[{"article_processing_charge":"Yes (in subscription journal)","oa":1,"issue":"1","publisher":"Nature Publishing Group","file":[{"checksum":"29a1b5db458048d3bd5c67e0e2a56818","creator":"system","access_level":"open_access","content_type":"application/pdf","file_size":998157,"file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","date_created":"2018-12-12T10:14:14Z","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","file_id":"5064"},{"creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_id":"5065","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","date_updated":"2020-07-14T12:48:16Z","relation":"main_file","date_created":"2018-12-12T10:14:15Z","file_size":9715993}],"external_id":{"isi":["000407198800005"]},"status":"public","_id":"955","date_published":"2017-08-09T00:00:00Z","corr_author":"1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"ec_funded":1,"title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","date_updated":"2026-04-08T13:54:24Z","file_date_updated":"2020-07-14T12:48:16Z","oa_version":"Published Version","volume":8,"article_number":"216","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6071"}]},"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Friedlander","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","full_name":"Prizak, Roshan"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["539","576"],"day":"09","scopus_import":"1","doi":"10.1038/s41467-017-00238-8","has_accepted_license":"1","quality_controlled":"1","year":"2017","citation":{"ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.","apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216."},"date_created":"2018-12-11T11:49:23Z","publist_id":"6459","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"publication":"Nature Communications","type":"journal_article","month":"08","intvolume":" 8","publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","pubrep_id":"864","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1},{"language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"doi":"10.1016/j.jfa.2017.05.003","scopus_import":"1","day":"01","author":[{"last_name":"Carlen","full_name":"Carlen, Eric","first_name":"Eric"},{"full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","first_name":"Jan"}],"title":"Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance","date_updated":"2025-06-04T08:14:53Z","volume":273,"oa_version":"Submitted Version","date_published":"2017-09-01T00:00:00Z","_id":"956","arxiv":1,"publisher":"Academic Press","oa":1,"issue":"5","article_processing_charge":"No","status":"public","external_id":{"arxiv":["1609.01254"],"isi":["000406082300005"]},"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 273","publication_identifier":{"issn":["0022-1236"]},"publication_status":"published","month":"09","publist_id":"6452","abstract":[{"lang":"eng","text":"We study a class of ergodic quantum Markov semigroups on finite-dimensional unital C⁎-algebras. These semigroups have a unique stationary state σ, and we are concerned with those that satisfy a quantum detailed balance condition with respect to σ. We show that the evolution on the set of states that is given by such a quantum Markov semigroup is gradient flow for the relative entropy with respect to σ in a particular Riemannian metric on the set of states. This metric is a non-commutative analog of the 2-Wasserstein metric, and in several interesting cases we are able to show, in analogy with work of Otto on gradient flows with respect to the classical 2-Wasserstein metric, that the relative entropy is strictly and uniformly convex with respect to the Riemannian metric introduced here. As a consequence, we obtain a number of new inequalities for the decay of relative entropy for ergodic quantum Markov semigroups with detailed balance."}],"date_created":"2018-12-11T11:49:24Z","quality_controlled":"1","citation":{"apa":"Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003","mla":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis, vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.","short":"E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.","ama":"Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869. doi:10.1016/j.jfa.2017.05.003","ista":"Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5), 1810–1869.","ieee":"E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum Markov semigroups with detailed balance,” Journal of Functional Analysis, vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.","chicago":"Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis. Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003."},"year":"2017","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.01254"}],"page":"1810 - 1869","publication":"Journal of Functional Analysis","type":"journal_article"},{"editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Methods in Molecular Biology"],"intvolume":" 1596","publication_identifier":{"issn":["1064-3745"]},"publication_status":"published","month":"03","year":"2017","citation":{"ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87."