[{"year":"2017","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"9855"}]},"author":[{"full_name":"Chalk, Matthew J","first_name":"Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436"},{"full_name":"Masset, Paul","last_name":"Masset","first_name":"Paul"},{"full_name":"Gutkin, Boris","first_name":"Boris","last_name":"Gutkin"},{"full_name":"Denève, Sophie","last_name":"Denève","first_name":"Sophie"}],"volume":13,"date_created":"2018-12-11T11:47:53Z","date_updated":"2023-02-23T14:10:54Z","article_number":"e1005582","publist_id":"7035","file_date_updated":"2020-07-14T12:47:40Z","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":"10.1371/journal.pcbi.1005582","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553734X"]},"month":"06","_id":"680","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","ddc":["571"],"status":"public","title":"Sensory noise predicts divisive reshaping of receptive fields","pubrep_id":"898","file":[{"file_name":"IST-2017-898-v1+1_journal.pcbi.1005582.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":14555676,"file_id":"4645","relation":"main_file","date_created":"2018-12-12T10:07:47Z","date_updated":"2020-07-14T12:47:40Z","checksum":"796a1026076af6f4405a47d985bc7b68"}],"oa_version":"Published Version","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics."}],"citation":{"chicago":"Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.","mla":"Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational Biology, vol. 13, no. 6, e1005582, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582.","short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017).","ista":"Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582.","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts divisive reshaping of receptive fields,” PLoS Computational Biology, vol. 13, no. 6. Public Library of Science, 2017.","apa":"Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582","ama":"Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 2017;13(6). doi:10.1371/journal.pcbi.1005582"},"publication":"PLoS Computational Biology","date_published":"2017-06-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"type":"research_data_reference","abstract":[{"text":"Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations.","lang":"eng"}],"year":"2017","_id":"9851","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"status":"public","title":"Heuristic prediction for multiple stresses","related_material":{"record":[{"id":"696","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Lukacisinova, Marta","last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"}],"oa_version":"Published Version","date_created":"2021-08-09T14:08:14Z","date_updated":"2023-02-23T12:55:39Z","article_processing_charge":"No","day":"18","month":"07","citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.","ama":"Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","mla":"Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003."},"date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s003"},{"date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s004","citation":{"short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","mla":"Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004.","ama":"Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004."},"month":"07","day":"18","article_processing_charge":"No","author":[{"full_name":"Lukacisinova, Marta","last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"}],"related_material":{"record":[{"id":"696","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-09T14:11:40Z","date_updated":"2023-02-23T12:55:39Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9852","year":"2017","status":"public","title":"Resistance frequencies for different combination strategies","publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"We show how different combination strategies affect the fraction of individuals that are multi-resistant."}],"type":"research_data_reference"},{"oa_version":"Published Version","date_created":"2021-08-10T07:05:10Z","date_updated":"2023-02-23T12:52:17Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"680"}]},"author":[{"full_name":"Chalk, Matthew J","last_name":"Chalk","first_name":"Matthew J","orcid":"0000-0001-7782-4436","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Masset, Paul","first_name":"Paul","last_name":"Masset"},{"full_name":"Gutkin, Boris","last_name":"Gutkin","first_name":"Boris"},{"full_name":"Denève, Sophie","last_name":"Denève","first_name":"Sophie"}],"publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"title":"Supplementary appendix","status":"public","year":"2017","_id":"9855","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Includes derivation of optimal estimation algorithm, generalisation to non-poisson noise statistics, correlated input noise, and implementation of in a multi-layer neural network.","lang":"eng"}],"type":"research_data_reference","date_published":"2017-06-01T00:00:00Z","doi":"10.1371/journal.pcbi.1005582.s001","citation":{"short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).","mla":"Chalk, Matthew J., et al. Supplementary Appendix. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582.s001.","chicago":"Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001.","ama":"Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017.","apa":"Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Supplementary appendix. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582.s001","ista":"Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public Library of Science, 10.1371/journal.pcbi.1005582.s001."},"article_processing_charge":"No","month":"06","day":"01"},{"scopus_import":1,"day":"10","month":"07","citation":{"chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.","mla":"Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379.","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379.","apa":"Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis (pp. 376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa Barbara, CA, United States, 2017, pp. 376–379.","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ACM; 2017:376-379. doi:10.1145/3092703.3098225"},"publication":"Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis","page":"376 - 379 ","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1145/3092703.3098225","date_published":"2017-07-10T00:00:00Z","conference":{"location":"Santa Barbara, CA, United States","start_date":"2017-07-10","end_date":"2017-07-14","name":"ISSTA: International Symposium on Software Testing and Analysis"},"language":[{"iso":"eng"}],"type":"conference","publist_id":"6478","abstract":[{"text":"Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ ","lang":"eng"}],"year":"2017","_id":"941","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","department":[{"_id":"ToHe"}],"publication_status":"published","title":"JFIX: Semantics-based repair of Java programs via symbolic PathFinder","status":"public","author":[{"first_name":"Xuan","last_name":"Le","full_name":"Le, Xuan"},{"full_name":"Chu, Duc Hiep","id":"3598E630-F248-11E8-B48F-1D18A9856A87","last_name":"Chu","first_name":"Duc Hiep"},{"full_name":"Lo, David","first_name":"David","last_name":"Lo"},{"first_name":"Claire","last_name":"Le Goues","full_name":"Le Goues, Claire"},{"last_name":"Visser","first_name":"Willem","full_name":"Visser, Willem"}],"oa_version":"None","date_updated":"2021-01-12T08:22:05Z","date_created":"2018-12-11T11:49:19Z"},{"day":"09","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2017-05-09T00:00:00Z","publication":"Genome Biology","citation":{"chicago":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.","short":"D. Zilberman, Genome Biology 18 (2017).","mla":"Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature, 2017, doi:10.1186/s13059-017-1230-2.","ieee":"D. Zilberman, “An evolutionary case for functional gene body methylation in plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.","apa":"Zilberman, D. (2017). An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2","ista":"Zilberman D. 2017. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 18(1), 87.","ama":"Zilberman D. An evolutionary case for functional gene body methylation in plants and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2"},"abstract":[{"lang":"eng","text":"Methylation in the bodies of active genes is common in animals and vascular plants. Evolutionary patterns indicate homeostatic functions for this type of methylation."}],"issue":"1","type":"journal_article","file":[{"file_id":"9507","relation":"main_file","date_created":"2021-06-07T12:31:36Z","date_updated":"2021-06-07T12:31:36Z","success":1,"checksum":"5a455ad914e7d225b1baa4ab07fd925e","file_name":"2017_GenomeBiology_Zilberman.pdf","access_level":"open_access","creator":"asandaue","file_size":278183,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9506","status":"public","title":"An evolutionary case for functional gene body methylation in plants and animals","ddc":["570"],"intvolume":" 18","month":"05","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"doi":"10.1186/s13059-017-1230-2","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"},"external_id":{"pmid":["28486944"]},"oa":1,"quality_controlled":"1","file_date_updated":"2021-06-07T12:31:36Z","extern":"1","article_number":"87","author":[{"full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"date_created":"2021-06-07T12:27:39Z","date_updated":"2021-12-14T07:55:02Z","volume":18,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"DaZi"}],"publisher":"Springer Nature"},{"day":"15","scopus_import":1,"series_title":"Synthetic Protein Switches","date_published":"2017-05-15T00:00:00Z","citation":{"mla":"Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.","short":"J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 89–99.","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.","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.","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","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."},"publication":"Synthetic Protein Switches","page":"89 - 99","abstract":[{"lang":"eng","text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors."}],"type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"958","intvolume":" 1596","title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","status":"public","publication_identifier":{"issn":["10643745"]},"month":"05","doi":"10.1007/978-1-4939-6940-1_6","language":[{"iso":"eng"}],"quality_controlled":"1","publist_id":"6450","author":[{"full_name":"Mitchell, Joshua","last_name":"Mitchell","first_name":"Joshua"},{"full_name":"Zhang, William","first_name":"William","last_name":"Zhang"},{"full_name":"Herde, Michel","last_name":"Herde","first_name":"Michel"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"}],"volume":1596,"date_updated":"2021-01-12T08:22:13Z","date_created":"2018-12-11T11:49:24Z","year":"2017","publisher":"Springer","editor":[{"first_name":"Viktor","last_name":"Stein","full_name":"Stein, Viktor"}],"department":[{"_id":"HaJa"}],"publication_status":"published"},{"date_created":"2021-07-23T09:39:34Z","date_updated":"2022-08-25T13:34:55Z","oa_version":"Published Version","author":[{"first_name":"Paul","last_name":"Riccio","full_name":"Riccio, Paul"},{"full_name":"Cebrián, Christina","first_name":"Christina","last_name":"Cebrián"},{"full_name":"Zong, Hui","last_name":"Zong","first_name":"Hui"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon","last_name":"Hippenmeyer"},{"full_name":"Costantini, Frank","first_name":"Frank","last_name":"Costantini"}],"related_material":{"record":[{"status":"deleted","relation":"used_in_publication","id":"9702"}]},"status":"public","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","publisher":"Dryad","department":[{"_id":"SiHi"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9707","year":"2017","abstract":[{"lang":"eng","text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis."}],"type":"research_data_reference","doi":"10.5061/dryad.pk16b","date_published":"2017-01-14T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.pk16b","open_access":"1"}],"citation":{"ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:10.5061/dryad.pk16b","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.","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","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).","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,"month":"01","day":"14","article_processing_charge":"No"},{"citation":{"short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","mla":"Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s018.","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures and Tables.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s018.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:10.1371/journal.pgen.1007122.s018","ieee":"N. Nikolic et al., “Source data for figures and tables.” Public Library of Science, 2017.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s018","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science, 10.1371/journal.pgen.1007122.s018."},"date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122.s018","article_processing_charge":"No","month":"12","day":"18","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","status":"public","title":"Source data for figures and tables","year":"2017","_id":"9844","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2021-08-09T13:27:16Z","date_updated":"2023-02-23T12:25:04Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"541"}]},"author":[{"orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","first_name":"Nela","full_name":"Nikolic, Nela"},{"full_name":"Schreiber, Frank","first_name":"Frank","last_name":"Schreiber"},{"last_name":"Dal Co","first_name":"Alma","full_name":"Dal Co, Alma"},{"last_name":"Kiviet","first_name":"Daniel","full_name":"Kiviet, Daniel"},{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"first_name":"Sten","last_name":"Littmann","full_name":"Littmann, Sten"},{"first_name":"Marcel","last_name":"Kuypers","full_name":"Kuypers, Marcel"},{"last_name":"Ackermann","first_name":"Martin","full_name":"Ackermann, Martin"}],"type":"research_data_reference"},{"conference":{"end_date":"2017-03-03","location":"Grundlsee, Austria","start_date":"2017-03-01","name":"AHPC: Austrian HPC Meeting"},"date_published":"2017-03-03T00:00:00Z","language":[{"iso":"eng"}],"publication":"AHPC17 – Austrian HPC Meeting 2017","citation":{"short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","chicago":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In AHPC17 – Austrian HPC Meeting 2017, 28. FSP Scientific Computing, 2017.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: AHPC17 – Austrian HPC Meeting 2017. FSP Scientific Computing; 2017:28.","ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in AHPC17 – Austrian HPC Meeting 2017, Grundlsee, Austria, 2017, p. 28.","apa":"Schlögl, A., & Kiss, J. (2017). Scientific Computing at IST Austria. In AHPC17 – Austrian HPC Meeting 2017 (p. 28). Grundlsee, Austria: FSP Scientific Computing.