"Bojsen-Hansen, M., & Wojtan, C. (2016). Generalized non-reflecting boundaries for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925963","ista":"Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96."}},{"file":[{"file_name":"IST-2017-763-v1+1_wirebending.pdf","access_level":"open_access","content_type":"application/pdf","file_size":44766392,"creator":"system","relation":"main_file","file_id":"4853","date_updated":"2020-07-14T12:44:47Z","date_created":"2018-12-12T10:11:01Z","checksum":"d00c2664a43d945df8876ea0193734e3"}],"oa_version":"Preprint","pubrep_id":"763","intvolume":" 35","ddc":["006"],"title":"Computational design of stable planar-rod structures","status":"public","_id":"1364","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"4","abstract":[{"lang":"eng","text":"We present a computational method for designing wire sculptures consisting of interlocking wires. Our method allows the computation of aesthetically pleasing structures that are structurally stable, efficiently fabricatable with a 2D wire bending machine, and assemblable without the need of additional connectors. Starting from a set of planar contours provided by the user, our method automatically tests for the feasibility of a design, determines a discrete ordering of wires at intersection points, and optimizes for the rest shape of the individual wires to maximize structural stability under frictional contact. In addition to their application to art, wire sculptures present an extremely efficient and fast alternative for low-fidelity rapid prototyping because manufacturing time and required material linearly scales with the physical size of objects. We demonstrate the effectiveness of our approach on a varied set of examples, all of which we fabricated."}],"alternative_title":["ACM Transactions on Graphics"],"type":"conference","date_published":"2016-07-01T00:00:00Z","citation":{"ama":"Miguel Villalba E, Lepoutre M, Bickel B. Computational design of stable planar-rod structures. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925978","ista":"Miguel Villalba E, Lepoutre M, Bickel B. 2016. Computational design of stable planar-rod structures. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 86.","ieee":"E. Miguel Villalba, M. Lepoutre, and B. Bickel, “Computational design of stable planar-rod structures,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","apa":"Miguel Villalba, E., Lepoutre, M., & Bickel, B. (2016). Computational design of stable planar-rod structures (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925978","mla":"Miguel Villalba, Eder, et al. Computational Design of Stable Planar-Rod Structures. Vol. 35, no. 4, 86, ACM, 2016, doi:10.1145/2897824.2925978.","short":"E. Miguel Villalba, M. Lepoutre, B. Bickel, in:, ACM, 2016.","chicago":"Miguel Villalba, Eder, Mathias Lepoutre, and Bernd Bickel. “Computational Design of Stable Planar-Rod Structures,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925978."},"has_accepted_license":"1","day":"01","scopus_import":1,"volume":35,"date_updated":"2021-01-12T06:50:10Z","date_created":"2018-12-11T11:51:36Z","author":[{"full_name":"Miguel Villalba, Eder","first_name":"Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lepoutre, Mathias","last_name":"Lepoutre","first_name":"Mathias"},{"full_name":"Bickel, Bernd","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385"}],"publisher":"ACM","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2016","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 645599.","ec_funded":1,"publist_id":"5878","file_date_updated":"2020-07-14T12:44:47Z","article_number":"86","language":[{"iso":"eng"}],"doi":"10.1145/2897824.2925978","conference":{"end_date":"2016-07-28","start_date":"2016-07-24","location":"Anaheim, CA, USA","name":"ACM SIGGRAPH"},"project":[{"grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation"}],"quality_controlled":"1","oa":1,"month":"07"},{"date_published":"2016-07-11T00:00:00Z","citation":{"ieee":"F. Da, D. Hahn, C. Batty, C. Wojtan, and E. Grinspun, “Surface only liquids,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4.","apa":"Da, F., Hahn, D., Batty, C., Wojtan, C., & Grinspun, E. (2016). Surface only liquids (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. https://doi.org/10.1145/2897824.2925899","ista":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. 2016. Surface only liquids. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, a78.","ama":"Da F, Hahn D, Batty C, Wojtan C, Grinspun E. Surface only liquids. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925899","chicago":"Da, Fang, David Hahn, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Surface Only Liquids,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925899.","short":"F. Da, D. Hahn, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2016.","mla":"Da, Fang, et al. Surface Only Liquids. Vol. 35, no. 4, a78, ACM, 2016, doi:10.1145/2897824.2925899."},"has_accepted_license":"1","day":"11","scopus_import":1,"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-637-v1+1_2016_Da_SOL.pdf","creator":"system","content_type":"application/pdf","file_size":10561865,"file_id":"4660","relation":"main_file","checksum":"6d662893bd447d4f575b4961a2247811","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:08:01Z"}],"pubrep_id":"637","intvolume":" 35","ddc":["000"],"title":"Surface only liquids","status":"public","_id":"1361","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"4","abstract":[{"text":"We propose a novel surface-only technique for simulating incompressible, inviscid and uniform-density liquids with surface tension in three dimensions. The liquid surface is captured by a triangle mesh on which a Lagrangian velocity field is stored. Because advection of the velocity field may violate the incompressibility condition, we devise an orthogonal projection technique to remove the divergence while requiring the evaluation of only two boundary integrals. The forces of surface tension, gravity, and solid contact are all treated by a boundary element solve, allowing us to perform detailed simulations of a wide range of liquid phenomena, including waterbells, droplet and jet collisions, fluid chains, and crown splashes.","lang":"eng"}],"alternative_title":["ACM Transactions on Graphics"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1145/2897824.2925899","conference":{"name":"ACM SIGGRAPH","end_date":"2016-07-28","location":"Anaheim, CA, USA","start_date":"2016-07-24"},"project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"month":"07","volume":35,"date_updated":"2023-02-21T10:36:07Z","date_created":"2018-12-11T11:51:35Z","author":[{"full_name":"Da, Fang","first_name":"Fang","last_name":"Da"},{"full_name":"Hahn, David","first_name":"David","last_name":"Hahn","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christopher","last_name":"Batty","full_name":"Batty, Christopher"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"},{"first_name":"Eitan","last_name":"Grinspun","full_name":"Grinspun, Eitan"}],"publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published","year":"2016","publist_id":"5881","ec_funded":1,"file_date_updated":"2020-07-14T12:44:46Z","article_number":"a78"},{"main_file_link":[{"url":"http://eprint.iacr.org/2016/115","open_access":"1"}],"oa":1,"citation":{"chicago":"Alwen, Joel F, and Jeremiah Blocki. “Efficiently Computing Data-Independent Memory-Hard Functions,” 9815:241–71. Springer, 2016. https://doi.org/10.1007/978-3-662-53008-5_9.","mla":"Alwen, Joel F., and Jeremiah Blocki. Efficiently Computing Data-Independent Memory-Hard Functions. Vol. 9815, Springer, 2016, pp. 241–71, doi:10.1007/978-3-662-53008-5_9.","short":"J.F. Alwen, J. Blocki, in:, Springer, 2016, pp. 241–271.","ista":"Alwen JF, Blocki J. 2016. Efficiently computing data-independent memory-hard functions. CRYPTO: International Cryptology Conference, LNCS, vol. 9815, 241–271.","apa":"Alwen, J. F., & Blocki, J. (2016). Efficiently computing data-independent memory-hard functions (Vol. 9815, pp. 241–271). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-53008-5_9","ieee":"J. F. Alwen and J. Blocki, “Efficiently computing data-independent memory-hard functions,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2016, vol. 9815, pp. 241–271.","ama":"Alwen JF, Blocki J. Efficiently computing data-independent memory-hard functions. In: Vol 9815. Springer; 2016:241-271. doi:10.1007/978-3-662-53008-5_9"},"quality_controlled":"1","page":"241 - 271","conference":{"start_date":"2016-08-14","location":"Santa Barbara, CA, USA","end_date":"2016-08-18","name":"CRYPTO: International Cryptology Conference"},"doi":"10.1007/978-3-662-53008-5_9","date_published":"2016-08-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"08","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1365","year":"2016","publication_status":"published","title":"Efficiently computing data-independent memory-hard functions","status":"public","department":[{"_id":"KrPi"}],"publisher":"Springer","intvolume":" 9815","author":[{"full_name":"Alwen, Joel F","first_name":"Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"}],"date_updated":"2021-01-12T06:50:11Z","date_created":"2018-12-11T11:51:36Z","volume":9815,"oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"A memory-hard function (MHF) f is equipped with a space cost σ and time cost τ parameter such that repeatedly computing fσ,τ on an application specific integrated circuit (ASIC) is not economically advantageous relative to a general purpose computer. Technically we would like that any (generalized) circuit for evaluating an iMHF fσ,τ has area × time (AT) complexity at Θ(σ2 ∗ τ). A data-independent MHF (iMHF) has the added property that it can be computed with almost optimal memory and time complexity by an algorithm which accesses memory in a pattern independent of the input value. Such functions can be specified by fixing a directed acyclic graph (DAG) G on n = Θ(σ ∗ τ) nodes representing its computation graph. In this work we develop new tools for analyzing iMHFs. First we define and motivate a new complexity measure capturing the amount of energy (i.e. electricity) required to compute a function. We argue that, in practice, this measure is at least as important as the more traditional AT-complexity. Next we describe an algorithm A for repeatedly evaluating an iMHF based on an arbitrary DAG G. We upperbound both its energy and AT complexities per instance evaluated in terms of a certain combinatorial property of G. Next we instantiate our attack for several general classes of DAGs which include those underlying many of the most important iMHF candidates in the literature. In particular, we obtain the following results which hold for all choices of parameters σ and τ (and thread-count) such that n = σ ∗ τ. -The Catena-Dragonfly function of [FLW13] has AT and energy complexities O(n1.67). -The Catena-Butterfly function of [FLW13] has complexities is O(n1.67). -The Double-Buffer and the Linear functions of [CGBS16] both have complexities in O(n1.67). -The Argon2i function of [BDK15] (winner of the Password Hashing Competition [PHC]) has complexities O(n7/4 log(n)). -The Single-Buffer function of [CGBS16] has complexities O(n7/4 log(n)). -Any iMHF can be computed by an algorithm with complexities O(n2/ log1 −ε(n)) for all ε > 0. In particular when τ = 1 this shows that the goal of constructing an iMHF with AT-complexity Θ(σ2 ∗ τ ) is unachievable. Along the way we prove a lemma upper-bounding the depth-robustness of any DAG which may prove to be of independent interest."