},"quality_controlled":"1","abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"publist_id":"6451","date_created":"2018-12-11T11:49:24Z","publication":"Synthetic Protein Switches","type":"book_chapter","page":"71 - 87","department":[{"_id":"HaJa"}],"language":[{"iso":"eng"}],"day":"15","author":[{"last_name":"Clifton","full_name":"Clifton, Ben","first_name":"Ben"},{"first_name":"Jason","full_name":"Whitfield, Jason","last_name":"Whitfield"},{"full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","full_name":"Janovjak, Harald L"},{"last_name":"Jackson","full_name":"Jackson, Colin","first_name":"Colin"}],"scopus_import":"1","doi":"10.1007/978-1-4939-6940-1_5","project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors"}],"date_updated":"2025-07-10T12:01:52Z","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","volume":1596,"oa_version":"None","_id":"957","date_published":"2017-03-15T00:00:00Z","series_title":"Synthetic Protein Switches","article_processing_charge":"No","publisher":"Springer","status":"public"},{"doi":"10.1007/978-1-4939-6940-1_6","scopus_import":"1","day":"15","author":[{"last_name":"Mitchell","full_name":"Mitchell, Joshua","first_name":"Joshua"},{"last_name":"Zhang","full_name":"Zhang, William","first_name":"William"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"language":[{"iso":"eng"}],"department":[{"_id":"HaJa"}],"volume":1596,"oa_version":"None","date_updated":"2025-07-10T12:01:54Z","title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","date_published":"2017-05-15T00:00:00Z","_id":"958","status":"public","publisher":"Springer","series_title":"Synthetic Protein Switches","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"publication_status":"published","publication_identifier":{"issn":["1064-3745"]},"alternative_title":["Methods in Molecular Biology"],"intvolume":" 1596","month":"05","page":"89 - 99","publication":"Synthetic Protein Switches","type":"book_chapter","publist_id":"6450","abstract":[{"text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors.","lang":"eng"}],"date_created":"2018-12-11T11:49:24Z","citation":{"ieee":"J. Mitchell et al., “Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 89–99.","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.","mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.","apa":"Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer. https://doi.org/10.1007/978-1-4939-6940-1_6","short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99.","ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6","ista":"Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2017.Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 89–99."},"year":"2017","quality_controlled":"1"},{"publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"825","page":"109","type":"dissertation","degree_awarded":"PhD","date_created":"2018-12-11T11:49:25Z","publist_id":"6444","abstract":[{"text":"Cell-cell contact formation constitutes the first step in the emergence of multicellularity in evolution, thereby allowing the differentiation of specialized cell types. In metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell fate specification has been implicated in cell-cell contact formation. However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and mesendoderm cell fate specification during zebrafish gastrulation. We show that long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an effective positive feedback loop between ppl cell-cell contact duration and cell fate specification. Finally, by using a combination of theoretical modeling and experimentation, we show that this feedback loop determines whether anterior axial mesendoderm cells become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal that the gene regulatory networks leading to cell fate diversification within the developing embryo are controlled by the interdependent activities of cell-cell signaling and contact formation.","lang":"eng"}],"citation":{"ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:10.15479/AT:ISTA:th_825","mla":"Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_825.","apa":"Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_825","short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria.","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.","chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_825."},"year":"2017","month":"03","OA_place":"publisher","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:16Z","date_updated":"2026-06-18T18:12:40Z","title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","doi":"10.15479/AT:ISTA:th_825","has_accepted_license":"1","author":[{"first_name":"Vanessa","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570","590"],"day":"01","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"735","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"1100","relation":"part_of_dissertation"},{"id":"1537","status":"public","relation":"part_of_dissertation"},{"id":"3246","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"2926","relation":"part_of_dissertation"},{"id":"676","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1912"}]},"department":[{"_id":"CaHe"}],"status":"public","file":[{"creator":"dernst","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"242f88c87f2cf267bf05049fa26a687b","file_name":"2017_Barone_thesis_final.docx","date_created":"2019-04-05T08:36:52Z","date_updated":"2020-07-14T12:48:16Z","relation":"source_file","file_id":"6205","file_size":14497822},{"checksum":"ba5b0613ed8bade73a409acdd880fb8a","access_level":"open_access","content_type":"application/pdf","creator":"dernst","file_size":14995941,"file_id":"6206","date_created":"2019-04-05T08:36:52Z","relation":"main_file","date_updated":"2020-07-14T12:48:16Z","file_name":"2017_Barone_thesis_.pdf"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","acknowledgement":"Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall the good science I witnessed and participated in. It has been a \r\nblast, an incredibly \r\nexciting one! Thanks to JLo, for teaching me how to master my pipettes and showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout zebrafish and being always there to advice, sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether for all the good laughs we\r\nhad. My start in Vienna would have been a lot more \r\ndifficult without you guys. Also it would not have been possible without Elena and Inês: \r\nthanks for helping setting up this lab and for the dinners in Gugging. Thanks to Martin, for \r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp, for the interest and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat. To