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf"}],"page":"28","month":"03","day":"03","has_accepted_license":"1","article_processing_charge":"No","author":[{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"full_name":"Kiss, Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss","first_name":"Janos"}],"date_created":"2023-05-05T12:58:53Z","date_updated":"2023-05-16T07:22:23Z","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12969","checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","success":1,"date_created":"2023-05-16T07:20:50Z","date_updated":"2023-05-16T07:20:50Z","access_level":"open_access","file_name":"2017_AHPC_Schloegl.pdf","file_size":1005486,"content_type":"application/pdf","creator":"dernst"}],"_id":"12905","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","ddc":["000"],"status":"public","publication_status":"published","title":"Scientific Computing at IST Austria","publisher":"FSP Scientific Computing","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-05-16T07:20:50Z","type":"conference_abstract"},{"oa":1,"external_id":{"arxiv":["1701.05738"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1701.05738","open_access":"1"}],"quality_controlled":"1","doi":"10.1007/978-3-662-54577-5_26","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2017-04-29","location":"Uppsala, Sweden","start_date":"2017-04-22"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783662545775"],"isbn":["9783662545768"],"eissn":["1611-3349"]},"month":"03","acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","year":"2017","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"full_name":"Waldmann, Clara","last_name":"Waldmann","first_name":"Clara"},{"last_name":"Weininger","first_name":"Maximilian","full_name":"Weininger, Maximilian"}],"volume":10205,"date_updated":"2023-06-21T13:29:46Z","date_created":"2023-06-21T13:21:14Z","citation":{"ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 10205. Springer; 2017:443-460. doi:10.1007/978-3-662-54577-5_26","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., & Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_26","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 10205, Springer, 2017, pp. 443–60, doi:10.1007/978-3-662-54577-5_26.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In Tools and Algorithms for the Construction and Analysis of Systems, 10205:443–60. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_26."},"publication":"Tools and Algorithms for the Construction and Analysis of Systems","page":"443-460","date_published":"2017-03-31T00:00:00Z","article_processing_charge":"No","day":"31","_id":"13160","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10205","status":"public","title":"Index appearance record for transforming Rabin automata into parity automata","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae."}]},{"month":"09","publication_identifier":{"issn":["1868-8969"]},"conference":{"start_date":"2017-09-05","location":"Berlin, Germany","end_date":"2017-09-07","name":"CONCUR: Concurrency Theory"},"doi":"10.4230/LIPIcs.CONCUR.2017.21","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"},"external_id":{"arxiv":["1705.01433"]},"oa":1,"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"file_date_updated":"2020-07-14T12:48:16Z","publist_id":"6466","article_number":"17","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","first_name":"Guy"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Ventsislav K","last_name":"Chonev","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K"}],"related_material":{"record":[{"id":"6752","relation":"later_version","status":"public"}]},"date_created":"2018-12-11T11:49:22Z","date_updated":"2023-08-29T07:02:13Z","volume":85,"year":"2017","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","citation":{"chicago":"Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21.","mla":"Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21.","short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.","apa":"Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21","ieee":"G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,” presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.","ama":"Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21"},"abstract":[{"text":"Two-player games on graphs are widely studied in formal methods as they model the interaction between a system and its environment. The game is played by moving a token throughout a graph to produce an infinite path. There are several common modes to determine how the players move the token through the graph; e.g., in turn-based games the players alternate turns in moving the token. We study the bidding mode of moving the token, which, to the best of our knowledge, has never been studied in infinite-duration games. Both players have separate budgets, which sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously, and a bid is legal if it does not exceed the available budget. The winner of the bidding pays his bid to the other player and moves the token. For reachability objectives, repeated bidding games have been studied and are called Richman games. There, a central question is the existence and computation of threshold budgets; namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity games and mean-payoff games. We show the existence of threshold budgets in these games, and reduce the problem of finding them to Richman games. We also determine the strategy-complexity of an optimal strategy. Our most interesting result shows that memoryless strategies suffice for mean-payoff bidding games. \r\n","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"844","file":[{"file_name":"IST-2017-844-v1+1_concur-cr.pdf","access_level":"open_access","content_type":"application/pdf","file_size":335170,"creator":"system","relation":"main_file","file_id":"5318","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:18:00Z","checksum":"6d5cccf755207b91ccbef95d8275b013"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"950","ddc":["000"],"status":"public","title":"Infinite-duration bidding games","intvolume":" 85"},{"file":[{"checksum":"24fdde981cc513352a78dcf9b0660ae9","date_updated":"2020-07-14T12:47:41Z","date_created":"2018-12-12T10:17:12Z","file_id":"5265","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":710007,"access_level":"open_access","file_name":"IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf"}],"oa_version":"Published Version","pubrep_id":"896","title":"A proof of the orbit conjecture for flipping edge labelled triangulations","status":"public","ddc":["514","516"],"intvolume":" 77","_id":"683","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2017-06-01T00:00:00Z","citation":{"chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.49.","short":"A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Lubiw, Anna, et al. A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations. Vol. 77, 49, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.SoCG.2017.49.","apa":"Lubiw, A., Masárová, Z., & Wagner, U. (2017). A proof of the orbit conjecture for flipping edge labelled triangulations (Vol. 77). Presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.49","ieee":"A. Lubiw, Z. Masárová, and U. Wagner, “A proof of the orbit conjecture for flipping edge labelled triangulations,” presented at the SoCG: Symposium on Computational Geometry, Brisbane, Australia, 2017, vol. 77.","ista":"Lubiw A, Masárová Z, Wagner U. 2017. A proof of the orbit conjecture for flipping edge labelled triangulations. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 77, 49.","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.SoCG.2017.49"},"day":"01","has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T11:47:54Z","date_updated":"2023-09-05T15:01:43Z","volume":77,"author":[{"full_name":"Lubiw, Anna","last_name":"Lubiw","first_name":"Anna"},{"full_name":"Masárová, Zuzana","orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","first_name":"Zuzana"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"5986"}]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"year":"2017","file_date_updated":"2020-07-14T12:47:41Z","publist_id":"7033","article_number":"49","language":[{"iso":"eng"}],"conference":{"end_date":"2017-07-07","start_date":"2017-07-04","location":"Brisbane, Australia","name":"SoCG: Symposium on Computational Geometry"},"doi":"10.4230/LIPIcs.SoCG.2017.49","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"},{"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results."}],"status":"public","title":"Statistical and logical methods for property checking","ddc":["004","005"],"_id":"1155","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":1028586,"access_level":"open_access","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","checksum":"1406a681cb737508234fde34766be2c2","date_created":"2018-12-12T10:11:26Z","date_updated":"2020-07-14T12:44:34Z","file_id":"4880","relation":"main_file"}],"pubrep_id":"730","has_accepted_license":"1","article_processing_charge":"No","day":"02","page":"163","citation":{"chicago":"Daca, Przemyslaw. “Statistical and Logical Methods for Property Checking.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:TH_730.","mla":"Daca, Przemyslaw. Statistical and Logical Methods for Property Checking. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730.","short":"P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017.","ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","apa":"Daca, P. (2017). Statistical and logical methods for property checking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_730","ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730"},"date_published":"2017-01-02T00:00:00Z","ec_funded":1,"publist_id":"6203","file_date_updated":"2020-07-14T12:44:34Z","department":[{"_id":"ToHe"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":" First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ","year":"2017","date_updated":"2023-09-07T11:58:34Z","date_created":"2018-12-11T11:50:27Z","related_material":{"record":[{"id":"1093","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1230"},{"relation":"part_of_dissertation","status":"public","id":"1234"},{"relation":"part_of_dissertation","status":"public","id":"1391"},{"id":"1501","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"1502"},{"id":"2063","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"2167"}]},"author":[{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"month":"01","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:TH_730"},{"year":"2017","_id":"6291","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Bacterial herd and social immunity to phages","publication_status":"published","status":"public","ddc":["570"],"author":[{"orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","first_name":"Pavel","full_name":"Payne, Pavel"}],"oa_version":"Published Version","file":[{"checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","date_created":"2019-04-09T15:15:32Z","date_updated":"2020-07-14T12:47:27Z","relation":"main_file","file_id":"6292","file_size":3025175,"content_type":"application/pdf","creator":"dernst","access_level":"closed","file_name":"thesis_pavel_payne_final_w_signature_page.pdf"},{"relation":"main_file","file_id":"9187","checksum":"af531e921a7f64a9e0af4cd8783b2226","success":1,"date_created":"2021-02-22T13:45:59Z","date_updated":"2021-02-22T13:45:59Z","access_level":"open_access","file_name":"2017_Payne_Thesis.pdf","content_type":"application/pdf","file_size":3111536,"creator":"dernst"}],"date_created":"2019-04-09T15:16:45Z","date_updated":"2023-09-07T12:00:00Z","type":"dissertation","alternative_title":["ISTA Thesis"],"file_date_updated":"2021-02-22T13:45:59Z","abstract":[{"lang":"eng","text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population."}],"citation":{"ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","apa":"Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017."},"oa":1,"page":"83","date_published":"2017-02-01T00:00:00Z","language":[{"iso":"eng"}],"supervisor":[{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","has_accepted_license":"1","article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"01","month":"02"},{"article_number":"20170646","publist_id":"7253","year":"2017","acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","pmid":1,"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"The Royal Society","author":[{"last_name":"Pleska","first_name":"Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9847"},{"id":"202","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-09-07T11:59:32Z","date_created":"2018-12-11T11:47:11Z","volume":13,"month":"12","publication_identifier":{"issn":["1744-9561"]},"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2017.0646","open_access":"1"}],"oa":1,"external_id":{"pmid":["29237814"]},"quality_controlled":"1","project":[{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011","_id":"251BCBEC-B435-11E9-9278-68D0E5697425"},{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"doi":"10.1098/rsbl.2017.0646","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape."}],"issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"561","status":"public","title":"Effects of mutations in phage restriction sites during escape from restriction–modification","intvolume":" 13","oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Biology Letters","citation":{"ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646","apa":"Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0646","ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646.","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646."},"article_type":"original","date_published":"2017-12-01T00:00:00Z"},{"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,"doi":"10.15479/AT:ISTA:th_862","degree_awarded":"PhD","supervisor":[{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["2663-337X"]},"year":"2017","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin"}],"related_material":{"record":[{"id":"2001","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"666"}]},"date_updated":"2023-09-07T12:00:26Z","date_created":"2018-12-11T11:48:40Z","file_date_updated":"2020-07-14T12:48:09Z","publist_id":"6831","citation":{"ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","apa":"Mitosch, K. (2017). Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017.","mla":"Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862."},"page":"113","date_published":"2017-09-27T00:00:00Z","day":"27","has_accepted_license":"1","article_processing_charge":"No","_id":"818","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","ddc":["571","579"],"status":"public","pubrep_id":"862","oa_version":"Published Version","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":6331071,"creator":"dernst","file_name":"Thesis_KarinMitosch.docx","access_level":"closed","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T08:48:51Z","checksum":"da3993c5f90f59a8e8623cc31ad501dd","relation":"source_file","file_id":"6210"},{"relation":"main_file","file_id":"6211","date_created":"2019-04-05T08:48:51Z","date_updated":"2020-07-14T12:48:09Z","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","file_name":"Thesis_KarinMitosch.pdf","access_level":"open_access","content_type":"application/pdf","file_size":9289852,"creator":"dernst"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. ","lang":"eng"}]},{"type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"intvolume":" 4","status":"public","title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","ddc":["576","610"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"666","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5041","checksum":"04ff20011c3d9a601c514aa999a5fe1a","date_updated":"2020-07-14T12:47:35Z","date_created":"2018-12-12T10:13:54Z","access_level":"open_access","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","file_size":2438660,"content_type":"application/pdf","creator":"system"}],"pubrep_id":"901","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"26","page":"393 - 403","citation":{"ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” Cell Systems, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","apa":"Mitosch, K., Rieckh, G., & Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2017.03.001","ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 2017;4(4):393-403. doi:10.1016/j.cels.2017.03.001","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems. Cell Press, 2017. https://doi.org/10.1016/j.cels.2017.03.001.","mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” Cell Systems, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:10.1016/j.cels.2017.03.001.","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403."