[{"publist_id":"6993","issue":"399","abstract":[{"lang":"eng","text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n"}],"type":"journal_article","volume":9,"oa_version":"None","date_updated":"2021-01-12T08:11:31Z","date_created":"2018-12-11T11:48:01Z","author":[{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"}],"department":[{"_id":"GaNo"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","status":"public","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"702","year":"2017","publication_identifier":{"issn":["19466234"]},"day":"19","month":"07","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aao0972","date_published":"2017-07-19T00:00:00Z","page":"eaao0972","quality_controlled":"1","citation":{"ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 2017;9(399):eaao0972. doi:10.1126/scitranslmed.aao0972","ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao0972","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” Science Translational Medicine, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:10.1126/scitranslmed.aao0972.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao0972."},"publication":"Science Translational Medicine"},{"scopus_import":1,"month":"08","day":"01","publication_identifier":{"issn":["13569597"]},"publication":"Genes to Cells","citation":{"apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. Wiley-Blackwell. https://doi.org/10.1111/gtc.12508","ieee":"X. Geng et al., “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” Genes to Cells, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722.","ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 2017;22(8):715-722. doi:10.1111/gtc.12508","chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells. Wiley-Blackwell, 2017. https://doi.org/10.1111/gtc.12508.","short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:10.1111/gtc.12508."},"quality_controlled":"1","page":"715 - 722","date_published":"2017-08-01T00:00:00Z","doi":"10.1111/gtc.12508","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse."}],"publist_id":"6987","issue":"8","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"706","year":"2017","status":"public","publication_status":"published","title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","department":[{"_id":"PeJo"}],"publisher":"Wiley-Blackwell","intvolume":" 22","author":[{"id":"3395256A-F248-11E8-B48F-1D18A9856A87","first_name":"Xiaoqi","last_name":"Geng","full_name":"Geng, Xiaoqi"},{"last_name":"Maruo","first_name":"Tomohiko","full_name":"Maruo, Tomohiko"},{"full_name":"Mandai, Kenji","first_name":"Kenji","last_name":"Mandai"},{"first_name":"Irwan","last_name":"Supriyanto","full_name":"Supriyanto, Irwan"},{"first_name":"Muneaki","last_name":"Miyata","full_name":"Miyata, Muneaki"},{"full_name":"Sakakibara, Shotaro","first_name":"Shotaro","last_name":"Sakakibara"},{"full_name":"Mizoguchi, Akira","first_name":"Akira","last_name":"Mizoguchi"},{"full_name":"Takai, Yoshimi","last_name":"Takai","first_name":"Yoshimi"},{"full_name":"Mori, Masahiro","first_name":"Masahiro","last_name":"Mori"}],"date_updated":"2021-01-12T08:11:37Z","date_created":"2018-12-11T11:48:02Z","oa_version":"None","volume":22},{"volume":49,"date_updated":"2021-01-12T08:11:41Z","date_created":"2018-12-11T11:48:02Z","author":[{"last_name":"Akopyan","first_name":"Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"first_name":"Roman","last_name":"Karasev","full_name":"Karasev, Roman"}],"publisher":"Wiley-Blackwell","department":[{"_id":"HeEd"}],"publication_status":"published","year":"2017","publist_id":"6982","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1112/blms.12062","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.06279"}],"oa":1,"publication_identifier":{"issn":["00246093"]},"month":"08","oa_version":"Preprint","intvolume":" 49","title":"A tight estimate for the waist of the ball ","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"707","issue":"4","abstract":[{"text":"We answer a question of M. Gromov on the waist of the unit ball.","lang":"eng"}],"type":"journal_article","date_published":"2017-08-01T00:00:00Z","page":"690 - 693","citation":{"ista":"Akopyan A, Karasev R. 2017. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 49(4), 690–693.","ieee":"A. Akopyan and R. Karasev, “A tight estimate for the waist of the ball ,” Bulletin of the London Mathematical Society, vol. 49, no. 4. Wiley-Blackwell, pp. 690–693, 2017.","apa":"Akopyan, A., & Karasev, R. (2017). A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. Wiley-Blackwell. https://doi.org/10.1112/blms.12062","ama":"Akopyan A, Karasev R. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 2017;49(4):690-693. doi:10.1112/blms.12062","chicago":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society. Wiley-Blackwell, 2017. https://doi.org/10.1112/blms.12062.","mla":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society, vol. 49, no. 4, Wiley-Blackwell, 2017, pp. 690–93, doi:10.1112/blms.12062.","short":"A. Akopyan, R. Karasev, Bulletin of the London Mathematical Society 49 (2017) 690–693."