Shayan, for being such a motivated student. To Matt, for helping out\r\nwith coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor setting up an amazing imaging facility and for building the best team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand to Patrick Lemaire f\r\nor the helpful insight and extremely interesting discussion we had \r\nabout the project. Also, this journey would not have been the same without all the friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William, e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!","oa":1,"corr_author":"1","date_published":"2017-03-01T00:00:00Z","_id":"961"},{"conference":{"end_date":"2017-07-28","name":"CAV: Computer Aided Verification","location":"Heidelberg, Germany","start_date":"2017-07-24"},"month":"01","quality_controlled":"1","year":"2017","citation":{"chicago":"Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer, 2017. https://doi.org/10.1007/978-3-319-63390-9_21.","ieee":"M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 399–418.","ista":"Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings. CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.","ama":"Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21","apa":"Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21","mla":"Trinh, Minh, et al. Model Counting for Recursively-Defined Strings. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418, doi:10.1007/978-3-319-63390-9_21.","short":"M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 399–418."},"abstract":[{"text":"We present a new algorithm for model counting of a class of string constraints. In addition to the classic operation of concatenation, our class includes some recursively defined operations such as Kleene closure, and replacement of substrings. Additionally, our class also includes length constraints on the string expressions, which means, by requiring reasoning about numbers, that we face a multi-sorted logic. In the end, our string constraints are motivated by their use in programming for web applications. Our algorithm comprises two novel features: the ability to use a technique of (1) partial derivatives for constraints that are already in a solved form, i.e. a form where its (string) satisfiability is clearly displayed, and (2) non-progression, where cyclic reasoning in the reduction process may be terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally compare our model counter with two recent works on model counting of similar constraints, SMC [18] and ABC [5], to demonstrate its superior performance.","lang":"eng"}],"publist_id":"6443","date_created":"2018-12-11T11:49:26Z","type":"conference","page":"399 - 418","editor":[{"last_name":"Majumdar","full_name":"Majumdar, Rupak","first_name":"Rupak"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["LNCS"],"intvolume":" 10427","publication_status":"published","publication_identifier":{"issn":["0302-9743"]},"_id":"962","date_published":"2017-01-01T00:00:00Z","article_processing_charge":"No","publisher":"Springer","status":"public","external_id":{"isi":["000431900900021"]},"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"day":"01","author":[{"first_name":"Minh","full_name":"Trinh, Minh","last_name":"Trinh"},{"full_name":"Chu, Duc Hiep","last_name":"Chu","id":"3598E630-F248-11E8-B48F-1D18A9856A87","first_name":"Duc Hiep"},{"first_name":"Joxan","last_name":"Jaffar","full_name":"Jaffar, Joxan"}],"doi":"10.1007/978-3-319-63390-9_21","scopus_import":"1","project":[{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"date_updated":"2026-04-16T09:58:05Z","title":"Model counting for recursively-defined strings","volume":10427,"oa_version":"None"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pubrep_id":"829","publication_identifier":{"issn":["1868-8969"]},"publication_status":"published","intvolume":" 83","alternative_title":["LIPIcs"],"month":"06","conference":{"start_date":"2017-08-21","end_date":"2017-08-25","location":"Aalborg, Denmark","name":"MFCS: Mathematical Foundations of Computer Science"},"type":"conference","date_created":"2018-12-11T11:49:26Z","abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. "}],"publist_id":"6438","quality_controlled":"1","citation":{"chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Aalborg, Denmark, 2017, vol. 83.","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 83, 37.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science, Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37"},"year":"2017","scopus_import":"1","doi":"10.4230/LIPIcs.MFCS.2017.37","has_accepted_license":"1","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","full_name":"Avni, Guy","first_name":"Guy","orcid":"0000-0001-5588-8287"},{"first_name":"Shibashis","full_name":"Guha, Shibashis","last_name":"Guha"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"day":"01","ddc":["004"],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"6005","relation":"later_version"}]},"department":[{"_id":"ToHe"}],"volume":83,"oa_version":"Published Version","article_number":"37","file_date_updated":"2020-07-14T12:48:18Z","title":"Timed network games with clocks","date_updated":"2025-07-10T12:01:59Z","project":[{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"date_published":"2017-06-01T00:00:00Z","_id":"963","file":[{"file_name":"IST-2017-829-v1+1_mfcs-cr.pdf","relation":"main_file","date_created":"2018-12-12T10:14:10Z","date_updated":"2020-07-14T12:48:18Z","file_id":"5059","file_size":369730,"creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"f55eaf7f3c36ea07801112acfedd17d5"}],"status":"public","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_processing_charge":"No","oa":1},{"oa_version":"Published