}],"publist_id":"5876"},{"abstract":[{"lang":"eng","text":"We study the problem of devising provably secure PRNGs with input based on the sponge paradigm. Such constructions are very appealing, as efficient software/hardware implementations of SHA-3 can easily be translated into a PRNG in a nearly black-box way. The only existing sponge-based construction, proposed by Bertoni et al. (CHES 2010), fails to achieve the security notion of robustness recently considered by Dodis et al. (CCS 2013), for two reasons: (1) The construction is deterministic, and thus there are high-entropy input distributions on which the construction fails to extract random bits, and (2) The construction is not forward secure, and presented solutions aiming at restoring forward security have not been rigorously analyzed. We propose a seeded variant of Bertoni et al.’s PRNG with input which we prove secure in the sense of robustness, delivering in particular concrete security bounds. On the way, we make what we believe to be an important conceptual contribution, developing a variant of the security framework of Dodis et al. tailored at the ideal permutation model that captures PRNG security in settings where the weakly random inputs are provided from a large class of possible adversarial samplers which are also allowed to query the random permutation. As a further application of our techniques, we also present an efficient sponge-based key-derivation function (which can be instantiated from SHA-3 in a black-box fashion), which we also prove secure when fed with samples from permutation-dependent distributions."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Preprint","intvolume":" 9665","title":"Provably robust sponge-based PRNGs and KDFs","status":"public","_id":"1366","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":1,"date_published":"2016-05-01T00:00:00Z","page":"87 - 116","citation":{"ieee":"P. Gazi and S. Tessaro, “Provably robust sponge-based PRNGs and KDFs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria, 2016, vol. 9665, pp. 87–116.","apa":"Gazi, P., & Tessaro, S. (2016). Provably robust sponge-based PRNGs and KDFs (Vol. 9665, pp. 87–116). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-662-49890-3_4","ista":"Gazi P, Tessaro S. 2016. Provably robust sponge-based PRNGs and KDFs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 9665, 87–116.","ama":"Gazi P, Tessaro S. Provably robust sponge-based PRNGs and KDFs. In: Vol 9665. Springer; 2016:87-116. doi:10.1007/978-3-662-49890-3_4","chicago":"Gazi, Peter, and Stefano Tessaro. “Provably Robust Sponge-Based PRNGs and KDFs,” 9665:87–116. Springer, 2016. https://doi.org/10.1007/978-3-662-49890-3_4.","short":"P. Gazi, S. Tessaro, in:, Springer, 2016, pp. 87–116.","mla":"Gazi, Peter, and Stefano Tessaro. Provably Robust Sponge-Based PRNGs and KDFs. Vol. 9665, Springer, 2016, pp. 87–116, doi:10.1007/978-3-662-49890-3_4."},"publist_id":"5872","ec_funded":1,"volume":9665,"date_created":"2018-12-11T11:51:36Z","date_updated":"2021-01-12T06:50:11Z","author":[{"first_name":"Peter","last_name":"Gazi","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","full_name":"Gazi, Peter"},{"full_name":"Tessaro, Stefano","first_name":"Stefano","last_name":"Tessaro"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2016","month":"05","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-49890-3_4","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","location":"Vienna, Austria","start_date":"2016-05-08","end_date":"2016-05-12"},"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2016/169/20160219:201940","open_access":"1"}]},{"day":"01","article_processing_charge":"No","scopus_import":1,"date_published":"2016-10-01T00:00:00Z","publication":"Proceedings of the American Mathematical Society","citation":{"mla":"Akopyan, Arseniy, et al. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society, vol. 144, no. 10, American Mathematical Society, 2016, pp. 4501–13, doi:10.1090/proc/13062.","short":"A. Akopyan, A. Balitskiy, R. Karasev, A. Sharipova, Proceedings of the American Mathematical Society 144 (2016) 4501–4513.","chicago":"Akopyan, Arseniy, Alexey Balitskiy, Roman Karasev, and Anastasia Sharipova. “Elementary Approach to Closed Billiard Trajectories in Asymmetric Normed Spaces.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/13062.","ama":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 2016;144(10):4501-4513. doi:10.1090/proc/13062","ista":"Akopyan A, Balitskiy A, Karasev R, Sharipova A. 2016. Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. 144(10), 4501–4513.","ieee":"A. Akopyan, A. Balitskiy, R. Karasev, and A. Sharipova, “Elementary approach to closed billiard trajectories in asymmetric normed spaces,” Proceedings of the American Mathematical Society, vol. 144, no. 10. American Mathematical Society, pp. 4501–4513, 2016.","apa":"Akopyan, A., Balitskiy, A., Karasev, R., & Sharipova, A. (2016). Elementary approach to closed billiard trajectories in asymmetric normed spaces. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13062"},"page":"4501 - 4513","abstract":[{"text":"We apply the technique of Károly Bezdek and Daniel Bezdek to study billiard trajectories in convex bodies, when the length is measured with a (possibly asymmetric) norm. We prove a lower bound for the length of the shortest closed billiard trajectory, related to the non-symmetric Mahler problem. With this technique we are able to give short and elementary proofs to some known results. ","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1360","status":"public","title":"Elementary approach to closed billiard trajectories in asymmetric normed spaces","intvolume":" 144","month":"10","doi":"10.1090/proc/13062","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.0442"}],"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publist_id":"5885","ec_funded":1,"author":[{"first_name":"Arseniy","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"last_name":"Balitskiy","first_name":"Alexey","full_name":"Balitskiy, Alexey"},{"last_name":"Karasev","first_name":"Roman","full_name":"Karasev, Roman"},{"full_name":"Sharipova, Anastasia","first_name":"Anastasia","last_name":"Sharipova"}],"date_created":"2018-12-11T11:51:34Z","date_updated":"2021-01-12T06:50:09Z","volume":144,"year":"2016","acknowledgement":"The first and third authors were supported by the Dynasty Foundation. The first, second and third authors were supported by the Russian Foundation for Basic Re- search grant 15-31-20403 (mol a ved).","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"American Mathematical Society"},{"intvolume":" 212","status":"public","ddc":["581"],"title":"Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis","_id":"1372","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"file_size":972763,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2018-1006-v1+1_Pernisova_NewPhytol_2016_peer_review.pdf","checksum":"27fd841ceaf0403559d7048ef51500f9","date_created":"2018-12-12T10:14:53Z","date_updated":"2020-07-14T12:44:47Z","relation":"main_file","file_id":"5108"}],"pubrep_id":"1006","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism."}],"page":"497 - 509","citation":{"ieee":"M. Pernisová et al., “Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis,” New Phytologist, vol. 212, no. 2. Wiley-Blackwell, pp. 497–509, 2016.","apa":"Pernisová, M., Prat, T., Grones, P., Haruštiaková, D., Matonohova, M., Spíchal, L., … Hejátko, J. (2016). Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.14049","ista":"Pernisová M, Prat T, Grones P, Haruštiaková D, Matonohova M, Spíchal L, Nodzyński T, Friml J, Hejátko J. 2016. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 212(2), 497–509.","ama":"Pernisová M, Prat T, Grones P, et al. Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis. New Phytologist. 2016;212(2):497-509. doi:10.1111/nph.14049","chicago":"Pernisová, Markéta, Tomas Prat, Peter Grones, Danka Haruštiaková, Martina Matonohova, Lukáš Spíchal, Tomasz Nodzyński, Jiří Friml, and Jan Hejátko. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist. Wiley-Blackwell, 2016. https://doi.org/10.1111/nph.14049.","short":"M. Pernisová, T. Prat, P. Grones, D. Haruštiaková, M. Matonohova, L. Spíchal, T. Nodzyński, J. Friml, J. Hejátko, New Phytologist 212 (2016) 497–509.","mla":"Pernisová, Markéta, et al. “Cytokinins Influence Root Gravitropism via Differential Regulation of Auxin Transporter Expression and Localization in Arabidopsis.” New Phytologist, vol. 212, no. 2, Wiley-Blackwell, 2016, pp. 497–509, doi:10.1111/nph.14049."},"publication":"New Phytologist","date_published":"2016-10-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"publication_status":"published","year":"2016","acknowledgement":"Funded by Ministry of Education, Youth and Sports Czech Republic. Grant Numbers: CEITEC 2020, LQ1601, LO1204, LH14104 and The European Research Council. Grant Number: ERC-2011-StG-20101109-PSDP and The Czech Science Foundation. Grant Numbers: GAP501/11/1150, GA13-40637S, GP14-30004P","volume":212,"date_created":"2018-12-11T11:51:38Z","date_updated":"2021-01-12T06:50:13Z","author":[{"full_name":"Pernisová, Markéta","first_name":"Markéta","last_name":"Pernisová"},{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","last_name":"Prat","first_name":"Tomas","full_name":"Prat, Tomas"},{"last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"full_name":"Haruštiaková, Danka","last_name":"Haruštiaková","first_name":"Danka"},{"last_name":"Matonohova","first_name":"Martina","full_name":"Matonohova, Martina"},{"full_name":"Spíchal, Lukáš","first_name":"Lukáš","last_name":"Spíchal"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hejátko","first_name":"Jan","full_name":"Hejátko, Jan"}],"publist_id":"5839","file_date_updated":"2020-07-14T12:44:47Z","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/nph.14049","month":"10"},{"date_published":"2016-09-15T00:00:00Z","page":"695 - 711","citation":{"ista":"Kolesnikov A, Lampert C. 2016. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. ECCV: European Conference on Computer Vision, LNCS, vol. 9908, 695–711.","apa":"Kolesnikov, A., & Lampert, C. (2016). Seed, expand and constrain: Three principles for weakly-supervised image segmentation (Vol. 9908, pp. 695–711). Presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands: Springer. https://doi.org/10.1007/978-3-319-46493-0_42","ieee":"A. Kolesnikov and C. Lampert, “Seed, expand and constrain: Three principles for weakly-supervised image segmentation,” presented at the ECCV: European Conference on Computer Vision, Amsterdam, The Netherlands, 2016, vol. 9908, pp. 695–711.","ama":"Kolesnikov A, Lampert C. Seed, expand and constrain: Three principles for weakly-supervised image segmentation. In: Vol 9908. Springer; 2016:695-711. doi:10.1007/978-3-319-46493-0_42","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation,” 9908:695–711. Springer, 2016. https://doi.org/10.1007/978-3-319-46493-0_42.","mla":"Kolesnikov, Alexander, and Christoph Lampert. Seed, Expand and Constrain: Three Principles for Weakly-Supervised Image Segmentation. Vol. 9908, Springer, 2016, pp. 695–711, doi:10.1007/978-3-319-46493-0_42.","short":"A. Kolesnikov, C. Lampert, in:, Springer, 2016, pp. 695–711."},"day":"15","scopus_import":1,"oa_version":"Preprint","status":"public","title":"Seed, expand and constrain: Three principles for weakly-supervised image segmentation","intvolume":" 9908","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1369","abstract":[{"lang":"eng","text":"We introduce a new loss function for the weakly-supervised training of semantic image segmentation models based on three guiding principles: to seed with weak localization cues, to expand objects based on the information about which classes can occur in an image, and to constrain the segmentations to coincide with object boundaries. We show experimentally that training a deep convolutional neural network using the proposed loss function leads to substantially better segmentations than previous state-of-the-art methods on the challenging PASCAL VOC 2012 dataset. We furthermore give insight into the working mechanism of our method by a detailed experimental study that illustrates how the segmentation quality is affected by each term of the proposed loss function as well as their combinations."