},"publication":"Cell Systems","date_published":"2017-04-26T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publist_id":"7061","ec_funded":1,"file_date_updated":"2020-07-14T12:47:35Z","publisher":"Cell Press","department":[{"_id":"ToBo"},{"_id":"GaTk"}],"publication_status":"published","year":"2017","volume":4,"date_created":"2018-12-11T11:47:48Z","date_updated":"2023-09-07T12:00:25Z","related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"author":[{"full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch"},{"full_name":"Rieckh, Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","last_name":"Rieckh","first_name":"Georg"},{"last_name":"Bollenbach","first_name":"Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Tobias"}],"publication_identifier":{"issn":["24054712"]},"month":"04","project":[{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507"},{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"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"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.cels.2017.03.001"},{"date_published":"2017-08-09T00:00:00Z","page":"418","citation":{"chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","mla":"Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854.","apa":"Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:10.15479/AT:ISTA:th_854"},"day":"09","article_processing_charge":"No","has_accepted_license":"1","file":[{"file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4103115,"creator":"system","relation":"main_file","file_id":"4900","date_created":"2018-12-12T10:11:44Z","date_updated":"2020-07-14T12:48:10Z","checksum":"3a3ec003f6ee73f41f82a544d63dfc77"},{"content_type":"application/zip","file_size":14744374,"creator":"dernst","file_name":"2017_thesis_Pavlogiannis.zip","access_level":"closed","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T07:59:31Z","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","relation":"source_file","file_id":"6201"}],"oa_version":"Published Version","pubrep_id":"854","ddc":["000"],"title":"Algorithmic advances in program analysis and their applications","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"821","abstract":[{"lang":"eng","text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_854","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"month":"08","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:48:41Z","date_updated":"2023-09-07T12:01:59Z","author":[{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"related_material":{"record":[{"id":"1071","relation":"part_of_dissertation","status":"public"},{"id":"1437","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1602"},{"id":"1604","status":"public","relation":"part_of_dissertation"},{"id":"1607","status":"public","relation":"part_of_dissertation"},{"id":"1714","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Institute of Science and Technology Austria","year":"2017","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna, Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","file_date_updated":"2020-07-14T12:48:10Z","publist_id":"6828","ec_funded":1},{"publist_id":"6829","ec_funded":1,"file_date_updated":"2020-07-14T12:48:10Z","department":[{"_id":"JoBo"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","year":"2017","date_created":"2018-12-11T11:48:41Z","date_updated":"2023-09-07T12:01:21Z","author":[{"full_name":"Jesse, Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","last_name":"Jesse","first_name":"Fabienne"}],"publication_identifier":{"issn":["2663-337X"]},"month":"08","project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"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"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:th_857","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background."}],"status":"public","ddc":["576","577","579"],"title":"The lac operon in the wild","_id":"820","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_size":3417773,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","access_level":"open_access","date_created":"2018-12-12T10:17:00Z","date_updated":"2020-07-14T12:48:10Z","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","relation":"main_file","file_id":"5252"},{"date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T08:51:59Z","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_id":"6212","relation":"source_file","creator":"dernst","file_size":215899,"content_type":"application/x-tex","file_name":"2017_thesis_Jesse_source.tex","access_level":"closed"}],"pubrep_id":"857","has_accepted_license":"1","article_processing_charge":"No","day":"25","page":"87","citation":{"ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","apa":"Jesse, F. (2017). The lac operon in the wild. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857","ama":"Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857","chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857.","mla":"Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017."},"date_published":"2017-08-25T00:00:00Z"},{"month":"06","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_828","oa":1,"file_date_updated":"2020-07-14T12:48:12Z","publist_id":"6810","date_updated":"2023-09-07T12:02:28Z","date_created":"2018-12-11T11:48:46Z","author":[{"full_name":"Rybar, Michal","last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"2082","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"6196"}]},"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrPi"}],"year":"2017","day":"26","article_processing_charge":"No","has_accepted_license":"1","date_published":"2017-06-26T00:00:00Z","page":"86","citation":{"chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_828.","mla":"Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","apa":"Rybar, M. (2017). (The exact security of) Message authentication codes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_828","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:10.15479/AT:ISTA:th_828"},"abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k > 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. "}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"file_id":"4799","relation":"main_file","checksum":"ff8639ec4bded6186f44c7bd3ee26804","date_created":"2018-12-12T10:10:13Z","date_updated":"2020-07-14T12:48:12Z","access_level":"open_access","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","creator":"system","content_type":"application/pdf","file_size":847400},{"date_created":"2019-04-05T08:24:11Z","date_updated":"2020-07-14T12:48:12Z","checksum":"3462101745ce8ad199c2d0f75dae4a7e","relation":"source_file","file_id":"6202","content_type":"application/zip","file_size":26054879,"creator":"dernst","file_name":"2017_Thesis_Rybar_source.zip","access_level":"closed"}],"pubrep_id":"828","ddc":["000"],"status":"public","title":"(The exact security of) Message authentication codes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"838"},{"date_published":"2017-02-03T00:00:00Z","publication":"IACR Transactions on Symmetric Cryptology","citation":{"short":"P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 145–161.","mla":"Gazi, Peter, et al. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2, Ruhr University Bochum, 2017, pp. 145–61, doi:10.13154/TOSC.V2016.I2.145-161.","chicago":"Gazi, Peter, Krzysztof Z Pietrzak, and Michal Rybar. “The Exact Security of PMAC.” IACR Transactions on Symmetric Cryptology. Ruhr University Bochum, 2017. https://doi.org/10.13154/TOSC.V2016.I2.145-161.","ama":"Gazi P, Pietrzak KZ, Rybar M. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2017;2016(2):145-161. doi:10.13154/TOSC.V2016.I2.145-161","ieee":"P. Gazi, K. Z. Pietrzak, and M. Rybar, “The exact security of PMAC,” IACR Transactions on Symmetric Cryptology, vol. 2016, no. 2. Ruhr University Bochum, pp. 145–161, 2017.","apa":"Gazi, P., Pietrzak, K. Z., & Rybar, M. (2017). The exact security of PMAC. IACR Transactions on Symmetric Cryptology. Ruhr University Bochum. https://doi.org/10.13154/TOSC.V2016.I2.145-161","ista":"Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 145–161."},"page":"145-161","day":"03","has_accepted_license":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":597335,"access_level":"open_access","file_name":"2017_IACR_Gazi.pdf","checksum":"f23161d685dd957ae8d7274132999684","date_updated":"2020-07-14T12:47:24Z","date_created":"2019-04-04T13:53:58Z","file_id":"6197","relation":"main_file"}],"_id":"6196","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"The exact security of PMAC","status":"public","ddc":["000"],"intvolume":" 2016","abstract":[{"lang":"eng","text":"PMAC is a simple and parallel block-cipher mode of operation, which was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a (pseudo)random permutation over n-bit strings, PMAC constitutes a provably secure variable input-length (pseudo)random function. For adversaries making q queries, each of length at most l (in n-bit blocks), and of total length σ ≤ ql, the original paper proves an upper bound on the distinguishing advantage of Ο(σ2/2n), while the currently best bound is Ο (qσ/2n).In this work we show that this bound is tight by giving an attack with advantage Ω (q2l/2n). In the PMAC construction one initially XORs a mask to every message block, where the mask for the ith block is computed as τi := γi·L, where L is a (secret) random value, and γi is the i-th codeword of the Gray code. Our attack applies more generally to any sequence of γi’s which contains a large coset of a subgroup of GF(2n). We then investigate if the security of PMAC can be further improved by using τi’s that are k-wise independent, for k > 1 (the original distribution is only 1-wise independent). We observe that the security of PMAC will not increase in general, even if the masks are chosen from a 2-wise independent distribution, and then prove that the security increases to O(q<2/2n), if the τi are 4-wise independent. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether 3-wise independence is already sufficient to get this level of security is left as an open problem."}],"issue":"2","type":"journal_article","doi":"10.13154/TOSC.V2016.I2.145-161","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":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"month":"02","publication_identifier":{"eissn":["2519-173X"]},"author":[{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"},{"last_name":"Rybar","first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal"}],"related_material":{"record":[{"id":"838","relation":"dissertation_contains","status":"public"}]},"date_updated":"2023-09-07T12:02:27Z","date_created":"2019-04-04T13:48:23Z","volume":2016,"year":"2017","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Ruhr University Bochum","file_date_updated":"2020-07-14T12:47:24Z","ec_funded":1},{"file_date_updated":"2020-07-14T12:48:12Z","publist_id":"6811","year":"2017","acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Xu, Haibing","last_name":"Xu","first_name":"Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"5828","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2023-09-07T12:06:38Z","date_created":"2018-12-11T11:48:46Z","month":"08","publication_identifier":{"issn":["2663-337X"]},"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"},"doi":"10.15479/AT:ISTA:th_858","supervisor":[{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"837","ddc":["571"],"status":"public","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","pubrep_id":"858","file":[{"creator":"dernst","file_size":3589490,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_name":"2017_Xu_Haibing_Thesis_Source.docx","checksum":"f11925fbbce31e495124b6bc4f10573c","date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:59:51Z","file_id":"6213","relation":"source_file"},{"relation":"main_file","file_id":"6214","checksum":"ffb10749a537d615fab1ef0937ccb157","date_updated":"2020-07-14T12:48:12Z","date_created":"2019-04-05T08:59:51Z","access_level":"open_access","file_name":"2017_Xu_Thesis_IST.pdf","content_type":"application/pdf","file_size":11668613,"creator":"dernst"}],"oa_version":"Published Version","day":"23","has_accepted_license":"1","article_processing_charge":"No","citation":{"ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858","ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","apa":"Xu, H. (2017). Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_858","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","mla":"Xu, Haibing. Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_858.","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_858."},"page":"93","date_published":"2017-08-23T00:00:00Z"},{"abstract":[{"lang":"eng","text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:20Z","checksum":"193425764d9aaaed3ac57062a867b315","file_id":"6215","relation":"source_file","creator":"dernst","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":46903863,"file_name":"2017_Adamowski-Thesis_Source.docx","access_level":"closed"},{"relation":"main_file","file_id":"6216","checksum":"df5ab01be81f821e1b958596a1ec8d21","date_updated":"2020-07-14T12:48:15Z","date_created":"2019-04-05T09:03:19Z","access_level":"open_access","file_name":"2017_Adamowski-Thesis.pdf","file_size":8698888,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","pubrep_id":"842","status":"public","ddc":["581","583","580"],"title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"938","day":"02","has_accepted_license":"1","article_processing_charge":"No","date_published":"2017-06-02T00:00:00Z","page":"117","citation":{"mla":"Adamowski, Maciek. Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_842.","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_842.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","apa":"Adamowski, M. (2017). Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_842","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017."},"file_date_updated":"2020-07-14T12:48:15Z","publist_id":"6483","date_created":"2018-12-11T11:49:18Z","date_updated":"2023-09-07T12:06:09Z","author":[{"full_name":"Adamowski, Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6463-5257","first_name":"Maciek","last_name":"Adamowski"}],"related_material":{"record":[{"id":"1591","relation":"part_of_dissertation","status":"public"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","year":"2017","month":"06","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","supervisor":[{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_842","oa":1},{"degree_awarded":"PhD","supervisor":[{"last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_815","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7"}],"oa":1,"month":"05","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:49:35Z","date_updated":"2023-09-07T12:05:41Z","author":[{"full_name":"Rolinek, Michal","first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"VlKo"}],"acknowledgement":"FP7/2007-2013/ERC grant agreement no 616160","year":"2017","file_date_updated":"2020-07-14T12:48:18Z","ec_funded":1,"publist_id":"6407","date_published":"2017-05-01T00:00:00Z","page":"97","citation":{"chicago":"Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815.","mla":"Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815.","short":"M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017.","ista":"Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria.","ieee":"M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017.","apa":"Rolinek, M. (2017). Complexity of constraint satisfaction. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815","ama":"Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815"},"day":"01","has_accepted_license":"1","article_processing_charge":"No","file":[{"file_id":"4654","relation":"main_file","date_updated":"2020-07-14T12:48:18Z","date_created":"2018-12-12T10:07:55Z","checksum":"81761fb939acb7585c36629f765b4373","file_name":"IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf","access_level":"open_access","creator":"system","file_size":786145,"content_type":"application/pdf"},{"creator":"dernst","file_size":5936337,"content_type":"application/zip","file_name":"2017_Thesis_Rolinek_source.zip","access_level":"closed","date_created":"2019-04-05T08:43:24Z","date_updated":"2020-07-14T12:48:18Z","checksum":"2b2d7e1d6c1c79a9795a7aa0f860baf3","file_id":"6208","relation":"source_file"}],"oa_version":"Published Version","pubrep_id":"815","status":"public","title":"Complexity of constraint satisfaction","ddc":["004"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"992","abstract":[{"text":"An instance of the Constraint Satisfaction Problem (CSP) is given by a finite set of\r\nvariables, a finite domain of labels, and a set of constraints, each constraint acting on\r\na subset of the variables. The goal is to find an assignment of labels to its variables\r\nthat satisfies all constraints (or decide whether one exists). If we allow more general\r\n“soft” constraints, which come with (possibly infinite) costs of particular assignments,\r\nwe obtain instances from a richer class called Valued Constraint Satisfaction Problem\r\n(VCSP). There the goal is to find an assignment with minimum total cost.\r\nIn this thesis, we focus (assuming that P\r\n6\r\n=\r\nNP) on classifying computational com-\r\nplexity of CSPs and VCSPs under certain restricting conditions. Two results are the core\r\ncontent of the work. In one of them, we consider VCSPs parametrized by a constraint\r\nlanguage, that is the set of “soft” constraints allowed to form the instances, and finish\r\nthe complexity classification modulo (missing pieces of) complexity classification for\r\nanalogously parametrized CSP. The other result is a generalization of Edmonds’ perfect\r\nmatching algorithm. This generalization contributes to complexity classfications in two\r\nways. First, it gives a new (largest known) polynomial-time solvable class of Boolean\r\nCSPs in which every variable may appear in at most two constraints and second, it\r\nsettles full classification of Boolean CSPs with planar drawing (again parametrized by a\r\nconstraint language).","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"quality_controlled":"1","project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems","call_identifier":"FP7"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"external_id":{"arxiv":["1607.05915"]},"main_file_link":[{"url":"https://arxiv.org/abs/1607.05915","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1017/apr.2017.20","month":"09","publication_identifier":{"issn":["00018678"]},"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Cambridge University Press","year":"2017","date_updated":"2023-09-07T12:07:12Z","date_created":"2018-12-11T11:48:07Z","volume":49,"author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-0659-3201","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","last_name":"Nikitenko","first_name":"Anton","full_name":"Nikitenko, Anton"},{"first_name":"Matthias","last_name":"Reitzner","full_name":"Reitzner, Matthias"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6287"}]},"publist_id":"6962","ec_funded":1,"page":"745 - 767","publication":"Advances in Applied Probability","citation":{"mla":"Edelsbrunner, Herbert, et al. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability, vol. 49, no. 3, Cambridge University Press, 2017, pp. 745–67, doi:10.1017/apr.2017.20.","short":"H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767.","chicago":"Edelsbrunner, Herbert, Anton Nikitenko, and Matthias Reitzner. “Expected Sizes of Poisson Delaunay Mosaics and Their Discrete Morse Functions.” Advances in Applied Probability. Cambridge University Press, 2017. https://doi.org/10.1017/apr.2017.20.","ama":"Edelsbrunner H, Nikitenko A, Reitzner M. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 2017;49(3):745-767. doi:10.1017/apr.2017.20","ista":"Edelsbrunner H, Nikitenko A, Reitzner M. 2017. Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. 49(3), 745–767.","apa":"Edelsbrunner, H., Nikitenko, A., & Reitzner, M. (2017). Expected sizes of poisson Delaunay mosaics and their discrete Morse functions. Advances in Applied Probability. Cambridge University Press. https://doi.org/10.1017/apr.2017.20","ieee":"H. Edelsbrunner, A. Nikitenko, and M. Reitzner, “Expected sizes of poisson Delaunay mosaics and their discrete Morse functions,” Advances in Applied Probability, vol. 49, no. 3. Cambridge University Press, pp. 745–767, 2017."},"date_published":"2017-09-01T00:00:00Z","scopus_import":1,"day":"01","status":"public","title":"Expected sizes of poisson Delaunay mosaics and their discrete Morse functions","intvolume":" 49","_id":"718","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Mapping every simplex in the Delaunay mosaic of a discrete point set to the radius of the smallest empty circumsphere gives a generalized discrete Morse function. Choosing the points from a Poisson point process in ℝ n , we study the expected number of simplices in the Delaunay mosaic as well as the expected number of critical simplices and nonsingular intervals in the corresponding generalized discrete gradient. Observing connections with other probabilistic models, we obtain precise expressions for the expected numbers in low dimensions. In particular, we obtain the expected numbers of simplices in the Poisson–Delaunay mosaic in dimensions n ≤ 4."}],"issue":"3"},{"intvolume":" 10625","status":"public","title":"Beyond Hellman’s time-memory trade-offs with applications to proofs of space","_id":"559","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2)."}],"page":"357 - 379","citation":{"short":"H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379.","mla":"Abusalah, Hamza M., et al. Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space. Vol. 10625, Springer, 2017, pp. 357–79, doi:10.1007/978-3-319-70697-9_13.","chicago":"Abusalah, Hamza M, Joel F Alwen, Bram Cohen, Danylo Khilko, Krzysztof Z Pietrzak, and Leonid Reyzin. “Beyond Hellman’s Time-Memory Trade-Offs with Applications to Proofs of Space,” 10625:357–79. Springer, 2017. https://doi.org/10.1007/978-3-319-70697-9_13.","ama":"Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. In: Vol 10625. Springer; 2017:357-379. doi:10.1007/978-3-319-70697-9_13","apa":"Abusalah, H. M., Alwen, J. F., Cohen, B., Khilko, D., Pietrzak, K. Z., & Reyzin, L. (2017). Beyond Hellman’s time-memory trade-offs with applications to proofs of space (Vol. 10625, pp. 357–379). Presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China: Springer. https://doi.org/10.1007/978-3-319-70697-9_13","ieee":"H. M. Abusalah, J. F. Alwen, B. Cohen, D. Khilko, K. Z. Pietrzak, and L. Reyzin, “Beyond Hellman’s time-memory trade-offs with applications to proofs of space,” presented at the ASIACRYPT: Theory and Applications of Cryptology and Information Security, Hong Kong, China, 2017, vol. 10625, pp. 357–379.","ista":"Abusalah HM, Alwen JF, Cohen B, Khilko D, Pietrzak KZ, Reyzin L. 2017. Beyond Hellman’s time-memory trade-offs with applications to proofs of space. ASIACRYPT: Theory and Applications of Cryptology and Information Security, LNCS, vol. 10625, 357–379."},"date_published":"2017-11-18T00:00:00Z","scopus_import":1,"day":"18","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2017","volume":10625,"date_created":"2018-12-11T11:47:10Z","date_updated":"2023-09-07T12:30:22Z","related_material":{"record":[{"id":"83","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","last_name":"Abusalah","full_name":"Abusalah, Hamza M"},{"last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alwen, Joel F"},{"first_name":"Bram","last_name":"Cohen","full_name":"Cohen, Bram"},{"full_name":"Khilko, Danylo","last_name":"Khilko","first_name":"Danylo"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Reyzin","first_name":"Leonid","full_name":"Reyzin, Leonid"}],"ec_funded":1,"publist_id":"7257","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2017/893.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-70697-9_13","conference":{"name":"ASIACRYPT: Theory and Applications of Cryptology and Information Security","end_date":"2017-12-07","start_date":"2017-12-03","location":"Hong Kong, China"},"publication_identifier":{"isbn":["978-331970696-2"]},"month":"11"},{"scopus_import":1,"has_accepted_license":"1","day":"21","citation":{"short":"J. Alt, Electronic Communications in Probability 22 (2017).","mla":"Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability, vol. 22, 63, Institute of Mathematical Statistics, 2017, doi:10.1214/17-ECP97.","chicago":"Alt, Johannes. “Singularities of the Density of States of Random Gram Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/17-ECP97.","ama":"Alt J. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 2017;22. doi:10.1214/17-ECP97","apa":"Alt, J. (2017). Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/17-ECP97","ieee":"J. Alt, “Singularities of the density of states of random Gram matrices,” Electronic Communications in Probability, vol. 22. Institute of Mathematical Statistics, 2017.","ista":"Alt J. 2017. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 22, 63."},"publication":"Electronic Communications in Probability","date_published":"2017-11-21T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities."}],"intvolume":" 22","status":"public","title":"Singularities of the density of states of random Gram matrices","ddc":["539"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"550","oa_version":"Published Version","file":[{"file_name":"IST-2018-926-v1+1_euclid.ecp.1511233247.pdf","access_level":"open_access","creator":"system","file_size":470876,"content_type":"application/pdf","file_id":"4663","relation":"main_file","date_created":"2018-12-12T10:08:04Z","date_updated":"2020-07-14T12:47:00Z","checksum":"0ec05303a0de190de145654237984c79"}],"pubrep_id":"926","publication_identifier":{"issn":["1083589X"]},"month":"11","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"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":"10.1214/17-ECP97","article_number":"63","ec_funded":1,"publist_id":"7265","file_date_updated":"2020-07-14T12:47:00Z","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","publication_status":"published","year":"2017","volume":22,"date_updated":"2023-09-07T12:38:08Z","date_created":"2018-12-11T11:47:07Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"149"}]},"author":[{"last_name":"Alt","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","full_name":"Alt, Johannes"}]},{"publist_id":"7129","file_date_updated":"2020-07-14T12:47:31Z","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","year":"2017","volume":"10419 ","date_updated":"2023-09-07T12:53:00Z","date_created":"2018-12-11T11:47:41Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6894"}]},"author":[{"full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Giacobbe, Mirco","last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kong, Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","first_name":"Hui","last_name":"Kong"}],"publication_identifier":{"isbn":["978-331965764-6"]},"month":"09","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-65765-3_7","conference":{"name":"FORMATS: Formal Modelling and Analysis of Timed Systems","end_date":"2017-09-07","location":"Berlin, Germany","start_date":"2017-09-05"},"alternative_title":["LNCS"],"type":"conference","abstract":[{"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.","lang":"eng"}],"title":"Conic abstractions for hybrid systems","ddc":["005"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"647","file":[{"file_id":"4956","relation":"main_file","date_created":"2018-12-12T10:12:38Z","date_updated":"2020-07-14T12:47:31Z","checksum":"faf546914ba29bcf9974ee36b6b16750","file_name":"IST-2017-831-v1+1_main.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":3806864}],"oa_version":"Submitted Version","pubrep_id":"831","scopus_import":1,"has_accepted_license":"1","day":"01","page":"116 - 132","citation":{"short":"S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017, pp. 116–132.","mla":"Bogomolov, Sergiy, et al. Conic Abstractions for Hybrid Systems. Vol. 10419, Springer, 2017, pp. 116–32, doi:10.1007/978-3-319-65765-3_7.","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.","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","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.","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","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."},"date_published":"2017-09-01T00:00:00Z"},{"language":[{"iso":"eng"}],"conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2017-04-22","location":"Uppsala, Sweden","end_date":"2017-04-29"},"doi":"10.1007/978-3-662-54577-5_34","quality_controlled":"1","project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"oa":1,"month":"03","publication_identifier":{"isbn":["978-366254576-8"]},"date_created":"2018-12-11T11:47:36Z","date_updated":"2023-09-07T12:53:00Z","volume":10205,"author":[{"orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"full_name":"Frehse, Goran","first_name":"Goran","last_name":"Frehse"},{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904","first_name":"Mirco","last_name":"Giacobbe","full_name":"Giacobbe, Mirco"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"}],"related_material":{"record":[{"id":"6894","relation":"dissertation_contains","status":"public"}]},"publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","year":"2017","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), by the European Commission under grant 643921 (UnCoVerCPS), and by the ARC project DP140104219 (Robust AI Planning for Hybrid Systems).","file_date_updated":"2020-07-14T12:47:27Z","publist_id":"7162","date_published":"2017-03-31T00:00:00Z","page":"589 - 606","citation":{"ieee":"S. Bogomolov, G. Frehse, M. Giacobbe, and T. A. Henzinger, “Counterexample guided refinement of template polyhedra,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden, 2017, vol. 10205, pp. 589–606.","apa":"Bogomolov, S., Frehse, G., Giacobbe, M., & Henzinger, T. A. (2017). Counterexample guided refinement of template polyhedra (Vol. 10205, pp. 589–606). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Uppsala, Sweden: Springer. https://doi.org/10.1007/978-3-662-54577-5_34","ista":"Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. 2017. Counterexample guided refinement of template polyhedra. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 589–606.","ama":"Bogomolov S, Frehse G, Giacobbe M, Henzinger TA. Counterexample guided refinement of template polyhedra. In: Vol 10205. Springer; 2017:589-606. doi:10.1007/978-3-662-54577-5_34","chicago":"Bogomolov, Sergiy, Goran Frehse, Mirco Giacobbe, and Thomas A Henzinger. “Counterexample Guided Refinement of Template Polyhedra,” 10205:589–606. Springer, 2017. https://doi.org/10.1007/978-3-662-54577-5_34.","short":"S. Bogomolov, G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2017, pp. 589–606.","mla":"Bogomolov, Sergiy, et al. Counterexample Guided Refinement of Template Polyhedra. Vol. 10205, Springer, 2017, pp. 589–606, doi:10.1007/978-3-662-54577-5_34."