Version","date_updated":"2022-08-25T13:34:55Z","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.pk16b","day":"14","author":[{"first_name":"Paul","last_name":"Riccio","full_name":"Riccio, Paul"},{"first_name":"Christina","last_name":"Cebrián","full_name":"Cebrián, Christina"},{"first_name":"Hui","full_name":"Zong, Hui","last_name":"Zong"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"first_name":"Frank","last_name":"Costantini","full_name":"Costantini, Frank"}],"department":[{"_id":"SiHi"}],"related_material":{"record":[{"id":"9702","status":"deleted","relation":"used_in_publication"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.pk16b"}],"type":"research_data_reference","status":"public","publisher":"Dryad","abstract":[{"text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.","lang":"eng"}],"date_created":"2021-07-23T09:39:34Z","citation":{"mla":"Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.","short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:10.5061/dryad.pk16b","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, 10.5061/dryad.pk16b.","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.","chicago":"Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b."},"oa":1,"year":"2017","article_processing_charge":"No","month":"01","date_published":"2017-01-14T00:00:00Z","_id":"9707"},{"date_updated":"2025-09-22T09:43:12Z","title":"Data from: Error-robust modes of the retinal population code","oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"1197","relation":"used_in_publication"}]},"department":[{"_id":"GaTk"}],"author":[{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"full_name":"Ioffe, Mark","last_name":"Ioffe","first_name":"Mark"},{"full_name":"Loback, Adrianna","last_name":"Loback","first_name":"Adrianna"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}],"day":"18","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.1f1rc","article_processing_charge":"No","year":"2017","citation":{"ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","mla":"Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc."},"oa":1,"date_created":"2021-07-23T11:34:34Z","publisher":"Dryad","abstract":[{"text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.","lang":"eng"}],"type":"research_data_reference","status":"public","main_file_link":[{"url":"https://doi.org/10.5061/dryad.1f1rc","open_access":"1"}],"_id":"9709","date_published":"2017-10-18T00:00:00Z","month":"10"},{"oa_version":"Published Version","date_updated":"2025-04-15T07:11:04Z","title":"Data for: Establishment in a new habitat by polygenic adaptation","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.17632/nw68fxzjpm.1","day":"29","author":[{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"used_in_publication","id":"564","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.17632/nw68fxzjpm.1"}],"type":"research_data_reference","status":"public","abstract":[{"lang":"eng","text":"Mathematica notebooks used to generate figures."}],"publisher":"Mendeley Data","date_created":"2021-08-09T13:18:55Z","citation":{"ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","chicago":"Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.","short":"A. Etheridge, N.H. Barton, (2017).","apa":"Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1","mla":"Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:10.17632/nw68fxzjpm.1","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1."},"oa":1,"year":"2017","article_processing_charge":"No","month":"12","date_published":"2017-12-29T00:00:00Z","_id":"9842"},{"department":[{"_id":"JaMa"}],"language":[{"iso":"eng"}],"day":"01","author":[{"first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"full_name":"Gyöngy, István","last_name":"Gyöngy","first_name":"István"}],"doi":"10.1090/mcom/3201","scopus_import":"1","title":"Localization errors in solving stochastic partial differential equations in the whole space","date_updated":"2025-09-11T07:20:20Z","oa_version":"Submitted Version","volume":86,"_id":"642","date_published":"2017-01-01T00:00:00Z","corr_author":"1","arxiv":1,"oa":1,"issue":"307","article_processing_charge":"No","publisher":"American Mathematical Society","status":"public","external_id":{"arxiv":["1508.05535"],"isi":["000400929100013"]},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":" 86","publication_status":"published","publication_identifier":{"issn":["0025-5718"]},"month":"01","citation":{"mla":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation, vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201.","short":"M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.","apa":"Gerencser, M., & Gyöngy, I. (2017). Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. American Mathematical Society. https://doi.org/10.1090/mcom/3201","ama":"Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397. doi:10.1090/mcom/3201","ista":"Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 86(307), 2373–2397.","ieee":"M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial differential equations in the whole space,” Mathematics of Computation, vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017.","chicago":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation. American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201."