}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"ECCV: European Conference on Computer Vision","start_date":"2016-10-11","location":"Amsterdam, The Netherlands","end_date":"2016-10-14"},"doi":"10.1007/978-3-319-46493-0_42","quality_controlled":"1","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/1603.06098","open_access":"1"}],"oa":1,"month":"09","date_updated":"2021-01-12T06:50:12Z","date_created":"2018-12-11T11:51:37Z","volume":9908,"author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander","full_name":"Kolesnikov, Alexander"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"publication_status":"published","department":[{"_id":"ChLa"}],"publisher":"Springer","year":"2016","ec_funded":1,"publist_id":"5842"},{"issue":"2","abstract":[{"text":"Superconductivity in heavy-fermion systems has an unconventional nature and is considered to originate from the universal features of the electronic structure. Here, the Anderson lattice model is studied by means of the full variational Gutzwiller wave function incorporating nonlocal effects of the on-site interaction. We show that the d-wave superconducting ground state can be driven solely by interelectronic correlations. The proposed microscopic mechanism leads to a multigap superconductivity with the dominant contribution due to f electrons and in the dx2−y2-wave channel. Our results rationalize several important observations for CeCoIn5.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 94","title":"Correlation driven d wave superconductivity in Anderson lattice model: Two gaps","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1368","day":"01","scopus_import":1,"date_published":"2016-07-01T00:00:00Z","citation":{"ieee":"M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Correlation driven d wave superconductivity in Anderson lattice model: Two gaps,” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 2. American Physical Society, 2016.","apa":"Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2016). Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.94.024517","ista":"Wysokiński M, Kaczmarczyk J, Spałek J. 2016. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 94(2), 024517.","ama":"Wysokiński M, Kaczmarczyk J, Spałek J. Correlation driven d wave superconductivity in Anderson lattice model: Two gaps. Physical Review B - Condensed Matter and Materials Physics. 2016;94(2). doi:10.1103/PhysRevB.94.024517","chicago":"Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevB.94.024517.","short":"M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B - Condensed Matter and Materials Physics 94 (2016).","mla":"Wysokiński, Marcin, et al. “Correlation Driven d Wave Superconductivity in Anderson Lattice Model: Two Gaps.” Physical Review B - Condensed Matter and Materials Physics, vol. 94, no. 2, 024517, American Physical Society, 2016, doi:10.1103/PhysRevB.94.024517."},"publication":"Physical Review B - Condensed Matter and Materials Physics","publist_id":"5844","ec_funded":1,"article_number":"024517","volume":94,"date_created":"2018-12-11T11:51:37Z","date_updated":"2021-01-12T06:50:12Z","author":[{"last_name":"Wysokiński","first_name":"Marcin","full_name":"Wysokiński, Marcin"},{"first_name":"Jan","last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1629-3675","full_name":"Kaczmarczyk, Jan"},{"full_name":"Spałek, Jozef","last_name":"Spałek","first_name":"Jozef"}],"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"The work has been supported by the National Science Center (NCN) under the Grant MAESTRO, No.\r\nDEC-2012/04/A/ST3/00342. ","year":"2016","month":"07","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevB.94.024517","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1510.00224","open_access":"1"}]},{"day":"01","month":"07","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2016-07-01T00:00:00Z","doi":"10.1016/j.plrev.2016.06.002","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"page":"124 - 158","quality_controlled":"1","citation":{"short":"O. Martin, A. Krzywicki, M.P. Zagórski, Physics of Life Reviews 17 (2016) 124–158.","mla":"Martin, Olivier, et al. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 124–58, doi:10.1016/j.plrev.2016.06.002.","chicago":"Martin, Olivier, André Krzywicki, and Marcin P Zagórski. “Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.002.","ama":"Martin O, Krzywicki A, Zagórski MP. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 2016;17:124-158. doi:10.1016/j.plrev.2016.06.002","apa":"Martin, O., Krzywicki, A., & Zagórski, M. P. (2016). Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.002","ieee":"O. Martin, A. Krzywicki, and M. P. Zagórski, “Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function,” Physics of Life Reviews, vol. 17. Elsevier, pp. 124–158, 2016.","ista":"Martin O, Krzywicki A, Zagórski MP. 2016. Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function. Physics of Life Reviews. 17, 124–158."},"publication":"Physics of Life Reviews","ec_funded":1,"publist_id":"5840","abstract":[{"lang":"eng","text":"Living cells can maintain their internal states, react to changing environments, grow, differentiate, divide, etc. All these processes are tightly controlled by what can be called a regulatory program. The logic of the underlying control can sometimes be guessed at by examining the network of influences amongst genetic components. Some associated gene regulatory networks have been studied in prokaryotes and eukaryotes, unveiling various structural features ranging from broad distributions of out-degrees to recurrent "motifs", that is small subgraphs having a specific pattern of interactions. To understand what factors may be driving such structuring, a number of groups have introduced frameworks to model the dynamics of gene regulatory networks. In that context, we review here such in silico approaches and show how selection for phenotypes, i.e., network function, can shape network structure."}],"type":"journal_article","oa_version":"None","volume":17,"date_created":"2018-12-11T11:51:38Z","date_updated":"2021-01-12T06:50:13Z","author":[{"full_name":"Martin, Olivier","first_name":"Olivier","last_name":"Martin"},{"full_name":"Krzywicki, André","last_name":"Krzywicki","first_name":"André"},{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P"}],"department":[{"_id":"AnKi"}],"intvolume":" 17","publisher":"Elsevier","title":"Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function","status":"public","publication_status":"published","acknowledgement":"MZ has been supported by Polish National Science Centre Grant No. DEC-2012/07/N/NZ2/00107 and by Foundation of Polish Science award START. ","_id":"1371","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publist_id":"5841","article_number":"033846","author":[{"full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir"},{"last_name":"Vitali","first_name":"David","full_name":"Vitali, David"}],"volume":93,"date_updated":"2023-02-21T10:36:32Z","date_created":"2018-12-11T11:51:38Z","year":"2016","acknowledgement":"The work of S.B. has been supported by the European Commission (Belgium) via the SCALEQIT program and by the Alexander von Humboldt Foundation. ","department":[{"_id":"JoFi"}],"publisher":"American Physical Society","publication_status":"published","month":"03","doi":"10.1103/PhysRevA.93.033846","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1601.01818"}],"quality_controlled":"1","issue":"3","abstract":[{"lang":"eng","text":"We study coherent phonon oscillations and tunneling between two coupled nonlinear nanomechanical resonators. We show that the coupling between two nanomechanical resonators creates an effective phonon Josephson junction, which exhibits two different dynamical behaviors: Josephson oscillation (phonon-Rabi oscillation) and macroscopic self-trapping (phonon blockade). Self-trapping originates from mechanical nonlinearities, meaning that when the nonlinearity exceeds its critical value, the energy exchange between the two resonators is suppressed, and phonon Josephson oscillations between them are completely blocked. An effective classical Hamiltonian for the phonon Josephson junction is derived and its mean-field dynamics is studied in phase space. Finally, we study the phonon-phonon coherence quantified by the mean fringe visibility, and show that the interaction between the two resonators may lead to the loss of coherence in the phononic junction."}],"type":"journal_article","oa_version":"Preprint","_id":"1370","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 93","status":"public","title":"Phonon Josephson junction with nanomechanical resonators","day":"28","scopus_import":1,"date_published":"2016-03-28T00:00:00Z","citation":{"ama":"Barzanjeh S, Vitali D. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 2016;93(3). doi:10.1103/PhysRevA.93.033846","apa":"Barzanjeh, S., & Vitali, D. (2016). Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.93.033846","ieee":"S. Barzanjeh and D. Vitali, “Phonon Josephson junction with nanomechanical resonators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3. American Physical Society, 2016.","ista":"Barzanjeh S, Vitali D. 2016. Phonon Josephson junction with nanomechanical resonators. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 033846.","short":"S. Barzanjeh, D. Vitali, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","mla":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 93, no. 3, 033846, American Physical Society, 2016, doi:10.1103/PhysRevA.93.033846.","chicago":"Barzanjeh, Shabir, and David Vitali. “Phonon Josephson Junction with Nanomechanical Resonators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2016. https://doi.org/10.1103/PhysRevA.93.033846."},"publication":"Physical Review A - Atomic, Molecular, and Optical Physics"},{"publist_id":"5838","type":"journal_article","date_created":"2018-12-11T11:51:39Z","date_updated":"2022-08-26T09:39:27Z","oa_version":"Preprint","volume":17,"author":[{"first_name":"Olivier","last_name":"Martin","full_name":"Martin, Olivier"},{"orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P","full_name":"Zagórski, Marcin P"}],"status":"public","title":"Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function"","publication_status":"published","intvolume":" 17","publisher":"Elsevier","department":[{"_id":"AnKi"}],"year":"2016","_id":"1373","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","month":"07","article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.plrev.2016.06.006","date_published":"2016-07-01T00:00:00Z","quality_controlled":"1","page":"168 - 171","publication":"Physics of Life Reviews","citation":{"chicago":"Martin, Olivier, and Marcin P Zagórski. “Network Architectures and Operating Principles. Reply to Comments on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.06.006.","short":"O. Martin, M.P. Zagórski, Physics of Life Reviews 17 (2016) 168–171.","mla":"Martin, Olivier, and Marcin P. Zagórski. “Network Architectures and Operating Principles. Reply to Comments on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 168–71, doi:10.1016/j.plrev.2016.06.006.","ieee":"O. Martin and M. P. Zagórski, “Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function",” Physics of Life Reviews, vol. 17. Elsevier, pp. 168–171, 2016.","apa":"Martin, O., & Zagórski, M. P. (2016). Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.006","ista":"Martin O, Zagórski MP. 2016. Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. 17, 168–171.","ama":"Martin O, Zagórski MP. Network architectures and operating principles. Reply to comments on "Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function" Physics of Life Reviews. 