[{"oa_version":"None","abstract":[{"text":"Adipose tissues play key roles in energy homeostasis. Brown adipocytes and beige adipocytes in white adipose tissue (WAT) share the similar characters of thermogenesis, both of them could be potential targets for obesity management. Several thermo-sensitive transient receptor potential channels (thermoTRPs) are shown to be involved in adipocyte biology. However, the expression pattern of thermoTRPs in adipose tissues from obese mice is still unknown. The mRNA expression of thermoTRPs in subcutaneous WAT (sWAT) and interscapular brown adipose tissue (iBAT) from lean and obese mice were measured using reverse transcriptase-quantitative PCRs (RT-qPCR). The results demonstrated that all 10 thermoTRPs are expressed in both iBAT and sWAT, and without significant difference in the mRNA expression level of thermoTRPs between these two tissues. Moreover, Trpv1 and Trpv3 mRNA expression levels in both iBAT and sWAT were significantly decreased in high fat diet (HFD)-induced obese mice and db/db (leptin receptor deficient) mice. Trpm2 mRNA expression level was significantly decreased only in sWAT from HFD-induced obese mice and db/db mice. On the other hand, Trpv2 and Trpv4 mRNA expression levels in iBAT and sWAT were significantly increased in HFD-induced obese mice and db/db mice. Taken together, we conclude that all 10 thermoTRPs are expressed in iBAT and sWAT. And several thermoTRPs differentially expressed in adipose tissues from HFD-induced obese mice and db/db mice, suggesting a potential involvement in anti-obesity regulations.","lang":"eng"}],"intvolume":" 41","month":"08","publisher":"Wiley-Blackwell","scopus_import":1,"quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Cell Biology International","day":"01","year":"2017","publication_status":"published","publication_identifier":{"issn":["10656995"]},"date_created":"2018-12-11T11:48:04Z","issue":"8","date_published":"2017-08-01T00:00:00Z","doi":"10.1002/cbin.10783","volume":41,"page":"908 - 913","_id":"709","status":"public","type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:47Z","citation":{"mla":"Sun, Wuping, et al. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International, vol. 41, no. 8, Wiley-Blackwell, 2017, pp. 908–13, doi:10.1002/cbin.10783.","ama":"Sun W, Li C, Zhang Y, et al. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 2017;41(8):908-913. doi:10.1002/cbin.10783","apa":"Sun, W., Li, C., Zhang, Y., Jiang, C., Zhai, M.-Z., Zhou, Q., … Deng, Q. (2017). Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. Wiley-Blackwell. https://doi.org/10.1002/cbin.10783","ieee":"W. Sun et al., “Gene expression changes of thermo sensitive transient receptor potential channels in obese mice,” Cell Biology International, vol. 41, no. 8. Wiley-Blackwell, pp. 908–913, 2017.","short":"W. Sun, C. Li, Y. Zhang, C. Jiang, M.-Z. Zhai, Q. Zhou, L. Xiao, Q. Deng, Cell Biology International 41 (2017) 908–913.","chicago":"Sun, Wuping, Chen Li, Yonghong Zhang, Changyu Jiang, Ming-Zhu Zhai, Qian Zhou, Lizu Xiao, and Qiwen Deng. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International. Wiley-Blackwell, 2017. https://doi.org/10.1002/cbin.10783.","ista":"Sun W, Li C, Zhang Y, Jiang C, Zhai M-Z, Zhou Q, Xiao L, Deng Q. 2017. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 41(8), 908–913."},"department":[{"_id":"RySh"}],"title":"Gene expression changes of thermo sensitive transient receptor potential channels in obese mice","author":[{"last_name":"Sun","full_name":"Sun, Wuping","first_name":"Wuping"},{"first_name":"Chen","full_name":"Li, Chen","last_name":"Li"},{"last_name":"Zhang","full_name":"Zhang, Yonghong","first_name":"Yonghong"},{"last_name":"Jiang","full_name":"Jiang, Changyu","first_name":"Changyu"},{"last_name":"Zhai","full_name":"Zhai, Ming-Zhu","first_name":"Ming-Zhu","id":"34009CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Qian","full_name":"Zhou, Qian","last_name":"Zhou"},{"first_name":"Lizu","last_name":"Xiao","full_name":"Xiao, Lizu"},{"first_name":"Qiwen","full_name":"Deng, Qiwen","last_name":"Deng"}],"publist_id":"6981"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Obremski, Maciej, and Maciej Skórski. “Renyi Entropy Estimation Revisited,” Vol. 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20.","ista":"Obremski M, Skórski M. 2017. Renyi entropy estimation revisited. 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, LIPIcs, vol. 81, 20.","mla":"Obremski, Maciej, and Maciej Skórski. Renyi Entropy Estimation Revisited. Vol. 81, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20.","short":"M. Obremski, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"M. Obremski and M. Skórski, “Renyi entropy estimation revisited,” presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA, 2017, vol. 81.","ama":"Obremski M, Skórski M. Renyi entropy estimation revisited. In: Vol 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20","apa":"Obremski, M., & Skórski, M. (2017). Renyi entropy estimation revisited (Vol. 81). Presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20"},"title":"Renyi entropy estimation revisited","author":[{"first_name":"Maciej","last_name":"Obremski","full_name":"Obremski, Maciej"},{"full_name":"Skórski, Maciej","last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"publist_id":"6979","article_number":"20","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:48:04Z","doi":"10.4230/LIPIcs.APPROX-RANDOM.2017.20","date_published":"2017-08-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["005","600"],"date_updated":"2021-01-12T08:11:50Z","file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"KrPi"}],"_id":"710","pubrep_id":"888","status":"public","conference":{"name":"20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX","location":"Berkeley, USA","end_date":"2017-08-18","start_date":"2017-08-18"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4991","checksum":"89225c7dcec2c93838458c9102858985","creator":"system","file_size":604813,"date_updated":"2020-07-14T12:47:49Z","file_name":"IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf","date_created":"2018-12-12T10:13:10Z"}],"publication_status":"published","publication_identifier":{"issn":["18688969"]},"ec_funded":1,"volume":81,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"We revisit the problem of estimating entropy of discrete distributions from independent samples, studied recently by Acharya, Orlitsky, Suresh and Tyagi (SODA 2015), improving their upper and lower bounds on the necessary sample size n. For estimating Renyi entropy of order alpha, up to constant accuracy and error probability, we show the following * Upper bounds n = O(1) 2^{(1-1/alpha)H_alpha} for integer alpha>1, as the worst case over distributions with Renyi entropy equal to H_alpha. * Lower bounds n = Omega(1) K^{1-1/alpha} for any real alpha>1, with the constant being an inverse polynomial of the accuracy, as the worst case over all distributions on K elements. Our upper bounds essentially replace the alphabet size by a factor exponential in the entropy, which offers improvements especially in low or medium entropy regimes (interesting for example in anomaly detection). As for the lower bounds, our proof explicitly shows how the complexity depends on both alphabet and accuracy, partially solving the open problem posted in previous works. The argument for upper bounds derives a clean identity for the variance of falling-power sum of a multinomial distribution. Our approach for lower bounds utilizes convex optimization to find a distribution with possibly worse estimation performance, and may be of independent interest as a tool to work with Le Cam’s two point method. "}],"intvolume":" 81","month":"08","alternative_title":["LIPIcs"],"scopus_import":1},{"date_updated":"2021-01-12T08:11:57Z","ddc":["576"],"file_date_updated":"2020-07-14T12:47:50Z","department":[{"_id":"GaNo"},{"_id":"SiHi"}],"_id":"713","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"885","publication_identifier":{"issn":["2050084X"]},"publication_status":"published","file":[{"date_created":"2018-12-12T10:13:36Z","file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf","date_updated":"2020-07-14T12:47:50Z","file_size":6399510,"creator":"system","file_id":"5020","checksum":"1ace3462e64a971b9ead896091829549","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf","date_created":"2018-12-12T10:13:36Z","file_size":4264398,"date_updated":"2020-07-14T12:47:50Z","creator":"system","checksum":"6241dc31eeb87b03facadec3a53a6827","file_id":"5021","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"volume":6,"abstract":[{"text":"To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"08","intvolume":" 6","citation":{"ista":"Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 6, e25125.","chicago":"Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25125.","ama":"Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 2017;6. doi:10.7554/eLife.25125","apa":"Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber, M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25125","short":"D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber, D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler, Q. Hudson, ELife 6 (2017).","ieee":"D. Andergassen et al., “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” eLife, vol. 6. eLife Sciences Publications, 2017.","mla":"Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife, vol. 6, e25125, eLife Sciences Publications, 2017, doi:10.7554/eLife.25125."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6971","author":[{"last_name":"Andergassen","full_name":"Andergassen, Daniel","first_name":"Daniel"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","last_name":"Dotter"},{"first_name":"Dyniel","full_name":"Wenzel, Dyniel","last_name":"Wenzel"},{"full_name":"Sigl, Verena","last_name":"Sigl","first_name":"Verena"},{"first_name":"Philipp","full_name":"Bammer, Philipp","last_name":"Bammer"},{"first_name":"Markus","full_name":"Muckenhuber, Markus","last_name":"Muckenhuber"},{"last_name":"Mayer","full_name":"Mayer, Daniela","first_name":"Daniela"},{"first_name":"Tomasz","full_name":"Kulinski, Tomasz","last_name":"Kulinski"},{"first_name":"Hans","last_name":"Theussl","full_name":"Theussl, Hans"},{"last_name":"Penninger","full_name":"Penninger, Josef","first_name":"Josef"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"last_name":"Barlow","full_name":"Barlow, Denise","first_name":"Denise"},{"first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","last_name":"Pauler","full_name":"Pauler, Florian"},{"first_name":"Quanah","full_name":"Hudson, Quanah","last_name":"Hudson"}],"title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","article_number":"e25125","project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","year":"2017","day":"14","publication":"eLife","doi":"10.7554/eLife.25125","date_published":"2017-08-14T00:00:00Z","date_created":"2018-12-11T11:48:05Z","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1},{"conference":{"name":"28th International Conference on Concurrency Theory, CONCUR","start_date":"2017-09-05","end_date":"2017-09-08","location":"Berlin, Germany"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"886","status":"public","_id":"711","file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_updated":"2021-01-12T08:11:53Z","ddc":["004","005"],"alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 85","month":"08","abstract":[{"lang":"eng","text":"Nested weighted automata (NWA) present a robust and convenient automata-theoretic formalism for quantitative specifications. Previous works have considered NWA that processed input words only in the forward direction. It is natural to allow the automata to process input words backwards as well, for example, to measure the maximal or average time between a response and the preceding request. We therefore introduce and study bidirectional NWA that can process input words in both directions. First, we show that bidirectional NWA can express interesting quantitative properties that are not expressible by forward-only NWA. Second, for the fundamental decision problems of emptiness and universality, we establish decidability and complexity results for the new framework which match the best-known results for the special case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality is achieved at no additional computational complexity. This is in stark contrast to the unweighted case, where bidirectional finite automata are no more expressive but exponentially more succinct than their forward-only counterparts."}],"oa_version":"Published Version","volume":85,"publication_status":"published","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"d2bda4783821a6358333fe27f11f4737","file_id":"4661","date_updated":"2020-07-14T12:47:49Z","file_size":570294,"creator":"system","date_created":"2018-12-12T10:08:02Z","file_name":"IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf"}],"article_number":"5","publist_id":"6976","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop"}],"title":"Bidirectional nested weighted automata","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Bidirectional Nested Weighted Automata,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5.","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 5.","mla":"Chatterjee, Krishnendu, et al. Bidirectional Nested Weighted Automata. Vol. 85, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.5.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Bidirectional nested weighted automata (Vol. 85). Presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5","ama":"Chatterjee K, Henzinger TA, Otop J. Bidirectional nested weighted automata. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.5","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Bidirectional nested weighted automata,” presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany, 2017, vol. 85.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","date_created":"2018-12-11T11:48:04Z","doi":"10.4230/LIPIcs.CONCUR.2017.5","date_published":"2017-08-01T00:00:00Z","year":"2017","has_accepted_license":"1","day":"01"},{"abstract":[{"text":"We establish a weak–strong uniqueness principle for solutions to entropy-dissipating reaction–diffusion equations: As long as a strong solution to the reaction–diffusion equation exists, any weak solution and even any renormalized solution must coincide with this strong solution. Our assumptions on the reaction rates are just the entropy condition and local Lipschitz continuity; in particular, we do not impose any growth restrictions on the reaction rates. Therefore, our result applies to any single reversible reaction with mass-action kinetics as well as to systems of reversible reactions with mass-action kinetics satisfying the detailed balance condition. Renormalized solutions are known to exist globally in time for reaction–diffusion equations with entropy-dissipating reaction rates; in contrast, the global-in-time existence of weak solutions is in general still an open problem–even for smooth data–, thereby motivating the study of renormalized solutions. The key ingredient of our result is a careful adjustment of the usual relative entropy functional, whose evolution cannot be controlled properly for weak solutions or renormalized solutions.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1703.00730","open_access":"1"}],"oa":1,"scopus_import":1,"quality_controlled":"1","publisher":"Elsevier","intvolume":" 159","month":"08","year":"2017","publication_status":"published","publication_identifier":{"issn":["0362546X"]},"publication":"Nonlinear Analysis: Theory, Methods and Applications","language":[{"iso":"eng"}],"day":"01","page":"181 - 207","date_created":"2018-12-11T11:48:05Z","date_published":"2017-08-01T00:00:00Z","volume":159,"doi":"10.1016/j.na.2017.03.001","_id":"712","type":"journal_article","status":"public","citation":{"apa":"Fischer, J. L. (2017). Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. Elsevier. https://doi.org/10.1016/j.na.2017.03.001","ama":"Fischer JL. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 2017;159:181-207. doi:10.1016/j.na.2017.03.001","ieee":"J. L. Fischer, “Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations,” Nonlinear Analysis: Theory, Methods and Applications, vol. 159. Elsevier, pp. 181–207, 2017.","short":"J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207.","mla":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications, vol. 159, Elsevier, 2017, pp. 181–207, doi:10.1016/j.na.2017.03.001.","ista":"Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207.","chicago":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications. Elsevier, 2017. https://doi.org/10.1016/j.na.2017.03.001."},"date_updated":"2021-01-12T08:11:55Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"6975","author":[{"orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JuFi"}],"title":"Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations"},{"page":"7 - 14","doi":"10.1016/j.drugalcdep.2017.04.015","date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:48:05Z","year":"2017","day":"01","publication":"Drug and Alcohol Dependence","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","author":[{"full_name":"Brailoiu, Gabriela","last_name":"Brailoiu","first_name":"Gabriela"},{"last_name":"Deliu","full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293","first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barr","full_name":"Barr, Jeffrey","first_name":"Jeffrey"},{"last_name":"Console Bram","full_name":"Console Bram, Linda","first_name":"Linda"},{"first_name":"Alexandra","full_name":"Ciuciu, Alexandra","last_name":"Ciuciu"},{"full_name":"Abood, Mary","last_name":"Abood","first_name":"Mary"},{"first_name":"Ellen","last_name":"Unterwald","full_name":"Unterwald, Ellen"},{"first_name":"Eugen","full_name":"Brǎiloiu, Eugen","last_name":"Brǎiloiu"}],"publist_id":"6967","article_processing_charge":"No","external_id":{"pmid":["28623807"]},"title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens","citation":{"ista":"Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14.","chicago":"Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence. Elsevier, 2017. https://doi.org/10.1016/j.drugalcdep.2017.04.015.","ama":"Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 2017;178:7-14. doi:10.1016/j.drugalcdep.2017.04.015","apa":"Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. Elsevier. https://doi.org/10.1016/j.drugalcdep.2017.04.015","ieee":"G. Brailoiu et al., “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” Drug and Alcohol Dependence, vol. 178. Elsevier, pp. 7–14, 2017.","short":"G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.","mla":"Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence, vol. 178, Elsevier, 2017, pp. 7–14, doi:10.1016/j.drugalcdep.2017.04.015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":178,"publication_identifier":{"issn":["03768716"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705"}],"month":"09","intvolume":" 178","abstract":[{"text":"Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"department":[{"_id":"GaNo"}],"date_updated":"2021-01-12T08:12:00Z","type":"journal_article","article_type":"original","status":"public","_id":"714"},{"_id":"715","article_number":"aao4218","type":"journal_article","status":"public","citation":{"ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218.","chicago":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218.","apa":"Novarino, G. (2017). More excitation for Rett syndrome. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218","ama":"Novarino G. More excitation for Rett syndrome. Science Translational Medicine. 2017;9(405). doi:10.1126/scitranslmed.aao4218","ieee":"G. Novarino, “More excitation for Rett syndrome,” Science Translational Medicine, vol. 9, no. 405. American Association for the Advancement of Science, 2017.","short":"G. Novarino, Science Translational Medicine 9 (2017).","mla":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aao4218."},"date_updated":"2021-01-12T08:12:04Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"publist_id":"6968","title":"More excitation for Rett syndrome","department":[{"_id":"GaNo"}],"abstract":[{"lang":"eng","text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome."}],"oa_version":"None","publisher":"American Association for the Advancement of Science","quality_controlled":"1","scopus_import":1,"month":"08","intvolume":" 9","publication_identifier":{"issn":["19466234"]},"year":"2017","publication_status":"published","day":"30","publication":"Science Translational Medicine","language":[{"iso":"eng"}],"volume":9,"doi":"10.1126/scitranslmed.aao4218","date_published":"2017-08-30T00:00:00Z","issue":"405","date_created":"2018-12-11T11:48:06Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.","ieee":"K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017.","apa":"Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408","ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):34. doi:10.1145/3121408","mla":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408.","ista":"Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408."},"title":"The complexity of mean-payoff pushdown games","external_id":{"arxiv":["1201.2829"]},"author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"publist_id":"6964","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"publication":"Journal of the ACM","day":"01","year":"2017","date_created":"2018-12-11T11:48:06Z","date_published":"2017-09-01T00:00:00Z","doi":"10.1145/3121408","page":"34","oa":1,"quality_controlled":"1","publisher":"ACM","date_updated":"2021-01-12T08:12:08Z","department":[{"_id":"KrCh"}],"_id":"716","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00045411"]},"ec_funded":1,"volume":64,"issue":"5","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded."}],"intvolume":" 64","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1201.2829","open_access":"1"}],"scopus_import":1},{"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"publist_id":"6963","title":"Hyperplane separation technique for multidimensional mean-payoff games","citation":{"ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences. Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005.","apa":"Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259. doi:10.1016/j.jcss.2017.04.005","short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic Press, pp. 236–259, 2017.","mla":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences, vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Academic Press","oa":1,"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.","page":"236 - 259","date_published":"2017-09-01T00:00:00Z","doi":"10.1016/j.jcss.2017.04.005","date_created":"2018-12-11T11:48:07Z","year":"2017","day":"01","publication":"Journal of Computer and System Sciences","type":"journal_article","status":"public","_id":"717","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T10:38:15Z","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1210.3141","open_access":"1"}],"month":"09","intvolume":" 88","abstract":[{"lang":"eng","text":"We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard."}],"oa_version":"Preprint","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2329"}]},"volume":88,"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}]},{"title":"Special issue: Synthesis and SYNT 2014","department":[{"_id":"KrCh"}],"publist_id":"6961","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Rüdiger","full_name":"Ehlers, Rüdiger","last_name":"Ehlers"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:10.1007/s00236-017-0299-0.","short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544.","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.","apa":"Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica. 2017;54(6):543-544. doi:10.1007/s00236-017-0299-0","chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0.","ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544."},"date_updated":"2021-01-12T08:12:18Z","status":"public","type":"journal_article","_id":"719","doi":"10.1007/s00236-017-0299-0","issue":"6","date_published":"2017-09-01T00:00:00Z","volume":54,"date_created":"2018-12-11T11:48:07Z","page":"543 - 544","day":"01","publication":"Acta Informatica","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00015903"]},"year":"2017","publication_status":"published","month":"09","intvolume":" 54","scopus_import":1,"quality_controlled":"1","publisher":"Springer","oa_version":"None","abstract":[{"lang":"eng","text":"The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains."}]},{"author":[{"first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","last_name":"Humplik","full_name":"Humplik, Jan"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"publist_id":"6960","article_processing_charge":"Yes","title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","citation":{"ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.","apa":"Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.","mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups"},{"call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes"}],"article_number":"e1005763","doi":"10.1371/journal.pcbi.1005763","date_published":"2017-09-19T00:00:00Z","date_created":"2018-12-11T11:48:08Z","has_accepted_license":"1","year":"2017","day":"19","publication":"PLoS Computational Biology","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"file_date_updated":"2020-07-14T12:47:53Z","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T08:12:21Z","ddc":["530","571"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"884","_id":"720","issue":"9","volume":13,"publication_identifier":{"issn":["1553734X"]},"publication_status":"published","file":[{"checksum":"81107096c19771c36ddbe6f0282a3acb","file_id":"5352","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","date_created":"2018-12-12T10:18:30Z","creator":"system","file_size":14167050,"date_updated":"2020-07-14T12:47:53Z"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"09","intvolume":" 13","abstract":[{"lang":"eng","text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality."}],"oa_version":"Published Version"},{"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"publist_id":"6959","author":[{"full_name":"Ajanki, Oskari H","last_name":"Ajanki","first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","orcid":"0000-0002-4821-3297","full_name":"Krüger, Torben H","last_name":"Krüger"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"}],"title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","citation":{"chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639.","ista":"Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705.","mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639.","ieee":"O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” Communications on Pure and Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705.","ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639","apa":"Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"page":"1672 - 1705","doi":"10.1002/cpa.21639","date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:48:08Z","year":"2017","day":"01","publication":"Communications on Pure and Applied Mathematics","type":"journal_article","status":"public","_id":"721","department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T08:12:24Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1512.03703"}],"month":"09","intvolume":" 70","abstract":[{"lang":"eng","text":"Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur."}],"oa_version":"Submitted Version","issue":"9","volume":70,"ec_funded":1,"publication_identifier":{"issn":["00103640"]},"publication_status":"published","language":[{"iso":"eng"}]},{"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"external_id":{"pmid":["28898665"]},"publist_id":"6956","author":[{"full_name":"Morris, Emily","last_name":"Morris","first_name":"Emily"},{"first_name":"Marcus","full_name":"Griffiths, Marcus","last_name":"Griffiths"},{"first_name":"Agata","full_name":"Golebiowska, Agata","last_name":"Golebiowska"},{"first_name":"Stefan","last_name":"Mairhofer","full_name":"Mairhofer, Stefan"},{"last_name":"Burr Hersey","full_name":"Burr Hersey, Jasmine","first_name":"Jasmine"},{"first_name":"Tatsuaki","last_name":"Goh","full_name":"Goh, Tatsuaki"},{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247"},{"full_name":"Atkinson, Brian","last_name":"Atkinson","first_name":"Brian"},{"first_name":"Craig","last_name":"Sturrock","full_name":"Sturrock, Craig"},{"first_name":"Jonathan","full_name":"Lynch, Jonathan","last_name":"Lynch"},{"first_name":"Kris","full_name":"Vissenberg, Kris","last_name":"Vissenberg"},{"full_name":"Ritz, Karl","last_name":"Ritz","first_name":"Karl"},{"first_name":"Darren","full_name":"Wells, Darren","last_name":"Wells"},{"first_name":"Sacha","last_name":"Mooney","full_name":"Mooney, Sacha"},{"first_name":"Malcolm","full_name":"Bennett, Malcolm","last_name":"Bennett"}],"title":"Shaping 3D root system architecture","citation":{"mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043.","short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.","ieee":"E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043","ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043.","ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Cell Press","quality_controlled":"1","page":"R919 - R930","date_created":"2018-12-11T11:48:08Z","doi":"10.1016/j.cub.2017.06.043","date_published":"2017-09-11T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Current Biology","day":"11","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"982","status":"public","_id":"722","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:54Z","date_updated":"2021-01-12T08:12:29Z","ddc":["581"],"scopus_import":1,"intvolume":" 27","month":"09","abstract":[{"text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"ec_funded":1,"issue":"17","volume":27,"publication_status":"published","publication_identifier":{"issn":["09609822"]},"language":[{"iso":"eng"}],"file":[{"file_id":"6332","checksum":"e45588b21097b408da6276a3e5eedb2e","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_CurrentBiology_Morris.pdf","date_created":"2019-04-17T07:46:40Z","creator":"dernst","file_size":1576593,"date_updated":"2020-07-14T12:47:54Z"}]},{"publication_status":"published","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"volume":114,"issue":"38","abstract":[{"text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/"}],"scopus_import":1,"intvolume":" 114","month":"09","date_updated":"2021-01-12T08:12:36Z","department":[{"_id":"GaTk"}],"_id":"725","type":"journal_article","status":"public","year":"2017","publication":"PNAS","day":"19","page":"10149 - 10154","date_created":"2018-12-11T11:48:10Z","date_published":"2017-09-19T00:00:00Z","doi":"10.1073/pnas.1703817114","oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","citation":{"chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114.","ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114","apa":"Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28874581"]},"publist_id":"6953","author":[{"last_name":"Harpaz","full_name":"Harpaz, Roy","first_name":"Roy"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"}],"title":"Discrete modes of social information processing predict individual behavior of fish in a group"},{"doi":"10.1103/PhysRevB.96.104203","date_published":"2017-09-13T00:00:00Z","date_created":"2018-12-11T11:48:09Z","day":"13","publication":"Physical Review B","year":"2017","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"We would like to thank Dmitry Abanin, Christophe De\r\nBeule, Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions. Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1.","title":"Noninteracting central site model localization and logarithmic entanglement growth","author":[{"last_name":"Hetterich","full_name":"Hetterich, Daniel","first_name":"Daniel"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn"},{"first_name":"Fernando","full_name":"Domínguez, Fernando","last_name":"Domínguez"},{"last_name":"Pollmann","full_name":"Pollmann, Frank","first_name":"Frank"},{"first_name":"Björn","last_name":"Trauzettel","full_name":"Trauzettel, Björn"}],"publist_id":"6955","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104203.","ista":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 96(10), 104203.","mla":"Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203.","short":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017).","ieee":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” Physical Review B, vol. 96, no. 10. American Physical Society, 2017.","ama":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203","apa":"Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203"},"article_number":"104203","volume":96,"issue":"10","language":[{"iso":"eng"}],"publication_identifier":{"issn":["24699950"]},"publication_status":"published","month":"09","intvolume":" 96","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1701.02744","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"text":"We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic.","lang":"eng"}],"department":[{"_id":"MaSe"}],"date_updated":"2021-01-12T08:12:35Z","status":"public","type":"journal_article","_id":"724"},{"department":[{"_id":"GaNo"}],"title":"The science of love in ASD and ADHD","publist_id":"6938","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:12:57Z","citation":{"short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “The science of love in ASD and ADHD,” Science Translational Medicine, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). The science of love in ASD and ADHD. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aap8168","ama":"Novarino G. The science of love in ASD and ADHD. Science Translational Medicine. 2017;9(411). doi:10.1126/scitranslmed.aap8168","mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aap8168.","ista":"Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168.","chicago":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aap8168."},"status":"public","type":"journal_article","article_number":"eaap8168","_id":"731","doi":"10.1126/scitranslmed.aap8168","issue":"411","volume":9,"date_published":"2017-10-11T00:00:00Z","date_created":"2018-12-11T11:48:12Z","day":"11","publication":"Science Translational Medicine","language":[{"iso":"eng"}],"publication_identifier":{"issn":["19466234"]},"publication_status":"published","year":"2017","month":"10","intvolume":" 9","quality_controlled":"1","scopus_import":1,"publisher":"American Association for the Advancement of Science","oa_version":"None","abstract":[{"text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently.","lang":"eng"}]},{"language":[{"iso":"eng"}],"file":[{"date_created":"2020-03-03T10:55:13Z","file_name":"2017_MolecularTherapy_Smole.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:56Z","file_size":3404806,"checksum":"ea8b1b28606dd1edab7379ba4fa3641f","file_id":"7561","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["1525-0016"]},"volume":25,"issue":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy.","lang":"eng"}],"intvolume":" 25","month":"01","ddc":["570"],"date_updated":"2021-01-12T08:13:14Z","file_date_updated":"2020-07-14T12:47:56Z","department":[{"_id":"MaLo"}],"_id":"7360","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","publication":"Molecular Therapy","day":"01","year":"2017","has_accepted_license":"1","date_created":"2020-01-25T15:55:39Z","doi":"10.1016/j.ymthe.2016.10.005","date_published":"2017-01-01T00:00:00Z","page":"102-119","oa":1,"quality_controlled":"1","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier, 2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005.","short":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119.","ieee":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation,” Molecular Therapy, vol. 25, no. 1. Elsevier, pp. 102–119, 2017.","ama":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005","apa":"Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017). A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005","chicago":"Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.","ista":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 25(1), 102–119."},"title":"A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation","article_processing_charge":"No","external_id":{"pmid":["28129106"]},"author":[{"last_name":"Smole","full_name":"Smole, Anže","first_name":"Anže"},{"first_name":"Duško","last_name":"Lainšček","full_name":"Lainšček, Duško"},{"first_name":"Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","full_name":"Bezeljak, Urban","orcid":"0000-0003-1365-5631","last_name":"Bezeljak"},{"last_name":"Horvat","full_name":"Horvat, Simon","first_name":"Simon"},{"last_name":"Jerala","full_name":"Jerala, Roman","first_name":"Roman"}]},{"publication_status":"published","year":"2017","publication_identifier":{"isbn":["978-153862714-3"]},"language":[{"iso":"eng"}],"publication":"2017 IEEE International Conference on Big Data","day":"01","page":"3760 - 3763","date_created":"2018-12-11T11:48:18Z","doi":"10.1109/BigData.2017.8258375","date_published":"2017-12-01T00:00:00Z","abstract":[{"text":"Modern communication technologies allow first responders to contact thousands of potential volunteers simultaneously for support during a crisis or disaster event. However, such volunteer efforts must be well coordinated and monitored, in order to offer an effective relief to the professionals. In this paper we extend earlier work on optimally assigning volunteers to selected landmark locations. In particular, we emphasize the aspect that obtaining good assignments requires not only advanced computational tools, but also a realistic measure of distance between volunteers and landmarks. Specifically, we propose the use of the Open Street Map (OSM) driving distance instead of he previously used flight distance. We find the OSM driving distance to be better aligned with the interests of volunteers and first responders. Furthermore, we show that relying on the flying distance leads to a substantial underestimation of the number of required volunteers, causing negative side effects in case of an actual crisis situation.","lang":"eng"}],"oa_version":"None","quality_controlled":"1","scopus_import":1,"publisher":"IEEE","month":"12","citation":{"ista":"Pielorz J, Prandtstetter M, Straub M, Lampert C. 2017. Optimal geospatial volunteer allocation needs realistic distances. 2017 IEEE International Conference on Big Data. Big Data, 3760–3763.","chicago":"Pielorz, Jasmin, Matthias Prandtstetter, Markus Straub, and Christoph Lampert. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” In 2017 IEEE International Conference on Big Data, 3760–63. IEEE, 2017. https://doi.org/10.1109/BigData.2017.8258375.","short":"J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763.","ieee":"J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial volunteer allocation needs realistic distances,” in 2017 IEEE International Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.","ama":"Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer allocation needs realistic distances. In: 2017 IEEE International Conference on Big Data. IEEE; 2017:3760-3763. doi:10.1109/BigData.2017.8258375","apa":"Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal geospatial volunteer allocation needs realistic distances. In 2017 IEEE International Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375","mla":"Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–63, doi:10.1109/BigData.2017.8258375."},"date_updated":"2021-01-12T08:13:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jasmin","id":"49BC895A-F248-11E8-B48F-1D18A9856A87","full_name":"Pielorz, Jasmin","last_name":"Pielorz"},{"full_name":"Prandtstetter, Matthias","last_name":"Prandtstetter","first_name":"Matthias"},{"last_name":"Straub","full_name":"Straub, Markus","first_name":"Markus"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"publist_id":"6906","title":"Optimal geospatial volunteer allocation needs realistic distances","department":[{"_id":"ChLa"}],"_id":"750","conference":{"name":"Big Data","location":"Boston, MA, United States","end_date":"2017-12-14","start_date":"2017-12-11"},"type":"conference","status":"public"},{"oa":1,"publisher":"International Press","quality_controlled":"1","date_created":"2018-12-11T11:48:32Z","doi":"10.37236/6663","date_published":"2017-07-28T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Electronic Journal of Combinatorics","day":"28","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"P3.18","article_processing_charge":"No","publist_id":"6859","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"first_name":"Dömötör","last_name":"Pálvölgyi","full_name":"Pálvölgyi, Dömötör"}],"title":"Unified Hanani Tutte theorem","citation":{"mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663.","short":"R. Fulek, J. Kynčl, D. Pálvölgyi, Electronic Journal of Combinatorics 24 (2017).","ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.","ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 2017;24(3). doi:10.37236/6663","apa":"Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics. International Press, 2017. https://doi.org/10.37236/6663.","ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","intvolume":" 24","month":"07","abstract":[{"lang":"eng","text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof."}],"oa_version":"Published Version","ec_funded":1,"issue":"3","volume":24,"publication_status":"published","publication_identifier":{"issn":["10778926"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2017_ElectrCombi_Fulek.pdf","date_created":"2019-01-18T14:04:08Z","creator":"dernst","file_size":236944,"date_updated":"2020-07-14T12:48:06Z","file_id":"5853","checksum":"ef320cff0f062051e858f929be6a3581","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","article_type":"original","status":"public","_id":"795","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:48:06Z","date_updated":"2022-03-18T12:58:53Z","ddc":["000"]},{"abstract":[{"text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden.","lang":"ger"}],"oa_version":"None","quality_controlled":"1","publisher":"Wiley","month":"05","intvolume":" 48","year":"2017","publication_status":"published","day":"01","publication":"Physik in unserer Zeit","language":[{"iso":"eng"}],"page":"111 - 113","volume":48,"doi":"10.1002/piuz.201770305","issue":"3","date_published":"2017-05-01T00:00:00Z","date_created":"2018-12-11T11:48:33Z","_id":"797","type":"journal_article","article_type":"original","status":"public","citation":{"ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit. Wiley, 2017. https://doi.org/10.1002/piuz.201770305.","ieee":"J. M. Fink, “Photonenblockade aufgelöst,” Physik in unserer Zeit, vol. 48, no. 3. Wiley, pp. 111–113, 2017.","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","ama":"Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113. doi:10.1002/piuz.201770305","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit. Wiley. https://doi.org/10.1002/piuz.201770305","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305."},"date_updated":"2022-03-24T09:16:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6856","author":[{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"}],"article_processing_charge":"No","title":"Photonenblockade aufgelöst","department":[{"_id":"JoFi"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","ieee":"M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","apa":"Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898","ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1898."},"title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung","publist_id":"6843","author":[{"first_name":"Magdalena","last_name":"Andrae","full_name":"Andrae, Magdalena"},{"full_name":"Villányi, Márton","orcid":"0000-0001-8126-0426","last_name":"Villányi","first_name":"Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87"}],"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","day":"01","year":"2017","has_accepted_license":"1","popular_science":"1","date_created":"2018-12-11T11:48:36Z","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1898","page":"274 - 280","oa":1,"publisher":"VÖB","ddc":["020"],"date_updated":"2021-01-12T08:16:45Z","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:48:09Z","_id":"807","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"date_created":"2019-01-18T13:39:26Z","file_name":"2017_VOEB_Andrae.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:09Z","file_size":125065,"file_id":"5851","checksum":"558c18bcf5580d87dd371ec626d52075","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["10222588"]},"issue":"2","volume":70,"oa_version":"Published Version","abstract":[{"text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.","lang":"eng"}],"intvolume":" 70","month":"08","scopus_import":1},{"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:48:42Z","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1678","page":"200 - 207","oa":1,"publisher":"VÖB","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1678","ama":"Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207. doi:10.31263/voebm.v70i2.1678","ieee":"B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 70 (2017) 200–207.","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1678."},"title":"Metadata for research data in practice","author":[{"first_name":"Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch","orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara"}],"publist_id":"6823","language":[{"iso":"eng"}],"file":[{"date_created":"2019-01-18T13:32:17Z","file_name":"2017_VOEB_Petritsch.pdf","date_updated":"2020-07-14T12:48:11Z","file_size":7843975,"creator":"dernst","file_id":"5850","checksum":"7c4544d07efa2c2add8612b489abb4e2","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["10222588"]},"issue":"2","volume":70,"oa_version":"Published Version","abstract":[{"text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.","lang":"eng"}],"intvolume":" 70","month":"08","scopus_import":1,"ddc":["020"],"date_updated":"2021-01-12T08:17:44Z","file_date_updated":"2020-07-14T12:48:11Z","department":[{"_id":"E-Lib"}],"_id":"825","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article"},{"external_id":{"pmid":["29140247"]},"article_processing_charge":"No","author":[{"first_name":"David B","full_name":"Lyons, David B","last_name":"Lyons"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"}],"title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","citation":{"ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"e30674","date_created":"2021-06-02T14:28:58Z","doi":"10.7554/elife.30674","date_published":"2017-11-15T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"eLife","day":"15","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","file_date_updated":"2021-06-02T14:33:36Z","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T07:54:36Z","ddc":["570"],"extern":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"9445","volume":6,"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"4cfcdd67511ae4aed3d993550e46e146","file_id":"9446","success":1,"date_updated":"2021-06-02T14:33:36Z","file_size":1603102,"creator":"cziletti","date_created":"2021-06-02T14:33:36Z","file_name":"2017_eLife_Lyons.pdf"}],"scopus_import":"1","intvolume":" 6","month":"11","abstract":[{"text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation.","lang":"eng"}],"pmid":1,"oa_version":"Published Version"},{"type":"book_chapter","status":"public","_id":"957","series_title":"Synthetic Protein Switches","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T08:22:13Z","scopus_import":1,"alternative_title":["Methods in Molecular Biology"],"intvolume":" 1596","month":"03","abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"oa_version":"None","volume":1596,"publication_status":"published","publication_identifier":{"issn":["10643745"]},"language":[{"iso":"eng"}],"project":[{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"}],"publist_id":"6451","author":[{"first_name":"Ben","full_name":"Clifton, Ben","last_name":"Clifton"},{"last_name":"Whitfield","full_name":"Whitfield, Jason","first_name":"Jason"},{"id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada"},{"last_name":"Herde","full_name":"Herde, Michel","first_name":"Michel"},{"first_name":"Christian","full_name":"Henneberger, Christian","last_name":"Henneberger"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Colin","full_name":"Jackson, Colin","last_name":"Jackson"}],"editor":[{"last_name":"Stein","full_name":"Stein, Viktor","first_name":"Viktor"}],"title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","citation":{"chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer","page":"71 - 87","date_created":"2018-12-11T11:49:24Z","date_published":"2017-03-15T00:00:00Z","doi":"10.1007/978-1-4939-6940-1_5","year":"2017","publication":"Synthetic Protein Switches","day":"15"},{"day":"01","has_accepted_license":"1","year":"2017","date_published":"2017-06-01T00:00:00Z","doi":"10.4230/LIPIcs.MFCS.2017.37","date_created":"2018-12-11T11:49:26Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37"},"title":"Timed network games with clocks","author":[{"last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"publist_id":"6438","article_number":"37","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"file":[{"creator":"system","file_size":369730,"date_updated":"2020-07-14T12:48:18Z","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf","date_created":"2018-12-12T10:14:10Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5059","checksum":"f55eaf7f3c36ea07801112acfedd17d5"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"]},"publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"6005","status":"public"}]},"volume":83,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. 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Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc."},"date_updated":"2023-02-21T16:34:41Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"full_name":"Ioffe, Mark","last_name":"Ioffe","first_name":"Mark"},{"last_name":"Loback","full_name":"Loback, Adrianna","first_name":"Adrianna"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}],"article_processing_charge":"No","title":"Data from: Error-robust modes of the retinal population code","department":[{"_id":"GaTk"}],"abstract":[{"text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.","lang":"eng"}],"oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"url":"https://doi.org/10.5061/dryad.1f1rc","open_access":"1"}],"oa":1,"month":"10","year":"2017","day":"18","date_published":"2017-10-18T00:00:00Z","doi":"10.5061/dryad.1f1rc","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1197"}]},"date_created":"2021-07-23T11:34:34Z"},{"date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122","date_created":"2018-12-11T11:47:04Z","day":"18","publication":"PLoS Genetics","has_accepted_license":"1","year":"2017","publisher":"Public Library of Science","quality_controlled":"1","oa":1,"title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic"},{"first_name":"Frank","last_name":"Schreiber","full_name":"Schreiber, Frank"},{"first_name":"Alma","last_name":"Dal Co","full_name":"Dal Co, Alma"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller"},{"first_name":"Sten","last_name":"Littmann","full_name":"Littmann, Sten"},{"full_name":"Kuypers, Marcel","last_name":"Kuypers","first_name":"Marcel"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"}],"publist_id":"7275","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12). doi:10.1371/journal.pgen.1007122","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122","ieee":"N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12. Public Library of Science, 2017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).","mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122."},"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"e1007122","issue":"12","volume":13,"related_material":{"record":[{"id":"9844","status":"public","relation":"research_data"},{"id":"9845","status":"public","relation":"research_data"},{"status":"public","id":"9846","relation":"research_data"}]},"ec_funded":1,"file":[{"date_created":"2018-12-12T10:14:35Z","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","date_updated":"2020-07-14T12:46:46Z","file_size":1308475,"creator":"system","checksum":"22426d9382f21554bad5fa5967afcfd0","file_id":"5088","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15537390"]},"publication_status":"published","month":"12","intvolume":" 13","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed."}],"department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:46:46Z","ddc":["576","579"],"date_updated":"2023-02-23T14:10:34Z","status":"public","pubrep_id":"959","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"541"},{"_id":"9847","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T12:29:44Z","citation":{"chicago":"Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1.","ista":"Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification, The Royal Society, 10.6084/m9.figshare.5633917.v1.","mla":"Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1.","apa":"Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1","ama":"Pleska M, Guet CC. Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification. 2017. doi:10.6084/m9.figshare.5633917.v1","short":"M. Pleska, C.C. Guet, (2017).","ieee":"M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification.” The Royal Society, 2017."},"title":"Supplementary materials and methods; Full data set from effects of mutations in phage restriction sites during escape from restriction–modification","department":[{"_id":"CaGu"}],"article_processing_charge":"No","author":[{"first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479","last_name":"Pleska"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"information on culture conditions, phage mutagenesis, verification and lysate preparation; Raw data"}],"month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.5633917.v1"}],"publisher":"The Royal Society","day":"27","year":"2017","date_created":"2021-08-09T13:54:38Z","date_published":"2017-11-27T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"561","status":"public"}]},"doi":"10.6084/m9.figshare.5633917.v1"},{"_id":"9845","status":"public","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T12:25:04Z","citation":{"chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017.","ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017.","mla":"Nikolic, Nela, et al. Mathematical Model. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s017.","ieee":"N. Nikolic et al., “Mathematical model.” Public Library of Science, 2017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017"},"department":[{"_id":"CaGu"}],"title":"Mathematical model","article_processing_charge":"No","author":[{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"last_name":"Dal Co","full_name":"Dal Co, Alma","first_name":"Alma"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"full_name":"Littmann, Sten","last_name":"Littmann","first_name":"Sten"},{"first_name":"Marcel","full_name":"Kuypers, Marcel","last_name":"Kuypers"},{"first_name":"Martin","full_name":"Ackermann, Martin","last_name":"Ackermann"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of heavy isotopes measured\tin single cells"}],"month":"12","publisher":"Public Library of Science","day":"18","year":"2017","date_created":"2021-08-09T13:31:51Z","related_material":{"record":[{"status":"public","id":"541","relation":"used_in_publication"}]},"date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122.s017"},{"_id":"9849","type":"research_data_reference","status":"public","citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001","ama":"Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:10.1371/journal.pcbi.1005609.s001","mla":"Lukacisinova, Marta, et al. Modelling and Simulation Details. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. 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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."}],"oa_version":"Published Version"},{"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"}],"oa_version":"Published Version","publisher":"Public Library of Science","month":"07","year":"2017","day":"18","date_created":"2021-08-09T14:08:14Z","related_material":{"record":[{"id":"696","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pcbi.1005609.s003","date_published":"2017-07-18T00:00:00Z","_id":"9851","type":"research_data_reference","status":"public","citation":{"mla":"Lukacisinova, Marta, et al. 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Supplementary appendix, Public Library of Science, 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","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","short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017.","mla":"Chalk, Matthew J., et al. Supplementary Appendix. 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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. 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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.","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.","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","ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. 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Genome Biology. 18(1), 87.","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"87","date_created":"2021-06-07T12:27:39Z","doi":"10.1186/s13059-017-1230-2","date_published":"2017-05-09T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Genome Biology","day":"09","oa":1,"quality_controlled":"1","publisher":"Springer Nature","department":[{"_id":"DaZi"}],"file_date_updated":"2021-06-07T12:31:36Z","date_updated":"2021-12-14T07:55:02Z","ddc":["570"],"extern":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"9506","issue":"1","volume":18,"publication_status":"published","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"language":[{"iso":"eng"}],"file":[{"file_size":278183,"date_updated":"2021-06-07T12:31:36Z","creator":"asandaue","file_name":"2017_GenomeBiology_Zilberman.pdf","date_created":"2021-06-07T12:31:36Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"9507","checksum":"5a455ad914e7d225b1baa4ab07fd925e"}],"scopus_import":"1","intvolume":" 18","month":"05","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1},{"quality_controlled":"1","publisher":"Springer","page":"89 - 99","date_published":"2017-05-15T00:00:00Z","doi":"10.1007/978-1-4939-6940-1_6","date_created":"2018-12-11T11:49:24Z","year":"2017","day":"15","publication":"Synthetic Protein Switches","publist_id":"6450","author":[{"last_name":"Mitchell","full_name":"Mitchell, Joshua","first_name":"Joshua"},{"first_name":"William","full_name":"Zhang, William","last_name":"Zhang"},{"last_name":"Herde","full_name":"Herde, Michel","first_name":"Michel"},{"last_name":"Henneberger","full_name":"Henneberger, Christian","first_name":"Christian"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"first_name":"Colin","full_name":"Jackson, Colin","last_name":"Jackson"}],"title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"citation":{"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.","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.","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.","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.","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","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","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"month":"05","intvolume":" 1596","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."}],"oa_version":"None","volume":1596,"publication_identifier":{"issn":["10643745"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"book_chapter","status":"public","series_title":"Synthetic Protein Switches","_id":"958","department":[{"_id":"HaJa"}],"date_updated":"2021-01-12T08:22:13Z"},{"date_published":"2017-01-14T00:00:00Z","doi":"10.5061/dryad.pk16b","related_material":{"record":[{"status":"deleted","id":"9702","relation":"used_in_publication"}]},"date_created":"2021-07-23T09:39:34Z","year":"2017","day":"14","publisher":"Dryad","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.pk16b"}],"month":"01","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."}],"oa_version":"Published Version","author":[{"full_name":"Riccio, Paul","last_name":"Riccio","first_name":"Paul"},{"first_name":"Christina","last_name":"Cebrián","full_name":"Cebrián, Christina"},{"full_name":"Zong, Hui","last_name":"Zong","first_name":"Hui"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"},{"last_name":"Costantini","full_name":"Costantini, Frank","first_name":"Frank"}],"article_processing_charge":"No","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","department":[{"_id":"SiHi"}],"citation":{"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.","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.","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","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","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.","short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).","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."},"date_updated":"2022-08-25T13:34:55Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9707"},{"publisher":"Public Library of Science","month":"12","oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","id":"541","status":"public"}]},"date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122.s018","date_created":"2021-08-09T13:27:16Z","year":"2017","day":"18","type":"research_data_reference","status":"public","_id":"9844","author":[{"orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"full_name":"Dal Co, Alma","last_name":"Dal Co","first_name":"Alma"},{"last_name":"Kiviet","full_name":"Kiviet, Daniel","first_name":"Daniel"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"last_name":"Littmann","full_name":"Littmann, Sten","first_name":"Sten"},{"last_name":"Kuypers","full_name":"Kuypers, Marcel","first_name":"Marcel"},{"first_name":"Martin","full_name":"Ackermann, Martin","last_name":"Ackermann"}],"article_processing_charge":"No","title":"Source data for figures and tables","department":[{"_id":"CaGu"}],"date_updated":"2023-02-23T12:25:04Z","citation":{"mla":"Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s018.","ieee":"N. Nikolic et al., “Source data for figures and tables.” Public Library of Science, 2017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:10.1371/journal.pgen.1007122.s018","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","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.","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"date_created":"2023-05-05T12:58:53Z","date_published":"2017-03-03T00:00:00Z","page":"28","publication":"AHPC17 – Austrian HPC Meeting 2017","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","file_id":"12969","creator":"dernst","file_size":1005486,"date_updated":"2023-05-16T07:20:50Z","file_name":"2017_AHPC_Schloegl.pdf","date_created":"2023-05-16T07:20:50Z"}],"day":"03","year":"2017","publication_status":"published","has_accepted_license":"1","month":"03","main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf"}],"oa":1,"publisher":"FSP Scientific Computing","oa_version":"Published Version","department":[{"_id":"ScienComp"}],"file_date_updated":"2023-05-16T07:20:50Z","title":"Scientific Computing at IST Austria","article_processing_charge":"No","author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"full_name":"Kiss, Janos","last_name":"Kiss","first_name":"Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2023-05-16T07:22:23Z","citation":{"mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: AHPC17 – Austrian HPC Meeting 2017. FSP Scientific Computing; 2017:28.","apa":"Schlögl, A., & Kiss, J. (2017). Scientific Computing at IST Austria. In AHPC17 – Austrian HPC Meeting 2017 (p. 28). Grundlsee, Austria: FSP Scientific Computing.","short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in AHPC17 – Austrian HPC Meeting 2017, Grundlsee, Austria, 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.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28."},"status":"public","conference":{"name":"AHPC: Austrian HPC Meeting","start_date":"2017-03-01","end_date":"2017-03-03","location":"Grundlsee, Austria"},"type":"conference_abstract","_id":"12905"},{"author":[{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky"},{"first_name":"Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer"},{"last_name":"Waldmann","full_name":"Waldmann, Clara","first_name":"Clara"},{"full_name":"Weininger, Maximilian","last_name":"Weininger","first_name":"Maximilian"}],"external_id":{"arxiv":["1701.05738"]},"article_processing_charge":"No","title":"Index appearance record for transforming Rabin automata into parity automata","citation":{"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.","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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"443-460","date_published":"2017-03-31T00:00:00Z","doi":"10.1007/978-3-662-54577-5_26","date_created":"2023-06-21T13:21:14Z","year":"2017","day":"31","publication":"Tools and Algorithms for the Construction and Analysis of Systems","quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","department":[{"_id":"KrCh"}],"date_updated":"2023-06-21T13:29:46Z","type":"conference","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"},"status":"public","_id":"13160","volume":10205,"publication_identifier":{"eisbn":["9783662545775"],"eissn":["1611-3349"],"isbn":["9783662545768"],"issn":["0302-9743"]},"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1701.05738","open_access":"1"}],"month":"03","intvolume":" 10205","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."}],"oa_version":"Preprint"},{"status":"public","pubrep_id":"844","type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2017-09-07","location":"Berlin, Germany","start_date":"2017-09-05","name":"CONCUR: Concurrency Theory"},"_id":"950","file_date_updated":"2020-07-14T12:48:16Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-08-29T07:02:13Z","month":"09","intvolume":" 85","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","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"}],"volume":85,"related_material":{"record":[{"id":"6752","status":"public","relation":"later_version"}]},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6d5cccf755207b91ccbef95d8275b013","file_id":"5318","date_updated":"2020-07-14T12:48:16Z","file_size":335170,"creator":"system","date_created":"2018-12-12T10:18:00Z","file_name":"IST-2017-844-v1+1_concur-cr.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1868-8969"]},"publication_status":"published","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"article_number":"17","title":"Infinite-duration bidding games","publist_id":"6466","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Chonev","full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1705.01433"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17.","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.","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","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"},"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"doi":"10.4230/LIPIcs.CONCUR.2017.21","date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:49:22Z","day":"01","has_accepted_license":"1","year":"2017"},{"alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 77","month":"06","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","id":"5986","status":"public"}]},"volume":77,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_id":"5265","checksum":"24fdde981cc513352a78dcf9b0660ae9","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:12Z","file_name":"IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf","date_updated":"2020-07-14T12:47:41Z","file_size":710007,"creator":"system"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Brisbane, Australia","end_date":"2017-07-07","start_date":"2017-07-04"},"type":"conference","pubrep_id":"896","status":"public","_id":"683","file_date_updated":"2020-07-14T12:47:41Z","department":[{"_id":"UlWa"}],"date_updated":"2023-09-05T15:01:43Z","ddc":["514","516"],"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_created":"2018-12-11T11:47:54Z","doi":"10.4230/LIPIcs.SoCG.2017.49","date_published":"2017-06-01T00:00:00Z","year":"2017","has_accepted_license":"1","day":"01","article_number":"49","author":[{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"last_name":"Masárová","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana","first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"publist_id":"7033","title":"A proof of the orbit conjecture for flipping edge labelled triangulations","citation":{"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.","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","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.","short":"A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file_date_updated":"2020-07-14T12:44:34Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-07T11:58:34Z","supervisor":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"ddc":["004","005"],"type":"dissertation","pubrep_id":"730","status":"public","_id":"1155","ec_funded":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1093"},{"relation":"part_of_dissertation","status":"public","id":"1230"},{"id":"1234","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1391"},{"relation":"part_of_dissertation","status":"public","id":"1501"},{"relation":"part_of_dissertation","id":"1502","status":"public"},{"id":"2063","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2167"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_size":1028586,"date_updated":"2020-07-14T12:44:34Z","creator":"system","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","date_created":"2018-12-12T10:11:26Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"1406a681cb737508234fde34766be2c2","file_id":"4880"}],"alternative_title":["ISTA Thesis"],"month":"01","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","article_processing_charge":"No","author":[{"last_name":"Daca","full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw"}],"publist_id":"6203","title":"Statistical and logical methods for property checking","citation":{"ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","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.","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","short":"P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017.","ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730","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","mla":"Daca, Przemyslaw. Statistical and Logical Methods for Property Checking. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"page":"163","date_created":"2018-12-11T11:50:27Z","doi":"10.15479/AT:ISTA:TH_730","date_published":"2017-01-02T00:00:00Z","year":"2017","has_accepted_license":"1","day":"02","oa":1,"publisher":"Institute of Science and Technology Austria","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. "},{"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."}],"oa_version":"Published Version","oa":1,"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"month":"02","publication_status":"published","degree_awarded":"PhD","year":"2017","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"day":"01","file":[{"file_name":"thesis_pavel_payne_final_w_signature_page.pdf","date_created":"2019-04-09T15:15:32Z","file_size":3025175,"date_updated":"2020-07-14T12:47:27Z","creator":"dernst","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","file_id":"6292","content_type":"application/pdf","relation":"main_file","access_level":"closed"},{"file_id":"9187","checksum":"af531e921a7f64a9e0af4cd8783b2226","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2021-02-22T13:45:59Z","file_name":"2017_Payne_Thesis.pdf","creator":"dernst","date_updated":"2021-02-22T13:45:59Z","file_size":3111536}],"page":"83","date_created":"2019-04-09T15:16:45Z","date_published":"2017-02-01T00:00:00Z","_id":"6291","type":"dissertation","status":"public","date_updated":"2023-09-07T12:00:00Z","citation":{"ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","apa":"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.","short":"P. Payne, 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.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017."},"supervisor":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["570"],"article_processing_charge":"No","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453","last_name":"Payne"}],"title":"Bacterial herd and social immunity to phages","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2021-02-22T13:45:59Z"},{"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.","oa":1,"publisher":"The Royal Society","quality_controlled":"1","publication":"Biology Letters","day":"01","year":"2017","date_created":"2018-12-11T11:47:11Z","doi":"10.1098/rsbl.2017.0646","date_published":"2017-12-01T00:00:00Z","article_number":"20170646","project":[{"_id":"251BCBEC-B435-11E9-9278-68D0E5697425","name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","grant_number":"RGY0079/2011"},{"_id":"251D65D8-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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","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.","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","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","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.","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","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."},"title":"Effects of mutations in phage restriction sites during escape from restriction–modification","article_processing_charge":"No","external_id":{"pmid":["29237814"]},"author":[{"first_name":"Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","full_name":"Pleska, Maros","orcid":"0000-0001-7460-7479"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"publist_id":"7253","oa_version":"Published Version","pmid":1,"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."}],"intvolume":" 13","month":"12","main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2017.0646","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1744-9561"]},"volume":13,"related_material":{"record":[{"status":"public","id":"9847","relation":"research_data"},{"status":"public","id":"202","relation":"dissertation_contains"}]},"issue":"12","_id":"561","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-07T11:59:32Z","department":[{"_id":"CaGu"}]},{"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. ","oa":1,"publisher":"Institute of Science and Technology Austria","day":"27","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:48:40Z","doi":"10.15479/AT:ISTA:th_862","date_published":"2017-09-27T00:00:00Z","page":"113","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","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.","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."