},"day":"31","has_accepted_license":"1","scopus_import":1,"file":[{"file_size":569863,"content_type":"application/pdf","creator":"system","file_name":"IST-2017-741-v1+1_main.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:27Z","date_created":"2018-12-12T10:11:41Z","checksum":"f395d0d20102b89aeaad8b4ef4f18f4f","relation":"main_file","file_id":"4897"},{"access_level":"open_access","file_name":"IST-2018-741-v2+2_main.pdf","creator":"system","file_size":563276,"content_type":"application/pdf","file_id":"4898","relation":"main_file","checksum":"f416ee1ae4497b23ecdf28b1f18bb8df","date_updated":"2020-07-14T12:47:27Z","date_created":"2018-12-12T10:11:42Z"}],"oa_version":"Submitted Version","pubrep_id":"966","status":"public","title":"Counterexample guided refinement of template polyhedra","ddc":["000"],"intvolume":" 10205","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"631","abstract":[{"lang":"eng","text":"Template polyhedra generalize intervals and octagons to polyhedra whose facets are orthogonal to a given set of arbitrary directions. They have been employed in the abstract interpretation of programs and, with particular success, in the reachability analysis of hybrid automata. While previously, the choice of directions has been left to the user or a heuristic, we present a method for the automatic discovery of directions that generalize and eliminate spurious counterexamples. We show that for the class of convex hybrid automata, i.e., hybrid automata with (possibly nonlinear) convex constraints on derivatives, such directions always exist and can be found using convex optimization. We embed our method inside a CEGAR loop, thus enabling the time-unbounded reachability analysis of an important and richer class of hybrid automata than was previously possible. We evaluate our method on several benchmarks, demonstrating also its superior efficiency for the special case of linear hybrid automata."}],"alternative_title":["LNCS"],"type":"conference"},{"type":"journal_article","abstract":[{"text":"We show that matrix elements of functions of N × N Wigner matrices fluctuate on a scale of order N−1/2 and we identify the limiting fluctuation. Our result holds for any function f of the matrix that has bounded variation thus considerably relaxing the regularity requirement imposed in [7, 11].","lang":"eng"}],"intvolume":" 21","status":"public","title":"Fluctuations of functions of Wigner matrices","ddc":["510"],"_id":"1144","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"5329","relation":"main_file","date_updated":"2018-12-12T10:18:10Z","date_created":"2018-12-12T10:18:10Z","file_name":"IST-2017-747-v1+1_euclid.ecp.1483347665.pdf","access_level":"open_access","creator":"system","file_size":440770,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"747","scopus_import":1,"has_accepted_license":"1","day":"02","citation":{"short":"L. Erdös, D.J. Schröder, Electronic Communications in Probability 21 (2017).","mla":"Erdös, László, and Dominik J. Schröder. “Fluctuations of Functions of Wigner Matrices.” Electronic Communications in Probability, vol. 21, 86, Institute of Mathematical Statistics, 2017, doi:10.1214/16-ECP38.","chicago":"Erdös, László, and Dominik J Schröder. “Fluctuations of Functions of Wigner Matrices.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-ECP38.","ama":"Erdös L, Schröder DJ. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 2017;21. doi:10.1214/16-ECP38","apa":"Erdös, L., & Schröder, D. J. (2017). Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/16-ECP38","ieee":"L. Erdös and D. J. Schröder, “Fluctuations of functions of Wigner matrices,” Electronic Communications in Probability, vol. 21. Institute of Mathematical Statistics, 2017.","ista":"Erdös L, Schröder DJ. 2017. Fluctuations of functions of Wigner matrices. 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Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 2017;36(6). doi:10.1145/3130800.3130890","apa":"Elek, O., Sumin, D., Zhang, R., Weyrich, T., Myszkowski, K., Bickel, B., … Krivanek, J. (2017). Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3130800.3130890","ieee":"O. Elek et al., “Scattering-aware texture reproduction for 3D printing,” ACM Transactions on Graphics, vol. 36, no. 6. ACM, 2017.","ista":"Elek O, Sumin D, Zhang R, Weyrich T, Myszkowski K, Bickel B, Wilkie A, Krivanek J. 2017. Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 36(6), 241.","short":"O. Elek, D. Sumin, R. Zhang, T. Weyrich, K. Myszkowski, B. Bickel, A. Wilkie, J. Krivanek, ACM Transactions on Graphics 36 (2017).","mla":"Elek, Oskar, et al. “Scattering-Aware Texture Reproduction for 3D Printing.” ACM Transactions on Graphics, vol. 36, no. 6, 241, ACM, 2017, doi:10.1145/3130800.3130890.","chicago":"Elek, Oskar, Denis Sumin, Ran Zhang, Tim Weyrich, Karol Myszkowski, Bernd Bickel, Alexander Wilkie, and Jaroslav Krivanek. “Scattering-Aware Texture Reproduction for 3D Printing.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3130800.3130890."},"publication":"ACM Transactions on Graphics","article_type":"original","date_published":"2017-11-20T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"Color texture reproduction in 3D printing commonly ignores volumetric light transport (cross-talk) between surface points on a 3D print. Such light diffusion leads to significant blur of details and color bleeding, and is particularly severe for highly translucent resin-based print materials. Given their widely varying scattering properties, this cross-talk between surface points strongly depends on the internal structure of the volume surrounding each surface point. Existing scattering-aware methods use simplified models for light diffusion, and often accept the visual blur as an immutable property of the print medium. In contrast, our work counteracts heterogeneous scattering to obtain the impression of a crisp albedo texture on top of the 3D print, by optimizing for a fully volumetric material distribution that preserves the target appearance. Our method employs an efficient numerical optimizer on top of a general Monte-Carlo simulation of heterogeneous scattering, supported by a practical calibration procedure to obtain scattering parameters from a given set of printer materials. Despite the inherent translucency of the medium, we reproduce detailed surface textures on 3D prints. We evaluate our system using a commercial, five-tone 3D print process and compare against the printer’s native color texturing mode, demonstrating that our method preserves high-frequency features well without having to compromise on color gamut."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"486","intvolume":" 36","status":"public","title":"Scattering-aware texture reproduction for 3D printing","ddc":["003","000","005"],"pubrep_id":"1052","file":[{"file_id":"4836","relation":"main_file","checksum":"48386fa6956c3645fc89594dc898b147","date_updated":"2020-07-14T12:46:35Z","date_created":"2018-12-12T10:10:46Z","access_level":"open_access","file_name":"IST-2018-1052-v1+1_ElekSumin2017SGA.pdf","creator":"system","file_size":107349827,"content_type":"application/pdf"},{"checksum":"21c89c28fb8d70f6602f752bf997aa0f","date_created":"2019-12-16T14:48:57Z","date_updated":"2020-07-14T12:46:35Z","relation":"main_file","file_id":"7189","file_size":4683145,"content_type":"application/pdf","creator":"bbickel","access_level":"open_access","file_name":"ElekSumin2017SGA_reduced_file_size.pdf"}],"oa_version":"Submitted Version"},{"scopus_import":1,"day":"01","citation":{"chicago":"Jafargholi, Zahra, Chethan Kamath Hosdurg, Karen Klein, Ilan Komargodski, Krzysztof Z Pietrzak, and Daniel Wichs. “Be Adaptive Avoid Overcommitting.” edited by Jonathan Katz and Hovav Shacham, 10401:133–63. Springer, 2017. https://doi.org/10.1007/978-3-319-63688-7_5.","short":"Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K.Z. Pietrzak, D. Wichs, in:, J. Katz, H. Shacham (Eds.), Springer, 2017, pp. 133–163.","mla":"Jafargholi, Zahra, et al. Be Adaptive Avoid Overcommitting. Edited by Jonathan Katz and Hovav Shacham, vol. 10401, Springer, 2017, pp. 133–63, doi:10.1007/978-3-319-63688-7_5.","apa":"Jafargholi, Z., Kamath Hosdurg, C., Klein, K., Komargodski, I., Pietrzak, K. Z., & Wichs, D. (2017). Be adaptive avoid overcommitting. In J. Katz & H. Shacham (Eds.) (Vol. 10401, pp. 133–163). Presented at the CRYPTO: Cryptology, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-319-63688-7_5","ieee":"Z. Jafargholi, C. Kamath Hosdurg, K. Klein, I. Komargodski, K. Z. Pietrzak, and D. Wichs, “Be adaptive avoid overcommitting,” presented at the CRYPTO: Cryptology, Santa Barbara, CA, United States, 2017, vol. 10401, pp. 133–163.","ista":"Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs D. 2017. Be adaptive avoid overcommitting. CRYPTO: Cryptology, LNCS, vol. 10401, 133–163.","ama":"Jafargholi Z, Kamath Hosdurg C, Klein K, Komargodski I, Pietrzak KZ, Wichs D. Be adaptive avoid overcommitting. In: Katz J, Shacham H, eds. Vol 10401. Springer; 2017:133-163. doi:10.1007/978-3-319-63688-7_5"},"page":"133 - 163","date_published":"2017-01-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"For many cryptographic primitives, it is relatively easy to achieve selective security (where the adversary commits a-priori to some of the choices to be made later in the attack) but appears difficult to achieve the more natural notion of adaptive security (where the adversary can make all choices on the go as the attack progresses). A series of several recent works shows how to cleverly achieve adaptive security in several such scenarios including generalized selective decryption (Panjwani, TCC ’07 and Fuchsbauer et al., CRYPTO ’15), constrained PRFs (Fuchsbauer et al., ASIACRYPT ’14), and Yao garbled circuits (Jafargholi and Wichs, TCC ’16b). Although the above works expressed vague intuition that they share a common technique, the connection was never made precise. In this work we present a new framework that connects all of these works and allows us to present them in a unified and simplified fashion. Moreover, we use the framework to derive a new result for adaptively secure secret sharing over access structures defined via monotone circuits. We envision that further applications will follow in the future. Underlying our framework is the following simple idea. It is well known that selective security, where the adversary commits to n-bits of information about his future choices, automatically implies adaptive security at the cost of amplifying the adversary’s advantage by a factor of up to 2n. However, in some cases the proof of selective security proceeds via a sequence of hybrids, where each pair of adjacent hybrids locally only requires some smaller partial information consisting of m ≪ n bits. The partial information needed might be completely different between different pairs of hybrids, and if we look across all the hybrids we might rely on the entire n-bit commitment. Nevertheless, the above is sufficient to prove adaptive security, at the cost of amplifying the adversary’s advantage by a factor of only 2m ≪ 2n. In all of our examples using the above framework, the different hybrids are captured by some sort of a graph pebbling game and the amount of information that the adversary needs to commit to in each pair of hybrids is bounded by the maximum number of pebbles in play at any point in time. Therefore, coming up with better strategies for proving adaptive security translates to various pebbling strategies for different types of graphs."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"637","title":"Be adaptive avoid overcommitting","status":"public","intvolume":" 10401","oa_version":"Submitted Version","month":"01","publication_identifier":{"isbn":["978-331963687-0"]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/515"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"conference":{"name":"CRYPTO: Cryptology","end_date":"2017-07-24","location":"Santa Barbara, CA, United States","start_date":"2017-07-20"},"doi":"10.1007/978-3-319-63688-7_5","language":[{"iso":"eng"}],"publist_id":"7151","ec_funded":1,"year":"2017","publication_status":"published","editor":[{"last_name":"Katz","first_name":"Jonathan","full_name":"Katz, Jonathan"},{"full_name":"Shacham, Hovav","last_name":"Shacham","first_name":"Hovav"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"author":[{"first_name":"Zahra","last_name":"Jafargholi","full_name":"Jafargholi, Zahra"},{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","last_name":"Klein","first_name":"Karen"},{"last_name":"Komargodski","first_name":"Ilan","full_name":"Komargodski, Ilan"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"related_material":{"record":[{"id":"10035","relation":"dissertation_contains","status":"public"}]},"date_created":"2018-12-11T11:47:38Z","date_updated":"2023-09-07T13:32:11Z","volume":10401},{"citation":{"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.","mla":"Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.","short":"A. Etheridge, N.H. Barton, (2017).","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.","apa":"Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:10.17632/nw68fxzjpm.1"},"main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}],"oa":1,"date_published":"2017-12-29T00:00:00Z","doi":"10.17632/nw68fxzjpm.1","article_processing_charge":"No","month":"12","day":"29","department":[{"_id":"NiBa"}],"publisher":"Mendeley Data","title":"Data for: Establishment in a new habitat by polygenic adaptation","status":"public","year":"2017","_id":"9842","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_updated":"2023-09-11T13:41:21Z","date_created":"2021-08-09T13:18:55Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"564"}]},"author":[{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Mathematica notebooks used to generate figures."}]},{"extern":"1","abstract":[{"text":"Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe (FW) algorithms regained popularity in recent years due to their simplicity, effectiveness and theoretical guarantees. MP and FW address optimization over the linear span and the convex hull of a set of atoms, respectively. In this paper, we consider the intermediate case of optimization over the convex cone, parametrized as the conic hull of a generic atom set, leading to the first principled definitions of non-negative MP algorithms for which we give explicit convergence rates and demonstrate excellent empirical performance. In particular, we derive sublinear (O(1/t)) convergence on general smooth and convex objectives, and linear convergence (O(e−t)) on strongly convex objectives, in both cases for general sets of atoms. Furthermore, we establish a clear correspondence of our algorithms to known algorithms from the MP and FW literature. Our novel algorithms and analyses target general atom sets and general objective functions, and hence are directly applicable to a large variety of learning settings.","lang":"eng"}],"type":"conference","date_updated":"2023-09-13T08:32:23Z","date_created":"2023-08-22T14:17:38Z","oa_version":"Preprint","author":[{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Jaggi","first_name":"Martin","full_name":"Jaggi, Martin"}],"publication_status":"published","title":"Greedy algorithms for cone constrained optimization with convergence guarantees","status":"public","department":[{"_id":"FrLo"}],"_id":"14206","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","day":"31","publication_identifier":{"isbn":["9781510860964"]},"article_processing_charge":"No","language":[{"iso":"eng"}],"conference":{"start_date":"2017-12-04","location":"Long Beach, CA, United States","end_date":"2017-12-09","name":"NeurIPS: Neural Information Processing Systems"},"date_published":"2017-05-31T00:00:00Z","quality_controlled":"1","publication":"Advances in Neural Information Processing Systems","citation":{"ista":"Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for cone constrained optimization with convergence guarantees. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","ieee":"F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for cone constrained optimization with convergence guarantees,” in Advances in Neural Information Processing Systems, Long Beach, CA, United States, 2017.","apa":"Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms for cone constrained optimization with convergence guarantees. In Advances in Neural Information Processing Systems. Long Beach, CA, United States.","ama":"Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained optimization with convergence guarantees. In: Advances in Neural Information Processing Systems. ; 2017.","chicago":"Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” In Advances in Neural Information Processing Systems, 2017.","mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” Advances in Neural Information Processing Systems, 2017.","short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017."},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.11041","open_access":"1"}],"external_id":{"arxiv":["1705.11041"]}},{"abstract":[{"lang":"eng","text":"Two of the most fundamental prototypes of greedy optimization are the matching pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both classes of methods, leading to the first explicit convergence rates of matching pursuit methods in an optimization sense, for general sets of atoms. We derive sublinear (1/t) convergence for both classes on general smooth objectives, and linear convergence on strongly convex objectives, as well as a clear correspondence of algorithm variants. Our presented algorithms and rates are affine invariant, and do not need any incoherence or sparsity assumptions."}],"extern":"1","type":"conference","author":[{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco"},{"full_name":"Khanna, Rajiv","last_name":"Khanna","first_name":"Rajiv"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"},{"first_name":"Martin","last_name":"Jaggi","full_name":"Jaggi, Martin"}],"volume":54,"oa_version":"Preprint","date_created":"2023-08-22T14:17:19Z","date_updated":"2023-09-13T09:49:10Z","_id":"14205","year":"2017","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"FrLo"}],"intvolume":" 54","publisher":"ML Research Press","status":"public","publication_status":"published","title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","article_processing_charge":"No","month":"02","day":"21","date_published":"2017-02-21T00:00:00Z","conference":{"name":"AISTATS: Conference on Artificial Intelligence and Statistics","start_date":"2017-04-20","location":"Fort Lauderdale, FL, United States","end_date":"2017-04-22"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1702.06457"}],"citation":{"chicago":"Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 54:860–68. ML Research Press, 2017.","mla":"Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017, pp. 860–68.","short":"F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, ML Research Press, 2017, pp. 860–868.","ista":"Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics vol. 54, 860–868.","ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. 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First, I analyze how mutations in phage restriction sites affect the probability of phage escape – an inherently stochastic process, during which phages accidently get modified instead of restricted. Next, I use single-cell experiments to show that RM systems can, with a low probability, attack the genome of their bacterial host and that this primitive form of autoimmunity leads to a tradeoff between the evolutionary cost and benefit of RM systems. Finally, I investigate the nature of interactions between bacteria, RM systems and temperate bacteriophages to find that, as a consequence of phage escape and its impact on population dynamics, RM systems can promote acquisition of symbiotic bacteriophages, rather than limit it. The results presented here uncover new fundamental biological properties of RM systems and highlight their importance in the ecology and evolution of bacteria, bacteriophages and their interactions.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"202","ddc":["576","579"],"title":"Biology of restriction-modification systems at the single-cell and population level","status":"public","pubrep_id":"916","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4710","checksum":"33cfb59674e91f82e3738396d3fb3776","date_created":"2018-12-12T10:08:48Z","date_updated":"2020-07-14T12:45:24Z","access_level":"open_access","file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","content_type":"application/pdf","file_size":18569590,"creator":"system"},{"file_id":"6204","relation":"source_file","checksum":"dcc239968decb233e7f98cf1083d8c26","date_updated":"2020-07-14T12:45:24Z","date_created":"2019-04-05T08:33:14Z","access_level":"closed","file_name":"2017_Pleska_Maros_Thesis.docx","creator":"dernst","file_size":2801649,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"day":"01","has_accepted_license":"1","article_processing_charge":"No","citation":{"ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria.","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","apa":"Pleska, M. (2017). Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_916","ama":"Pleska M. Biology of restriction-modification systems at the single-cell and population level. 2017. doi:10.15479/AT:ISTA:th_916","chicago":"Pleska, Maros. “Biology of Restriction-Modification Systems at the Single-Cell and Population Level.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_916.","mla":"Pleska, Maros. Biology of Restriction-Modification Systems at the Single-Cell and Population Level. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_916.","short":"M. Pleska, Biology of Restriction-Modification Systems at the Single-Cell and Population Level, Institute of Science and Technology Austria, 2017."},"page":"126","date_published":"2017-10-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:24Z","publist_id":"7711","acknowledgement":"During my PhD studies, I received help from many people, all of which unfortunately cannot be listed here. I thank them deeply and hope that I never made them regret their kindness.\r\nI would like to express my deepest gratitude to Călin Guet, who went far beyond his responsibilities as an advisor and was to me also a great mentor and a friend. Călin never questioned my potential or lacked compassion and I cannot thank him enough for cultivating in me an independent scientist. I was amazed by his ability to recognize the most fascinating scientific problems in objects of study that others would find mundane. I hope I adopted at least a fraction of this ability.\r\nI will be forever grateful to Bruce Levin for all his support and especially for giving me the best possible example of how one can practice excellent science with humor and style. Working with Bruce was a true privilege.\r\nI thank Jonathan Bollback and Gašper Tkačik for serving in my PhD committee and the Austrian Academy of Science for funding my PhD research via the DOC fellowship.\r\nI thank all our lab members: Tobias Bergmiller for his guidance, especially in the first years of my research, and for being a good friend throughout; Remy Chait for staying in the lab at unreasonable hours and for the good laughs at bad jokes we shared; Anna Staron for supportively listening to my whines whenever I had to run a gel; Magdalena Steinrück for her pioneering work in the lab; Kathrin Tomasek for keeping the entropic forces in check and for her FACS virtuosity; Isabella Tomanek for always being nice to me, no matter how much bench space I took from her.\r\nI thank all my collaborators: Reiko Okura and Yuichi Wakamoto for performing and analyzing the microfluidic experiments; Long Qian and Edo Kussell for their bioinformatics analysis; Dominik Refardt for the λ kan phage; Moritz for his help with the mathematical modeling. I thank Fabienne Jesse for her tireless editorial work on all our manuscripts.\r\nFinally, I would like to thank my family and especially my wife Edita, who sacrificed a lot so that I can pursue my goals and dreams.\r\n","year":"2017","publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Pleska","first_name":"Maros","orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1243"},{"status":"public","relation":"part_of_dissertation","id":"561"},{"status":"public","relation":"part_of_dissertation","id":"457"}]},"date_updated":"2023-09-15T12:04:56Z","date_created":"2018-12-11T11:45:10Z","month":"10","publication_identifier":{"issn":["2663-337X"]},"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":"251D65D8-B435-11E9-9278-68D0E5697425","grant_number":"24210","name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)"}],"doi":"10.15479/AT:ISTA:th_916","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"}],"language":[{"iso":"eng"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"27","date_published":"2017-10-27T00:00:00Z","page":"86","citation":{"mla":"Nikitenko, Anton. Discrete Morse Theory for Random Complexes . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_873.","short":"A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science and Technology Austria, 2017.","chicago":"Nikitenko, Anton. “Discrete Morse Theory for Random Complexes .” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_873.","ama":"Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:10.15479/AT:ISTA:th_873","ista":"Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria.","ieee":"A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of Science and Technology Austria, 2017.","apa":"Nikitenko, A. (2017). Discrete Morse theory for random complexes . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_873"},"abstract":[{"lang":"eng","text":"The main objects considered in the present work are simplicial and CW-complexes with vertices forming a random point cloud. In particular, we consider a Poisson point process in R^n and study Delaunay and Voronoi complexes of the first and higher orders and weighted Delaunay complexes obtained as sections of Delaunay complexes, as well as the Čech complex. Further, we examine theDelaunay complex of a Poisson point process on the sphere S^n, as well as of a uniform point cloud, which is equivalent to the convex hull, providing a connection to the theory of random polytopes. Each of the complexes in question can be endowed with a radius function, which maps its cells to the radii of appropriately chosen circumspheres, called the radius of the cell. Applying and developing discrete Morse theory for these functions, joining it together with probabilistic and sometimes analytic machinery, and developing several integral geometric tools, we aim at getting the distributions of circumradii of typical cells. For all considered complexes, we are able to generalize and obtain up to constants the distribution of radii of typical intervals of all types. In low dimensions the constants can be computed explicitly, thus providing the explicit expressions for the expected numbers of cells. In particular, it allows to find the expected density of simplices of every dimension for a Poisson point process in R^4, whereas the result for R^3 was known already in 1970's."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2017_Thesis_Nikitenko.pdf","creator":"dernst","file_size":2324870,"content_type":"application/pdf","file_id":"6289","relation":"main_file","checksum":"ece7e598a2f060b263c2febf7f3fe7f9","date_created":"2019-04-09T14:54:51Z","date_updated":"2020-07-14T12:47:26Z"},{"checksum":"99b7ad76e317efd447af60f91e29b49b","date_updated":"2020-07-14T12:47:26Z","date_created":"2019-04-09T14:54:51Z","file_id":"6290","relation":"source_file","creator":"dernst","file_size":2863219,"content_type":"application/zip","access_level":"closed","file_name":"2017_Thesis_Nikitenko_source.zip"}],"pubrep_id":"873","title":"Discrete Morse theory for random complexes ","status":"public","ddc":["514","516","519"],"_id":"6287","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"month":"10","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"doi":"10.15479/AT:ISTA:th_873","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,"file_date_updated":"2020-07-14T12:47:26Z","date_updated":"2023-09-15T12:10:34Z","date_created":"2019-04-09T15:04:32Z","related_material":{"record":[{"id":"718","status":"public","relation":"part_of_dissertation"},{"id":"5678","status":"public","relation":"part_of_dissertation"},{"id":"87","status":"public","relation":"part_of_dissertation"}]},"author":[{"id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201","first_name":"Anton","last_name":"Nikitenko","full_name":"Nikitenko, Anton"}],"department":[{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2017"},{"file_date_updated":"2021-02-22T11:52:56Z","publist_id":"6233","date_updated":"2023-09-19T10:39:33Z","date_created":"2018-12-11T11:50:17Z","author":[{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","last_name":"Prat","full_name":"Prat, Tomas"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"449"}]},"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"Institute of Science and Technology Austria","acknowledgement":"I would like to first acknowledge my supervisor Jiří Friml for support, kind advice and patience. It was a pleasure to be a part of your lab, Jiří. I will remember the atmosphere present in auxin lab at VIB in Ghent and at IST in Klosterneuburg forever. I would like to thank all past and present lab members for the friendship and friendly and scientific environment in the groups. It was so nice to cooperate with you, guys. There was always someone who helped me with experiments, troubleshoot issues coming from our work etc. At this place, I would like to thank especially to Gergo Molnár. I’m happy (and lucky) that I have met him; he naturally became my tutor and guide through my PhD. From no one else during my entire professional career, I’ve learned that much.","year":"2017","month":"01","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"abstract":[{"text":"Plant hormone auxin and its transport between cells belong to the most important\r\nmechanisms controlling plant development. Auxin itself could change localization of PINs and\r\nthereby control direction of its own flow. We performed an expression profiling experiment\r\nin Arabidopsis roots to identify potential regulators of PIN polarity which are transcriptionally\r\nregulated by auxin signalling. We identified several novel regulators and performed a detailed\r\ncharacterization of the transcription factor WRKY23 (At2g47260) and its role in auxin\r\nfeedback on PIN polarity. Gain-of-function and dominant-negative mutants revealed that\r\nWRKY23 plays a crucial role in mediating the auxin effect on PIN polarity. In concordance,\r\ntypical polar auxin transport processes such as gravitropism and leaf vascular pattern\r\nformation were disturbed by interfering with WRKY23 function.