2016;17:168-171. doi:10.1016/j.plrev.2016.06.006"},"oa":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01531698","open_access":"1"}]},{"month":"05","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1502.07770","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1137/15M1010257","ec_funded":1,"publist_id":"5834","department":[{"_id":"VlKo"}],"publisher":"Society for Industrial and Applied Mathematics ","publication_status":"published","year":"2016","volume":9,"date_created":"2018-12-11T11:51:40Z","date_updated":"2021-01-12T06:50:15Z","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"},{"first_name":"Thomas","last_name":"Pock","full_name":"Pock, Thomas"},{"first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"}],"scopus_import":1,"day":"03","page":"605 - 636","citation":{"ista":"Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636.","apa":"Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree. SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M1010257","ieee":"V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied Mathematics , pp. 605–636, 2016.","ama":"Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257","chicago":"Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M1010257.","mla":"Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics , 2016, pp. 605–36, doi:10.1137/15M1010257.","short":"V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636."},"publication":"SIAM Journal on Imaging Sciences","date_published":"2016-05-03T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels."}],"intvolume":" 9","title":"Total variation on a tree","status":"public","_id":"1377","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint"},{"file":[{"file_size":622969,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-621-v1+1_LIPIcs-SoCG-2016-51.pdf","checksum":"92c0c3735fe908f8ded6e484005cb3b1","date_created":"2018-12-12T10:10:06Z","date_updated":"2020-07-14T12:44:47Z","relation":"main_file","file_id":"4791"}],"oa_version":"Published Version","pubrep_id":"621","intvolume":" 51","status":"public","ddc":["510"],"title":"Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1381","abstract":[{"lang":"eng","text":"Motivated by Tverberg-type problems in topological combinatorics and by classical results about embeddings (maps without double points), we study the question whether a finite simplicial complex K can be mapped into double-struck Rd without higher-multiplicity intersections. We focus on conditions for the existence of almost r-embeddings, i.e., maps f : K → double-struck Rd such that f(σ1) ∩ ⋯ ∩ f(σr) = ∅ whenever σ1, ..., σr are pairwise disjoint simplices of K. Generalizing the classical Haefliger-Weber embeddability criterion, we show that a well-known necessary deleted product condition for the existence of almost r-embeddings is sufficient in a suitable r-metastable range of dimensions: If rd ≥ (r + 1) dim K + 3, then there exists an almost r-embedding K → double-struck Rd if and only if there exists an equivariant map (K)Δ r → Sr Sd(r-1)-1, where (K)Δ r is the deleted r-fold product of K, the target Sd(r-1)-1 is the sphere of dimension d(r - 1) - 1, and Sr is the symmetric group. This significantly extends one of the main results of our previous paper (which treated the special case where d = rk and dim K = (r - 1)k for some k ≥ 3), and settles an open question raised there."}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2016-06-01T00:00:00Z","page":"51.1 - 51.12","citation":{"ama":"Mabillard I, Wagner U. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. In: Vol 51. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH; 2016:51.1-51.12. doi:10.4230/LIPIcs.SoCG.2016.51","ista":"Mabillard I, Wagner U. 2016. Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 51, 51.1-51.12.","ieee":"I. Mabillard and U. Wagner, “Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range,” presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA, 2016, vol. 51, p. 51.1-51.12.","apa":"Mabillard, I., & Wagner, U. (2016). Eliminating higher-multiplicity intersections, II. The deleted product criterion in the r-metastable range (Vol. 51, p. 51.1-51.12). Presented at the SoCG: Symposium on Computational Geometry, Medford, MA, USA: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH. https://doi.org/10.4230/LIPIcs.SoCG.2016.51","mla":"Mabillard, Isaac, and Uli Wagner. Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range. Vol. 51, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12, doi:10.4230/LIPIcs.SoCG.2016.51.","short":"I. Mabillard, U. Wagner, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016, p. 51.1-51.12.","chicago":"Mabillard, Isaac, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, II. The Deleted Product Criterion in the r-Metastable Range,” 51:51.1-51.12. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, 2016. https://doi.org/10.4230/LIPIcs.SoCG.2016.51."},"has_accepted_license":"1","day":"01","scopus_import":1,"volume":51,"date_created":"2018-12-11T11:51:41Z","date_updated":"2021-01-12T06:50:17Z","author":[{"full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard"},{"full_name":"Wagner, Uli","first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH","publication_status":"published","year":"2016","publist_id":"5830","file_date_updated":"2020-07-14T12:44:47Z","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2016.51","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Medford, MA, USA","start_date":"2016-06-14","end_date":"2016-06-17"},"project":[{"_id":"25FA3206-B435-11E9-9278-68D0E5697425","grant_number":"PP00P2_138948","name":"Embeddings in Higher Dimensions: Algorithms and Combinatorics"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"06"},{"scopus_import":1,"month":"06","day":"01","quality_controlled":"1","publication":"Journal of the ACM","citation":{"mla":"Chonev, Ventsislav K., et al. “On the Complexity of the Orbit Problem.” Journal of the ACM, vol. 63, no. 3, 23, ACM, 2016, doi:10.1145/2857050.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, Journal of the ACM 63 (2016).","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Complexity of the Orbit Problem.” Journal of the ACM. ACM, 2016. https://doi.org/10.1145/2857050.","ama":"Chonev VK, Ouaknine J, Worrell J. On the complexity of the orbit problem. Journal of the ACM. 2016;63(3). doi:10.1145/2857050","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the complexity of the orbit problem. Journal of the ACM. 63(3), 23.","apa":"Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On the complexity of the orbit problem. Journal of the ACM. ACM. https://doi.org/10.1145/2857050","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the complexity of the orbit problem,” Journal of the ACM, vol. 63, no. 3. ACM, 2016."},"main_file_link":[{"url":"http://arxiv.org/abs/1303.2981","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2857050","date_published":"2016-06-01T00:00:00Z","article_number":"23","type":"journal_article","abstract":[{"text":"We consider higher-dimensional versions of Kannan and Lipton's Orbit Problem - determining whether a target vector space V may be reached from a starting point x under repeated applications of a linear transformation A. Answering two questions posed by Kannan and Lipton in the 1980s, we show that when V has dimension one, this problem is solvable in polynomial time, and when V has dimension two or three, the problem is in NPRP.","lang":"eng"}],"issue":"3","publist_id":"5831","publication_status":"published","status":"public","title":"On the complexity of the orbit problem","publisher":"ACM","intvolume":" 63","department":[{"_id":"KrCh"}],"_id":"1380","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:50:17Z","date_created":"2018-12-11T11:51:41Z","oa_version":"Preprint","volume":63,"author":[{"last_name":"Chonev","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K"},{"full_name":"Ouaknine, Joël","last_name":"Ouaknine","first_name":"Joël"},{"first_name":"James","last_name":"Worrell","full_name":"Worrell, James"}]},{"month":"07","day":"05","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2016-07-05T00:00:00Z","doi":"10.1145/2933575.2934548","conference":{"name":"LICS: Logic in Computer Science","end_date":"2018-07-08","location":"New York, NY, USA","start_date":"2018-07-05"},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"page":"515 - 524","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1507.03632","open_access":"1"}],"citation":{"ama":"Chonev VK, Ouaknine J, Worrell J. On recurrent reachability for continuous linear dynamical systems. In: LICS ’16. IEEE; 2016:515-524. doi:10.1145/2933575.2934548","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On recurrent reachability for continuous linear dynamical systems,” in LICS ’16, New York, NY, USA, 2016, pp. 515–524.","apa":"Chonev, V. K., Ouaknine, J., & Worrell, J. (2016). On recurrent reachability for continuous linear dynamical systems. In LICS ’16 (pp. 515–524). New York, NY, USA: IEEE. https://doi.org/10.1145/2933575.2934548","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On recurrent reachability for continuous linear dynamical systems. LICS ’16. LICS: Logic in Computer Science, 515–524.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, LICS ’16, IEEE, 2016, pp. 515–524.","mla":"Chonev, Ventsislav K., et al. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” LICS ’16, IEEE, 2016, pp. 515–24, doi:10.1145/2933575.2934548.","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On Recurrent Reachability for Continuous Linear Dynamical Systems.” In LICS ’16, 515–24. IEEE, 2016. https://doi.org/10.1145/2933575.2934548."},"oa":1,"publication":"LICS '16","ec_funded":1,"publist_id":"5820","abstract":[{"lang":"eng","text":"The continuous evolution of a wide variety of systems, including continous-time Markov chains and linear hybrid automata, can be\r\ndescribed in terms of linear differential equations. In this paper we study the decision problem of whether the solution x(t) of a system of linear differential equations dx/dt = Ax reaches a target halfspace infinitely often. This recurrent reachability problem can\r\nequivalently be formulated as the following Infinite Zeros Problem: does a real-valued function f:R≥0 --> R satisfying a given linear\r\ndifferential equation have infinitely many zeros? Our main decidability result is that if the differential equation has order at most 7, then the Infinite Zeros Problem is decidable. On the other hand, we show that a decision procedure for the Infinite Zeros Problem at order 9 (and above) would entail a major breakthrough in Diophantine Approximation, specifically an algorithm for computing the Lagrange constants of arbitrary real algebraic numbers to arbitrary precision."}],"type":"conference","oa_version":"Preprint","date_updated":"2021-01-12T06:50:20Z","date_created":"2018-12-11T11:51:44Z","author":[{"last_name":"Chonev","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K"},{"full_name":"Ouaknine, Joël","last_name":"Ouaknine","first_name":"Joël"},{"full_name":"Worrell, James","first_name":"James","last_name":"Worrell"}],"department":[{"_id":"KrCh"}],"publisher":"IEEE","status":"public","publication_status":"published","title":"On recurrent reachability for continuous linear dynamical systems","year":"2016","_id":"1389","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"citation":{"short":"L. D’Antoni, R. Samanta, R. Singh, in:, Springer, 2016, pp. 383–401.","mla":"D’Antoni, Loris, et al. QLOSE: Program Repair with Quantitative Objectives. Vol. 9780, Springer, 2016, pp. 383–401, doi:10.1007/978-3-319-41540-6_21.","chicago":"D’Antoni, Loris, Roopsha Samanta, and Rishabh Singh. “QLOSE: Program Repair with Quantitative Objectives,” 9780:383–401. Springer, 2016. https://doi.org/10.1007/978-3-319-41540-6_21.","ama":"D’Antoni L, Samanta R, Singh R. QLOSE: Program repair with quantitative objectives. In: Vol 9780. Springer; 2016:383-401. doi:10.1007/978-3-319-41540-6_21","apa":"D’Antoni, L., Samanta, R., & Singh, R. (2016). QLOSE: Program repair with quantitative objectives (Vol. 9780, pp. 383–401). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. https://doi.org/10.1007/978-3-319-41540-6_21","ieee":"L. D’Antoni, R. Samanta, and R. Singh, “QLOSE: Program repair with quantitative objectives,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 383–401.","ista":"D’Antoni L, Samanta R, Singh R. 2016. QLOSE: Program repair with quantitative objectives. CAV: Computer Aided Verification, LNCS, vol. 9780, 383–401."