},"title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","article_processing_charge":"No","author":[{"first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","last_name":"Mitosch","full_name":"Mitosch, Karin"}],"publist_id":"6831","oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"month":"09","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"file_name":"Thesis_KarinMitosch.docx","date_created":"2019-04-05T08:48:51Z","file_size":6331071,"date_updated":"2020-07-14T12:48:09Z","creator":"dernst","file_id":"6210","checksum":"da3993c5f90f59a8e8623cc31ad501dd","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6211","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","date_updated":"2020-07-14T12:48:09Z","file_size":9289852,"creator":"dernst","date_created":"2019-04-05T08:48:51Z","file_name":"Thesis_KarinMitosch.pdf"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2001"},{"relation":"part_of_dissertation","status":"public","id":"666"}]},"_id":"818","pubrep_id":"862","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","ddc":["571","579"],"date_updated":"2023-09-07T12:00:26Z","supervisor":[{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"department":[{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:48:09Z"},{"department":[{"_id":"ToBo"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:35Z","ddc":["576","610"],"date_updated":"2023-09-07T12:00:25Z","pubrep_id":"901","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","_id":"666","ec_funded":1,"volume":4,"related_material":{"record":[{"relation":"dissertation_contains","id":"818","status":"public"}]},"issue":"4","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:47:35Z","file_size":2438660,"date_created":"2018-12-12T10:13:54Z","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"04ff20011c3d9a601c514aa999a5fe1a","file_id":"5041"}],"publication_status":"published","publication_identifier":{"issn":["24054712"]},"intvolume":" 4","month":"04","scopus_import":1,"oa_version":"Published Version","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."}],"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","full_name":"Mitosch, Karin","last_name":"Mitosch"},{"full_name":"Rieckh, Georg","last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"}],"publist_id":"7061","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 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.","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.","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."},"project":[{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"}],"date_created":"2018-12-11T11:47:48Z","doi":"10.1016/j.cels.2017.03.001","date_published":"2017-04-26T00:00:00Z","page":"393 - 403","publication":"Cell Systems","day":"26","year":"2017","has_accepted_license":"1","oa":1,"publisher":"Cell Press","quality_controlled":"1"},{"_id":"821","pubrep_id":"854","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"type":"dissertation","ddc":["000"],"date_updated":"2023-09-07T12:01:59Z","supervisor":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:48:10Z","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"08","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"file":[{"checksum":"3a3ec003f6ee73f41f82a544d63dfc77","file_id":"4900","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","date_created":"2018-12-12T10:11:44Z","file_size":4103115,"date_updated":"2020-07-14T12:48:10Z","creator":"system"},{"creator":"dernst","date_updated":"2020-07-14T12:48:10Z","file_size":14744374,"date_created":"2019-04-05T07:59:31Z","file_name":"2017_thesis_Pavlogiannis.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","file_id":"6201"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"1071","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1437"},{"id":"1602","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1604"},{"id":"1607","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"1714","relation":"part_of_dissertation"}]},"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 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.","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.","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","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."},"title":"Algorithmic advances in program analysis and their applications","article_processing_charge":"No","publist_id":"6828","author":[{"last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"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.","oa":1,"publisher":"Institute of Science and Technology Austria","day":"09","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:48:41Z","date_published":"2017-08-09T00:00:00Z","doi":"10.15479/AT:ISTA:th_854","page":"418"},{"date_created":"2018-12-11T11:48:41Z","date_published":"2017-08-25T00:00:00Z","doi":"10.15479/AT:ISTA:th_857","page":"87","day":"25","year":"2017","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","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. ","title":"The lac operon in the wild","article_processing_charge":"No","publist_id":"6829","author":[{"first_name":"Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","full_name":"Jesse, Fabienne","last_name":"Jesse"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","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.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","ama":"Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857","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"},"project":[{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","date_created":"2018-12-12T10:17:00Z","file_size":3417773,"date_updated":"2020-07-14T12:48:10Z","creator":"system","file_id":"5252","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"date_created":"2019-04-05T08:51:59Z","file_name":"2017_thesis_Jesse_source.tex","date_updated":"2020-07-14T12:48:10Z","file_size":215899,"creator":"dernst","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_id":"6212","content_type":"application/x-tex","access_level":"closed","relation":"source_file"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"08","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:48:10Z","ddc":["576","577","579"],"date_updated":"2023-09-07T12:01:21Z","supervisor":[{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"pubrep_id":"857","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","_id":"820"},{"date_created":"2018-12-11T11:48:46Z","doi":"10.15479/AT:ISTA:th_828","date_published":"2017-06-26T00:00:00Z","page":"86","day":"26","year":"2017","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","title":"(The exact security of) Message authentication codes","article_processing_charge":"No","author":[{"first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","full_name":"Rybar, Michal"}],"publist_id":"6810","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","short":"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","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","mla":"Rybar, Michal. (The Exact Security of) Message Authentication Codes. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_828.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","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."},"related_material":{"record":[{"status":"public","id":"2082","relation":"part_of_dissertation"},{"status":"public","id":"6196","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:10:13Z","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf","creator":"system","date_updated":"2020-07-14T12:48:12Z","file_size":847400,"file_id":"4799","checksum":"ff8639ec4bded6186f44c7bd3ee26804","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"3462101745ce8ad199c2d0f75dae4a7e","file_id":"6202","date_updated":"2020-07-14T12:48:12Z","file_size":26054879,"creator":"dernst","date_created":"2019-04-05T08:24:11Z","file_name":"2017_Thesis_Rybar_source.zip"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"06","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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. "}],"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:48:12Z","ddc":["000"],"date_updated":"2023-09-07T12:02:28Z","pubrep_id":"828","status":"public","type":"dissertation","_id":"838"},{"project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"title":"The exact security of PMAC","author":[{"full_name":"Gazi, Peter","last_name":"Gazi","first_name":"Peter","id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","full_name":"Rybar, Michal","last_name":"Rybar"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Gazi P, Pietrzak KZ, Rybar M. 2017. The exact security of PMAC. IACR Transactions on Symmetric Cryptology. 2016(2), 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.","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","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","short":"P. Gazi, K.Z. Pietrzak, M. Rybar, IACR Transactions on Symmetric Cryptology 2016 (2017) 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."},"publisher":"Ruhr University Bochum","quality_controlled":"1","oa":1,"doi":"10.13154/TOSC.V2016.I2.145-161","date_published":"2017-02-03T00:00:00Z","date_created":"2019-04-04T13:48:23Z","page":"145-161","day":"03","publication":"IACR Transactions on Symmetric Cryptology","has_accepted_license":"1","year":"2017","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"6196","file_date_updated":"2020-07-14T12:47:24Z","department":[{"_id":"KrPi"}],"ddc":["000"],"date_updated":"2023-09-07T12:02:27Z","month":"02","intvolume":" 2016","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"issue":"2","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"838"}]},"volume":2016,"ec_funded":1,"file":[{"creator":"dernst","date_updated":"2020-07-14T12:47:24Z","file_size":597335,"date_created":"2019-04-04T13:53:58Z","file_name":"2017_IACR_Gazi.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6197","checksum":"f23161d685dd957ae8d7274132999684"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2519-173X"]},"publication_status":"published"},{"title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","article_processing_charge":"No","author":[{"last_name":"Xu","full_name":"Xu, Haibing","id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing"}],"publist_id":"6811","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","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.","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:10.15479/AT:ISTA:th_858","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","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017.","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."},"oa":1,"publisher":"Institute of Science and Technology Austria","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. ","date_created":"2018-12-11T11:48:46Z","doi":"10.15479/AT:ISTA:th_858","date_published":"2017-08-23T00:00:00Z","page":"93","day":"23","year":"2017","has_accepted_license":"1","pubrep_id":"858","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","_id":"837","file_date_updated":"2020-07-14T12:48:12Z","department":[{"_id":"JoCs"}],"ddc":["571"],"date_updated":"2023-09-07T12:06:38Z","supervisor":[{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari"}],"month":"08","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"5828"}]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:48:12Z","file_size":3589490,"creator":"dernst","date_created":"2019-04-05T08:59:51Z","file_name":"2017_Xu_Haibing_Thesis_Source.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","checksum":"f11925fbbce31e495124b6bc4f10573c","file_id":"6213"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"ffb10749a537d615fab1ef0937ccb157","file_id":"6214","file_size":11668613,"date_updated":"2020-07-14T12:48:12Z","creator":"dernst","file_name":"2017_Xu_Thesis_IST.pdf","date_created":"2019-04-05T08:59:51Z"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]}},{"citation":{"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.","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","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.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:10.15479/AT:ISTA:th_842","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","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"last_name":"Adamowski","orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6483","article_processing_charge":"No","title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","publisher":"Institute of Science and Technology Austria","oa":1,"has_accepted_license":"1","year":"2017","day":"02","page":"117","doi":"10.15479/AT:ISTA:th_842","date_published":"2017-06-02T00:00:00Z","date_created":"2018-12-11T11:49:18Z","_id":"938","type":"dissertation","status":"public","pubrep_id":"842","supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:06:09Z","ddc":["581","583","580"],"file_date_updated":"2020-07-14T12:48:15Z","department":[{"_id":"JiFr"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"06","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"6215","checksum":"193425764d9aaaed3ac57062a867b315","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2017_Adamowski-Thesis_Source.docx","date_created":"2019-04-05T09:03:20Z","creator":"dernst","file_size":46903863,"date_updated":"2020-07-14T12:48:15Z"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"df5ab01be81f821e1b958596a1ec8d21","file_id":"6216","date_updated":"2020-07-14T12:48:15Z","file_size":8698888,"creator":"dernst","date_created":"2019-04-05T09:03:19Z","file_name":"2017_Adamowski-Thesis.pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"1591","status":"public","relation":"part_of_dissertation"}]}},{"status":"public","pubrep_id":"815","type":"dissertation","_id":"992","file_date_updated":"2020-07-14T12:48:18Z","department":[{"_id":"VlKo"}],"ddc":["004"],"supervisor":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"}],"date_updated":"2023-09-07T12:05:41Z","month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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"}],"ec_funded":1,"file":[{"file_id":"4654","checksum":"81761fb939acb7585c36629f765b4373","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-815-v1+3_final_blank_signature_maybe_pdfa.pdf","date_created":"2018-12-12T10:07:55Z","creator":"system","file_size":786145,"date_updated":"2020-07-14T12:48:18Z"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"6208","checksum":"2b2d7e1d6c1c79a9795a7aa0f860baf3","date_updated":"2020-07-14T12:48:18Z","file_size":5936337,"creator":"dernst","date_created":"2019-04-05T08:43:24Z","file_name":"2017_Thesis_Rolinek_source.zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"title":"Complexity of constraint satisfaction","publist_id":"6407","author":[{"first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","last_name":"Rolinek"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Rolinek M. 2017. Complexity of constraint satisfaction. Institute of Science and Technology Austria.","chicago":"Rolinek, Michal. “Complexity of Constraint Satisfaction.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_815.","ama":"Rolinek M. Complexity of constraint satisfaction. 2017. doi:10.15479/AT:ISTA:th_815","apa":"Rolinek, M. (2017). Complexity of constraint satisfaction. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_815","ieee":"M. Rolinek, “Complexity of constraint satisfaction,” Institute of Science and Technology Austria, 2017.","short":"M. Rolinek, Complexity of Constraint Satisfaction, Institute of Science and Technology Austria, 2017.","mla":"Rolinek, Michal. Complexity of Constraint Satisfaction. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_815."},"publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"FP7/2007-2013/ERC grant agreement no 616160","doi":"10.15479/AT:ISTA:th_815","date_published":"2017-05-01T00:00:00Z","date_created":"2018-12-11T11:49:35Z","page":"97","day":"01","has_accepted_license":"1","year":"2017"},{"type":"journal_article","status":"public","_id":"718","department":[{"_id":"HeEd"}],"date_updated":"2023-09-07T12:07:12Z","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.05915"}],"month":"09","intvolume":" 49","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","related_material":{"record":[{"relation":"dissertation_contains","id":"6287","status":"public"}]},"volume":49,"issue":"3","ec_funded":1,"publication_identifier":{"issn":["00018678"]},"publication_status":"published","language":[{"iso":"eng"}],"project":[{"name":"Topological Complex Systems","grant_number":"318493","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"publist_id":"6962","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"last_name":"Nikitenko","full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201","first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reitzner","full_name":"Reitzner, Matthias","first_name":"Matthias"}],"external_id":{"arxiv":["1607.05915"]},"title":"Expected sizes of poisson Delaunay mosaics and their discrete Morse functions","citation":{"short":"H. Edelsbrunner, A. Nikitenko, M. Reitzner, Advances in Applied Probability 49 (2017) 745–767.","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Cambridge University Press","quality_controlled":"1","oa":1,"page":"745 - 767","date_published":"2017-09-01T00:00:00Z","doi":"10.1017/apr.2017.20","date_created":"2018-12-11T11:48:07Z","year":"2017","day":"01","publication":"Advances in Applied Probability"},{"day":"18","year":"2017","date_published":"2017-11-18T00:00:00Z","doi":"10.1007/978-3-319-70697-9_13","date_created":"2018-12-11T11:47:10Z","page":"357 - 379","quality_controlled":"1","publisher":"Springer","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","short":"H.M. Abusalah, J.F. Alwen, B. Cohen, D. Khilko, K.Z. Pietrzak, L. Reyzin, in:, Springer, 2017, pp. 357–379.","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."},"title":"Beyond Hellman’s time-memory trade-offs with applications to proofs of space","publist_id":"7257","author":[{"last_name":"Abusalah","full_name":"Abusalah, Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M"},{"first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","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","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"first_name":"Leonid","full_name":"Reyzin, Leonid","last_name":"Reyzin"}],"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331970696-2"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"83"}]},"volume":10625,"ec_funded":1,"oa_version":"Submitted Version","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)."}],"month":"11","intvolume":" 10625","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/893.pdf"}],"date_updated":"2023-09-07T12:30:22Z","department":[{"_id":"KrPi"}],"_id":"559","status":"public","type":"conference","conference":{"name":"ASIACRYPT: Theory and Applications of Cryptology and Information Security","start_date":"2017-12-03","location":"Hong Kong, China","end_date":"2017-12-07"}},{"publication_identifier":{"issn":["1083589X"]},"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:47:00Z","file_size":470876,"date_created":"2018-12-12T10:08:04Z","file_name":"IST-2018-926-v1+1_euclid.ecp.1511233247.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4663","checksum":"0ec05303a0de190de145654237984c79"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"149","relation":"dissertation_contains"}]},"volume":22,"ec_funded":1,"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."}],"oa_version":"Published Version","scopus_import":1,"month":"11","intvolume":" 22","date_updated":"2023-09-07T12:38:08Z","ddc":["539"],"department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:47:00Z","_id":"550","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"926","has_accepted_license":"1","year":"2017","day":"21","publication":"Electronic Communications in Probability","doi":"10.1214/17-ECP97","date_published":"2017-11-21T00:00:00Z","date_created":"2018-12-11T11:47:07Z","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"citation":{"short":"J. Alt, Electronic Communications in Probability 22 (2017).","ieee":"J. Alt, “Singularities of the density of states of random Gram matrices,” Electronic Communications in Probability, vol. 22. Institute of Mathematical Statistics, 2017.","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","ama":"Alt J. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 2017;22. doi:10.1214/17-ECP97","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.","ista":"Alt J. 2017. Singularities of the density of states of random Gram matrices. Electronic Communications in Probability. 22, 63.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","full_name":"Alt, Johannes","last_name":"Alt"}],"publist_id":"7265","title":"Singularities of the density of states of random Gram matrices","article_number":"63","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}]},{"oa":1,"quality_controlled":"1","publisher":"Springer","day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:47:41Z","doi":"10.1007/978-3-319-65765-3_7","date_published":"2017-09-01T00:00:00Z","page":"116 - 132","project":[{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017, pp. 116–132.","ama":"Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid systems. In: Vol 10419. Springer; 2017:116-132. doi:10.1007/978-3-319-65765-3_7","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","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.","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.","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."},"title":"Conic abstractions for hybrid systems","publist_id":"7129","author":[{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"last_name":"Giacobbe","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","last_name":"Kong","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui"}],"oa_version":"Submitted Version","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"}],"month":"09","scopus_import":1,"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:12:38Z","file_name":"IST-2017-831-v1+1_main.pdf","creator":"system","date_updated":"2020-07-14T12:47:31Z","file_size":3806864,"file_id":"4956","checksum":"faf546914ba29bcf9974ee36b6b16750","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"isbn":["978-331965764-6"]},"volume":"10419 ","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6894"}]},"_id":"647","pubrep_id":"831","status":"public","conference":{"name":"FORMATS: Formal Modelling and Analysis of Timed Systems","location":"Berlin, Germany","end_date":"2017-09-07","start_date":"2017-09-05"},"type":"conference","ddc":["005"],"date_updated":"2023-09-07T12:53:00Z","file_date_updated":"2020-07-14T12:47:31Z","department":[{"_id":"ToHe"}]},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 10205","month":"03","publication_status":"published","publication_identifier":{"isbn":["978-366254576-8"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4897","checksum":"f395d0d20102b89aeaad8b4ef4f18f4f","file_size":569863,"date_updated":"2020-07-14T12:47:27Z","creator":"system","file_name":"IST-2017-741-v1+1_main.pdf","date_created":"2018-12-12T10:11:41Z"},{"creator":"system","date_updated":"2020-07-14T12:47:27Z","file_size":563276,"date_created":"2018-12-12T10:11:42Z","file_name":"IST-2018-741-v2+2_main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f416ee1ae4497b23ecdf28b1f18bb8df","file_id":"4898"}],"volume":10205,"related_material":{"record":[{"relation":"dissertation_contains","id":"6894","status":"public"}]},"_id":"631","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2017-04-22","end_date":"2017-04-29","location":"Uppsala, Sweden"},"type":"conference","pubrep_id":"966","status":"public","date_updated":"2023-09-07T12:53:00Z","ddc":["000"],"file_date_updated":"2020-07-14T12:47:27Z","department":[{"_id":"ToHe"}],"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).","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2017","has_accepted_license":"1","day":"31","page":"589 - 606","date_created":"2018-12-11T11:47:36Z","date_published":"2017-03-31T00:00:00Z","doi":"10.1007/978-3-662-54577-5_34","project":[{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"citation":{"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","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","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7162","author":[{"last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"first_name":"Goran","full_name":"Frehse, Goran","last_name":"Frehse"},{"orcid":"0000-0001-8180-0904","full_name":"Giacobbe, Mirco","last_name":"Giacobbe","first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"title":"Counterexample guided refinement of template polyhedra"},{"title":"Fluctuations of functions of Wigner matrices","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"last_name":"Schröder","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","first_name":"Dominik J","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"6214","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"L. Erdös, D.J. Schröder, Electronic Communications in Probability 21 (2017).","ieee":"L. Erdös and D. J. Schröder, “Fluctuations of functions of Wigner matrices,” Electronic Communications in Probability, vol. 21. Institute of Mathematical Statistics, 2017.","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","ama":"Erdös L, Schröder DJ. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 2017;21. 