\r\nIn order to identify direct targets of WRKY23, we performed consequential expression\r\nprofiling experiments using a WRKY23 inducible gain-of-function line and dominant-negative\r\nWRKY23 line that is defunct in PIN re-arrangement. Among several genes mostly related to\r\nthe groups of cell wall and defense process regulators, we identified LYSINE-HISTIDINE\r\nTRANSPORTER 1 (LHT1; At5g40780), a small amino acid permease gene from the amino\r\nacid/auxin permease family (AAAP), we present its detailed characterisation in auxin feedback\r\non PIN repolarization, identified its transcriptional regulation, we propose a potential\r\nmechanism of its action. Moreover, we identified also a member of receptor-like protein\r\nkinase LRR-RLK (LEUCINE-RICH REPEAT TRANSMEMBRANE PROTEIN KINASE PROTEIN 1;\r\nLRRK1; At1g05700), which also affects auxin-dependent PIN re-arrangement. We described\r\nits transcriptional behaviour, subcellular localization. Based on global expression data, we\r\ntried to identify ligand responsible for mechanism of signalling and suggest signalling partner\r\nand interactors. Additionally, we described role of novel phytohormone group, strigolactone,\r\nin auxin-dependent PIN re-arrangement, that could be a fundament for future studies in this\r\nfield.\r\nOur results provide first insights into an auxin transcriptional network targeting PIN\r\nlocalization and thus regulating plant development. We highlighted WRKY23 transcriptional\r\nnetwork and characterised its mediatory role in plant development. We identified direct\r\neffectors of this network, LHT1 and LRRK1, and describe their roles in PIN re-arrangement and\r\nPIN-dependent auxin transport processes.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"relation":"main_file","file_id":"6209","checksum":"d192c7c6c5ea32c8432437286dc4909e","date_updated":"2019-04-05T08:45:14Z","date_created":"2019-04-05T08:45:14Z","access_level":"closed","file_name":"IST_Austria_Thesis_Tomáš_Prát.pdf","content_type":"application/pdf","file_size":10285946,"creator":"dernst"},{"file_id":"9185","relation":"main_file","date_created":"2021-02-22T11:52:56Z","date_updated":"2021-02-22T11:52:56Z","success":1,"checksum":"bab18b52cf98145926042d8ed99fdb3b","file_name":"2017_Thesis_Prat.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":9802991}],"oa_version":"Published Version","ddc":["580"],"title":"Identification of novel regulators of PIN polarity and development of novel auxin sensor","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1127","day":"12","article_processing_charge":"No","has_accepted_license":"1","date_published":"2017-01-12T00:00:00Z","page":"131","citation":{"ista":"Prat T. 2017. Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria.","ieee":"T. Prat, “Identification of novel regulators of PIN polarity and development of novel auxin sensor,” Institute of Science and Technology Austria, 2017.","apa":"Prat, T. (2017). Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria.","ama":"Prat T. Identification of novel regulators of PIN polarity and development of novel auxin sensor. 2017.","chicago":"Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017.","mla":"Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017.","short":"T. Prat, Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor, Institute of Science and Technology Austria, 2017."}},{"page":"285 - 306","publication":"Scandinavian Journal of Statistics","citation":{"apa":"Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., & Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. Wiley-Blackwell. https://doi.org/10.1111/sjos.12251","ieee":"A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” Scandinavian Journal of Statistics, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.","ista":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.","ama":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 2017;44(2):285-306. doi:10.1111/sjos.12251","chicago":"Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal of Statistics. Wiley-Blackwell, 2017. https://doi.org/10.1111/sjos.12251.","short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","mla":"Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” Scandinavian Journal of Statistics, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:10.1111/sjos.12251."},"date_published":"2017-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Exact goodness-of-fit testing for the Ising model","status":"public","intvolume":" 44","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"2016","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane."}],"issue":"2","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.1242","open_access":"1"}],"external_id":{"isi":["000400985000001"],"arxiv":["1410.1242"]},"language":[{"iso":"eng"}],"doi":"10.1111/sjos.12251","month":"06","publication_identifier":{"issn":["03036898"]},"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"GaTk"}],"year":"2017","date_updated":"2023-09-19T15:13:27Z","date_created":"2018-12-11T11:55:13Z","volume":44,"author":[{"first_name":"Abraham","last_name":"Martin Del Campo Sanchez","full_name":"Martin Del Campo Sanchez, Abraham"},{"id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"publist_id":"5060"},{"file_date_updated":"2020-07-14T12:45:00Z","publist_id":"5644","ec_funded":1,"author":[{"full_name":"Bao, Zhigang","last_name":"Bao","first_name":"Zhigang","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"}],"date_created":"2018-12-11T11:52:32Z","date_updated":"2023-09-20T09:42:12Z","volume":167,"acknowledgement":"Z. Bao was supported by ERC Advanced Grant RANMAT No. 338804; L. Erdős was partially supported by ERC Advanced Grant RANMAT No. 338804.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to the anonymous referees for careful reading and valuable comments, which helped to improve the organization.","year":"2017","publication_status":"published","publisher":"Springer","department":[{"_id":"LaEr"}],"month":"04","publication_identifier":{"issn":["01788051"]},"doi":"10.1007/s00440-015-0692-y","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"},"external_id":{"isi":["000398842700004"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"We consider N×N Hermitian random matrices H consisting of blocks of size M≥N6/7. The matrix elements are i.i.d. within the blocks, close to a Gaussian in the four moment matching sense, but their distribution varies from block to block to form a block-band structure, with an essential band width M. We show that the entries of the Green’s function G(z)=(H−z)−1 satisfy the local semicircle law with spectral parameter z=E+iη down to the real axis for any η≫N−1, using a combination of the supersymmetry method inspired by Shcherbina (J Stat Phys 155(3): 466–499, 2014) and the Green’s function comparison strategy. Previous estimates were valid only for η≫M−1. The new estimate also implies that the eigenvectors in the middle of the spectrum are fully delocalized.","lang":"eng"}],"issue":"3-4","type":"journal_article","pubrep_id":"489","file":[{"checksum":"67afa85ff1e220cbc1f9f477a828513c","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:08:05Z","file_id":"4665","relation":"main_file","creator":"system","file_size":1615755,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-489-v1+1_s00440-015-0692-y.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1528","ddc":["530"],"status":"public","title":"Delocalization for a class of random block band matrices","intvolume":" 167","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2017-04-01T00:00:00Z","publication":"Probability Theory and Related Fields","citation":{"mla":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” Probability Theory and Related Fields, vol. 167, no. 3–4, Springer, 2017, pp. 673–776, doi:10.1007/s00440-015-0692-y.","short":"Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 673–776.","chicago":"Bao, Zhigang, and László Erdös. “Delocalization for a Class of Random Block Band Matrices.” Probability Theory and Related Fields. Springer, 2017. https://doi.org/10.1007/s00440-015-0692-y.","ama":"Bao Z, Erdös L. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 2017;167(3-4):673-776. doi:10.1007/s00440-015-0692-y","ista":"Bao Z, Erdös L. 2017. Delocalization for a class of random block band matrices. Probability Theory and Related Fields. 167(3–4), 673–776.","ieee":"Z. Bao and L. Erdös, “Delocalization for a class of random block band matrices,” Probability Theory and Related Fields, vol. 167, no. 3–4. Springer, pp. 673–776, 2017.","apa":"Bao, Z., & Erdös, L. (2017). Delocalization for a class of random block band matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-015-0692-y"},"article_type":"original","page":"673 - 776"},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jsc.2016.03.008"}],"external_id":{"isi":["000384396000005"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"doi":"10.1016/j.jsc.2016.03.008","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"issn":[" 07477171"]},"year":"2017","publication_status":"published","publisher":"Academic Press","department":[{"_id":"HeEd"}],"author":[{"first_name":"Ulrich","last_name":"Bauer","full_name":"Bauer, Ulrich"},{"first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael"},{"last_name":"Reininghaus","first_name":"Jan","full_name":"Reininghaus, Jan"},{"full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","last_name":"Wagner"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10894"}]},"date_updated":"2023-09-20T09:42:40Z","date_created":"2018-12-11T11:51:59Z","volume":78,"ec_funded":1,"publist_id":"5765","publication":"Journal of Symbolic Computation","citation":{"ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology algorithms toolbox,” Journal of Symbolic Computation, vol. 78. Academic Press, pp. 76–90, 2017.","apa":"Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2017). Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. Academic Press. https://doi.org/10.1016/j.jsc.2016.03.008","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 2017;78:76-90. doi:10.1016/j.jsc.2016.03.008","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat - Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation. Academic Press, 2017. https://doi.org/10.1016/j.jsc.2016.03.008.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90.","mla":"Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation, vol. 78, Academic Press, 2017, pp. 76–90, doi:10.1016/j.jsc.2016.03.008."},"article_type":"original","page":"76 - 90","date_published":"2017-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1433","status":"public","title":"Phat - Persistent homology algorithms toolbox","intvolume":" 78","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology.","lang":"eng"}]},{"abstract":[{"lang":"eng","text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of all satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. While the proposed algorithm guarantees progress and soundness in every iteration, it is computationally demanding. We offer an alternative, more efficient solution for the reachability properties that decomposes the problem into a series of smaller problems of the same type. All algorithms are demonstrated on an illustrative case study."}],"issue":"2","type":"journal_article","oa_version":"Preprint","title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","status":"public","intvolume":" 23","_id":"1407","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2017-02-01T00:00:00Z","page":"230 - 253","publication":"Nonlinear Analysis: Hybrid Systems","citation":{"short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006.","chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006.","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no. 2. Elsevier, pp. 230–253, 2017.","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253."},"publist_id":"5800","ec_funded":1,"date_updated":"2023-09-20T09:43:09Z","date_created":"2018-12-11T11:51:50Z","volume":23,"author":[{"first_name":"Mária","last_name":"Svoreňová","full_name":"Svoreňová, Mária"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cěrná","first_name":"Ivana","full_name":"Cěrná, Ivana"},{"first_name":"Cǎlin","last_name":"Belta","full_name":"Belta, Cǎlin"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1689"}]},"publication_status":"published","publisher":"Elsevier","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"year":"2017","month":"02","language":[{"iso":"eng"}],"doi":"10.1016/j.nahs.2016.04.006","isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"external_id":{"isi":["000390637000014"],"arxiv":["1410.5387"]},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}]},{"title":"Adaptive physically based models in computer graphics","ddc":["000"],"status":"public","intvolume":" 36","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1367","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:44:47Z","date_created":"2018-12-12T10:16:21Z","checksum":"7676e9a9ead6d58c3000988c97deb2ef","file_id":"5208","relation":"main_file","creator":"system","file_size":1434439,"content_type":"application/pdf","file_name":"IST-2016-634-v1+1_starAdaptivity-cgf.pdf","access_level":"open_access"}],"pubrep_id":"634","type":"journal_article","abstract":[{"lang":"eng","text":"One of the major challenges in physically based modelling is making simulations efficient. Adaptive models provide an essential solution to these efficiency goals. These models are able to self-adapt in space and time, attempting to provide the best possible compromise between accuracy and speed. This survey reviews the adaptive solutions proposed so far in computer graphics. Models are classified according to the strategy they use for adaptation, from time-stepping and freezing techniques to geometric adaptivity in the form of structured grids, meshes and particles. Applications range from fluids, through deformable bodies, to articulated solids."}],"issue":"6","page":"312 - 337","publication":"Computer Graphics Forum","citation":{"mla":"Manteaux, Pierre, et al. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum, vol. 36, no. 6, Wiley-Blackwell, 2017, pp. 312–37, doi:10.1111/cgf.12941.","short":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337.","chicago":"Manteaux, Pierre, Chris Wojtan, Rahul Narain, Stéphane Redon, François Faure, and Marie Cani. “Adaptive Physically Based Models in Computer Graphics.” Computer Graphics Forum. Wiley-Blackwell, 2017. https://doi.org/10.1111/cgf.12941.","ama":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. Adaptive physically based models in computer graphics. Computer Graphics Forum. 2017;36(6):312-337. doi:10.1111/cgf.12941","ista":"Manteaux P, Wojtan C, Narain R, Redon S, Faure F, Cani M. 2017. Adaptive physically based models in computer graphics. Computer Graphics Forum. 36(6), 312–337.","apa":"Manteaux, P., Wojtan, C., Narain, R., Redon, S., Faure, F., & Cani, M. (2017). Adaptive physically based models in computer graphics. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12941","ieee":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, and M. Cani, “Adaptive physically based models in computer graphics,” Computer Graphics Forum, vol. 36, no. 6. Wiley-Blackwell, pp. 312–337, 2017."