},"quality_controlled":"1","page":"383 - 401","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"CAV: Computer Aided Verification","location":"Toronto, Canada","start_date":"2016-07-17","end_date":"2016-07-23"},"doi":"10.1007/978-3-319-41540-6_21","date_published":"2016-07-13T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"day":"13","month":"07","_id":"1390","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","title":"QLOSE: Program repair with quantitative objectives","intvolume":" 9780","publisher":"Springer","department":[{"_id":"ToHe"}],"author":[{"full_name":"D'Antoni, Loris","first_name":"Loris","last_name":"D'Antoni"},{"full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","last_name":"Samanta"},{"full_name":"Singh, Rishabh","first_name":"Rishabh","last_name":"Singh"}],"date_created":"2018-12-11T11:51:45Z","date_updated":"2021-01-12T06:50:21Z","volume":9780,"oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"The goal of automatic program repair is to identify a set of syntactic changes that can turn a program that is incorrect with respect\r\nto a given specification into a correct one. Existing program repair techniques typically aim to find any program that meets the given specification. Such “best-effort” strategies can end up generating a program that is quite different from the original one. Novel techniques have been proposed to compute syntactically minimal program fixes, but the smallest syntactic fix to a program can still significantly alter the original program’s behaviour. We propose a new approach to program repair based on program distances, which can quantify changes not only to the program syntax but also to the program semantics. We call this the quantitative program repair problem where the “optimal” repair is derived using multiple distances. We implement a solution to the quantitative repair\r\nproblem in a prototype tool called Qlose\r\n(Quantitatively close), using the program synthesizer Sketch. We evaluate the effectiveness of different distances in obtaining desirable repairs by evaluating\r\nQlose on programs taken from educational tools such as CodeHunt and edX."}],"publist_id":"5819","ec_funded":1},{"publication":"Physical Biology","citation":{"mla":"De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/3/036005.","ama":"De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005","ista":"De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.","apa":"De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/3/036005","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016."},"date_published":"2016-05-27T00:00:00Z","scopus_import":1,"day":"27","status":"public","title":"Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli","intvolume":" 13","_id":"1394","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"The solution space of genome-scale models of cellular metabolism provides a map between physically\r\nviable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the\r\ncorresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat empirical growth rate distributions recently obtained in experiments at single-cell resolution can\r\nbe explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of\r\na large bacterial population that captures this trade-off. The scaling relationships observed in\r\nexperiments encode, in such frameworks, for the same distance from the maximum achievable growth\r\nrate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions, these results allow for multiple\r\nimplications and extensions in spite of the underlying conceptual simplicity.","lang":"eng"}],"issue":"3","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.03243"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1088/1478-3975/13/3/036005","month":"05","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"IOP Publishing Ltd.","acknowledgement":"The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038.","year":"2016","date_created":"2018-12-11T11:51:46Z","date_updated":"2021-01-12T06:50:23Z","volume":13,"author":[{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","first_name":"Daniele"},{"full_name":"Capuani, Fabrizio","last_name":"Capuani","first_name":"Fabrizio"},{"last_name":"De Martino","first_name":"Andrea","full_name":"De Martino, Andrea"}],"article_number":"036005","publist_id":"5815","ec_funded":1},{"month":"05","doi":"10.1111/cgf.12826","language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"quality_controlled":"1","ec_funded":1,"publist_id":"5795","file_date_updated":"2020-07-14T12:44:53Z","author":[{"full_name":"Goldade, Ryan","last_name":"Goldade","first_name":"Ryan"},{"full_name":"Batty, Christopher","first_name":"Christopher","last_name":"Batty"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"volume":35,"date_updated":"2023-02-21T10:38:30Z","date_created":"2018-12-11T11:51:52Z","acknowledgement":"This research was supported by NSERC (RGPIN-04360-2014) and IST Austria. ","year":"2016","department":[{"_id":"ChWo"}],"publisher":"Wiley-Blackwell","publication_status":"published","has_accepted_license":"1","day":"27","scopus_import":1,"date_published":"2016-05-27T00:00:00Z","citation":{"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","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.","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","ista":"Goldade R, Batty C, Wojtan C. 2016. A practical method for high-resolution embedded liquid surfaces. Computer Graphics Forum. 35(2), 233–242.","short":"R. Goldade, C. Batty, C. Wojtan, Computer Graphics Forum 35 (2016) 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.","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."},"publication":"Computer Graphics Forum","page":"233 - 242","issue":"2","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"}],"type":"journal_article","pubrep_id":"612","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":15873858,"access_level":"open_access","file_name":"IST-2016-612-v1+2_Wojtan_APracticalMethod_PostPrint_2016.pdf","checksum":"8e61387ee2e3bd0e776fbe301629bfd9","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:13:18Z","file_id":"5000","relation":"main_file"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1412","intvolume":" 35","title":"A practical method for high-resolution embedded liquid surfaces","status":"public","ddc":["000"]},{"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ista":"Ugalde J, Rodríguez Furlán C, De Rycke R, Norambuena L, Friml J, León G, Tejos R. 2016. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 250, 10–19.","apa":"Ugalde, J., Rodríguez Furlán, C., De Rycke, R., Norambuena, L., Friml, J., León, G., & Tejos, R. (2016). Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. Elsevier. https://doi.org/10.1016/j.plantsci.2016.05.014","ieee":"J. Ugalde et al., “Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development,” Plant Science, vol. 250. Elsevier, pp. 10–19, 2016.","ama":"Ugalde J, Rodríguez Furlán C, De Rycke R, et al. Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development. Plant Science. 2016;250:10-19. doi:10.1016/j.plantsci.2016.05.014","chicago":"Ugalde, José, Cecilia Rodríguez Furlán, Riet De Rycke, Lorena Norambuena, Jiří Friml, Gabriel León, and Ricardo Tejos. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science. Elsevier, 2016. https://doi.org/10.1016/j.plantsci.2016.05.014.","mla":"Ugalde, José, et al. “Phosphatidylinositol 4-Phosphate 5-Kinases 1 and 2 Are Involved in the Regulation of Vacuole Morphology during Arabidopsis Thaliana Pollen Development.” Plant Science, vol. 250, Elsevier, 2016, pp. 10–19, doi:10.1016/j.plantsci.2016.05.014.","short":"J. Ugalde, C. Rodríguez Furlán, R. De Rycke, L. Norambuena, J. Friml, G. León, R. Tejos, Plant Science 250 (2016) 10–19."},"publication":"Plant Science","page":"10 - 19","date_published":"2016-09-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1410","intvolume":" 250","title":"Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development","ddc":["581"],"status":"public","pubrep_id":"1005","file":[{"access_level":"open_access","file_name":"2016_PlantScience_Ugalde.pdf","creator":"dernst","content_type":"application/pdf","file_size":4338545,"file_id":"6331","relation":"main_file","checksum":"ca08de036e6ddc81e6f760e0ccdebd3f","date_updated":"2020-07-14T12:44:53Z","date_created":"2019-04-17T07:41:57Z"}],"oa_version":"Submitted Version","month":"09","oa":1,"external_id":{"pmid":["27457979"]},"quality_controlled":"1","doi":"10.1016/j.plantsci.2016.05.014","language":[{"iso":"eng"}],"publist_id":"5797","file_date_updated":"2020-07-14T12:44:53Z","pmid":1,"year":"2016","acknowledgement":"the Odysseus Program of the Research Foundation-Flanders [G091608] to JF.","department":[{"_id":"JiFr"}],"publisher":"Elsevier","publication_status":"published","author":[{"first_name":"José","last_name":"Ugalde","full_name":"Ugalde, José"},{"last_name":"Rodríguez Furlán","first_name":"Cecilia","full_name":"Rodríguez Furlán, Cecilia"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"last_name":"Norambuena","first_name":"Lorena","full_name":"Norambuena, Lorena"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"León, Gabriel","last_name":"León","first_name":"Gabriel"},{"last_name":"Tejos","first_name":"Ricardo","full_name":"Tejos, Ricardo"}],"volume":250,"date_updated":"2021-01-12T06:50:33Z","date_created":"2018-12-11T11:51:51Z"},{"department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","year":"2016","volume":25,"date_updated":"2021-01-12T06:50:33Z","date_created":"2018-12-11T11:51:51Z","author":[{"full_name":"Abbott, Richard","first_name":"Richard","last_name":"Abbott"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Good, Jeffrey","first_name":"Jeffrey","last_name":"Good"}],"publist_id":"5798","file_date_updated":"2020-07-14T12:44:53Z","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/mec.13685","month":"06","intvolume":" 25","ddc":["576"],"status":"public","title":"Genomics of hybridization and its evolutionary consequences","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1409","file":[{"relation":"main_file","file_id":"4797","checksum":"ede7d0b8a471754f71f17e2b20f3135b","date_created":"2018-12-12T10:10:12Z","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","file_name":"IST-2017-772-v1+1_AbbotEtAl2016-3.pdf","file_size":226137,"content_type":"application/pdf","creator":"system"}],"oa_version":"Submitted Version","pubrep_id":"772","type":"journal_article","issue":"11","page":"2325 - 2332","citation":{"ama":"Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685","apa":"Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.13685","ieee":"R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp. 2325–2332, 2016.","ista":"Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary consequences. Molecular Ecology. 25(11), 2325–2332.","short":"R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.","mla":"Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32, doi:10.1111/mec.13685.","chicago":"Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell, 2016. https://doi.org/10.1111/mec.13685."},"publication":"Molecular Ecology","date_published":"2016-06-08T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"08"},{"scopus_import":1,"month":"05","day":"01","publication":"Computer Graphics Forum","citation":{"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","ista":"Jeschke S. 2016. Generalized diffusion curves: An improved vector representation for smooth-shaded images. Computer Graphics Forum. 35(2), 71–79.","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.","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","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.","short":"S. Jeschke, Computer Graphics Forum 35 (2016) 71–79.","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."