},"publication":"Bulletin of the London Mathematical Society","day":"01","scopus_import":1},{"publisher":"Public Library of Science","department":[{"_id":"SaSi"}],"publication_status":"published","year":"2017","volume":15,"date_updated":"2021-01-12T08:11:45Z","date_created":"2018-12-11T11:48:03Z","author":[{"orcid":"0000-0002-4002-4686","id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","last_name":"Nagy","first_name":"Balint","full_name":"Nagy, Balint"},{"full_name":"Hovhannisyan, Anahit","first_name":"Anahit","last_name":"Hovhannisyan"},{"full_name":"Barzan, Ruxandra","first_name":"Ruxandra","last_name":"Barzan"},{"first_name":"Ting","last_name":"Chen","full_name":"Chen, Ting"},{"last_name":"Kukley","first_name":"Maria","full_name":"Kukley, Maria"}],"article_number":"e2001993","publist_id":"6983","file_date_updated":"2020-07-14T12:47:49Z","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2001993","publication_identifier":{"issn":["15449173"]},"month":"08","intvolume":" 15","status":"public","ddc":["576","610"],"title":"Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"708","file":[{"creator":"system","file_size":18155365,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-889-v1+1_journal.pbio.2001993.pdf","checksum":"0c974f430682dc832ea7b27ab5a93124","date_created":"2018-12-12T10:15:35Z","date_updated":"2020-07-14T12:47:49Z","file_id":"5156","relation":"main_file"}],"oa_version":"Published Version","pubrep_id":"889","type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"In the developing and adult brain, oligodendrocyte precursor cells (OPCs) are influenced by neuronal activity: they are involved in synaptic signaling with neurons, and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing. An important question that has been unanswered is whether OPCs can discriminate different patterns of neuronal activity and respond to them in a distinct way. Here, we demonstrate in brain slices that the pattern of neuronal activity determines the functional changes triggered at synapses between axons and OPCs. Furthermore, we show that stimulation of the corpus callosum at different frequencies in vivo affects proliferation and differentiation of OPCs in a dissimilar way. Our findings suggest that neurons do not influence OPCs in “all-or-none” fashion but use their firing pattern to tune the response and behavior of these nonneuronal cells."}],"citation":{"chicago":"Nagy, Balint, Anahit Hovhannisyan, Ruxandra Barzan, Ting Chen, and Maria Kukley. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001993.","mla":"Nagy, Balint, et al. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology, vol. 15, no. 8, e2001993, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001993.","short":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, M. Kukley, PLoS Biology 15 (2017).","ista":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. 2017. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 15(8), e2001993.","ieee":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, and M. Kukley, “Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum,” PLoS Biology, vol. 15, no. 8. Public Library of Science, 2017.","apa":"Nagy, B., Hovhannisyan, A., Barzan, R., Chen, T., & Kukley, M. (2017). Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001993","ama":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 2017;15(8). doi:10.1371/journal.pbio.2001993"},"publication":"PLoS Biology","date_published":"2017-08-22T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"22"},{"language":[{"iso":"eng"}],"doi":"10.1002/cbin.10783","date_published":"2017-08-01T00:00:00Z","page":"908 - 913","quality_controlled":"1","citation":{"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.","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.","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","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.","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.","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."},"publication":"Cell Biology International","publication_identifier":{"issn":["10656995"]},"day":"01","month":"08","scopus_import":1,"volume":41,"oa_version":"None","date_updated":"2021-01-12T08:11:47Z","date_created":"2018-12-11T11:48:04Z","author":[{"first_name":"Wuping","last_name":"Sun","full_name":"Sun, Wuping"},{"full_name":"Li, Chen","last_name":"Li","first_name":"Chen"},{"full_name":"Zhang, Yonghong","first_name":"Yonghong","last_name":"Zhang"},{"full_name":"Jiang, Changyu","last_name":"Jiang","first_name":"Changyu"},{"full_name":"Zhai, Ming-Zhu","id":"34009CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Ming-Zhu","last_name":"Zhai"},{"full_name":"Zhou, Qian","first_name":"Qian","last_name":"Zhou"},{"first_name":"Lizu","last_name":"Xiao","full_name":"Xiao, Lizu"},{"full_name":"Deng, Qiwen","last_name":"Deng","first_name":"Qiwen"}],"publisher":"Wiley-Blackwell","department":[{"_id":"RySh"}],"intvolume":" 41","title":"Gene expression changes of thermo sensitive transient receptor potential channels in obese mice","publication_status":"published","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"709","year":"2017","issue":"8","publist_id":"6981","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"}],"type":"journal_article"},{"department":[{"_id":"KrPi"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2017","volume":81,"date_created":"2018-12-11T11:48:04Z","date_updated":"2021-01-12T08:11:50Z","author":[{"last_name":"Obremski","first_name":"Maciej","full_name":"Obremski, Maciej"},{"full_name":"Skórski, Maciej","first_name":"Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"article_number":"20","ec_funded":1,"publist_id":"6979","file_date_updated":"2020-07-14T12:47:49Z","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.APPROX-RANDOM.2017.20","conference":{"end_date":"2017-08-18","start_date":"2017-08-18","location":"Berkeley, USA","name":"20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX"},"publication_identifier":{"issn":["18688969"]},"month":"08","intvolume":" 