},"quality_controlled":"1","year":"2017","abstract":[{"text":"Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable.","lang":"eng"}],"publist_id":"7144","date_created":"2018-12-11T11:47:40Z","publication":"Mathematics of Computation","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1508.05535","open_access":"1"}],"page":"2373 - 2397"},{"month":"08","date_published":"2017-08-04T00:00:00Z","_id":"6426","page":"28","status":"public","file":[{"checksum":"b48d42725182d7ca10107a118815f4cf","creator":"dernst","content_type":"application/pdf","access_level":"open_access","file_size":971347,"file_id":"6431","file_name":"main(1).pdf","relation":"main_file","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-13T08:14:44Z"}],"type":"technical_report","publisher":"IST Austria","abstract":[{"text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent asynchronous computation threads. We show that specifications and correctness proofs for asynchronous programs can be structured by introducing the fiction, for proof purposes, that intermediate, non-quiescent states of asynchronous operations can be ignored. Then, the task of specification becomes relatively simple and the task of verification can be naturally decomposed into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure of an asynchronous program, the atomic effect of non-atomic operations and the synchronous effect of asynchronous operations. This structuring of specifications and proofs corresponds to the introduction of multiple layers of stepwise refinement for asynchronous programs. We present the first proof rule, called synchronization, to reduce asynchronous invocations on a lower layer to synchronous invocations on a higher layer. We implemented our proof method in CIVL and evaluated it on a collection of benchmark programs.","lang":"eng"}],"date_created":"2019-05-13T08:15:55Z","oa":1,"citation":{"chicago":"Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. Synchronizing the Asynchronous. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2018-853-v2-2.","ieee":"T. A. Henzinger, B. Kragl, and S. Qadeer, Synchronizing the asynchronous. IST Austria, 2017.","ista":"Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST Austria, 28p.","ama":"Henzinger TA, Kragl B, Qadeer S. Synchronizing the Asynchronous. IST Austria; 2017. doi:10.15479/AT:IST-2018-853-v2-2","short":"T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST Austria, 2017.","mla":"Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria, 2017, doi:10.15479/AT:IST-2018-853-v2-2.","apa":"Henzinger, T. A., Kragl, B., & Qadeer, S. (2017). Synchronizing the asynchronous. IST Austria. https://doi.org/10.15479/AT:IST-2018-853-v2-2"},"year":"2017","has_accepted_license":"1","doi":"10.15479/AT:IST-2018-853-v2-2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"04","ddc":["000"],"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Kragl, Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","orcid":"0000-0001-7745-9117"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"}],"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"133"}]},"oa_version":"Published Version","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","file_date_updated":"2020-07-14T12:47:30Z","alternative_title":["IST Austria Technical Report"],"title":"Synchronizing the asynchronous","date_updated":"2025-04-15T08:11:53Z"},{"_id":"643","date_published":"2017-08-31T00:00:00Z","issue":"4","article_processing_charge":"No","publisher":"Chinese Physiological Society","pmid":1,"status":"public","external_id":{"isi":["000409566300002"],"pmid":["28847140"]},"department":[{"_id":"RySh"}],"language":[{"iso":"eng"}],"day":"31","ddc":["570"],"author":[{"last_name":"Sun","full_name":"Sun, Wuping","first_name":"Wuping"},{"first_name":"Ming-Zhu","full_name":"Zhai, Ming-Zhu","last_name":"Zhai","id":"34009CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhou","full_name":"Zhou, Qian","first_name":"Qian"},{"first_name":"Chengrui","full_name":"Qian, Chengrui","last_name":"Qian"},{"last_name":"Jiang","full_name":"Jiang, Changyu","first_name":"Changyu"}],"OA_type":"closed access","doi":"10.4077/CJP.2017.BAF469","scopus_import":"1","date_updated":"2025-09-11T07:19:13Z","title":"Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats","article_type":"original","oa_version":"None","volume":60,"month":"08","year":"2017","citation":{"ista":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 60(4), 207–214.","short":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology 60 (2017) 207–214.","apa":"Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469","mla":"Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology, vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:10.4077/CJP.2017.BAF469.","ama":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469","chicago":"Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469.","ieee":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp. 207–214, 2017."},"quality_controlled":"1","abstract":[{"lang":"eng","text":"It has been reported that nicotinamide-overload induces oxidative stress associated with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT) were also carried out in adult Sprague-Dawley rats treated with or without cumulative doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration significantly increased the plasma H2O2 levels associated with high insulin levels. Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration of nicotinic acid, another form of Vitamin B3, also significantly increased plasma insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic acid or nicotinamide impaired glucose metabolism. This study suggested that excess Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance."}],"publist_id":"7142","date_created":"2018-12-11T11:47:40Z","publication":"Chinese Journal of Physiology","type":"journal_article","page":"207 - 214","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"intvolume":" 60","publication_status":"published","publication_identifier":{"issn":["0304-4920"]}},{"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","intvolume":" 46","month":"06","page":"1087 - 1110","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.07327"}],"type":"journal_article","publication":"SIAM Journal on Computing","date_created":"2018-12-11T11:47:40Z","abstract":[{"text":"An instance of the valued constraint satisfaction problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P 6= NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in f0;1g corresponds to ordinary CSPs, where one deals only with the feasibility issue, and there is no optimization. This case is the subject of the algebraic CSP dichotomy conjecture predicting for which constraint languages CSPs are tractable (i.e., solvable in polynomial time) and for which they are NP-hard. The case when all allowed functions take only finite values corresponds to a finitevalued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Živný. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e., the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.","lang":"eng"}],"publist_id":"7138","year":"2017","citation":{"ieee":"V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” SIAM Journal on Computing, vol. 46, no. 3. SIAM, pp. 1087–1110, 2017.","chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2017. https://doi.org/10.1137/16M1091836.","apa":"Kolmogorov, V., Krokhin, A., & Rolinek, M. (2017). The complexity of general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16M1091836","short":"V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017) 1087–1110.","mla":"Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:10.1137/16M1091836.","ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. SIAM Journal on Computing. 2017;46(3):1087-1110. doi:10.1137/16M1091836","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued CSPs. SIAM Journal on Computing. 46(3), 1087–1110."},"quality_controlled":"1","doi":"10.1137/16M1091836","scopus_import":"1","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir"},{"first_name":"Andrei","full_name":"Krokhin, Andrei","last_name":"Krokhin"},{"first_name":"Michal","full_name":"Rolinek, Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"day":"29","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"1637","relation":"other"}]},"department":[{"_id":"VlKo"}],"volume":46,"oa_version":"Preprint","date_updated":"2025-09-23T13:45:56Z","title":"The complexity of general-valued CSPs","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"ec_funded":1,"arxiv":1,"date_published":"2017-06-29T00:00:00Z","_id":"644","external_id":{"arxiv":["1502.07327"],"isi":["000404774300010"]},"status":"public","publisher":"SIAM","article_processing_charge":"No","oa":1,"issue":"3"},{"volume":10426,"oa_version":"Submitted Version","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"ec_funded":1,"date_updated":"2025-09-11T07:18:04Z","title":"Value iteration for long run average reward in markov decision processes","day":"13","author":[{"full_name":"Ashok, Pranav","last_name":"Ashok","first_name":"Pranav"},{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw"},{"first_name":"Jan","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer"}],"doi":"10.1007/978-3-319-63387-9_10","scopus_import":"1","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000432196400010"],"arxiv":["1705.02326"]},"status":"public","oa":1,"article_processing_charge":"No","publisher":"Springer","arxiv":1,"_id":"645","date_published":"2017-07-13T00:00:00Z","publication_status":"published","publication_identifier":{"isbn":["978-331963386-2"]},"alternative_title":["LNCS"],"intvolume":" 10426","editor":[{"last_name":"Majumdar","full_name":"Majumdar, Rupak","first_name":"Rupak"},{"last_name":"Kunčak","full_name":"Kunčak, Viktor","first_name":"Viktor"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1705.02326","open_access":"1"}],"page":"201 - 221","citation":{"ieee":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, and T. Meggendorfer, “Value iteration for long run average reward in markov decision processes,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 201–221.","chicago":"Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_10.","mla":"Ashok, Pranav, et al. Value Iteration for Long Run Average Reward in Markov Decision Processes. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 201–21, doi:10.1007/978-3-319-63387-9_10.","short":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221.","apa":"Ashok, P., Chatterjee, K., Daca, P., Kretinsky, J., & Meggendorfer, T. (2017). Value iteration for long run average reward in markov decision processes. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 201–221). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_10","ama":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration for long run average reward in markov decision processes. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:201-221. doi:10.1007/978-3-319-63387-9_10","ista":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration for long run average reward in markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 10426, 201–221."},"year":"2017","quality_controlled":"1","publist_id":"7135","abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks."}],"date_created":"2018-12-11T11:47:41Z","month":"07","conference":{"end_date":"2017-07-28","name":"CAV: Computer Aided Verification","location":"Heidelberg, Germany","start_date":"2017-07-24"}},{"publisher":"Springer","oa":1,"article_processing_charge":"No","external_id":{"arxiv":["1703.03769"],"isi":["000432210900019"]},"status":"public","date_published":"2017-06-01T00:00:00Z","_id":"646","arxiv":1,"title":"A novel convex relaxation for non binary discrete tomography","date_updated":"2025-09-11T07:16:00Z","ec_funded":1,"project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"oa_version":"Submitted Version","volume":10302,"language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"scopus_import":"1","doi":"10.1007/978-3-319-58771-4_19","day":"01","author":[{"full_name":"Kuske, Jan","last_name":"Kuske","first_name":"Jan"},{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"first_name":"Stefanie","full_name":"Petra, Stefanie","last_name":"Petra"}],"abstract":[{"lang":"eng","text":"We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations."}],"publist_id":"7132","date_created":"2018-12-11T11:47:41Z","year":"2017","citation":{"ieee":"J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary discrete tomography,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246.","chicago":"Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_19.","short":"J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 235–246.","apa":"Kuske, J., Swoboda, P., & Petra, S. (2017). A novel convex relaxation for non binary discrete tomography. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_19","mla":"Kuske, Jan, et al. A Novel Convex Relaxation for Non Binary Discrete Tomography. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:10.1007/978-3-319-58771-4_19.","ama":"Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246. doi:10.1007/978-3-319-58771-4_19","ista":"Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 235–246."},"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1703.03769","open_access":"1"}],"page":"235 - 246","type":"conference","conference":{"end_date":"2017-06-08","name":"SSVM: Scale Space and Variational Methods in Computer Vision","location":"Kolding, Denmark","start_date":"2017-06-04"},"month":"06","intvolume":" 10302","alternative_title":["LNCS"],"publication_identifier":{"isbn":["978-331958770-7"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"editor":[{"last_name":"Lauze","full_name":"Lauze, François","first_name":"François"},{"first_name":"Yiqiu","full_name":"Dong, Yiqiu","last_name":"Dong"},{"first_name":"Anders","full_name":"Bjorholm Dahl, Anders","last_name":"Bjorholm Dahl"}]},{"publication_status":"published","publication_identifier":{"isbn":["978-331965764-6"]},"alternative_title":["LNCS"],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"831","type":"conference","page":"116 - 132","citation":{"ista":"Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 116–132.","ama":"Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid systems. In: Vol 10419. Springer; 2017:116-132. doi:10.1007/978-3-319-65765-3_7","mla":"Bogomolov, Sergiy, et al. Conic Abstractions for Hybrid Systems. Vol. 10419, Springer, 2017, pp. 116–32, doi:10.1007/978-3-319-65765-3_7.","short":"S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017, pp. 116–132.","apa":"Bogomolov, S., Giacobbe, M., Henzinger, T. A., & Kong, H. (2017). Conic abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_7","chicago":"Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_7.","ieee":"S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132."},"year":"2017","quality_controlled":"1","abstract":[{"lang":"eng","text":"Despite researchers’ efforts in the last couple of decades, reachability analysis is still a challenging problem even for linear hybrid systems. Among the existing approaches, the most practical ones are mainly based on bounded-time reachable set over-approximations. For the purpose of unbounded-time analysis, one important strategy is to abstract the original system and find an invariant for the abstraction. In this paper, we propose an approach to constructing a new kind of abstraction called conic abstraction for affine hybrid systems, and to computing reachable sets based on this abstraction. The essential feature of a conic abstraction is that it partitions the state space of a system into a set of convex polyhedral cones which is derived from a uniform conic partition of the derivative space. Such a set of polyhedral cones is able to cut all trajectories of the system into almost straight segments so that every segment of a reach pipe in a polyhedral cone tends to be straight as well, and hence can be over-approximated tightly by polyhedra using similar techniques as HyTech or PHAVer. In particular, for diagonalizable affine systems, our approach can guarantee to find an invariant for unbounded reachable sets, which is beyond the capability of bounded-time reachability analysis tools. We implemented the approach in a tool and experiments on benchmarks show that our approach is more powerful than SpaceEx and PHAVer in dealing with diagonalizable systems."}],"publist_id":"7129","date_created":"2018-12-11T11:47:41Z","month":"09","conference":{"start_date":"2017-09-05","name":"FORMATS: Formal Modelling and Analysis of Timed Systems","location":"Berlin, Germany","end_date":"2017-09-07"},"file_date_updated":"2020-07-14T12:47:31Z","oa_version":"Submitted Version","volume":"10419 ","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"date_updated":"2026-04-08T07:47:13Z","title":"Conic abstractions for hybrid systems","day":"01","ddc":["005"],"author":[{"first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov"},{"orcid":"0000-0001-8180-0904","first_name":"Mirco","full_name":"Giacobbe, Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","full_name":"Kong, Hui","last_name":"Kong","orcid":"0000-0002-3066-6941","first_name":"Hui"}],"has_accepted_license":"1","doi":"10.1007/978-3-319-65765-3_7","scopus_import":"1","department":[{"_id":"ToHe"}],"related_material":{"record":[{"status":"public","id":"6894","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:38Z","relation":"main_file","date_updated":"2020-07-14T12:47:31Z","file_name":"IST-2017-831-v1+1_main.pdf","file_id":"4956","file_size":3806864,"content_type":"application/pdf","access_level":"open_access","creator":"system","checksum":"faf546914ba29bcf9974ee36b6b16750"}],"status":"public","external_id":{"isi":["000611678300007"]},"oa":1,"article_processing_charge":"No","publisher":"Springer","corr_author":"1","_id":"647","date_published":"2017-09-01T00:00:00Z"},{"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","editor":[{"last_name":"Jäger","full_name":"Jäger, Gerhard","first_name":"Gerhard"},{"full_name":"Steila, Silvia","last_name":"Steila","first_name":"Silvia"}],"intvolume":" 10185","alternative_title":["LNCS"],"publication_status":"published","publication_identifier":{"isbn":["978-331955910-0"]},"conference":{"end_date":"2017-04-22","name":"TAMC: Theory and Applications of Models of Computation","location":"Bern, Switzerland","start_date":"2017-04-20"},"month":"04","date_created":"2018-12-11T11:47:42Z","publist_id":"7125","abstract":[{"lang":"eng","text":"Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) differs from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method."