},"date_published":"2017-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"Wiley-Blackwell","acknowledgement":"This work was partly supported by the starting grants ADAPT and BigSplash, as well as the advanced grant EXPRESSIVE from the European Research Council (ERC-2012-StG_20111012, ERC-2014-StG_638176 and ERC-2011-ADG_20110209).","year":"2017","date_updated":"2023-09-20T11:05:36Z","date_created":"2018-12-11T11:51:37Z","volume":36,"author":[{"full_name":"Manteaux, Pierre","first_name":"Pierre","last_name":"Manteaux"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"full_name":"Narain, Rahul","first_name":"Rahul","last_name":"Narain"},{"full_name":"Redon, Stéphane","last_name":"Redon","first_name":"Stéphane"},{"full_name":"Faure, François","last_name":"Faure","first_name":"François"},{"full_name":"Cani, Marie","first_name":"Marie","last_name":"Cani"}],"file_date_updated":"2020-07-14T12:44:47Z","publist_id":"5873","quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000408634200019"]},"language":[{"iso":"eng"}],"doi":"10.1111/cgf.12941","month":"09","publication_identifier":{"issn":["01677055"]}},{"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"},"external_id":{"isi":["000399888900001"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"doi":"10.1007/s10703-016-0256-5","language":[{"iso":"eng"}],"month":"06","year":"2017","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","author":[{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","first_name":"Pavol"},{"full_name":"Clarke, Edmund","last_name":"Clarke","first_name":"Edmund"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun","full_name":"Radhakrishna, Arjun"},{"full_name":"Ryzhyk, Leonid","last_name":"Ryzhyk","first_name":"Leonid"},{"last_name":"Samanta","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","full_name":"Samanta, Roopsha"},{"full_name":"Tarrach, Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","first_name":"Thorsten","last_name":"Tarrach"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1729"}]},"date_created":"2018-12-11T11:51:27Z","date_updated":"2023-09-20T11:13:51Z","volume":50,"file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5929","ec_funded":1,"publication":"Formal Methods in System Design","citation":{"apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., & Tarrach, T. (2017). From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-016-0256-5","ieee":"P. Cerny et al., “From non-preemptive to preemptive scheduling using synchronization synthesis,” Formal Methods in System Design, vol. 50, no. 2–3. Springer, pp. 97–139, 2017.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2017. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 50(2–3), 97–139.","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. Formal Methods in System Design. 2017;50(2-3):97-139. doi:10.1007/s10703-016-0256-5","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Formal Methods in System Design. Springer, 2017. https://doi.org/10.1007/s10703-016-0256-5.","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, Formal Methods in System Design 50 (2017) 97–139.","mla":"Cerny, Pavol, et al. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Formal Methods in System Design, vol. 50, no. 2–3, Springer, 2017, pp. 97–139, doi:10.1007/s10703-016-0256-5."},"page":"97 - 139","date_published":"2017-06-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","_id":"1338","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"From non-preemptive to preemptive scheduling using synchronization synthesis","status":"public","ddc":["000"],"intvolume":" 50","pubrep_id":"656","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4985","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:13:05Z","checksum":"1163dfd997e8212c789525d4178b1653","file_name":"IST-2016-656-v1+1_s10703-016-0256-5.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1416170,"creator":"system"}],"type":"journal_article","abstract":[{"text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We guarantee that our synthesis does not introduce deadlocks and that the synchronization inserted is optimal w.r.t. a given objective function. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and generation of a set of global constraints over synchronization placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronization placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronization solution. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient. The implicit specification helped us find one concurrency bug previously missed when model-checking using an explicit, user-provided specification. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronization placements are produced for our experiments, favoring a minimal number of synchronization operations or maximum concurrency, respectively.","lang":"eng"}],"issue":"2-3"},{"file_date_updated":"2020-07-14T12:44:46Z","ec_funded":1,"publist_id":"5898","author":[{"full_name":"Giacobbe, Mirco","last_name":"Giacobbe","first_name":"Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana"}],"related_material":{"record":[{"id":"1835","status":"public","relation":"earlier_version"}]},"date_created":"2018-12-11T11:51:32Z","date_updated":"2023-09-20T11:06:03Z","volume":54,"year":"2017","publication_status":"published","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"month":"12","publication_identifier":{"issn":["00015903"]},"doi":"10.1007/s00236-016-0278-x","language":[{"iso":"eng"}],"external_id":{"isi":["000414343200003"]},"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","isi":1,"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"issue":"8","type":"journal_article","pubrep_id":"649","file":[{"file_size":755241,"content_type":"application/pdf","creator":"dernst","file_name":"2017_ActaInformatica_Giacobbe.pdf","access_level":"open_access","date_created":"2019-01-17T15:57:29Z","date_updated":"2020-07-14T12:44:46Z","checksum":"4e661d9135d7f8c342e8e258dee76f3e","relation":"main_file","file_id":"5841"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1351","title":"Model checking the evolution of gene regulatory networks","ddc":["006","576"],"status":"public","intvolume":" 54","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2017-12-01T00:00:00Z","publication":"Acta Informatica","citation":{"chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer. https://doi.org/10.1007/s00236-016-0278-x","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8. Springer, pp. 765–787, 2017.","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x"},"page":"765 - 787"},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2017-06-01T00:00:00Z","page":"681 - 713","citation":{"chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica. Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica. Springer. https://doi.org/10.1007/s00453-016-0212-1","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2. Springer, pp. 681–713, 2017.","ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1"},"publication":"Algorithmica","issue":"2","abstract":[{"text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":710206,"creator":"system","access_level":"open_access","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","checksum":"7873f665a0c598ac747c908f34cb14b9","date_created":"2018-12-12T10:10:19Z","date_updated":"2020-07-14T12:44:44Z","relation":"main_file","file_id":"4805"}],"pubrep_id":"658","intvolume":" 78","ddc":["576"],"status":"public","title":"Towards a runtime comparison of natural and artificial evolution","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1336","publication_identifier":{"issn":["01784617"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1007/s00453-016-0212-1","project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"quality_controlled":"1","isi":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,"external_id":{"isi":["000400379500013"]},"publist_id":"5931","ec_funded":1,"file_date_updated":"2020-07-14T12:44:44Z","volume":78,"date_created":"2018-12-11T11:51:27Z","date_updated":"2023-09-20T11:14:42Z","author":[{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"},{"full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia","first_name":"Jorge"},{"full_name":"Sudholt, Dirk","last_name":"Sudholt","first_name":"Dirk"},{"orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora"}],"publisher":"Springer","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","year":"2017"},{"date_published":"2017-12-01T00:00:00Z","page":"667 - 727","publication":"Probability Theory and Related Fields","citation":{"apa":"Ajanki, O. H., Erdös, L., & Krüger, T. H. (2017). Universality for general Wigner-type matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-016-0740-2","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Universality for general Wigner-type matrices,” Probability Theory and Related Fields, vol. 169, no. 3–4. Springer, pp. 667–727, 2017.","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727.","ama":"Ajanki OH, Erdös L, Krüger TH. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 2017;169(3-4):667-727. doi:10.1007/s00440-016-0740-2","chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Universality for General Wigner-Type Matrices.” Probability Theory and Related Fields. Springer, 2017. https://doi.org/10.1007/s00440-016-0740-2.","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727.","mla":"Ajanki, Oskari H., et al. “Universality for General Wigner-Type Matrices.” Probability Theory and Related Fields, vol. 169, no. 3–4, Springer, 2017, pp. 667–727, doi:10.1007/s00440-016-0740-2."},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","file":[{"access_level":"open_access","file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf","file_size":988843,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4686","checksum":"29f5a72c3f91e408aeb9e78344973803","date_created":"2018-12-12T10:08:25Z","date_updated":"2020-07-14T12:44:44Z"}],"oa_version":"Published Version","pubrep_id":"657","title":"Universality for general Wigner-type matrices","ddc":["510","530"],"status":"public","intvolume":" 169","_id":"1337","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes.","lang":"eng"}],"issue":"3-4","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s00440-016-0740-2","quality_controlled":"1","isi":1,"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"external_id":{"isi":["000414358400002"]},"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,"month":"12","publication_identifier":{"issn":["01788051"]},"date_created":"2018-12-11T11:51:27Z","date_updated":"2023-09-20T11:14:17Z","volume":169,"author":[{"full_name":"Ajanki, Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki"},{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Springer","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","year":"2017","file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5930","ec_funded":1},{"oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:11:30Z","checksum":"91271b23cf884d7c06d33bef0cd623b1","file_id":"4885","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":708657,"file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","access_level":"open_access"}],"pubrep_id":"717","intvolume":" 84","ddc":["004","006"],"title":"Trading performance for stability in Markov decision processes","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1294","abstract":[{"text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints.","lang":"eng"}],"type":"journal_article","date_published":"2017-03-01T00:00:00Z","page":"144 - 170","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” Journal of Computer and System Sciences. Elsevier, 2017. https://doi.org/10.1016/j.jcss.2016.09.009.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170.","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” Journal of Computer and System Sciences, vol. 84, Elsevier, 2017, pp. 144–70, doi:10.1016/j.jcss.2016.09.009.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” Journal of Computer and System Sciences, vol. 84. Elsevier, pp. 144–170, 2017.","apa":"Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2017). Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. Elsevier. https://doi.org/10.1016/j.jcss.2016.09.009","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 2017;84:144-170. doi:10.1016/j.jcss.2016.09.009"},"publication":"Journal of Computer and System Sciences","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","volume":84,"date_updated":"2023-09-20T11:15:31Z","date_created":"2018-12-11T11:51:12Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2305"}]},"author":[{"full_name":"Brázdil, Tomáš","last_name":"Brázdil","first_name":"Tomáš"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Forejt","first_name":"Vojtěch","full_name":"Forejt, Vojtěch"},{"last_name":"Kučera","first_name":"Antonín","full_name":"Kučera, Antonín"}],"publisher":"Elsevier","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2017","publist_id":"6009","ec_funded":1,"file_date_updated":"2020-07-14T12:44:42Z","language":[{"iso":"eng"}],"doi":"10.1016/j.jcss.2016.09.009","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","isi":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"},"external_id":{"isi":["000388430000011"]},"month":"03"},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2017-01-01T00:00:00Z","citation":{"mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” European Journal of Neuroscience, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:10.1111/ejn.13418.","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.","chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” European Journal of Neuroscience. Wiley-Blackwell, 2017. https://doi.org/10.1111/ejn.13418.","ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 2017;45(1):45-57. doi:10.1111/ejn.13418","ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57.","ieee":"U. Sauerzopf et al., “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” European Journal of Neuroscience, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1111/ejn.13418"},"publication":"European Journal of Neuroscience","page":"45 - 57","article_type":"review","issue":"1","abstract":[{"lang":"eng","text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD."}],"type":"journal_article","pubrep_id":"738","oa_version":"Published Version","file":[{"file_id":"4838","relation":"main_file","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:10:48Z","checksum":"c572cf02be8fbb7020cfcfb892182e4c","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","access_level":"open_access","creator":"system","file_size":169145,"content_type":"application/pdf"}],"_id":"1228","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 45","status":"public","title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","ddc":["616"],"month":"01","doi":"10.1111/ejn.13418","language":[{"iso":"eng"}],"external_id":{"isi":["000392487100005"],"pmid":["27690184"]},"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,"isi":1,"quality_controlled":"1","publist_id":"6106","file_date_updated":"2020-07-14T12:44:39Z","author":[{"first_name":"Ulrich","last_name":"Sauerzopf","full_name":"Sauerzopf, Ulrich"},{"first_name":"Roberto","last_name":"Sacco","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","full_name":"Sacco, Roberto"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"full_name":"Niello, Marco","first_name":"Marco","last_name":"Niello"},{"full_name":"Weidenauer, Ana","first_name":"Ana","last_name":"Weidenauer"},{"first_name":"Nicole","last_name":"Praschak Rieder","full_name":"Praschak Rieder, Nicole"},{"full_name":"Sitte, Harald","last_name":"Sitte","first_name":"Harald"},{"first_name":"Matthaeus","last_name":"Willeit","full_name":"Willeit, Matthaeus"}],"volume":45,"date_created":"2018-12-11T11:50:50Z","date_updated":"2023-09-20T11:16:01Z","pmid":1,"year":"2017","acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W.","department":[{"_id":"GaNo"}],"publisher":"Wiley-Blackwell","publication_status":"published"}]