81","status":"public","title":"Renyi entropy estimation revisited","ddc":["005","600"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"710","oa_version":"Published Version","file":[{"file_name":"IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf","access_level":"open_access","content_type":"application/pdf","file_size":604813,"creator":"system","relation":"main_file","file_id":"4991","date_updated":"2020-07-14T12:47:49Z","date_created":"2018-12-12T10:13:10Z","checksum":"89225c7dcec2c93838458c9102858985"}],"pubrep_id":"888","alternative_title":["LIPIcs"],"type":"conference","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. "}],"citation":{"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","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.","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.","short":"M. Obremski, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","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.","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."},"date_published":"2017-08-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"year":"2017","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"GaNo"},{"_id":"SiHi"}],"author":[{"full_name":"Andergassen, Daniel","first_name":"Daniel","last_name":"Andergassen"},{"last_name":"Dotter","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph"},{"full_name":"Wenzel, Dyniel","first_name":"Dyniel","last_name":"Wenzel"},{"full_name":"Sigl, Verena","last_name":"Sigl","first_name":"Verena"},{"last_name":"Bammer","first_name":"Philipp","full_name":"Bammer, Philipp"},{"first_name":"Markus","last_name":"Muckenhuber","full_name":"Muckenhuber, Markus"},{"full_name":"Mayer, Daniela","first_name":"Daniela","last_name":"Mayer"},{"last_name":"Kulinski","first_name":"Tomasz","full_name":"Kulinski, Tomasz"},{"last_name":"Theussl","first_name":"Hans","full_name":"Theussl, Hans"},{"full_name":"Penninger, Josef","last_name":"Penninger","first_name":"Josef"},{"full_name":"Bock, Christoph","first_name":"Christoph","last_name":"Bock"},{"full_name":"Barlow, Denise","last_name":"Barlow","first_name":"Denise"},{"full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pauler"},{"full_name":"Hudson, Quanah","last_name":"Hudson","first_name":"Quanah"}],"date_updated":"2021-01-12T08:11:57Z","date_created":"2018-12-11T11:48:05Z","volume":6,"article_number":"e25125","file_date_updated":"2020-07-14T12:47:50Z","publist_id":"6971","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"}],"doi":"10.7554/eLife.25125","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["2050084X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"713","status":"public","title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","ddc":["576"],"intvolume":" 6","pubrep_id":"885","oa_version":"Published Version","file":[{"file_id":"5020","relation":"main_file","checksum":"1ace3462e64a971b9ead896091829549","date_updated":"2020-07-14T12:47:50Z","date_created":"2018-12-12T10:13:36Z","access_level":"open_access","file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf","creator":"system","content_type":"application/pdf","file_size":6399510},{"date_updated":"2020-07-14T12:47:50Z","date_created":"2018-12-12T10:13:36Z","checksum":"6241dc31eeb87b03facadec3a53a6827","file_id":"5021","relation":"main_file","creator":"system","file_size":4264398,"content_type":"application/pdf","file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","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."}],"publication":"eLife","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.","ieee":"D. Andergassen et al., “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” eLife, vol. 6. eLife Sciences Publications, 2017.","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","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","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.","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.","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)."},"date_published":"2017-08-14T00:00:00Z","scopus_import":1,"day":"14","has_accepted_license":"1"},{"date_published":"2017-08-01T00:00:00Z","citation":{"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","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","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.","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 5.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","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.","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."},"has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"checksum":"d2bda4783821a6358333fe27f11f4737","date_created":"2018-12-12T10:08:02Z","date_updated":"2020-07-14T12:47:49Z","file_id":"4661","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":570294,"access_level":"open_access","file_name":"IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf"}],"oa_version":"Published Version","pubrep_id":"886","intvolume":" 85","ddc":["004","005"],"title":"Bidirectional nested weighted automata","status":"public","_id":"711","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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."