}],"quality_controlled":"1","citation":{"ieee":"M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 600–613.","chicago":"Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_43.","ama":"Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:600-613. doi:10.1007/978-3-319-55911-7_43","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.","mla":"Skórski, Maciej. On the Complexity of Breaking Pseudoentropy. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:10.1007/978-3-319-55911-7_43.","apa":"Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_43","ista":"Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 600–613."},"year":"2017","page":"600 - 613","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/1186.pdf"}],"type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"doi":"10.1007/978-3-319-55911-7_43","scopus_import":"1","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","full_name":"Skórski, Maciej","first_name":"Maciej"}],"day":"01","title":"On the complexity of breaking pseudoentropy","date_updated":"2025-09-11T07:14:42Z","oa_version":"Submitted Version","volume":10185,"date_published":"2017-04-01T00:00:00Z","_id":"648","corr_author":"1","publisher":"Springer","article_processing_charge":"No","oa":1,"external_id":{"isi":["000425175500043"]},"status":"public"},{"status":"public","publisher":"Springer","article_processing_charge":"No","series_title":"Lecture Notes in Mathematics","corr_author":"1","date_published":"2017-10-05T00:00:00Z","_id":"649","volume":2184,"oa_version":"None","title":"Entropic Ricci curvature for discrete spaces","date_updated":"2026-04-16T08:59:01Z","doi":"10.1007/978-3-319-58002-9_5","scopus_import":"1","author":[{"first_name":"Jan","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"day":"05","language":[{"iso":"eng"}],"department":[{"_id":"JaMa"}],"page":"159 - 174","publication":"Modern Approaches to Discrete Curvature","type":"book_chapter","date_created":"2018-12-11T11:47:42Z","publist_id":"7123","abstract":[{"lang":"eng","text":"We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani."}],"year":"2017","quality_controlled":"1","citation":{"ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.","ama":"Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. Modern Approaches to Discrete Curvature. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:10.1007/978-3-319-58002-9_5","apa":"Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman & P. Romon (Eds.), Modern Approaches to Discrete Curvature (Vol. 2184, pp. 159–174). Springer. https://doi.org/10.1007/978-3-319-58002-9_5","mla":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:10.1007/978-3-319-58002-9_5.","short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174.","chicago":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. https://doi.org/10.1007/978-3-319-58002-9_5.","ieee":"J. Maas, “Entropic Ricci curvature for discrete spaces,” in Modern Approaches to Discrete Curvature, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174."},"month":"10","publication_status":"published","publication_identifier":{"isbn":["9783319580012"],"eisbn":["9783319580029"]},"intvolume":" 2184","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","editor":[{"first_name":"Laurent","last_name":"Najman","full_name":"Najman, Laurent"},{"full_name":"Romon, Pascal","last_name":"Romon","first_name":"Pascal"}]},{"scopus_import":"1","doi":"10.1007/978-3-319-55911-7_42","day":"01","author":[{"first_name":"Maciej","full_name":"Skórski, Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"oa_version":"Submitted Version","volume":10185,"title":"A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds","date_updated":"2026-04-16T09:59:38Z","corr_author":"1","date_published":"2017-01-01T00:00:00Z","_id":"650","external_id":{"isi":["000425175500042"]},"status":"public","publisher":"Springer","oa":1,"article_processing_charge":"No","isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","editor":[{"first_name":"Gerhard","full_name":"Jäger, Gerhard","last_name":"Jäger"},{"full_name":"Steila, Silvia","last_name":"Steila","first_name":"Silvia"}],"publication_identifier":{"issn":["0302-9743"]},"publication_status":"published","alternative_title":["LNCS"],"intvolume":" 10185","month":"01","conference":{"start_date":"2017-04-20","name":"TAMC: Theory and Applications of Models of Computation","location":"Bern, Switzerland","end_date":"2017-04-22"},"main_file_link":[{"url":"https://eprint.iacr.org/2016/965.pdf","open_access":"1"}],"page":"586 - 599","type":"conference","abstract":[{"lang":"eng","text":"In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy."}],"publist_id":"7119","date_created":"2018-12-11T11:47:42Z","year":"2017","citation":{"ieee":"M. Skórski, “A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 586–599.","chicago":"Skórski, Maciej. “A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds.” edited by Gerhard Jäger and Silvia Steila, 10185:586–99. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_42.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599.","apa":"Skórski, M. (2017). A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 586–599). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_42","mla":"Skórski, Maciej. A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 586–99, doi:10.1007/978-3-319-55911-7_42.","ama":"Skórski M. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:586-599. doi:10.1007/978-3-319-55911-7_42","ista":"Skórski M. 2017. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 586–599."},"quality_controlled":"1"}]