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.","ista":"Erdös L, Schröder DJ. 2017. Fluctuations of functions of Wigner matrices. Electronic Communications in Probability. 21, 86."},"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"86","date_created":"2018-12-11T11:50:23Z","doi":"10.1214/16-ECP38","date_published":"2017-01-02T00:00:00Z","publication":"Electronic Communications in Probability","day":"02","year":"2017","has_accepted_license":"1","oa":1,"publisher":"Institute of Mathematical Statistics","quality_controlled":"1","acknowledgement":"Partially supported by the IST Austria Excellence Scholarship.","file_date_updated":"2018-12-12T10:18:10Z","department":[{"_id":"LaEr"}],"ddc":["510"],"date_updated":"2023-09-07T12:54:12Z","pubrep_id":"747","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"1144","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"6179","status":"public"}]},"volume":21,"language":[{"iso":"eng"}],"file":[{"file_id":"5329","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:18:10Z","file_name":"IST-2017-747-v1+1_euclid.ecp.1483347665.pdf","creator":"system","date_updated":"2018-12-12T10:18:10Z","file_size":440770}],"publication_status":"published","intvolume":" 21","month":"01","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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]."}]},{"department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:46:35Z","ddc":["003","000","005"],"date_updated":"2023-09-07T13:11:15Z","status":"public","pubrep_id":"1052","type":"journal_article","article_type":"original","_id":"486","volume":36,"issue":"6","related_material":{"record":[{"id":"8386","status":"public","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"date_created":"2018-12-12T10:10:46Z","file_name":"IST-2018-1052-v1+1_ElekSumin2017SGA.pdf","date_updated":"2020-07-14T12:46:35Z","file_size":107349827,"creator":"system","file_id":"4836","checksum":"48386fa6956c3645fc89594dc898b147","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"checksum":"21c89c28fb8d70f6602f752bf997aa0f","file_id":"7189","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-12-16T14:48:57Z","file_name":"ElekSumin2017SGA_reduced_file_size.pdf","creator":"bbickel","date_updated":"2020-07-14T12:46:35Z","file_size":4683145}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["07300301"]},"publication_status":"published","month":"11","intvolume":" 36","scopus_import":1,"oa_version":"Submitted Version","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."}],"title":"Scattering-aware texture reproduction for 3D printing","publist_id":"7334","author":[{"full_name":"Elek, Oskar","last_name":"Elek","first_name":"Oskar"},{"first_name":"Denis","last_name":"Sumin","full_name":"Sumin, Denis"},{"first_name":"Ran","id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X"},{"first_name":"Tim","last_name":"Weyrich","full_name":"Weyrich, Tim"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel"},{"first_name":"Alexander","last_name":"Wilkie","full_name":"Wilkie, Alexander"},{"first_name":"Jaroslav","full_name":"Krivanek, Jaroslav","last_name":"Krivanek"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","ama":"Elek O, Sumin D, Zhang R, et al. Scattering-aware texture reproduction for 3D printing. ACM Transactions on Graphics. 2017;36(6). doi: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.","short":"O. Elek, D. Sumin, R. Zhang, T. Weyrich, K. Myszkowski, B. Bickel, A. Wilkie, J. Krivanek, ACM Transactions on Graphics 36 (2017)."},"project":[{"call_identifier":"H2020","_id":"2508E324-B435-11E9-9278-68D0E5697425","grant_number":"642841","name":"Distributed 3D Object Design"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"article_number":"241","doi":"10.1145/3130800.3130890","date_published":"2017-11-20T00:00:00Z","date_created":"2018-12-11T11:46:44Z","day":"20","publication":"ACM Transactions on Graphics","has_accepted_license":"1","year":"2017","quality_controlled":"1","publisher":"ACM","oa":1},{"date_updated":"2023-09-07T13:32:11Z","department":[{"_id":"KrPi"}],"_id":"637","status":"public","conference":{"start_date":"2017-07-20","location":"Santa Barbara, CA, United States","end_date":"2017-07-24","name":"CRYPTO: Cryptology"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-331963687-0"]},"ec_funded":1,"related_material":{"record":[{"id":"10035","status":"public","relation":"dissertation_contains"}]},"volume":10401,"oa_version":"Submitted Version","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."}],"intvolume":" 10401","month":"01","main_file_link":[{"url":"https://eprint.iacr.org/2017/515","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","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.","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.","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.","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.","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."},"title":"Be adaptive avoid overcommitting","editor":[{"full_name":"Katz, Jonathan","last_name":"Katz","first_name":"Jonathan"},{"first_name":"Hovav","last_name":"Shacham","full_name":"Shacham, Hovav"}],"author":[{"last_name":"Jafargholi","full_name":"Jafargholi, Zahra","first_name":"Zahra"},{"first_name":"Chethan","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Klein, Karen","last_name":"Klein","first_name":"Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Komargodski","full_name":"Komargodski, Ilan","first_name":"Ilan"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"last_name":"Wichs","full_name":"Wichs, Daniel","first_name":"Daniel"}],"publist_id":"7151","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"day":"01","year":"2017","date_created":"2018-12-11T11:47:38Z","doi":"10.1007/978-3-319-63688-7_5","date_published":"2017-01-01T00:00:00Z","page":"133 - 163","oa":1,"publisher":"Springer","quality_controlled":"1"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-11T13:41:21Z","citation":{"ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","short":"A. Etheridge, N.H. Barton, (2017).","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi: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","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.","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.","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."},"department":[{"_id":"NiBa"}],"title":"Data for: Establishment in a new habitat by polygenic adaptation","author":[{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"article_processing_charge":"No","_id":"9842","status":"public","type":"research_data_reference","day":"29","year":"2017","doi":"10.17632/nw68fxzjpm.1","related_material":{"record":[{"id":"564","status":"public","relation":"used_in_publication"}]},"date_published":"2017-12-29T00:00:00Z","date_created":"2021-08-09T13:18:55Z","oa_version":"Published Version","abstract":[{"text":"Mathematica notebooks used to generate figures.","lang":"eng"}],"month":"12","publisher":"Mendeley Data","oa":1,"main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}]},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.11041"}],"quality_controlled":"1","month":"05","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"}],"oa_version":"Preprint","date_created":"2023-08-22T14:17:38Z","date_published":"2017-05-31T00:00:00Z","publication_status":"published","year":"2017","publication_identifier":{"isbn":["9781510860964"]},"publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"day":"31","conference":{"location":"Long Beach, CA, United States","end_date":"2017-12-09","start_date":"2017-12-04","name":"NeurIPS: Neural Information Processing Systems"},"type":"conference","status":"public","_id":"14206","article_processing_charge":"No","external_id":{"arxiv":["1705.11041"]},"author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Michael","last_name":"Tschannen","full_name":"Tschannen, Michael"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"last_name":"Jaggi","full_name":"Jaggi, Martin","first_name":"Martin"}],"title":"Greedy algorithms for cone constrained optimization with convergence guarantees","department":[{"_id":"FrLo"}],"date_updated":"2023-09-13T08:32:23Z","citation":{"short":"F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural Information Processing Systems, 2017.","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.","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.","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.","mla":"Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.” Advances in Neural Information Processing Systems, 2017.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1"},{"language":[{"iso":"eng"}],"publication":"Proceedings of the 20th International Conference on Artificial Intelligence and Statistics","day":"21","year":"2017","publication_status":"published","date_created":"2023-08-22T14:17:19Z","date_published":"2017-02-21T00:00:00Z","volume":54,"page":"860-868","oa_version":"Preprint","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."}],"intvolume":" 54","month":"02","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1702.06457","open_access":"1"}],"oa":1,"quality_controlled":"1","publisher":"ML Research Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","extern":"1","date_updated":"2023-09-13T09:49:10Z","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.","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.","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.","apa":"Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics (Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.","ama":"Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International Conference on Artificial Intelligence and Statistics. Vol 54. ML Research Press; 2017:860-868.","ieee":"F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, Fort Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.","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."},"department":[{"_id":"FrLo"}],"title":"A unified optimization view on generalized matching pursuit and Frank-Wolfe","external_id":{"arxiv":["1702.06457"]},"article_processing_charge":"No","author":[{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Rajiv","full_name":"Khanna, Rajiv","last_name":"Khanna"},{"first_name":"Michael","full_name":"Tschannen, Michael","last_name":"Tschannen"},{"full_name":"Jaggi, Martin","last_name":"Jaggi","first_name":"Martin"}],"_id":"14205","status":"public","conference":{"location":"Fort Lauderdale, FL, United States","end_date":"2017-04-22","start_date":"2017-04-20","name":"AISTATS: Conference on Artificial Intelligence and Statistics"},"type":"conference"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","ieee":"M. Pleska, “Biology of restriction-modification systems at the single-cell and population level,” Institute of Science and Technology Austria, 2017.","short":"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.","ista":"Pleska M. 2017. Biology of restriction-modification systems at the single-cell and population level. Institute of Science and Technology Austria."},"title":"Biology of restriction-modification systems at the single-cell and population level","publist_id":"7711","author":[{"last_name":"Pleska","orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros"}],"article_processing_charge":"No","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)"}],"day":"01","has_accepted_license":"1","year":"2017","date_published":"2017-10-01T00:00:00Z","doi":"10.15479/AT:ISTA:th_916","date_created":"2018-12-11T11:45:10Z","page":"126","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","publisher":"Institute of Science and Technology Austria","oa":1,"ddc":["576","579"],"supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"date_updated":"2023-09-15T12:04:56Z","file_date_updated":"2020-07-14T12:45:24Z","department":[{"_id":"CaGu"}],"_id":"202","status":"public","pubrep_id":"916","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"file_name":"IST-2018-916-v1+3_2017_Pleska_Maros_Thesis.pdf","date_created":"2018-12-12T10:08:48Z","creator":"system","file_size":18569590,"date_updated":"2020-07-14T12:45:24Z","checksum":"33cfb59674e91f82e3738396d3fb3776","file_id":"4710","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_name":"2017_Pleska_Maros_Thesis.docx","date_created":"2019-04-05T08:33:14Z","file_size":2801649,"date_updated":"2020-07-14T12:45:24Z","creator":"dernst","file_id":"6204","checksum":"dcc239968decb233e7f98cf1083d8c26","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","related_material":{"record":[{"relation":"part_of_dissertation","id":"1243","status":"public"},{"relation":"part_of_dissertation","id":"561","status":"public"},{"id":"457","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"text":"Restriction-modification (RM) represents the simplest and possibly the most widespread mechanism of self/non-self discrimination in nature. In order to provide bacteria with immunity against bacteriophages and other parasitic genetic elements, RM systems rely on a balance between two enzymes: the restriction enzyme, which cleaves non-self DNA at specific restriction sites, and the modification enzyme, which tags the host’s DNA as self and thus protects it from cleavage. In this thesis, I use population and single-cell level experiments in combination with mathematical modeling to study different aspects of the interplay between RM systems, bacteria and bacteriophages. 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"}],"month":"10","alternative_title":["ISTA Thesis"]},{"author":[{"first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","full_name":"Nikitenko, Anton","orcid":"0000-0002-0659-3201","last_name":"Nikitenko"}],"article_processing_charge":"No","title":"Discrete Morse theory for random complexes ","citation":{"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","ama":"Nikitenko A. Discrete Morse theory for random complexes . 2017. doi:10.15479/AT:ISTA:th_873","ieee":"A. Nikitenko, “Discrete Morse theory for random complexes ,” Institute of Science and Technology Austria, 2017.","short":"A. Nikitenko, Discrete Morse Theory for Random Complexes , Institute of Science and Technology Austria, 2017.","mla":"Nikitenko, Anton. Discrete Morse Theory for Random Complexes . Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_873.","ista":"Nikitenko A. 2017. Discrete Morse theory for random complexes . Institute of Science and Technology Austria.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","oa":1,"page":"86","doi":"10.15479/AT:ISTA:th_873","date_published":"2017-10-27T00:00:00Z","date_created":"2019-04-09T15:04:32Z","has_accepted_license":"1","year":"2017","day":"27","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"873","_id":"6287","file_date_updated":"2020-07-14T12:47:26Z","department":[{"_id":"HeEd"}],"supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"}],"date_updated":"2023-09-15T12:10:34Z","ddc":["514","516","519"],"alternative_title":["ISTA Thesis"],"month":"10","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"718","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"5678","status":"public"},{"relation":"part_of_dissertation","id":"87","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_created":"2019-04-09T14:54:51Z","file_name":"2017_Thesis_Nikitenko.pdf","date_updated":"2020-07-14T12:47:26Z","file_size":2324870,"creator":"dernst","checksum":"ece7e598a2f060b263c2febf7f3fe7f9","file_id":"6289","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"checksum":"99b7ad76e317efd447af60f91e29b49b","file_id":"6290","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"2017_Thesis_Nikitenko_source.zip","date_created":"2019-04-09T14:54:51Z","file_size":2863219,"date_updated":"2020-07-14T12:47:26Z","creator":"dernst"}],"language":[{"iso":"eng"}]},{"supervisor":[{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"date_updated":"2023-09-19T10:39:33Z","ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2021-02-22T11:52:56Z","_id":"1127","type":"dissertation","status":"public","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"checksum":"d192c7c6c5ea32c8432437286dc4909e","file_id":"6209","access_level":"closed","relation":"main_file","content_type":"application/pdf","date_created":"2019-04-05T08:45:14Z","file_name":"IST_Austria_Thesis_Tomáš_Prát.pdf","creator":"dernst","date_updated":"2019-04-05T08:45:14Z","file_size":10285946},{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9185","checksum":"bab18b52cf98145926042d8ed99fdb3b","creator":"dernst","file_size":9802991,"date_updated":"2021-02-22T11:52:56Z","file_name":"2017_Thesis_Prat.pdf","date_created":"2021-02-22T11:52:56Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"449","relation":"part_of_dissertation"}]},"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"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"01","citation":{"ieee":"T. Prat, “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.","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.","mla":"Prat, Tomas. Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor. Institute of Science and Technology Austria, 2017.","ista":"Prat T. 2017. Identification of novel regulators of PIN polarity and development of novel auxin sensor. Institute of Science and Technology Austria.","chicago":"Prat, Tomas. “Identification of Novel Regulators of PIN Polarity and Development of Novel Auxin Sensor.” Institute of Science and Technology Austria, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"id":"3DA3BFEE-F248-11E8-B48F-1D18A9856A87","first_name":"Tomas","full_name":"Prat, Tomas","last_name":"Prat"}],"publist_id":"6233","article_processing_charge":"No","title":"Identification of novel regulators of PIN polarity and development of novel auxin sensor","has_accepted_license":"1","year":"2017","day":"12","page":"131","date_published":"2017-01-12T00:00:00Z","date_created":"2018-12-11T11:50:17Z","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.","publisher":"Institute of Science and Technology Austria","oa":1},{"isi":1,"year":"2017","day":"01","publication":"Scandinavian Journal of Statistics","page":"285 - 306","doi":"10.1111/sjos.12251","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:55:13Z","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"citation":{"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.","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.","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","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","short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez","first_name":"Abraham"},{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez"},{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5060","external_id":{"isi":["000400985000001"],"arxiv":["1410.1242"]},"article_processing_charge":"No","title":"Exact goodness-of-fit testing for the Ising model","publication_identifier":{"issn":["03036898"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":44,"issue":"2","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"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."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"http://arxiv.org/abs/1410.1242","open_access":"1"}],"month":"06","intvolume":" 44","date_updated":"2023-09-19T15:13:27Z","department":[{"_id":"GaTk"}],"_id":"2016","type":"journal_article","status":"public"},{"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"title":"Delocalization for a class of random block band matrices","external_id":{"isi":["000398842700004"]},"article_processing_charge":"Yes (via OA deal)","publist_id":"5644","author":[{"id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","last_name":"Bao","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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","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","short":"Z. Bao, L. Erdös, Probability Theory and Related Fields 167 (2017) 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.","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.","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.","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."},"oa":1,"quality_controlled":"1","publisher":"Springer","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.","date_created":"2018-12-11T11:52:32Z","date_published":"2017-04-01T00:00:00Z","doi":"10.1007/s00440-015-0692-y","page":"673 - 776","publication":"Probability Theory and Related Fields","day":"01","year":"2017","isi":1,"has_accepted_license":"1","pubrep_id":"489","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"1528","file_date_updated":"2020-07-14T12:45:00Z","department":[{"_id":"LaEr"}],"ddc":["530"],"date_updated":"2023-09-20T09:42:12Z","intvolume":" 167","month":"04","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"ec_funded":1,"issue":"3-4","volume":167,"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-12T10:08:05Z","file_name":"IST-2016-489-v1+1_s00440-015-0692-y.pdf","creator":"system","date_updated":"2020-07-14T12:45:00Z","file_size":1615755,"checksum":"67afa85ff1e220cbc1f9f477a828513c","file_id":"4665","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["01788051"]}},{"status":"public","article_type":"original","type":"journal_article","_id":"1433","department":[{"_id":"HeEd"}],"date_updated":"2023-09-20T09:42:40Z","intvolume":" 78","month":"01","main_file_link":[{"url":"https://doi.org/10.1016/j.jsc.2016.03.008","open_access":"1"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"ec_funded":1,"related_material":{"record":[{"status":"public","id":"10894","relation":"earlier_version"}]},"volume":78,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":[" 07477171"]},"project":[{"grant_number":"318493","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Phat - Persistent homology algorithms toolbox","external_id":{"isi":["000384396000005"]},"article_processing_charge":"No","publist_id":"5765","author":[{"first_name":"Ulrich","last_name":"Bauer","full_name":"Bauer, Ulrich"},{"last_name":"Kerber","full_name":"Kerber, Michael","first_name":"Michael"},{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","first_name":"Jan"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","last_name":"Wagner","full_name":"Wagner, Hubert"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation 78 (2017) 76–90.","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","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.","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology algorithms toolbox. Journal of Symbolic Computation. 78, 76–90."},"oa":1,"publisher":"Academic Press","quality_controlled":"1","date_created":"2018-12-11T11:51:59Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.jsc.2016.03.008","page":"76 - 90","publication":"Journal of Symbolic Computation","day":"01","year":"2017","isi":1},{"citation":{"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.","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.","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.","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","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","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1410.5387"],"isi":["000390637000014"]},"publist_id":"5800","author":[{"full_name":"Svoreňová, Mária","last_name":"Svoreňová","first_name":"Mária"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Cěrná","full_name":"Cěrná, Ivana","first_name":"Ivana"},{"first_name":"Cǎlin","last_name":"Belta","full_name":"Belta, Cǎlin"}],"title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"year":"2017","isi":1,"publication":"Nonlinear Analysis: Hybrid Systems","day":"01","page":"230 - 253","date_created":"2018-12-11T11:51:50Z","doi":"10.1016/j.nahs.2016.04.006","date_published":"2017-02-01T00:00:00Z","oa":1,"publisher":"Elsevier","quality_controlled":"1","date_updated":"2023-09-20T09:43:09Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"_id":"1407","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"2","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1689"}]},"volume":23,"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"scopus_import":"1","intvolume":" 23","month":"02"},{"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).","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"day":"01","publication":"Computer Graphics Forum","isi":1,"has_accepted_license":"1","year":"2017","doi":"10.1111/cgf.12941","date_published":"2017-09-01T00:00:00Z","date_created":"2018-12-11T11:51:37Z","page":"312 - 337","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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","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","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.","short":"P. Manteaux, C. Wojtan, R. Narain, S. Redon, F. Faure, M. Cani, Computer Graphics Forum 36 (2017) 312–337.","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."