}],"alternative_title":["LIPIcs"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.CONCUR.2017.5","conference":{"name":"28th International Conference on Concurrency Theory, CONCUR","end_date":"2017-09-08","start_date":"2017-09-05","location":"Berlin, Germany"},"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["18688969"]},"month":"08","volume":85,"date_updated":"2021-01-12T08:11:53Z","date_created":"2018-12-11T11:48:04Z","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2017","publist_id":"6976","file_date_updated":"2020-07-14T12:47:49Z","article_number":"5"},{"day":"01","month":"08","publication_identifier":{"issn":["0362546X"]},"scopus_import":1,"doi":"10.1016/j.na.2017.03.001","date_published":"2017-08-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Nonlinear Analysis: Theory, Methods and Applications","oa":1,"citation":{"ista":"Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207.","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.","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","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.","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.","short":"J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.00730"}],"quality_controlled":"1","page":"181 - 207","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"}],"publist_id":"6975","type":"journal_article","author":[{"full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer","first_name":"Julian L"}],"date_updated":"2021-01-12T08:11:55Z","date_created":"2018-12-11T11:48:05Z","oa_version":"Submitted Version","volume":159,"_id":"712","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2017","publication_status":"published","title":"Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations","status":"public","department":[{"_id":"JuFi"}],"intvolume":" 159","publisher":"Elsevier"},{"_id":"714","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 178","status":"public","title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens","oa_version":"Submitted Version","type":"journal_article","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"}],"citation":{"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.","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.","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","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.","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."},"publication":"Drug and Alcohol Dependence","page":"7 - 14","article_type":"original","date_published":"2017-09-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"01","pmid":1,"acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","year":"2017","department":[{"_id":"GaNo"}],"publisher":"Elsevier","publication_status":"published","author":[{"first_name":"Gabriela","last_name":"Brailoiu","full_name":"Brailoiu, Gabriela"},{"orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","last_name":"Deliu","first_name":"Elena","full_name":"Deliu, Elena"},{"first_name":"Jeffrey","last_name":"Barr","full_name":"Barr, Jeffrey"},{"first_name":"Linda","last_name":"Console Bram","full_name":"Console Bram, Linda"},{"full_name":"Ciuciu, Alexandra","first_name":"Alexandra","last_name":"Ciuciu"},{"full_name":"Abood, Mary","first_name":"Mary","last_name":"Abood"},{"full_name":"Unterwald, Ellen","first_name":"Ellen","last_name":"Unterwald"},{"last_name":"Brǎiloiu","first_name":"Eugen","full_name":"Brǎiloiu, Eugen"}],"volume":178,"date_created":"2018-12-11T11:48:05Z","date_updated":"2021-01-12T08:12:00Z","publist_id":"6967","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705"}],"oa":1,"external_id":{"pmid":["28623807"]},"quality_controlled":"1","doi":"10.1016/j.drugalcdep.2017.04.015","language":[{"iso":"eng"}],"publication_identifier":{"issn":["03768716"]},"month":"09"},{"title":"More excitation for Rett syndrome","status":"public","publication_status":"published","department":[{"_id":"GaNo"}],"intvolume":" 9","publisher":"American Association for the Advancement of Science","_id":"715","year":"2017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:48:06Z","date_updated":"2021-01-12T08:12:04Z","oa_version":"None","volume":9,"author":[{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"article_number":"aao4218","type":"journal_article","abstract":[{"lang":"eng","text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome."}],"issue":"405","publist_id":"6968","quality_controlled":"1","publication":"Science Translational Medicine","citation":{"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.","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.","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.","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","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218."},"language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aao4218","date_published":"2017-08-30T00:00:00Z","scopus_import":1,"month":"08","day":"30","publication_identifier":{"issn":["19466234"]}},{"publication_identifier":{"issn":["00045411"]},"month":"09","language":[{"iso":"eng"}],"doi":"10.1145/3121408","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1201.2829"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1201.2829"}],"publist_id":"6964","ec_funded":1,"volume":64,"date_updated":"2021-01-12T08:12:08Z","date_created":"2018-12-11T11:48:06Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"publisher":"ACM","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2017","day":"01","scopus_import":1,"date_published":"2017-09-01T00:00:00Z","page":"34","article_type":"original","citation":{"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.","short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 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.","ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):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.","apa":"Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408","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."