},"quality_controlled":"1","project":[{"name":"Deep Pictures: Creating Visual and Haptic Vector Images","call_identifier":"FWF","_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23"}],"page":"71 - 79","date_published":"2016-05-01T00:00:00Z","doi":"10.1111/cgf.12812","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"2","publist_id":"5794","year":"2016","_id":"1413","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Generalized diffusion curves: An improved vector representation for smooth-shaded images","status":"public","department":[{"_id":"ChWo"}],"intvolume":" 35","publisher":"Wiley-Blackwell","author":[{"full_name":"Jeschke, Stefan","first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:50:34Z","date_created":"2018-12-11T11:51:53Z","oa_version":"None","volume":35},{"department":[{"_id":"BeBi"}],"publisher":"Wiley-Blackwell","intvolume":" 35","publication_status":"published","title":"Modeling and estimation of energy-based hyperelastic objects","status":"public","_id":"1414","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).","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":35,"date_created":"2018-12-11T11:51:53Z","date_updated":"2021-01-12T06:50:35Z","author":[{"last_name":"Miguel Villalba","first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","full_name":"Miguel Villalba, Eder"},{"full_name":"Miraut, David","first_name":"David","last_name":"Miraut"},{"first_name":"Miguel","last_name":"Otaduy","full_name":"Otaduy, Miguel"}],"type":"journal_article","issue":"2","publist_id":"5792","abstract":[{"lang":"eng","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."}],"page":"385 - 396","quality_controlled":"1","citation":{"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.","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.","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.","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."},"publication":"Computer Graphics Forum","language":[{"iso":"eng"}],"doi":"10.1111/cgf.12840","date_published":"2016-05-01T00:00:00Z","scopus_import":1,"month":"05","day":"01"},{"doi":"10.1111/nph.14019","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","month":"07","author":[{"last_name":"Simon","first_name":"Sibu","orcid":"0000-0002-1998-6741","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu"},{"full_name":"Skůpa, Petr","last_name":"Skůpa","first_name":"Petr"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"full_name":"Zwiewka, Marta","first_name":"Marta","last_name":"Zwiewka"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"full_name":"Klíma, Petr","first_name":"Petr","last_name":"Klíma"},{"full_name":"Čarná, Mária","first_name":"Mária","last_name":"Čarná"},{"full_name":"Rolčík, Jakub","last_name":"Rolčík","first_name":"Jakub"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"last_name":"Moreno","first_name":"Ignacio","full_name":"Moreno, Ignacio"},{"last_name":"Dobrev","first_name":"Petre","full_name":"Dobrev, Petre"},{"full_name":"Orellana, Ariel","last_name":"Orellana","first_name":"Ariel"},{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"volume":211,"date_created":"2018-12-11T11:51:54Z","date_updated":"2021-01-12T06:50:36Z","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 GACR (project no. 13-4063 7S to J.F.)","year":"2016","publisher":"Wiley-Blackwell","department":[{"_id":"JiFr"}],"publication_status":"published","publist_id":"5790","file_date_updated":"2020-07-14T12:44:53Z","date_published":"2016-07-01T00:00:00Z","citation":{"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.","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","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","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.","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.","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."},"publication":"New Phytologist","page":"65 - 74","has_accepted_license":"1","day":"01","scopus_import":1,"pubrep_id":"1004","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:13:32Z","checksum":"23522ced3508ffe7a4f247c4230e6493","relation":"main_file","file_id":"5016","content_type":"application/pdf","file_size":3828383,"creator":"system","file_name":"IST-2018-1004-v1+1_Simon_NewPhytol_2016_proof.pdf","access_level":"open_access"}],"_id":"1417","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 211","title":"PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis","status":"public","ddc":["581"],"issue":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article"},{"citation":{"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","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","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.","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.","short":"F. Ferstl, R. Ando, C. Wojtan, R. Westermann, N. Thuerey, Computer Graphics Forum 35 (2016) 225–232.","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.","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."},"publication":"Computer Graphics Forum","page":"225 - 232","date_published":"2016-05-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1415","intvolume":" 35","ddc":["000"],"title":"Narrow band FLIP for liquid simulations","status":"public","pubrep_id":"611","file":[{"date_created":"2018-12-12T10:12:22Z","date_updated":"2020-07-14T12:44:53Z","checksum":"984afbe510ed48019025dff1dcc7baad","file_id":"4940","relation":"main_file","creator":"system","file_size":5938324,"content_type":"application/pdf","file_name":"IST-2016-611-v1+3_CW_nbflip_postprint_2016.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","type":"journal_article","issue":"2","abstract":[{"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.","lang":"eng"}],"oa":1,"quality_controlled":"1","doi":"10.1111/cgf.12825","language":[{"iso":"eng"}],"month":"05","year":"2016","department":[{"_id":"ChWo"}],"publisher":"Wiley-Blackwell","publication_status":"published","author":[{"last_name":"Ferstl","first_name":"Florian","full_name":"Ferstl, Florian"},{"full_name":"Ando, Ryoichi","last_name":"Ando","first_name":"Ryoichi"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"first_name":"Rüdiger","last_name":"Westermann","full_name":"Westermann, Rüdiger"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"}],"volume":35,"date_updated":"2023-02-21T10:38:38Z","date_created":"2018-12-11T11:51:53Z","publist_id":"5793","file_date_updated":"2020-07-14T12:44:53Z"},{"date_published":"2016-05-15T00:00:00Z","doi":"10.1103/PhysRevB.93.195145","language":[{"iso":"eng"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","oa":1,"citation":{"short":"E. Van Loon, M. Katsnelson, L. Chomaz, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 93 (2016).","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.","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.","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.","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."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1603.09358"}],"quality_controlled":"1","month":"05","day":"15","scopus_import":1,"author":[{"first_name":"Erik","last_name":"Van Loon","full_name":"Van Loon, Erik"},{"last_name":"Katsnelson","first_name":"Mikhail","full_name":"Katsnelson, Mikhail"},{"first_name":"Lauriane","last_name":"Chomaz","full_name":"Chomaz, Lauriane"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:51:54Z","date_updated":"2021-01-12T06:50:36Z","oa_version":"Preprint","volume":93,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1416","year":"2016","title":"Interaction-driven Lifshitz transition with dipolar fermions in optical lattices","publication_status":"published","status":"public","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"intvolume":" 93","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."}],"publist_id":"5791","issue":"19","article_number":"195145","type":"journal_article"},{"scopus_import":1,"day":"29","month":"03","publication":"Journal of Physics: Condensed Matter","citation":{"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.","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","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.","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","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.","short":"A. Tomski, J. Kaczmarczyk, Journal of Physics: Condensed Matter 28 (2016).","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."},"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_published":"2016-03-29T00:00:00Z","doi":"10.1088/0953-8984/28/17/175701","language":[{"iso":"eng"}],"article_number":"175701","type":"journal_article","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"}],"issue":"17","ec_funded":1,"publist_id":"5788","year":"2016","_id":"1419","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Gutzwiller wave function for finite systems: Superconductivity in the Hubbard model","status":"public","publication_status":"published","publisher":"IOP Publishing Ltd.","department":[{"_id":"MiLe"}],"intvolume":" 28","author":[{"full_name":"Tomski, Andrzej","first_name":"Andrzej","last_name":"Tomski"},{"full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarczyk","first_name":"Jan"}],"date_updated":"2021-01-12T06:50:36Z","date_created":"2018-12-11T11:51:55Z","oa_version":"None","volume":28},{"pubrep_id":"588","oa_version":"Published Version","file":[{"file_id":"4751","relation":"main_file","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:09:27Z","checksum":"1f456ce1d2aa2f67176a1709f9702ecf","file_name":"IST-2016-588-v1+1_Mol_Biol_Evol-2016-Lagator-761-9.pdf","access_level":"open_access","creator":"system","file_size":648115,"content_type":"application/pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1427","title":"Epistatic interactions in the arabinose cis-regulatory element","status":"public","ddc":["570","576"],"intvolume":" 33","abstract":[{"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.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2016-03-01T00:00:00Z","publication":"Molecular Biology and Evolution","citation":{"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.","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.","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","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","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.","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.","short":"M. Lagator, C. Igler, A. Moreno, C.C. Guet, J.P. Bollback, Molecular Biology and Evolution 33 (2016) 761–769."},"page":"761 - 769","day":"01","has_accepted_license":"1","scopus_import":1,"author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Igler, Claudia","first_name":"Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Moreno","first_name":"Anaisa","full_name":"Moreno, Anaisa"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"date_updated":"2021-01-12T06:50:39Z","date_created":"2018-12-11T11:51:57Z","volume":33,"year":"2016","publication_status":"published","department":[{"_id":"CaGu"},{"_id":"JoBo"}],"publisher":"Oxford University Press","file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5772","ec_funded":1,"doi":"10.1093/molbev/msv269","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"month":"03"},{"doi":"10.1088/1742-6596/691/1/012016","conference":{"name":"24th International Laser Physics Workshop (LPHYS'15)","end_date":"2015-08-25","location":"Shanghai, China","start_date":"2015-08-21"},"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"quality_controlled":"1","month":"03","author":[{"first_name":"Martin","last_name":"Könenberg","full_name":"Könenberg, Martin"},{"full_name":"Moser, Thomas","last_name":"Moser","first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert"},{"full_name":"Yngvason, Jakob","last_name":"Yngvason","first_name":"Jakob"}],"volume":691,"date_updated":"2021-01-12T06:50:40Z","date_created":"2018-12-11T11:51:58Z","year":"2016","department":[{"_id":"RoSe"}],"publisher":"IOP Publishing Ltd.","publication_status":"published","publist_id":"5770","file_date_updated":"2020-07-14T12:44:53Z","article_number":"012016","date_published":"2016-03-07T00:00:00Z","citation":{"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.","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.","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","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","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.","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.