},"title":"Adaptive physically based models in computer graphics","publist_id":"5873","author":[{"full_name":"Manteaux, Pierre","last_name":"Manteaux","first_name":"Pierre"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"},{"full_name":"Narain, Rahul","last_name":"Narain","first_name":"Rahul"},{"last_name":"Redon","full_name":"Redon, Stéphane","first_name":"Stéphane"},{"first_name":"François","last_name":"Faure","full_name":"Faure, François"},{"first_name":"Marie","full_name":"Cani, Marie","last_name":"Cani"}],"external_id":{"isi":["000408634200019"]},"article_processing_charge":"No","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"09","intvolume":" 36","scopus_import":"1","file":[{"file_id":"5208","checksum":"7676e9a9ead6d58c3000988c97deb2ef","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:16:21Z","file_name":"IST-2016-634-v1+1_starAdaptivity-cgf.pdf","date_updated":"2020-07-14T12:44:47Z","file_size":1434439,"creator":"system"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["01677055"]},"publication_status":"published","volume":36,"issue":"6","_id":"1367","status":"public","pubrep_id":"634","type":"journal_article","ddc":["000"],"date_updated":"2023-09-20T11:05:36Z","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:44:47Z"},{"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"title":"From non-preemptive to preemptive scheduling using synchronization synthesis","author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Clarke","full_name":"Clarke, Edmund","first_name":"Edmund"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"},{"first_name":"Leonid","last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid"},{"full_name":"Samanta, Roopsha","last_name":"Samanta","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha"},{"orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten"}],"publist_id":"5929","article_processing_charge":"No","external_id":{"isi":["000399888900001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","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.","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.","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."},"publisher":"Springer","quality_controlled":"1","oa":1,"doi":"10.1007/s10703-016-0256-5","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:51:27Z","page":"97 - 139","day":"01","publication":"Formal Methods in System Design","isi":1,"has_accepted_license":"1","year":"2017","status":"public","pubrep_id":"656","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"1338","file_date_updated":"2020-07-14T12:44:44Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-09-20T11:13:51Z","month":"06","intvolume":" 50","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"status":"public","id":"1729","relation":"earlier_version"}]},"volume":50,"issue":"2-3","ec_funded":1,"file":[{"date_created":"2018-12-12T10:13:05Z","file_name":"IST-2016-656-v1+1_s10703-016-0256-5.pdf","creator":"system","date_updated":"2020-07-14T12:44:44Z","file_size":1416170,"checksum":"1163dfd997e8212c789525d4178b1653","file_id":"4985","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","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.","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","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","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."},"title":"Model checking the evolution of gene regulatory networks","external_id":{"isi":["000414343200003"]},"article_processing_charge":"No","author":[{"last_name":"Giacobbe","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao"},{"first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"}],"publist_id":"5898","oa":1,"publisher":"Springer","quality_controlled":"1","publication":"Acta Informatica","day":"01","year":"2017","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:51:32Z","doi":"10.1007/s00236-016-0278-x","date_published":"2017-12-01T00:00:00Z","page":"765 - 787","_id":"1351","pubrep_id":"649","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["006","576"],"date_updated":"2023-09-20T11:06:03Z","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:44:46Z","oa_version":"Published Version","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."}],"intvolume":" 54","month":"12","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"4e661d9135d7f8c342e8e258dee76f3e","file_id":"5841","creator":"dernst","date_updated":"2020-07-14T12:44:46Z","file_size":755241,"date_created":"2019-01-17T15:57:29Z","file_name":"2017_ActaInformatica_Giacobbe.pdf"}],"publication_status":"published","publication_identifier":{"issn":["00015903"]},"ec_funded":1,"issue":"8","volume":54,"related_material":{"record":[{"relation":"earlier_version","id":"1835","status":"public"}]}},{"scopus_import":"1","month":"06","intvolume":" 78","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","issue":"2","volume":78,"ec_funded":1,"publication_identifier":{"issn":["01784617"]},"publication_status":"published","file":[{"creator":"system","file_size":710206,"date_updated":"2020-07-14T12:44:44Z","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","date_created":"2018-12-12T10:10:19Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4805","checksum":"7873f665a0c598ac747c908f34cb14b9"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"658","_id":"1336","file_date_updated":"2020-07-14T12:44:44Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"date_updated":"2023-09-20T11:14:42Z","ddc":["576"],"publisher":"Springer","quality_controlled":"1","oa":1,"page":"681 - 713","doi":"10.1007/s00453-016-0212-1","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:51:27Z","has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"Algorithmica","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"5931","author":[{"orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jorge","last_name":"Pérez Heredia","full_name":"Pérez Heredia, Jorge"},{"first_name":"Dirk","full_name":"Sudholt, Dirk","last_name":"Sudholt"},{"orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","first_name":"Barbora"}],"external_id":{"isi":["000400379500013"]},"article_processing_charge":"No","title":"Towards a runtime comparison of natural and artificial evolution","citation":{"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.","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.","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","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.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"issue":"3-4","volume":169,"ec_funded":1,"publication_identifier":{"issn":["01788051"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4686","checksum":"29f5a72c3f91e408aeb9e78344973803","date_updated":"2020-07-14T12:44:44Z","file_size":988843,"creator":"system","date_created":"2018-12-12T10:08:25Z","file_name":"IST-2017-657-v1+2_s00440-016-0740-2.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"12","intvolume":" 169","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"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:44:44Z","department":[{"_id":"LaEr"}],"date_updated":"2023-09-20T11:14:17Z","ddc":["510","530"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"657","_id":"1337","page":"667 - 727","date_published":"2017-12-01T00:00:00Z","doi":"10.1007/s00440-016-0740-2","date_created":"2018-12-11T11:51:27Z","has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"Probability Theory and Related Fields","publisher":"Springer","quality_controlled":"1","oa":1,"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","publist_id":"5930","author":[{"full_name":"Ajanki, Oskari H","last_name":"Ajanki","first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","last_name":"Krüger"}],"external_id":{"isi":["000414358400002"]},"article_processing_charge":"Yes (via OA deal)","title":"Universality for general Wigner-type matrices","citation":{"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.","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","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","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields 169 (2017) 667–727.","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.","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.","ista":"Ajanki OH, Erdös L, Krüger TH. 2017. Universality for general Wigner-type matrices. Probability Theory and Related Fields. 169(3–4), 667–727."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}]},{"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publist_id":"6009","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"full_name":"Forejt, Vojtěch","last_name":"Forejt","first_name":"Vojtěch"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"}],"external_id":{"isi":["000388430000011"]},"article_processing_charge":"No","title":"Trading performance for stability in Markov decision processes","citation":{"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.","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.","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.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Elsevier","oa":1,"page":"144 - 170","doi":"10.1016/j.jcss.2016.09.009","date_published":"2017-03-01T00:00:00Z","date_created":"2018-12-11T11:51:12Z","isi":1,"has_accepted_license":"1","year":"2017","day":"01","publication":"Journal of Computer and System Sciences","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"717","_id":"1294","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:44:42Z","date_updated":"2023-09-20T11:15:31Z","ddc":["004","006"],"scopus_import":"1","month":"03","intvolume":" 84","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"}],"oa_version":"Published Version","volume":84,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2305"}]},"ec_funded":1,"publication_status":"published","file":[{"file_id":"4885","checksum":"91271b23cf884d7c06d33bef0cd623b1","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","date_created":"2018-12-12T10:11:30Z","file_size":708657,"date_updated":"2020-07-14T12:44:42Z","creator":"system"}],"language":[{"iso":"eng"}]},{"has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"European Journal of Neuroscience","page":"45 - 57","date_published":"2017-01-01T00:00:00Z","doi":"10.1111/ejn.13418","date_created":"2018-12-11T11:50:50Z","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.","quality_controlled":"1","publisher":"Wiley-Blackwell","oa":1,"citation":{"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.","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.","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.","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.","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","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","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6106","author":[{"first_name":"Ulrich","last_name":"Sauerzopf","full_name":"Sauerzopf, Ulrich"},{"full_name":"Sacco, Roberto","last_name":"Sacco","first_name":"Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marco","last_name":"Niello","full_name":"Niello, Marco"},{"full_name":"Weidenauer, Ana","last_name":"Weidenauer","first_name":"Ana"},{"full_name":"Praschak Rieder, Nicole","last_name":"Praschak Rieder","first_name":"Nicole"},{"first_name":"Harald","last_name":"Sitte","full_name":"Sitte, Harald"},{"full_name":"Willeit, Matthaeus","last_name":"Willeit","first_name":"Matthaeus"}],"article_processing_charge":"No","external_id":{"pmid":["27690184"],"isi":["000392487100005"]},"title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","publication_status":"published","file":[{"creator":"system","file_size":169145,"date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","date_created":"2018-12-12T10:10:48Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"c572cf02be8fbb7020cfcfb892182e4c","file_id":"4838"}],"language":[{"iso":"eng"}],"volume":45,"issue":"1","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"01","intvolume":" 45","date_updated":"2023-09-20T11:16:01Z","ddc":["616"],"department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:44:39Z","_id":"1228","type":"journal_article","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"738"},{"_id":"1213","type":"book_chapter","status":"public","date_updated":"2023-09-20T11:16:30Z","department":[{"_id":"MaLo"}],"acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Bacterial cytokinesis is commonly initiated by the Z-ring, a dynamic cytoskeletal structure that assembles at the site of division. Its primary component is FtsZ, a tubulin-like GTPase, that like its eukaryotic relative forms protein filaments in the presence of GTP. Since the discovery of the Z-ring 25 years ago, various models for the role of FtsZ have been suggested. However, important information about the architecture and dynamics of FtsZ filaments during cytokinesis is still missing. One reason for this lack of knowledge has been the small size of bacteria, which has made it difficult to resolve the orientation and dynamics of individual FtsZ filaments in the Z-ring. While superresolution microscopy experiments have helped to gain more information about the organization of the Z-ring in the dividing cell, they were not yet able to elucidate a mechanism of how FtsZ filaments reorganize during assembly and disassembly of the Z-ring. In this chapter, we explain how to use an in vitro reconstitution approach to investigate the self-organization of FtsZ filaments recruited to a biomimetic lipid bilayer by its membrane anchor FtsA. We show how to perform single-molecule experiments to study the behavior of individual FtsZ monomers during the constant reorganization of the FtsZ-FtsA filament network. We describe how to analyze the dynamics of single molecules and explain why this information can help to shed light onto possible mechanism of Z-ring constriction. We believe that similar experimental approaches will be useful to study the mechanism of membrane-based polymerization of other cytoskeletal systems, not only from prokaryotic but also eukaryotic origin."}],"oa_version":"None","alternative_title":["Methods in Cell Biology"],"scopus_import":"1","month":"12","intvolume":" 137","publication_identifier":{"issn":["0091679X"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":137,"ec_funded":1,"project":[{"_id":"2596EAB6-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 2015-1163","name":"Synthesis of bacterial cell wall"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"mla":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” Cytokinesis, edited by Arnaud Echard, vol. 137, Academic Press, 2017, pp. 355–70, doi:10.1016/bs.mcb.2016.03.036.","ieee":"N. S. Baranova and M. Loose, “Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers,” in Cytokinesis, vol. 137, A. Echard, Ed. Academic Press, 2017, pp. 355–370.","short":"N.S. Baranova, M. Loose, in:, A. Echard (Ed.), Cytokinesis, Academic Press, 2017, pp. 355–370.","ama":"Baranova NS, Loose M. Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Echard A, ed. Cytokinesis. Vol 137. Academic Press; 2017:355-370. doi:10.1016/bs.mcb.2016.03.036","apa":"Baranova, N. S., & Loose, M. (2017). Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In A. Echard (Ed.), Cytokinesis (Vol. 137, pp. 355–370). Academic Press. https://doi.org/10.1016/bs.mcb.2016.03.036","chicago":"Baranova, Natalia S., and Martin Loose. “Single-Molecule Measurements to Study Polymerization Dynamics of FtsZ-FtsA Copolymers.” In Cytokinesis, edited by Arnaud Echard, 137:355–70. Academic Press, 2017. https://doi.org/10.1016/bs.mcb.2016.03.036.","ista":"Baranova NS, Loose M. 2017.Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers. In: Cytokinesis. Methods in Cell Biology, vol. 137, 355–370."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6134","author":[{"full_name":"Baranova, Natalia","orcid":"0000-0002-3086-9124","last_name":"Baranova","first_name":"Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","last_name":"Loose"}],"external_id":{"isi":["000403542900022"]},"article_processing_charge":"No","title":"Single-molecule measurements to study polymerization dynamics of FtsZ-FtsA copolymers","editor":[{"full_name":"Echard, Arnaud ","last_name":"Echard","first_name":"Arnaud "}],"acknowledgement":"Natalia Baranova is supported by an EMBO Long-Term Fellowship (EMBO ALTF 1163-2015) and Martin Loose by an ERC Starting Grant (ERCStG-2015-SelfOrganiCell).","quality_controlled":"1","publisher":"Academic Press","isi":1,"year":"2017","day":"01","publication":"Cytokinesis","page":"355 - 370","doi":"10.1016/bs.mcb.2016.03.036","date_published":"2017-12-01T00:00:00Z","date_created":"2018-12-11T11:50:45Z"},{"project":[{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"citation":{"ieee":"T. Moser and R. Seiringer, “Triviality of a model of particles with point interactions in the thermodynamic limit,” Letters in Mathematical Physics, vol. 107, no. 3. Springer, pp. 533–552, 2017.","short":"T. Moser, R. Seiringer, Letters in Mathematical Physics 107 (2017) 533–552.","ama":"Moser T, Seiringer R. Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. 2017;107(3):533-552. doi:10.1007/s11005-016-0915-x","apa":"Moser, T., & Seiringer, R. (2017). Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-016-0915-x","mla":"Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics, vol. 107, no. 3, Springer, 2017, pp. 533–52, doi:10.1007/s11005-016-0915-x.","ista":"Moser T, Seiringer R. 2017. Triviality of a model of particles with point interactions in the thermodynamic limit. Letters in Mathematical Physics. 107(3), 533–552.","chicago":"Moser, Thomas, and Robert Seiringer. “Triviality of a Model of Particles with Point Interactions in the Thermodynamic Limit.” Letters in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s11005-016-0915-x."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6152","author":[{"first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","full_name":"Moser, Thomas","last_name":"Moser"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"external_id":{"isi":["000394280200007"]},"article_processing_charge":"Yes (via OA deal)","title":"Triviality of a model of particles with point interactions in the thermodynamic limit","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","publisher":"Springer","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"Letters in Mathematical Physics","page":" 533 - 552","doi":"10.1007/s11005-016-0915-x","date_published":"2017-03-01T00:00:00Z","date_created":"2018-12-11T11:50:40Z","_id":"1198","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"723","date_updated":"2023-09-20T11:18:13Z","ddc":["510","539"],"file_date_updated":"2020-07-14T12:44:38Z","department":[{"_id":"RoSe"}],"abstract":[{"lang":"eng","text":"We consider a model of fermions interacting via point interactions, defined via a certain weighted Dirichlet form. While for two particles the interaction corresponds to infinite scattering length, the presence of further particles effectively decreases the interaction strength. We show that the model becomes trivial in the thermodynamic limit, in the sense that the free energy density at any given particle density and temperature agrees with the corresponding expression for non-interacting particles."}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 107","publication_identifier":{"issn":["03779017"]},"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:44:38Z","file_size":587207,"date_created":"2018-12-12T10:17:40Z","file_name":"IST-2016-723-v1+1_s11005-016-0915-x.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5296","checksum":"c0c835def162c1bc52f978fad26e3c2f"}],"language":[{"iso":"eng"}],"issue":"3","related_material":{"record":[{"relation":"dissertation_contains","id":"52","status":"public"}]},"volume":107},{"page":"947 - 990","date_created":"2018-12-11T11:50:43Z","date_published":"2017-02-01T00:00:00Z","doi":"10.1007/s00220-016-2805-6","year":"2017","has_accepted_license":"1","isi":1,"publication":"Communications in Mathematical Physics","day":"01","oa":1,"quality_controlled":"1","publisher":"Springer","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000393696700005"]},"author":[{"first_name":"Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","last_name":"Bao","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin"}],"publist_id":"6141","title":"Local law of addition of random matrices on optimal scale","citation":{"short":"Z. Bao, L. Erdös, K. Schnelli, Communications in Mathematical Physics 349 (2017) 947–990.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local law of addition of random matrices on optimal scale,” Communications in Mathematical Physics, vol. 349, no. 3. Springer, pp. 947–990, 2017.","apa":"Bao, Z., Erdös, L., & Schnelli, K. (2017). Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-016-2805-6","ama":"Bao Z, Erdös L, Schnelli K. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 2017;349(3):947-990. doi:10.1007/s00220-016-2805-6","mla":"Bao, Zhigang, et al. “Local Law of Addition of Random Matrices on Optimal Scale.” Communications in Mathematical Physics, vol. 349, no. 3, Springer, 2017, pp. 947–90, doi:10.1007/s00220-016-2805-6.","ista":"Bao Z, Erdös L, Schnelli K. 2017. Local law of addition of random matrices on optimal scale. Communications in Mathematical Physics. 349(3), 947–990.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Law of Addition of Random Matrices on Optimal Scale.” Communications in Mathematical Physics. Springer, 2017. https://doi.org/10.1007/s00220-016-2805-6."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"ec_funded":1,"volume":349,"issue":"3","publication_status":"published","publication_identifier":{"issn":["00103616"]},"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":1033743,"date_updated":"2020-07-14T12:44:39Z","file_name":"IST-2016-722-v1+1_s00220-016-2805-6.pdf","date_created":"2018-12-12T10:14:47Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"ddff79154c3daf27237de5383b1264a9","file_id":"5102"}],"scopus_import":"1","intvolume":" 349","month":"02","abstract":[{"text":"The eigenvalue distribution of the sum of two large Hermitian matrices, when one of them is conjugated by a Haar distributed unitary matrix, is asymptotically given by the free convolution of their spectral distributions. We prove that this convergence also holds locally in the bulk of the spectrum, down to the optimal scales larger than the eigenvalue spacing. The corresponding eigenvectors are fully delocalized. Similar results hold for the sum of two real symmetric matrices, when one is conjugated by Haar orthogonal matrix.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"LaEr"}],"file_date_updated":"2020-07-14T12:44:39Z","date_updated":"2023-09-20T11:16:57Z","ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"722","status":"public","_id":"1207"},{"day":"01","publication":"Nonlinear Analysis: Hybrid Systems","isi":1,"year":"2017","doi":"10.1016/j.nahs.2016.09.001","date_published":"2017-02-01T00:00:00Z","date_created":"2018-12-11T11:50:39Z","page":"166 - 190","acknowledgement":"This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund1 (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.\r\nA Technical Report of this article is available via: https://repository.ist.ac.at/171/","quality_controlled":"1","publisher":"Elsevier","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Henzinger, T. A., & Otop, J. (2017). Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2016.09.001","ama":"Henzinger TA, Otop J. Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. 2017;23:166-190. doi:10.1016/j.nahs.2016.09.001","ieee":"T. A. Henzinger and J. Otop, “Model measuring for discrete and hybrid systems,” Nonlinear Analysis: Hybrid Systems, vol. 23. Elsevier, pp. 166–190, 2017.","short":"T.A. Henzinger, J. Otop, Nonlinear Analysis: Hybrid Systems 23 (2017) 166–190.","mla":"Henzinger, Thomas A., and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” Nonlinear Analysis: Hybrid Systems, vol. 23, Elsevier, 2017, pp. 166–90, doi:10.1016/j.nahs.2016.09.001.","ista":"Henzinger TA, Otop J. 2017. Model measuring for discrete and hybrid systems. Nonlinear Analysis: Hybrid Systems. 23, 166–190.","chicago":"Henzinger, Thomas A, and Jan Otop. “Model Measuring for Discrete and Hybrid Systems.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.09.001."},"title":"Model measuring for discrete and hybrid systems","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","full_name":"Otop, Jan"}],"publist_id":"6154","article_processing_charge":"No","external_id":{"isi":["000390637000011"]},"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":23,"ec_funded":1,"oa_version":"None","abstract":[{"lang":"eng","text":"We define the . model-measuring problem: given a model . M and specification . ϕ, what is the maximal distance . ρ such that all models . M' within distance . ρ from . M satisfy (or violate) . ϕ. The model-measuring problem presupposes a distance function on models. We concentrate on . automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification; robustness problems that measure how much a model can be perturbed without violating the specification; and parameter synthesis for hybrid systems. We show that for automatic distance functions, and (a) . ω-regular linear-time, (b) . ω-regular branching-time, and (c) hybrid specifications, the model-measuring problem can be solved.We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for word, tree, and hybrid automata by the . optimal-value question for the weighted versions of these automata. For automata over words and trees, we consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. For hybrid automata, we consider monotonic (parametric) hybrid automata, a hybrid counterpart of (discrete) weighted automata.We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications. Further, we propose the modeling framework for model measuring to ease the specification and reduce the likelihood of errors in modeling.Finally, we present a variant of the model-measuring problem, called the . model-repair problem. The model-repair problem applies to models that do not satisfy the specification; it can be used to derive restrictions, under which the model satisfies the specification, i.e., to repair the model."