},"publication":"Journal of the ACM","issue":"5","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."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 64","status":"public","title":"The complexity of mean-payoff pushdown games","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"716"},{"page":"236 - 259","citation":{"short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","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.","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.","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","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.","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","ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259."},"publication":"Journal of Computer and System Sciences","date_published":"2017-09-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 88","title":"Hyperplane separation technique for multidimensional mean-payoff games","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"717","oa_version":"Preprint","type":"journal_article","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."}],"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1210.3141"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jcss.2017.04.005","month":"09","publisher":"Academic Press","department":[{"_id":"KrCh"}],"publication_status":"published","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.","year":"2017","volume":88,"date_created":"2018-12-11T11:48:07Z","date_updated":"2023-02-23T10:38:15Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2329"}]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Yaron","last_name":"Velner","full_name":"Velner, Yaron"}],"ec_funded":1,"publist_id":"6963"},{"scopus_import":1,"publication_identifier":{"issn":["00015903"]},"month":"09","day":"01","page":"543 - 544","quality_controlled":"1","citation":{"ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","apa":"Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.","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.","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."},"publication":"Acta Informatica","language":[{"iso":"eng"}],"doi":"10.1007/s00236-017-0299-0","date_published":"2017-09-01T00:00:00Z","type":"journal_article","publist_id":"6961","issue":"6","abstract":[{"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.","lang":"eng"}],"intvolume":" 54","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","status":"public","title":"Special issue: Synthesis and SYNT 2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"719","year":"2017","oa_version":"None","volume":54,"date_updated":"2021-01-12T08:12:18Z","date_created":"2018-12-11T11:48:07Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Rüdiger","last_name":"Ehlers","full_name":"Ehlers, Rüdiger"}]},{"publication":"PLoS Computational Biology","citation":{"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.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (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.","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","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.","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","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"},"date_published":"2017-09-19T00:00:00Z","scopus_import":1,"day":"19","has_accepted_license":"1","article_processing_charge":"Yes","_id":"720","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["530","571"],"title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","status":"public","intvolume":" 13","pubrep_id":"884","file":[{"relation":"main_file","file_id":"5352","date_updated":"2020-07-14T12:47:53Z","date_created":"2018-12-12T10:18:30Z","checksum":"81107096c19771c36ddbe6f0282a3acb","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","access_level":"open_access","file_size":14167050,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"9","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"doi":"10.1371/journal.pcbi.1005763","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"issn":["1553734X"]},"year":"2017","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","author":[{"last_name":"Humplik","first_name":"Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","full_name":"Humplik, Jan"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:48:08Z","date_updated":"2021-01-12T08:12:21Z","volume":13,"article_number":"e1005763","file_date_updated":"2020-07-14T12:47:53Z","publist_id":"6960"},{"type":"journal_article","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."}],"issue":"9","status":"public","title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","intvolume":" 70","_id":"721","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"day":"01","page":"1672 - 1705","publication":"Communications on Pure and Applied Mathematics","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.","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 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.","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","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.","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.","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"},"date_published":"2017-09-01T00:00:00Z","publist_id":"6959","ec_funded":1,"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"LaEr"}],"year":"2017","date_updated":"2021-01-12T08:12:24Z","date_created":"2018-12-11T11:48:08Z","volume":70,"author":[{"full_name":"Ajanki, Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87","first_name":"Oskari