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, in:, Journal of Physics: Conference Series, IOP Publishing Ltd., 2016."},"publication":"Journal of Physics: Conference Series","has_accepted_license":"1","day":"07","scopus_import":1,"pubrep_id":"585","oa_version":"Published Version","file":[{"checksum":"109db801749072c3f6c8f1a1848700fa","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:10:55Z","relation":"main_file","file_id":"4847","content_type":"application/pdf","file_size":1434688,"creator":"system","access_level":"open_access","file_name":"IST-2016-585-v1+1_JPCS_691_1_012016.pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1428","intvolume":" 691","title":"Superfluidity and BEC in a Model of Interacting Bosons in a Random Potential","ddc":["510","530"],"status":"public","issue":"1","abstract":[{"lang":"eng","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."}],"type":"conference"},{"month":"05","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1098/rsos.160036","article_number":"160036","publist_id":"5776","file_date_updated":"2020-07-14T12:44:53Z","department":[{"_id":"KrCh"}],"publisher":"Royal Society, The","publication_status":"published","acknowledgement":"C.H. gratefully acknowledges funding by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475.","year":"2016","volume":3,"date_created":"2018-12-11T11:51:57Z","date_updated":"2021-01-12T06:50:39Z","author":[{"first_name":"Maria","last_name":"Chakra","full_name":"Chakra, Maria"},{"orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","first_name":"Christian","full_name":"Hilbe, Christian"},{"first_name":"Arne","last_name":"Traulsen","full_name":"Traulsen, Arne"}],"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"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","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.","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.","short":"M. Chakra, C. Hilbe, A. Traulsen, Royal Society Open Science 3 (2016).","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.","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."},"publication":"Royal Society Open Science","date_published":"2016-05-01T00:00:00Z","type":"journal_article","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"}],"intvolume":" 3","ddc":["000"],"status":"public","title":"Coevolutionary interactions between farmers and mafia induce host acceptance of avian brood parasites","_id":"1426","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_name":"IST-2016-589-v1+1_160036.full.pdf","access_level":"open_access","creator":"system","file_size":937002,"content_type":"application/pdf","file_id":"5104","relation":"main_file","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:14:49Z","checksum":"bf84211b31fe87451e738ba301d729c3"}],"pubrep_id":"589"},{"citation":{"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.","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.","short":"S. Baek, H. Jeong, C. Hilbe, M. Nowak, Scientific Reports 6 (2016).","ista":"Baek S, Jeong H, Hilbe C, Nowak M. 2016. Comparing reactive and memory-one strategies of direct reciprocity. Scientific Reports. 6, 25676.","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","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.","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"},"publication":"Scientific Reports","date_published":"2016-05-10T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1423","intvolume":" 6","ddc":["000"],"title":"Comparing reactive and memory-one strategies of direct reciprocity","status":"public","pubrep_id":"590","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2016-590-v1+1_srep25676.pdf","file_size":1349915,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5327","checksum":"ee17c482370d2e1b3add393710d3c696","date_created":"2018-12-12T10:18:08Z","date_updated":"2020-07-14T12:44:53Z"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1038/srep25676","language":[{"iso":"eng"}],"month":"05","year":"2016","acknowledgement":"C.H. acknowledges generous funding from the Schrödinger scholarship of the Austrian Science Fund (FWF), J3475.","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","publication_status":"published","author":[{"last_name":"Baek","first_name":"Seung","full_name":"Baek, Seung"},{"last_name":"Jeong","first_name":"Hyeongchai","full_name":"Jeong, Hyeongchai"},{"last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"volume":6,"date_created":"2018-12-11T11:51:56Z","date_updated":"2021-01-12T06:50:38Z","article_number":"25676","publist_id":"5784","file_date_updated":"2020-07-14T12:44:53Z"},{"month":"07","language":[{"iso":"eng"}],"doi":"10.1007/s11005-016-0847-5","quality_controlled":"1","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5785","date_updated":"2021-01-12T06:50:38Z","date_created":"2018-12-11T11:51:56Z","volume":106,"author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"},{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"publication_status":"published","publisher":"Springer","department":[{"_id":"RoSe"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","year":"2016","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":1,"date_published":"2016-07-01T00:00:00Z","page":"913 - 923","publication":"Letters in Mathematical Physics","citation":{"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","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","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.","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.","short":"R. Frank, C. Hainzl, B. Schlein, R. Seiringer, Letters in Mathematical Physics 106 (2016) 913–923.","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.","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."},"abstract":[{"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.","lang":"eng"}],"issue":"7","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"5181","relation":"main_file","checksum":"fb404923d8ca9a1faeb949561f26cbea","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:15:57Z","access_level":"open_access","file_name":"IST-2016-591-v1+1_s11005-016-0847-5.pdf","creator":"system","content_type":"application/pdf","file_size":458968}],"pubrep_id":"591","status":"public","ddc":["510","530"],"title":"Incompatibility of time-dependent Bogoliubov–de-Gennes and Ginzburg–Landau equations","intvolume":" 106","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1422"},{"day":"11","month":"04","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1145/2883817.2883837","date_published":"2016-04-11T00:00:00Z","conference":{"location":"Vienna, Austria","start_date":"2016-04-12","end_date":"2016-04-14","name":"HSCC 2016: International Conference on Hybrid Systems: Computation and Control"},"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"page":"155 - 164","quality_controlled":"1","citation":{"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","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.","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","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.","mla":"Bak, Stanley, et al. Scalable Static Hybridization Methods for Analysis of Nonlinear Systems. Springer, 2016, pp. 155–64, doi:10.1145/2883817.2883837.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, T. Johnson, P. Prakash, in:, Springer, 2016, pp. 155–164.","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."},"ec_funded":1,"publist_id":"5786","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"}],"type":"conference","oa_version":"None","date_updated":"2021-01-12T06:50:37Z","date_created":"2018-12-11T11:51:55Z","author":[{"first_name":"Stanley","last_name":"Bak","full_name":"Bak, Stanley"},{"orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Johnson, Taylor","last_name":"Johnson","first_name":"Taylor"},{"full_name":"Prakash, Pradyot","first_name":"Pradyot","last_name":"Prakash"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","status":"public","publication_status":"published","title":"Scalable static hybridization methods for analysis of nonlinear systems","_id":"1421","year":"2016","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publication":"Genetics","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","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","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.","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.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","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."},"page":"1523 - 1548","date_published":"2016-04-06T00:00:00Z","scopus_import":"1","day":"06","article_processing_charge":"No","_id":"1420","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"A general approximation for the dynamics of quantitative traits","intvolume":" 202","oa_version":"Preprint","type":"journal_article","abstract":[{"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. ","lang":"eng"}],"issue":"4","external_id":{"arxiv":["1510.08344"]},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08344"}],"oa":1,"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"}],"doi":"10.1534/genetics.115.184127","language":[{"iso":"eng"}],"month":"04","year":"2016","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"author":[{"last_name":"Bod'ová","first_name":"Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"date_updated":"2022-08-01T10:49:55Z","date_created":"2018-12-11T11:51:55Z","volume":202,"publist_id":"5787","ec_funded":1},{"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms11332","month":"04","publication_status":"published","department":[{"_id":"JoFi"}],"publisher":"Nature Publishing Group","year":"2016","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.","date_updated":"2021-01-12T06:50:40Z","date_created":"2018-12-11T11:51:58Z","volume":7,"author":[{"full_name":"Husko, Chad","last_name":"Husko","first_name":"Chad"},{"full_name":"Wulf, Matthias","first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378"},{"full_name":"Lefrançois, Simon","first_name":"Simon","last_name":"Lefrançois"},{"full_name":"Combrié, Sylvain","first_name":"Sylvain","last_name":"Combrié"},{"full_name":"Lehoucq, Gaëlle","last_name":"Lehoucq","first_name":"Gaëlle"},{"first_name":"Alfredo","last_name":"De Rossi","full_name":"De Rossi, Alfredo"},{"full_name":"Eggleton, Benjamin","first_name":"Benjamin","last_name":"Eggleton"},{"full_name":"Kuipers, Laurens","last_name":"Kuipers","first_name":"Laurens"}],"article_number":"11332 (2016)","file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5769","publication":"Nature Communications","citation":{"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","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","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.","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.","short":"C. Husko, M. Wulf, S. Lefrançois, S. Combrié, G. Lehoucq, A. De Rossi, B. Eggleton, L. Kuipers, Nature Communications 7 (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."