}],"month":"02","intvolume":" 23","scopus_import":"1","date_updated":"2023-09-20T11:18:50Z","department":[{"_id":"ToHe"}],"_id":"1196","status":"public","type":"journal_article"},{"title":"How does epistasis influence the response to selection?","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"publist_id":"6151","article_processing_charge":"No","external_id":{"isi":["000392229100011"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.","apa":"Barton, N. H. (2017). How does epistasis influence the response to selection? Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109","ama":"Barton NH. How does epistasis influence the response to selection? Heredity. 2017;118:96-109. doi:10.1038/hdy.2016.109","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” Heredity, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","short":"N.H. Barton, Heredity 118 (2017) 96–109.","chicago":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.","ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109."},"project":[{"call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"doi":"10.1038/hdy.2016.109","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:50:40Z","page":"96 - 109","day":"01","publication":"Heredity","isi":1,"year":"2017","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"department":[{"_id":"NiBa"}],"date_updated":"2023-09-20T11:17:47Z","status":"public","type":"journal_article","_id":"1199","volume":118,"related_material":{"record":[{"relation":"research_data","id":"9710","status":"public"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","month":"01","intvolume":" 118","scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}]},{"external_id":{"isi":["000411712300012"]},"article_processing_charge":"No","author":[{"last_name":"Zwiernik","full_name":"Zwiernik, Piotr","first_name":"Piotr"},{"last_name":"Uhler","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"last_name":"Richards","full_name":"Richards, Donald","first_name":"Donald"}],"publist_id":"6142","title":"Maximum likelihood estimation for linear Gaussian covariance models","citation":{"ieee":"P. Zwiernik, C. Uhler, and D. Richards, “Maximum likelihood estimation for linear Gaussian covariance models,” Journal of the Royal Statistical Society. Series B: Statistical Methodology, vol. 79, no. 4. Wiley-Blackwell, pp. 1269–1292, 2017.","short":"P. Zwiernik, C. Uhler, D. Richards, Journal of the Royal Statistical Society. Series B: Statistical Methodology 79 (2017) 1269–1292.","ama":"Zwiernik P, Uhler C, Richards D. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society Series B: Statistical Methodology. 2017;79(4):1269-1292. doi:10.1111/rssb.12217","apa":"Zwiernik, P., Uhler, C., & Richards, D. (2017). Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. Wiley-Blackwell. https://doi.org/10.1111/rssb.12217","mla":"Zwiernik, Piotr, et al. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical Methodology, vol. 79, no. 4, Wiley-Blackwell, 2017, pp. 1269–92, doi:10.1111/rssb.12217.","ista":"Zwiernik P, Uhler C, Richards D. 2017. Maximum likelihood estimation for linear Gaussian covariance models. Journal of the Royal Statistical Society. Series B: Statistical Methodology. 79(4), 1269–1292.","chicago":"Zwiernik, Piotr, Caroline Uhler, and Donald Richards. “Maximum Likelihood Estimation for Linear Gaussian Covariance Models.” Journal of the Royal Statistical Society. Series B: Statistical Methodology. Wiley-Blackwell, 2017. https://doi.org/10.1111/rssb.12217."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"2530CA10-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Gaussian Graphical Models: Theory and Applications","grant_number":"Y 903-N35"}],"page":"1269 - 1292","date_created":"2018-12-11T11:50:43Z","date_published":"2017-09-01T00:00:00Z","doi":"10.1111/rssb.12217","year":"2017","isi":1,"publication":"Journal of the Royal Statistical Society. Series B: Statistical Methodology","day":"01","oa":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","department":[{"_id":"CaUh"}],"date_updated":"2023-09-20T11:17:21Z","type":"journal_article","status":"public","_id":"1208","issue":"4","volume":79,"publication_status":"published","publication_identifier":{"issn":["13697412"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.5604"}],"scopus_import":"1","intvolume":" 79","month":"09","abstract":[{"text":"We study parameter estimation in linear Gaussian covariance models, which are p-dimensional Gaussian models with linear constraints on the covariance matrix. Maximum likelihood estimation for this class of models leads to a non-convex optimization problem which typically has many local maxima. Using recent results on the asymptotic distribution of extreme eigenvalues of the Wishart distribution, we provide sufficient conditions for any hill climbing method to converge to the global maximum. Although we are primarily interested in the case in which n≫p, the proofs of our results utilize large sample asymptotic theory under the scheme n/p→γ>1. Remarkably, our numerical simulations indicate that our results remain valid for p as small as 2. An important consequence of this analysis is that, for sample sizes n≃14p, maximum likelihood estimation for linear Gaussian covariance models behaves as if it were a convex optimization problem. © 2016 The Royal Statistical Society and Blackwell Publishing Ltd.","lang":"eng"}],"oa_version":"Submitted Version"},{"_id":"1174","status":"public","type":"conference","conference":{"location":"Hannover, Germany","end_date":"2017-03-11","start_date":"2017-03-08","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"date_updated":"2023-09-20T11:23:15Z","department":[{"_id":"KrPi"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Security of cryptographic applications is typically defined by security games. The adversary, within certain resources, cannot win with probability much better than 0 (for unpredictability applications, like one-way functions) or much better than 1/2 (indistinguishability applications for instance encryption schemes). In so called squared-friendly applications the winning probability of the adversary, for different values of the application secret randomness, is not only close to 0 or 1/2 on average, but also concentrated in the sense that its second central moment is small. The class of squared-friendly applications, which contains all unpredictability applications and many indistinguishability applications, is particularly important for key derivation. Barak et al. observed that for square-friendly applications one can beat the "RT-bound", extracting secure keys with significantly smaller entropy loss. In turn Dodis and Yu showed that in squared-friendly applications one can directly use a "weak" key, which has only high entropy, as a secure key. In this paper we give sharp lower bounds on square security assuming security for "weak" keys. We show that any application which is either (a) secure with weak keys or (b) allows for entropy savings for keys derived by universal hashing, must be square-friendly. Quantitatively, our lower bounds match the positive results of Dodis and Yu and Barak et al. (TCC\\'13, CRYPTO\\'11) Hence, they can be understood as a general characterization of squared-friendly applications. While the positive results on squared-friendly applications where derived by one clever application of the Cauchy-Schwarz Inequality, for tight lower bounds we need more machinery. In our approach we use convex optimization techniques and some theory of circular matrices."}],"month":"03","intvolume":" 66","scopus_import":"1","alternative_title":["LIPIcs"],"main_file_link":[{"open_access":"1","url":"http://drops.dagstuhl.de/opus/volltexte/2017/6976"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"]},"publication_status":"published","volume":66,"ec_funded":1,"article_number":"57","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Skórski, Maciej. “Lower Bounds on Key Derivation for Square-Friendly Applications,” Vol. 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.STACS.2017.57.","ista":"Skórski M. 2017. Lower bounds on key derivation for square-friendly applications. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 66, 57.","mla":"Skórski, Maciej. Lower Bounds on Key Derivation for Square-Friendly Applications. Vol. 66, 57, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.STACS.2017.57.","apa":"Skórski, M. (2017). Lower bounds on key derivation for square-friendly applications (Vol. 66). Presented at the STACS: Symposium on Theoretical Aspects of Computer Science, Hannover, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2017.57","ama":"Skórski M. Lower bounds on key derivation for square-friendly applications. In: Vol 66. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.STACS.2017.57","short":"M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"M. Skórski, “Lower bounds on key derivation for square-friendly applications,” presented at the STACS: Symposium on Theoretical Aspects of Computer Science, Hannover, Germany, 2017, vol. 66."},"title":"Lower bounds on key derivation for square-friendly applications","publist_id":"6180","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"external_id":{"isi":["000521077300057"]},"article_processing_charge":"No","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"day":"01","isi":1,"year":"2017","date_published":"2017-03-01T00:00:00Z","doi":"10.4230/LIPIcs.STACS.2017.57","date_created":"2018-12-11T11:50:32Z"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Alwen, J. F., & Blocki, J. (2017). Towards practical attacks on Argon2i and balloon hashing. Presented at the EuroS&P: European Symposium on Security and Privacy, Paris, France: IEEE. https://doi.org/10.1109/EuroSP.2017.47","ama":"Alwen JF, Blocki J. Towards practical attacks on Argon2i and balloon hashing. In: IEEE; 2017. doi:10.1109/EuroSP.2017.47","ieee":"J. F. Alwen and J. Blocki, “Towards practical attacks on Argon2i and balloon hashing,” presented at the EuroS&P: European Symposium on Security and Privacy, Paris, France, 2017.","short":"J.F. Alwen, J. Blocki, in:, IEEE, 2017.","mla":"Alwen, Joel F., and Jeremiah Blocki. Towards Practical Attacks on Argon2i and Balloon Hashing. 7961977, IEEE, 2017, doi:10.1109/EuroSP.2017.47.","ista":"Alwen JF, Blocki J. 2017. Towards practical attacks on Argon2i and balloon hashing. EuroS&P: European Symposium on Security and Privacy, 7961977.","chicago":"Alwen, Joel F, and Jeremiah Blocki. “Towards Practical Attacks on Argon2i and Balloon Hashing.” IEEE, 2017. https://doi.org/10.1109/EuroSP.2017.47."},"title":"Towards practical attacks on Argon2i and balloon hashing","external_id":{"isi":["000424197300011"]},"article_processing_charge":"No","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Blocki, Jeremiah","last_name":"Blocki","first_name":"Jeremiah"}],"publist_id":"6178","article_number":"7961977","day":"03","year":"2017","isi":1,"date_created":"2018-12-11T11:50:33Z","date_published":"2017-07-03T00:00:00Z","doi":"10.1109/EuroSP.2017.47","oa":1,"quality_controlled":"1","publisher":"IEEE","date_updated":"2023-09-20T11:22:25Z","department":[{"_id":"KrPi"}],"_id":"1176","status":"public","conference":{"start_date":"2017-04-26","location":"Paris, France","end_date":"2017-04-28","name":"EuroS&P: European Symposium on Security and Privacy"},"type":"conference","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-150905761-0"]},"oa_version":"Submitted Version","abstract":[{"text":"The algorithm Argon2i-B of Biryukov, Dinu and Khovratovich is currently being considered by the IRTF (Internet Research Task Force) as a new de-facto standard for password hashing. An older version (Argon2i-A) of the same algorithm was chosen as the winner of the recent Password Hashing Competition. An important competitor to Argon2i-B is the recently introduced Balloon Hashing (BH) algorithm of Corrigan-Gibs, Boneh and Schechter. A key security desiderata for any such algorithm is that evaluating it (even using a custom device) requires a large amount of memory amortized across multiple instances. Alwen and Blocki (CRYPTO 2016) introduced a class of theoretical attacks against Argon2i-A and BH. While these attacks yield large asymptotic reductions in the amount of memory, it was not, a priori, clear if (1) they can be extended to the newer Argon2i-B, (2) the attacks are effective on any algorithm for practical parameter ranges (e.g., 1GB of memory) and (3) if they can be effectively instantiated against any algorithm under realistic hardware constrains. In this work we answer all three of these questions in the affirmative for all three algorithms. This is also the first work to analyze the security of Argon2i-B. In more detail, we extend the theoretical attacks of Alwen and Blocki (CRYPTO 2016) to the recent Argon2i-B proposal demonstrating severe asymptotic deficiencies in its security. Next we introduce several novel heuristics for improving the attack's concrete memory efficiency even when on-chip memory bandwidth is bounded. We then simulate our attacks on randomly sampled Argon2i-A, Argon2i-B and BH instances and measure the resulting memory consumption for various practical parameter ranges and for a variety of upperbounds on the amount of parallelism available to the attacker. Finally we describe, implement, and test a new heuristic for applying the Alwen-Blocki attack to functions employing a technique developed by Corrigan-Gibs et al. for improving concrete security of memory-hard functions. We analyze the collected data and show the effects various parameters have on the memory consumption of the attack. In particular, we can draw several interesting conclusions about the level of security provided by these functions. · For the Alwen-Blocki attack to fail against practical memory parameters, Argon2i-B must be instantiated with more than 10 passes on memory - beyond the \"paranoid\" parameter setting in the current IRTF proposal. · The technique of Corrigan-Gibs for improving security can also be overcome by the Alwen-Blocki attack under realistic hardware constraints. · On a positive note, both the asymptotic and concrete security of Argon2i-B seem to improve on that of Argon2i-A.","lang":"eng"}],"month":"07","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/759"}],"scopus_import":"1"},{"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"7843","checksum":"c647520d115b772a1682fc06fa273eb1","file_size":516959,"date_updated":"2020-07-14T12:44:37Z","creator":"dernst","file_name":"2017_JournalCrypto_Kiltz.pdf","date_created":"2020-05-14T16:30:17Z"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"3238","status":"public","relation":"earlier_version"}]},"issue":"4","volume":30,"ec_funded":1,"abstract":[{"lang":"eng","text":"We construct efficient authentication protocols and message authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work—starting with the (Formula presented.) protocol of Hopper and Blum in 2001—until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle attacks. A MAC implies such a (two-round) protocol."}],"oa_version":"Submitted Version","scopus_import":"1","month":"10","intvolume":" 30","date_updated":"2023-09-20T11:20:58Z","ddc":["000"],"file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"KrPi"}],"_id":"1187","type":"journal_article","article_type":"original","status":"public","has_accepted_license":"1","isi":1,"year":"2017","day":"01","publication":"Journal of Cryptology","page":"1238 - 1275","doi":"10.1007/s00145-016-9247-3","date_published":"2017-10-01T00:00:00Z","date_created":"2018-12-11T11:50:37Z","publisher":"Springer","quality_controlled":"1","oa":1,"citation":{"chicago":"Kiltz, Eike, Krzysztof Z Pietrzak, Daniele Venturi, David Cash, and Abhishek Jain. “Efficient Authentication from Hard Learning Problems.” Journal of Cryptology. Springer, 2017. https://doi.org/10.1007/s00145-016-9247-3.","ista":"Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. 2017. Efficient authentication from hard learning problems. Journal of Cryptology. 30(4), 1238–1275.","mla":"Kiltz, Eike, et al. “Efficient Authentication from Hard Learning Problems.” Journal of Cryptology, vol. 30, no. 4, Springer, 2017, pp. 1238–75, doi:10.1007/s00145-016-9247-3.","ama":"Kiltz E, Pietrzak KZ, Venturi D, Cash D, Jain A. Efficient authentication from hard learning problems. Journal of Cryptology. 2017;30(4):1238-1275. doi:10.1007/s00145-016-9247-3","apa":"Kiltz, E., Pietrzak, K. Z., Venturi, D., Cash, D., & Jain, A. (2017). Efficient authentication from hard learning problems. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-016-9247-3","short":"E. Kiltz, K.Z. Pietrzak, D. Venturi, D. Cash, A. Jain, Journal of Cryptology 30 (2017) 1238–1275.","ieee":"E. Kiltz, K. Z. Pietrzak, D. Venturi, D. Cash, and A. Jain, “Efficient authentication from hard learning problems,” Journal of Cryptology, vol. 30, no. 4. Springer, pp. 1238–1275, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6166","author":[{"first_name":"Eike","full_name":"Kiltz, Eike","last_name":"Kiltz"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","last_name":"Pietrzak"},{"full_name":"Venturi, Daniele","last_name":"Venturi","first_name":"Daniele"},{"last_name":"Cash","full_name":"Cash, David","first_name":"David"},{"first_name":"Abhishek","full_name":"Jain, Abhishek","last_name":"Jain"}],"article_processing_charge":"No","external_id":{"isi":["000410788600007"]},"title":"Efficient authentication from hard learning problems","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668","name":"Provable Security for Physical Cryptography"}]},{"department":[{"_id":"VlKo"}],"date_updated":"2023-09-20T11:20:26Z","status":"public","conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2017-01-16","location":"Barcelona, Spain","end_date":"2017-01019"},"type":"conference","_id":"1192","ec_funded":1,"related_material":{"record":[{"relation":"later_version","id":"6032","status":"public"}]},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-161197478-2"]},"month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1602.03124","open_access":"1"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The main result of this paper is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δ-matroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Knowing that edge CSP is tractable for even Δ-matroid constraints allows us to extend the tractability result to a larger class of Δ-matroids that includes many classes that were known to be tractable before, namely co-independent, compact, local and binary."}],"title":"Even delta-matroids and the complexity of planar Boolean CSPs","article_processing_charge":"No","external_id":{"isi":["000426965800020"]},"publist_id":"6159","author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr","full_name":"Kazda, Alexandr","last_name":"Kazda"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rolinek","full_name":"Rolinek, Michal"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids and the Complexity of Planar Boolean CSPs,” 307–26. SIAM, 2017. https://doi.org/10.1137/1.9781611974782.20.","ista":"Kazda A, Kolmogorov V, Rolinek M. 2017. Even delta-matroids and the complexity of planar Boolean CSPs. SODA: Symposium on Discrete Algorithms, 307–326.","mla":"Kazda, Alexandr, et al. Even Delta-Matroids and the Complexity of Planar Boolean CSPs. SIAM, 2017, pp. 307–26, doi:10.1137/1.9781611974782.20.","ieee":"A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity of planar Boolean CSPs,” presented at the SODA: Symposium on Discrete Algorithms, Barcelona, Spain, 2017, pp. 307–326.","short":"A. Kazda, V. Kolmogorov, M. Rolinek, in:, SIAM, 2017, pp. 307–326.","ama":"Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of planar Boolean CSPs. In: SIAM; 2017:307-326. doi:10.1137/1.9781611974782.20","apa":"Kazda, A., Kolmogorov, V., & Rolinek, M. (2017). Even delta-matroids and the complexity of planar Boolean CSPs (pp. 307–326). Presented at the SODA: Symposium on Discrete Algorithms, Barcelona, Spain: SIAM. https://doi.org/10.1137/1.9781611974782.20"},"project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:38Z","doi":"10.1137/1.9781611974782.20","date_published":"2017-01-01T00:00:00Z","page":"307 - 326","day":"01","year":"2017","isi":1,"oa":1,"publisher":"SIAM","quality_controlled":"1"},{"month":"02","intvolume":" 308","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.07594"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In this article we define an algebraic vertex of a generalized polyhedron and show that the set of algebraic vertices is the smallest set of points needed to define the polyhedron. We prove that the indicator function of a generalized polytope P is a linear combination of indicator functions of simplices whose vertices are algebraic vertices of P. We also show that the indicator function of any generalized polyhedron is a linear combination, with integer coefficients, of indicator functions of cones with apices at algebraic vertices and line-cones. The concept of an algebraic vertex is closely related to the Fourier–Laplace transform. We show that a point v is an algebraic vertex of a generalized polyhedron P if and only if the tangent cone of P, at v, has non-zero Fourier–Laplace transform."}],"volume":308,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00018708"]},"publication_status":"published","status":"public","type":"journal_article","_id":"1180","department":[{"_id":"HeEd"}],"date_updated":"2023-09-20T11:21:27Z","publisher":"Academic Press","quality_controlled":"1","oa":1,"date_published":"2017-02-21T00:00:00Z","doi":"10.1016/j.aim.2016.12.026","date_created":"2018-12-11T11:50:34Z","page":"627 - 644","day":"21","publication":"Advances in Mathematics","isi":1,"year":"2017","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"title":"Algebraic vertices of non-convex polyhedra","publist_id":"6173","author":[{"last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Imre","last_name":"Bárány","full_name":"Bárány, Imre"},{"full_name":"Robins, Sinai","last_name":"Robins","first_name":"Sinai"}],"external_id":{"isi":["000409292900015"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Akopyan, Arseniy, Imre Bárány, and Sinai Robins. “Algebraic Vertices of Non-Convex Polyhedra.” Advances in Mathematics. Academic Press, 2017. https://doi.org/10.1016/j.aim.2016.12.026.","ista":"Akopyan A, Bárány I, Robins S. 2017. Algebraic vertices of non-convex polyhedra. Advances in Mathematics. 308, 627–644.","mla":"Akopyan, Arseniy, et al. “Algebraic Vertices of Non-Convex Polyhedra.” Advances in Mathematics, vol. 308, Academic Press, 2017, pp. 627–44, doi:10.1016/j.aim.2016.12.026.","apa":"Akopyan, A., Bárány, I., & Robins, S. (2017). Algebraic vertices of non-convex polyhedra. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2016.12.026","ama":"Akopyan A, Bárány I, Robins S. Algebraic vertices of non-convex polyhedra. Advances in Mathematics. 2017;308:627-644. doi:10.1016/j.aim.2016.12.026","short":"A. Akopyan, I. Bárány, S. Robins, Advances in Mathematics 308 (2017) 627–644.","ieee":"A. Akopyan, I. Bárány, and S. Robins, “Algebraic vertices of non-convex polyhedra,” Advances in Mathematics, vol. 308. Academic Press, pp. 627–644, 2017."}},{"status":"public","article_type":"original","type":"journal_article","_id":"1159","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:44:36Z","ddc":["580"],"date_updated":"2023-09-20T11:29:17Z","month":"01","intvolume":" 173","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"Auxin steers numerous physiological processes in plants, making the tight control of its endogenous levels and spatiotemporal distribution a necessity. This regulation is achieved by different mechanisms, including auxin biosynthesis, metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic acid (c-CA) as a novel and unique addition to a small group of endogenous molecules affecting in planta auxin concentrations. c-CA is the photo-isomerization product of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes characteristic for high auxin levels, including inhibition of primary root growth, induction of root hairs, and promotion of adventitious and lateral rooting. By molecular docking and receptor binding assays, we showed that c-CA itself is neither an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux. Auxin signaling reporters detected changes in spatiotemporal distribution of the auxin response along the root of c-CA-treated plants, and long-distance auxin transport assays showed no inhibition of rootward auxin transport. Overall, these results suggest that the phenotypes of c-CA-treated plants are the consequence of a local change in auxin accumulation, induced by the inhibition of auxin efflux. This work reveals a novel mechanism how plants may regulate auxin levels and adds a novel, naturally occurring molecule to the chemical toolbox for the studies of auxin homeostasis.","lang":"eng"}],"issue":"1","volume":173,"ec_funded":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"fd4d1cfe7ed70e54bb12ae3881f3fb91","file_id":"7040","date_updated":"2020-07-14T12:44:36Z","file_size":4109142,"creator":"dernst","date_created":"2019-11-18T16:12:25Z","file_name":"2016_PlantPhysi_Steenackers.