H","last_name":"Ajanki"},{"full_name":"Krüger, Torben H","last_name":"Krüger","first_name":"Torben H","orcid":"0000-0002-4821-3297","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös"}],"month":"09","publication_identifier":{"issn":["00103640"]},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1512.03703"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1002/cpa.21639"},{"month":"09","publication_identifier":{"issn":["09609822"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2017.06.043","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["28898665"]},"file_date_updated":"2020-07-14T12:47:54Z","publist_id":"6956","ec_funded":1,"date_updated":"2021-01-12T08:12:29Z","date_created":"2018-12-11T11:48:08Z","volume":27,"author":[{"last_name":"Morris","first_name":"Emily","full_name":"Morris, Emily"},{"full_name":"Griffiths, Marcus","first_name":"Marcus","last_name":"Griffiths"},{"first_name":"Agata","last_name":"Golebiowska","full_name":"Golebiowska, Agata"},{"full_name":"Mairhofer, Stefan","last_name":"Mairhofer","first_name":"Stefan"},{"full_name":"Burr Hersey, Jasmine","last_name":"Burr Hersey","first_name":"Jasmine"},{"full_name":"Goh, Tatsuaki","first_name":"Tatsuaki","last_name":"Goh"},{"full_name":"Von Wangenheim, Daniel","id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim"},{"first_name":"Brian","last_name":"Atkinson","full_name":"Atkinson, Brian"},{"last_name":"Sturrock","first_name":"Craig","full_name":"Sturrock, Craig"},{"full_name":"Lynch, Jonathan","first_name":"Jonathan","last_name":"Lynch"},{"full_name":"Vissenberg, Kris","last_name":"Vissenberg","first_name":"Kris"},{"first_name":"Karl","last_name":"Ritz","full_name":"Ritz, Karl"},{"full_name":"Wells, Darren","last_name":"Wells","first_name":"Darren"},{"full_name":"Mooney, Sacha","last_name":"Mooney","first_name":"Sacha"},{"full_name":"Bennett, Malcolm","first_name":"Malcolm","last_name":"Bennett"}],"publication_status":"published","publisher":"Cell Press","department":[{"_id":"JiFr"}],"year":"2017","pmid":1,"day":"11","has_accepted_license":"1","scopus_import":1,"date_published":"2017-09-11T00:00:00Z","page":"R919 - R930","publication":"Current Biology","citation":{"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","ieee":"E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","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.","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.","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.","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."},"abstract":[{"lang":"eng","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."}],"issue":"17","type":"journal_article","oa_version":"Submitted Version","file":[{"file_name":"2017_CurrentBiology_Morris.pdf","access_level":"open_access","creator":"dernst","file_size":1576593,"content_type":"application/pdf","file_id":"6332","relation":"main_file","date_updated":"2020-07-14T12:47:54Z","date_created":"2019-04-17T07:46:40Z","checksum":"e45588b21097b408da6276a3e5eedb2e"}],"pubrep_id":"982","ddc":["581"],"title":"Shaping 3D root system architecture","status":"public","intvolume":" 27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"722"},{"type":"journal_article","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"}],"issue":"38","_id":"725","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Discrete modes of social information processing predict individual behavior of fish in a group","intvolume":" 114","oa_version":"Submitted Version","scopus_import":1,"day":"19","publication":"PNAS","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.","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 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.","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","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.","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.","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"},"page":"10149 - 10154","date_published":"2017-09-19T00:00:00Z","publist_id":"6953","year":"2017","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"GaTk"}],"author":[{"last_name":"Harpaz","first_name":"Roy","full_name":"Harpaz, Roy"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"}],"date_created":"2018-12-11T11:48:10Z","date_updated":"2021-01-12T08:12:36Z","volume":114,"month":"09","publication_identifier":{"issn":["00278424"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/","open_access":"1"}],"external_id":{"pmid":["28874581"]},"quality_controlled":"1","doi":"10.1073/pnas.1703817114","language":[{"iso":"eng"}]},{"date_published":"2017-09-13T00:00:00Z","publication":"Physical Review B","citation":{"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","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.","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.","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","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).","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."},"day":"13","scopus_import":1,"oa_version":"Submitted Version","_id":"724","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Noninteracting central site model localization and logarithmic entanglement growth","status":"public","intvolume":" 96","abstract":[{"lang":"eng","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."