},"date_published":"2016-04-15T00:00:00Z","scopus_import":1,"day":"15","has_accepted_license":"1","status":"public","title":"Free-carrier-induced soliton fission unveiled by in situ measurements in nanophotonic waveguides","ddc":["530"],"intvolume":" 7","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1429","file":[{"file_name":"IST-2016-583-v1+1_ncomms11332.pdf","access_level":"open_access","file_size":965176,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5177","date_created":"2018-12-12T10:15:53Z","date_updated":"2020-07-14T12:44:53Z","checksum":"6484fa81a2e52e4fdd7935e1ae6091d4"}],"oa_version":"Published Version","pubrep_id":"583","type":"journal_article","abstract":[{"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.","lang":"eng"}]},{"pubrep_id":"584","file":[{"content_type":"application/pdf","file_size":1216360,"creator":"system","access_level":"open_access","file_name":"IST-2016-584-v1+1_peerj-1865.pdf","checksum":"c27d898598a1e3d7f629607a309254e1","date_created":"2018-12-12T10:17:19Z","date_updated":"2020-07-14T12:44:53Z","relation":"main_file","file_id":"5272"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1431","title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","status":"public","ddc":["570"],"intvolume":" 2016","abstract":[{"lang":"eng","text":"The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow."}],"issue":"3","type":"journal_article","date_published":"2016-01-01T00:00:00Z","publication":"PeerJ","citation":{"short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:10.7717/peerj.1865.","chicago":"Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” PeerJ. PeerJ, 2016. https://doi.org/10.7717/peerj.1865.","ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016;2016(3). doi:10.7717/peerj.1865","apa":"Tartally, A., Kelager, A., Fürst, M., & Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. PeerJ. https://doi.org/10.7717/peerj.1865","ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” PeerJ, vol. 2016, no. 3. PeerJ, 2016.","ista":"Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865."},"day":"01","has_accepted_license":"1","scopus_import":1,"author":[{"first_name":"András","last_name":"Tartally","full_name":"Tartally, András"},{"full_name":"Kelager, Andreas","first_name":"Andreas","last_name":"Kelager"},{"full_name":"Fürst, Matthias","first_name":"Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X"},{"full_name":"Nash, David","first_name":"David","last_name":"Nash"}],"date_created":"2018-12-11T11:51:59Z","date_updated":"2021-01-12T06:50:41Z","volume":2016,"year":"2016","publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"PeerJ","file_date_updated":"2020-07-14T12:44:53Z","publist_id":"5767","article_number":"1865","doi":"10.7717/peerj.1865","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","month":"01"},{"type":"journal_article","abstract":[{"text":"We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B on scales down to N−2/3N−2/3.","lang":"eng"}],"issue":"3","status":"public","title":"Local stability of the free additive convolution","intvolume":" 271","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1434","oa_version":"Preprint","scopus_import":1,"day":"01","page":"672 - 719","publication":"Journal of Functional Analysis","citation":{"ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. Journal of Functional Analysis. 2016;271(3):672-719. doi:10.1016/j.jfa.2016.04.006","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2016). Local stability of the free additive convolution. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2016.04.006","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” Journal of Functional Analysis, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719.","mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:10.1016/j.jfa.2016.04.006.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” Journal of Functional Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2016.04.006."},"date_published":"2016-08-01T00:00:00Z","publist_id":"5764","ec_funded":1,"publication_status":"published","publisher":"Academic Press","department":[{"_id":"LaEr"}],"year":"2016","date_updated":"2021-01-12T06:50:42Z","date_created":"2018-12-11T11:52:00Z","volume":271,"author":[{"full_name":"Bao, Zhigang","first_name":"Zhigang","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","first_name":"Kevin","last_name":"Schnelli","full_name":"Schnelli, Kevin"}],"month":"08","quality_controlled":"1","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1508.05905","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jfa.2016.04.006"},{"file_date_updated":"2020-07-14T12:44:54Z","ec_funded":1,"publist_id":"5763","publication_status":"published","publisher":"Elsevier","department":[{"_id":"RoSe"}],"year":"2016","date_updated":"2021-01-12T06:50:43Z","date_created":"2018-12-11T11:52:00Z","volume":105,"author":[{"last_name":"Bach","first_name":"Volker","full_name":"Bach, Volker"},{"full_name":"Breteaux, Sébastien","first_name":"Sébastien","last_name":"Breteaux"},{"id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","first_name":"Sören P","last_name":"Petrat","full_name":"Petrat, Sören P"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"},{"first_name":"Tim","last_name":"Tzaneteas","full_name":"Tzaneteas, Tim"}],"month":"01","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.matpur.2015.09.003","type":"journal_article","abstract":[{"lang":"eng","text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system."}],"issue":"1","status":"public","ddc":["510","530"],"title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction","intvolume":" 105","_id":"1436","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:44:54Z","date_created":"2018-12-12T10:10:36Z","checksum":"c5afe1f6935bc7f2b546adbde1d31a35","relation":"main_file","file_id":"4825","file_size":658491,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","access_level":"open_access"}],"pubrep_id":"581","scopus_import":1,"day":"01","has_accepted_license":"1","page":"1 - 30","publication":"Journal de Mathématiques Pures et Appliquées","citation":{"ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 2016;105(1):1-30. doi:10.1016/j.matpur.2015.09.003","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., & Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. Elsevier. https://doi.org/10.1016/j.matpur.2015.09.003","ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30.","mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:10.1016/j.matpur.2015.09.003.","chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” Journal de Mathématiques Pures et Appliquées. Elsevier, 2016. https://doi.org/10.1016/j.matpur.2015.09.003."},"date_published":"2016-01-01T00:00:00Z"},{"month":"01","language":[{"iso":"eng"}],"doi":"10.1155/2016/1207393","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publist_id":"5762","file_date_updated":"2020-07-14T12:44:54Z","article_number":"1207393","volume":2016,"date_updated":"2021-01-12T06:50:43Z","date_created":"2018-12-11T11:52:00Z","author":[{"id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","last_name":"Guzmán","full_name":"Guzmán, José"},{"full_name":"Gerevich, Zoltan","last_name":"Gerevich","first_name":"Zoltan"}],"publisher":"Hindawi Publishing Corporation","department":[{"_id":"PeJo"}],"publication_status":"published","year":"2016","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2016-01-01T00:00:00Z","citation":{"short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:10.1155/2016/1207393.","chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” Neural Plasticity. Hindawi Publishing Corporation, 2016. https://doi.org/10.1155/2016/1207393.","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016;2016. doi:10.1155/2016/1207393","apa":"Guzmán, J., & Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. Hindawi Publishing Corporation. https://doi.org/10.1155/2016/1207393","ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” Neural Plasticity, vol. 2016. Hindawi Publishing Corporation, 2016.","ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393."},"publication":"Neural Plasticity","abstract":[{"text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"IST-2016-580-v1+1_1207393.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1395180,"file_id":"4740","relation":"main_file","date_created":"2018-12-12T10:09:17Z","date_updated":"2020-07-14T12:44:54Z","checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da"}],"oa_version":"Published Version","pubrep_id":"580","intvolume":" 2016","title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","ddc":["570"],"status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1435"},{"citation":{"mla":"Dragoi, Cezara, et al. PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms. Vol. 20–22, ACM, 2016, pp. 400–15, doi:10.1145/2837614.2837650.","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. https://doi.org/10.1145/2837614.2837650.","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:10.1145/2837614.2837650","ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.","apa":"Dragoi, C., Henzinger, T. A., & Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. https://doi.org/10.1145/2837614.2837650","ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415."},"page":"400 - 415","date_published":"2016-01-11T00:00:00Z","scopus_import":1,"day":"11","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1439","title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","status":"public","oa_version":"Preprint","type":"conference","alternative_title":["ACM SIGPLAN Notices"],"abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification.","lang":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01251199/"}],"quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"conference":{"name":"POPL: Principles of Programming Languages","end_date":"2016-01-22","start_date":"2016-01-20","location":"St. Petersburg, FL, USA"},"doi":"10.1145/2837614.2837650","language":[{"iso":"eng"}],"month":"01","year":"2016","acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"ACM","author":[{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","first_name":"Cezara","last_name":"Dragoi","full_name":"Dragoi, Cezara"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","first_name":"Damien"}],"date_updated":"2021-01-12T06:50:45Z","date_created":"2018-12-11T11:52:01Z","volume":"20-22","ec_funded":1,"publist_id":"5759"},{"_id":"1440","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2016","acknowledgement":"The author thanks Banerjee et al. (2016) for providing coordinates prior to public release and apologizes to colleagues whose work was not cited or discussed due to the limited space available. The author is supported by grants from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232).","title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","publication_status":"published","status":"public","intvolume":" 24","department":[{"_id":"HaJa"}],"publisher":"Cell Press","author":[{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L"}],"date_updated":"2021-01-12T06:50:46Z","date_created":"2018-12-11T11:52:02Z","volume":24,"oa_version":"None","type":"journal_article","issue":"2","ec_funded":1,"publist_id":"5756","publication":"Structure","citation":{"ista":"Janovjak HL. 2016. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 24(2), 213–215.","apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. Cell Press. https://doi.org/10.1016/j.str.2016.01.002","ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” Structure, vol. 24, no. 2. Cell Press, pp. 213–215, 2016.","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 2016;24(2):213-215. doi:10.1016/j.str.2016.01.002","chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” Structure. Cell Press, 2016. https://doi.org/10.1016/j.str.2016.01.002.","mla":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” Structure, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:10.1016/j.str.2016.01.002.","short":"H.L. Janovjak, Structure 24 (2016) 213–215."},"quality_controlled":"1","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"},{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"},{"name":"Molecular Drug Targets","call_identifier":"FWF","grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425"}],"page":"213 - 215","date_published":"2016-02-02T00:00:00Z","doi":"10.1016/j.str.2016.01.002","language":[{"iso":"eng"}],"scopus_import":1,"day":"02","month":"02"}]