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0032-0889"]},"publication_status":"published","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"title":"Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation","publist_id":"6199","author":[{"full_name":"Steenackers, Ward","last_name":"Steenackers","first_name":"Ward"},{"last_name":"Klíma","full_name":"Klíma, Petr","first_name":"Petr"},{"last_name":"Quareshy","full_name":"Quareshy, Mussa","first_name":"Mussa"},{"first_name":"Igor","full_name":"Cesarino, Igor","last_name":"Cesarino"},{"last_name":"Kumpf","full_name":"Kumpf, Robert","first_name":"Robert"},{"last_name":"Corneillie","full_name":"Corneillie, Sander","first_name":"Sander"},{"full_name":"Araújo, Pedro","last_name":"Araújo","first_name":"Pedro"},{"last_name":"Viaene","full_name":"Viaene, Tom","first_name":"Tom"},{"full_name":"Goeminne, Geert","last_name":"Goeminne","first_name":"Geert"},{"first_name":"Moritz","full_name":"Nowack, Moritz","last_name":"Nowack"},{"first_name":"Karin","full_name":"Ljung, Karin","last_name":"Ljung"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"full_name":"Blakeslee, Joshua","last_name":"Blakeslee","first_name":"Joshua"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"first_name":"Richard","full_name":"Napier, Richard","last_name":"Napier"},{"first_name":"Wout","full_name":"Boerjan, Wout","last_name":"Boerjan"},{"full_name":"Vanholme, Bartel","last_name":"Vanholme","first_name":"Bartel"}],"article_processing_charge":"No","external_id":{"pmid":["27837086"],"isi":["000394135800041"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"W. Steenackers et al., “Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation,” Plant Physiology, vol. 173, no. 1. American Society of Plant Biologists, pp. 552–565, 2017.","short":"W. Steenackers, P. Klíma, M. Quareshy, I. Cesarino, R. Kumpf, S. Corneillie, P. Araújo, T. Viaene, G. Goeminne, M. Nowack, K. Ljung, J. Friml, J. Blakeslee, O. Novák, E. Zažímalová, R. Napier, W. Boerjan, B. Vanholme, Plant Physiology 173 (2017) 552–565.","apa":"Steenackers, W., Klíma, P., Quareshy, M., Cesarino, I., Kumpf, R., Corneillie, S., … Vanholme, B. (2017). Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.00943","ama":"Steenackers W, Klíma P, Quareshy M, et al. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 2017;173(1):552-565. doi:10.1104/pp.16.00943","mla":"Steenackers, Ward, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology, vol. 173, no. 1, American Society of Plant Biologists, 2017, pp. 552–65, doi:10.1104/pp.16.00943.","ista":"Steenackers W, Klíma P, Quareshy M, Cesarino I, Kumpf R, Corneillie S, Araújo P, Viaene T, Goeminne G, Nowack M, Ljung K, Friml J, Blakeslee J, Novák O, Zažímalová E, Napier R, Boerjan W, Vanholme B. 2017. Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation. Plant Physiology. 173(1), 552–565.","chicago":"Steenackers, Ward, Petr Klíma, Mussa Quareshy, Igor Cesarino, Robert Kumpf, Sander Corneillie, Pedro Araújo, et al. “Cis-Cinnamic Acid Is a Novel Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.00943."},"publisher":"American Society of Plant Biologists","quality_controlled":"1","oa":1,"doi":"10.1104/pp.16.00943","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:50:28Z","page":"552 - 565","day":"01","publication":"Plant Physiology","has_accepted_license":"1","isi":1,"year":"2017"},{"file_date_updated":"2020-07-14T12:44:37Z","department":[{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2023-09-20T11:24:21Z","status":"public","pubrep_id":"727","type":"journal_article","_id":"1169","volume":205,"issue":"1","ec_funded":1,"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4833","checksum":"7c8ab79cda1f92760bbbbe0f53175bfc","creator":"system","file_size":361500,"date_updated":"2020-07-14T12:44:37Z","file_name":"IST-2016-727-v1+1_SFC_Genetics_final.pdf","date_created":"2018-12-12T10:10:43Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00166731"]},"publication_status":"published","month":"01","intvolume":" 205","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies.","lang":"eng"}],"title":"Spatial gene frequency waves under genotype dependent dispersal","author":[{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kollár","full_name":"Kollár, Richard","first_name":"Richard"}],"publist_id":"6188","article_processing_charge":"No","external_id":{"isi":["000393677300025"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374.","chicago":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193946.","apa":"Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946","ama":"Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946","short":"S. Novak, R. Kollár, Genetics 205 (2017) 367–374.","ieee":"S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp. 367–374, 2017.","mla":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America, 2017, pp. 367–74, doi:10.1534/genetics.116.193946."},"project":[{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"doi":"10.1534/genetics.116.193946","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:50:31Z","page":"367 - 374","day":"01","publication":"Genetics","has_accepted_license":"1","isi":1,"year":"2017","quality_controlled":"1","publisher":"Genetics Society of America","oa":1},{"article_number":"40012","citation":{"ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio,” Scientific Reports, vol. 7. Nature Publishing Group, 2017.","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 7 (2017).","ama":"Altmeyer S, Do Y, Lai Y. Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. 2017;7. doi:10.1038/srep40012","apa":"Altmeyer, S., Do, Y., & Lai, Y. (2017). Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep40012","mla":"Altmeyer, Sebastian, et al. “Dynamics of Ferrofluidic Flow in the Taylor-Couette System with a Small Aspect Ratio.” Scientific Reports, vol. 7, 40012, Nature Publishing Group, 2017, doi:10.1038/srep40012.","ista":"Altmeyer S, Do Y, Lai Y. 2017. Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio. Scientific Reports. 7, 40012.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Dynamics of Ferrofluidic Flow in the Taylor-Couette System with a Small Aspect Ratio.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/srep40012."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-5964-0203","full_name":"Altmeyer, Sebastian","last_name":"Altmeyer","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Do","full_name":"Do, Younghae","first_name":"Younghae"},{"first_name":"Ying","full_name":"Lai, Ying","last_name":"Lai"}],"publist_id":"6198","external_id":{"isi":["000391269700001"]},"article_processing_charge":"No","title":"Dynamics of ferrofluidic flow in the Taylor-Couette system with a small aspect ratio","quality_controlled":"1","publisher":"Nature Publishing Group","oa":1,"isi":1,"has_accepted_license":"1","year":"2017","day":"06","publication":"Scientific Reports","doi":"10.1038/srep40012","date_published":"2017-01-06T00:00:00Z","date_created":"2018-12-11T11:50:28Z","_id":"1160","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"743","date_updated":"2023-09-20T11:28:49Z","ddc":["532"],"department":[{"_id":"BjHo"}],"file_date_updated":"2020-07-14T12:44:36Z","abstract":[{"text":"We investigate fundamental nonlinear dynamics of ferrofluidic Taylor-Couette flow - flow confined be-tween two concentric independently rotating cylinders - consider small aspect ratio by solving the ferro-hydrodynamical equations, carrying out systematic bifurcation analysis. Without magnetic field, we find steady flow patterns, previously observed with a simple fluid, such as those containing normal one- or two vortex cells, as well as anomalous one-cell and twin-cell flow states. However, when a symmetry-breaking transverse magnetic field is present, all flow states exhibit stimulated, finite two-fold mode. Various bifurcations between steady and unsteady states can occur, corresponding to the transitions between the two-cell and one-cell states. While unsteady, axially oscillating flow states can arise, we also detect the emergence of new unsteady flow states. In particular, we uncover two new states: one contains only the azimuthally oscillating solution in the configuration of the twin-cell flow state, and an-other a rotating flow state. Topologically, these flow states are a limit cycle and a quasiperiodic solution on a two-torus, respectively. Emergence of new flow states in addition to observed ones with classical fluid, indicates that richer but potentially more controllable dynamics in ferrofluidic flows, as such flow states depend on the external magnetic field.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"01","intvolume":" 7","publication_identifier":{"issn":["20452322"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"694aa70399444570825099c1a7ec91f2","file_id":"4802","file_size":4546835,"date_updated":"2020-07-14T12:44:36Z","creator":"system","file_name":"IST-2017-743-v1+1_srep40012.pdf","date_created":"2018-12-12T10:10:16Z"}],"language":[{"iso":"eng"}],"volume":7},{"date_created":"2018-12-11T11:50:29Z","doi":"10.1103/PhysRevB.95.024506","date_published":"2017-01-13T00:00:00Z","publication":"Physical Review B - Condensed Matter and Materials Physics","day":"13","year":"2017","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Physical Society","title":"Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment","external_id":{"isi":["000391852800006"]},"article_processing_charge":"No","author":[{"full_name":"Spałek, Jozef","last_name":"Spałek","first_name":"Jozef"},{"last_name":"Zegrodnik","full_name":"Zegrodnik, Michał","first_name":"Michał"},{"full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","last_name":"Kaczmarczyk","id":"46C405DE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publist_id":"6195","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Spałek, Jozef, et al. “Universal Properties of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.” Physical Review B - Condensed Matter and Materials Physics, vol. 95, no. 2, 024506, American Physical Society, 2017, doi:10.1103/PhysRevB.95.024506.","ieee":"J. Spałek, M. Zegrodnik, and J. Kaczmarczyk, “Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment,” Physical Review B - Condensed Matter and Materials Physics, vol. 95, no. 2. American Physical Society, 2017.","short":"J. Spałek, M. Zegrodnik, J. Kaczmarczyk, Physical Review B - Condensed Matter and Materials Physics 95 (2017).","apa":"Spałek, J., Zegrodnik, M., & Kaczmarczyk, J. (2017). Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.95.024506","ama":"Spałek J, Zegrodnik M, Kaczmarczyk J. Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. 2017;95(2). doi:10.1103/PhysRevB.95.024506","chicago":"Spałek, Jozef, Michał Zegrodnik, and Jan Kaczmarczyk. “Universal Properties of High Temperature Superconductors from Real Space Pairing T-J-U Model and Its Quantitative Comparison with Experiment.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.024506.","ista":"Spałek J, Zegrodnik M, Kaczmarczyk J. 2017. Universal properties of high temperature superconductors from real space pairing t-J-U model and its quantitative comparison with experiment. Physical Review B - Condensed Matter and Materials Physics. 95(2), 024506."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"024506","ec_funded":1,"issue":"2","volume":95,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["24699950"]},"intvolume":" 95","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1606.03247","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Selected universal experimental properties of high-temperature superconducting (HTS) cuprates have been singled out in the last decade. One of the pivotal challenges in this field is the designation of a consistent interpretation framework within which we can describe quantitatively the universal features of those systems. Here we analyze in a detailed manner the principal experimental data and compare them quantitatively with the approach based on a single-band model of strongly correlated electrons supplemented with strong antiferromagnetic (super)exchange interaction (the so-called t−J−U model). The model rationale is provided by estimating its microscopic parameters on the basis of the three-band approach for the Cu-O plane. We use our original full Gutzwiller wave-function solution by going beyond the renormalized mean-field theory (RMFT) in a systematic manner. Our approach reproduces very well the observed hole doping (δ) dependence of the kinetic-energy gain in the superconducting phase, one of the principal non-Bardeen-Cooper-Schrieffer features of the cuprates. The calculated Fermi velocity in the nodal direction is practically δ-independent and its universal value agrees very well with that determined experimentally. Also, a weak doping dependence of the Fermi wave vector leads to an almost constant value of the effective mass in a pure superconducting phase which is both observed in experiment and reproduced within our approach. An assessment of the currently used models (t−J, Hubbard) is carried out and the results of the canonical RMFT as a zeroth-order solution are provided for comparison to illustrate the necessity of the introduced higher-order contributions."}],"department":[{"_id":"MiLe"}],"date_updated":"2023-09-20T11:25:56Z","status":"public","type":"journal_article","_id":"1162"},{"status":"public","type":"journal_article","_id":"1152","file_date_updated":"2019-01-18T08:43:16Z","department":[{"_id":"ChWo"}],"ddc":["000"],"date_updated":"2023-09-20T11:29:44Z","month":"01","intvolume":" 18","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"We propose a new memetic strategy that can solve the multi-physics, complex inverse problems, formulated as the multi-objective optimization ones, in which objectives are misfits between the measured and simulated states of various governing processes. The multi-deme structure of the strategy allows for both, intensive, relatively cheap exploration with a moderate accuracy and more accurate search many regions of Pareto set in parallel. The special type of selection operator prefers the coherent alternative solutions, eliminating artifacts appearing in the particular processes. The additional accuracy increment is obtained by the parallel convex searches applied to the local scalarizations of the misfit vector. The strategy is dedicated for solving ill-conditioned problems, for which inverting the single physical process can lead to the ambiguous results. The skill of the selection in artifact elimination is shown on the benchmark problem, while the whole strategy was applied for identification of oil deposits, where the misfits are related to various frequencies of the magnetic and electric waves of the magnetotelluric measurements. 2016 Elsevier B.V.","lang":"eng"}],"volume":18,"file":[{"success":1,"file_id":"5842","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2016_jocs_ewa.pdf","date_created":"2019-01-18T08:43:16Z","file_size":1083911,"date_updated":"2019-01-18T08:43:16Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18777503"]},"publication_status":"published","title":"A multi objective memetic inverse solver reinforced by local optimization methods","author":[{"id":"47794CF0-F248-11E8-B48F-1D18A9856A87","first_name":"Ewa P","full_name":"Gajda-Zagorska, Ewa P","last_name":"Gajda-Zagorska"},{"full_name":"Schaefer, Robert","last_name":"Schaefer","first_name":"Robert"},{"last_name":"Smołka","full_name":"Smołka, Maciej","first_name":"Maciej"},{"full_name":"Pardo, David","last_name":"Pardo","first_name":"David"},{"first_name":"Julen","full_name":"Alvarez Aramberri, Julen","last_name":"Alvarez Aramberri"}],"publist_id":"6206","external_id":{"isi":["000393528700009"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Gajda-Zagorska, E. P., Schaefer, R., Smołka, M., Pardo, D., & Alvarez Aramberri, J. (2017). A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. Elsevier. https://doi.org/10.1016/j.jocs.2016.06.007","ama":"Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. 2017;18:85-94. doi:10.1016/j.jocs.2016.06.007","ieee":"E. P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, and J. Alvarez Aramberri, “A multi objective memetic inverse solver reinforced by local optimization methods,” Journal of Computational Science, vol. 18. Elsevier, pp. 85–94, 2017.","short":"E.P. Gajda-Zagorska, R. Schaefer, M. Smołka, D. Pardo, J. Alvarez Aramberri, Journal of Computational Science 18 (2017) 85–94.","mla":"Gajda-Zagorska, Ewa P., et al. “A Multi Objective Memetic Inverse Solver Reinforced by Local Optimization Methods.” Journal of Computational Science, vol. 18, Elsevier, 2017, pp. 85–94, doi:10.1016/j.jocs.2016.06.007.","ista":"Gajda-Zagorska EP, Schaefer R, Smołka M, Pardo D, Alvarez Aramberri J. 2017. A multi objective memetic inverse solver reinforced by local optimization methods. Journal of Computational Science. 18, 85–94.","chicago":"Gajda-Zagorska, Ewa P, Robert Schaefer, Maciej Smołka, David Pardo, and Julen Alvarez Aramberri. “A Multi Objective Memetic Inverse Solver Reinforced by Local Optimization Methods.” Journal of Computational Science. Elsevier, 2017. https://doi.org/10.1016/j.jocs.2016.06.007."},"publisher":"Elsevier","quality_controlled":"1","oa":1,"doi":"10.1016/j.jocs.2016.06.007","date_published":"2017-01-01T00:00:00Z","date_created":"2018-12-11T11:50:26Z","page":"85 - 94","day":"01","publication":"Journal of Computational Science","isi":1,"has_accepted_license":"1","year":"2017"},{"publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5199","checksum":"0b2d1b647ca96e9ef13a14b8b6775e0f","date_updated":"2020-07-14T12:44:37Z","file_size":56664,"creator":"system","date_created":"2018-12-12T10:16:13Z","file_name":"IST-2017-739-v1+2_10260_2016_375_MOESM1_ESM.pdf"},{"file_name":"IST-2017-739-v1+3_s10260-016-0375-6.pdf","date_created":"2018-12-12T10:16:14Z","creator":"system","file_size":688953,"date_updated":"2020-07-14T12:44:37Z","checksum":"3321ef34e02e28acfc427f77cf32812a","file_id":"5200","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"volume":26,"issue":"3","abstract":[{"lang":"eng","text":"Optimum experimental design theory has recently been extended for parameter estimation in copula models. The use of these models allows one to gain in flexibility by considering the model parameter set split into marginal and dependence parameters. However, this separation also leads to the natural issue of estimating only a subset of all model parameters. In this work, we treat this problem with the application of the (Formula presented.)-optimality to copula models. First, we provide an extension of the corresponding equivalence theory. Then, we analyze a wide range of flexible copula models to highlight the usefulness of (Formula presented.)-optimality in many possible scenarios. Finally, we discuss how the usage of the introduced design criterion also relates to the more general issue of copula selection and optimal design for model discrimination."}],"oa_version":"Submitted Version","scopus_import":"1","intvolume":" 26","month":"08","date_updated":"2023-09-20T11:25:09Z","ddc":["519"],"department":[{"_id":"CaUh"}],"file_date_updated":"2020-07-14T12:44:37Z","_id":"1168","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"739","status":"public","year":"2017","isi":1,"has_accepted_license":"1","publication":"Statistical Methods and Applications","day":"01","page":"403 - 418","date_created":"2018-12-11T11:50:31Z","date_published":"2017-08-01T00:00:00Z","doi":"10.1007/s10260-016-0375-6","acknowledgement":"This work has been supported by the project ANR-2011-IS01-001-01 “DESIRE” and Austrian Science Fund (FWF) I833-N18. Open access funding is provided by the Austrian Science Fund (FWF). ","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"ista":"Perrone E, Rappold A, Müller W. 2017. D inf s optimality in copula models. Statistical Methods and Applications. 26(3), 403–418.","chicago":"Perrone, Elisa, Andreas Rappold, and Werner Müller. “D Inf s Optimality in Copula Models.” Statistical Methods and Applications. Springer, 2017. https://doi.org/10.1007/s10260-016-0375-6.","ama":"Perrone E, Rappold A, Müller W. D inf s optimality in copula models. Statistical Methods and Applications. 2017;26(3):403-418. doi:10.1007/s10260-016-0375-6","apa":"Perrone, E., Rappold, A., & Müller, W. (2017). D inf s optimality in copula models. Statistical Methods and Applications. Springer. https://doi.org/10.1007/s10260-016-0375-6","ieee":"E. Perrone, A. Rappold, and W. Müller, “D inf s optimality in copula models,” Statistical Methods and Applications, vol. 26, no. 3. Springer, pp. 403–418, 2017.","short":"E. Perrone, A. Rappold, W. Müller, Statistical Methods and Applications 26 (2017) 403–418.","mla":"Perrone, Elisa, et al. “D Inf s Optimality in Copula Models.” Statistical Methods and Applications, vol. 26, no. 3, Springer, 2017, pp. 403–18, doi:10.1007/s10260-016-0375-6."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000407973200004"]},"article_processing_charge":"No","publist_id":"6189","author":[{"full_name":"Perrone, Elisa","orcid":"0000-0003-0370-9835","last_name":"Perrone","first_name":"Elisa","id":"2A5F8724-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rappold","full_name":"Rappold, Andreas","first_name":"Andreas"},{"full_name":"Müller, Werner","last_name":"Müller","first_name":"Werner"}],"title":"D inf s optimality in copula models"},{"title":"Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms","publist_id":"6194","author":[{"first_name":"Marcin","last_name":"Wysokiński","full_name":"Wysokiński, Marcin"},{"last_name":"Kaczmarczyk","full_name":"Kaczmarczyk, Jan","orcid":"0000-0002-1629-3675","first_name":"Jan","id":"46C405DE-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000393955500001"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Wysokiński M, Kaczmarczyk J. 2017. Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. 29(8), 085604.","chicago":"Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2017. https://doi.org/10.1088/1361-648X/aa532f.","short":"M. Wysokiński, J. Kaczmarczyk, Journal of Physics: Condensed Matter 29 (2017).","ieee":"M. Wysokiński and J. Kaczmarczyk, “Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms,” Journal of Physics: Condensed Matter, vol. 29, no. 8. IOP Publishing Ltd., 2017.","ama":"Wysokiński M, Kaczmarczyk J. Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. 2017;29(8). doi:10.1088/1361-648X/aa532f","apa":"Wysokiński, M., & Kaczmarczyk, J. (2017). Unconventional superconductivity in generalized Hubbard model role of electron–hole symmetry breaking terms. Journal of Physics: Condensed Matter. IOP Publishing Ltd. https://doi.org/10.1088/1361-648X/aa532f","mla":"Wysokiński, Marcin, and Jan Kaczmarczyk. “Unconventional Superconductivity in Generalized Hubbard Model Role of Electron–Hole Symmetry Breaking Terms.” Journal of Physics: Condensed Matter, vol. 29, no. 8, 085604, IOP Publishing Ltd., 2017, doi:10.1088/1361-648X/aa532f."},"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"article_number":"085604","date_published":"2017-01-16T00:00:00Z","doi":"10.1088/1361-648X/aa532f","date_created":"2018-12-11T11:50:29Z","day":"16","publication":"Journal of Physics: Condensed Matter","isi":1,"year":"2017","publisher":"IOP Publishing Ltd.","quality_controlled":"1","department":[{"_id":"MiLe"}],"date_updated":"2023-09-20T11:25:32Z","status":"public","type":"journal_article","_id":"1163","volume":29,"issue":"8","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09538984"]},"publication_status":"published","month":"01","intvolume":" 29","scopus_import":"1","oa_version":"None","abstract":[{"text":"We investigate the effect of the electron-hole (e-h) symmetry breaking on d-wave superconductivity induced by non-local effects of correlations in the generalized Hubbard model. The symmetry breaking is introduced in a two-fold manner: by the next-to-nearest neighbor hopping of electrons and by the charge-bond interaction - the off-diagonal term of the Coulomb potential. Both terms lead to a pronounced asymmetry of the superconducting order parameter. The next-to-nearest neighbor hopping enhances superconductivity for h-doping, while diminishes it for e-doping. The charge-bond interaction alone leads to the opposite effect and, additionally, to the kinetic-energy gain upon condensation in the underdoped regime. With both terms included, with similar amplitudes, the height of the superconducting dome and the critical doping remain in favor of h-doping. The influence of the charge-bond interaction on deviations from symmetry of the shape of the gap at the Fermi surface in the momentum space is briefly discussed.","lang":"eng"}]}]