}],"issue":"10","type":"journal_article","doi":"10.1103/PhysRevB.96.104203","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1701.02744","open_access":"1"}],"oa":1,"quality_controlled":"1","month":"09","publication_identifier":{"issn":["24699950"]},"author":[{"last_name":"Hetterich","first_name":"Daniel","full_name":"Hetterich, Daniel"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","first_name":"Maksym","last_name":"Serbyn"},{"first_name":"Fernando","last_name":"Domínguez","full_name":"Domínguez, Fernando"},{"full_name":"Pollmann, Frank","last_name":"Pollmann","first_name":"Frank"},{"first_name":"Björn","last_name":"Trauzettel","full_name":"Trauzettel, Björn"}],"date_created":"2018-12-11T11:48:09Z","date_updated":"2021-01-12T08:12:35Z","volume":96,"year":"2017","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.","publication_status":"published","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publist_id":"6955","article_number":"104203"},{"language":[{"iso":"eng"}],"doi":"10.1126/scitranslmed.aap8168","date_published":"2017-10-11T00:00:00Z","quality_controlled":"1","citation":{"ista":"Novarino G. 2017. The science of love in ASD and ADHD. Science Translational Medicine. 9(411), eaap8168.","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","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.","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.","short":"G. Novarino, Science Translational Medicine 9 (2017)."},"publication":"Science Translational Medicine","publication_identifier":{"issn":["19466234"]},"day":"11","month":"10","scopus_import":1,"oa_version":"None","volume":9,"date_updated":"2021-01-12T08:12:57Z","date_created":"2018-12-11T11:48:12Z","author":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"intvolume":" 9","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science","status":"public","title":"The science of love in ASD and ADHD","publication_status":"published","year":"2017","_id":"731","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6938","issue":"411","abstract":[{"text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently.","lang":"eng"}],"type":"journal_article","article_number":"eaap8168"},{"publication_identifier":{"issn":["1525-0016"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1016/j.ymthe.2016.10.005","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["28129106"]},"file_date_updated":"2020-07-14T12:47:56Z","volume":25,"date_updated":"2021-01-12T08:13:14Z","date_created":"2020-01-25T15:55:39Z","author":[{"full_name":"Smole, Anže","last_name":"Smole","first_name":"Anže"},{"full_name":"Lainšček, Duško","last_name":"Lainšček","first_name":"Duško"},{"last_name":"Bezeljak","first_name":"Urban","orcid":"0000-0003-1365-5631","id":"2A58201A-F248-11E8-B48F-1D18A9856A87","full_name":"Bezeljak, Urban"},{"full_name":"Horvat, Simon","first_name":"Simon","last_name":"Horvat"},{"full_name":"Jerala, Roman","first_name":"Roman","last_name":"Jerala"}],"publisher":"Elsevier","department":[{"_id":"MaLo"}],"publication_status":"published","pmid":1,"year":"2017","article_processing_charge":"No","has_accepted_license":"1","day":"01","date_published":"2017-01-01T00:00:00Z","page":"102-119","article_type":"original","citation":{"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","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.","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","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.","short":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119.","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.","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."},"publication":"Molecular Therapy","issue":"1","abstract":[{"lang":"eng","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."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2017_MolecularTherapy_Smole.pdf","access_level":"open_access","file_size":3404806,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7561","date_updated":"2020-07-14T12:47:56Z","date_created":"2020-03-03T10:55:13Z","checksum":"ea8b1b28606dd1edab7379ba4fa3641f"}],"intvolume":" 25","ddc":["570"],"title":"A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation","status":"public","_id":"7360","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"conference":{"name":"Big Data","end_date":"2017-12-14","location":"Boston, MA, United States","start_date":"2017-12-11"},"date_published":"2017-12-01T00:00:00Z","doi":"10.1109/BigData.2017.8258375","quality_controlled":"1","page":"3760 - 3763","publication":"2017 IEEE International Conference on Big Data","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.","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","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","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.","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.","short":"J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763."},"day":"01","month":"12","publication_identifier":{"isbn":["978-153862714-3"]},"scopus_import":1,"date_created":"2018-12-11T11:48:18Z","date_updated":"2021-01-12T08:13:55Z","oa_version":"None","author":[{"last_name":"Pielorz","first_name":"Jasmin","id":"49BC895A-F248-11E8-B48F-1D18A9856A87","full_name":"Pielorz, Jasmin"},{"first_name":"Matthias","last_name":"Prandtstetter","full_name":"Prandtstetter, Matthias"},{"full_name":"Straub, Markus","last_name":"Straub","first_name":"Markus"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"publication_status":"published","status":"public","title":"Optimal geospatial volunteer allocation needs realistic distances","publisher":"IEEE","department":[{"_id":"ChLa"}],"_id":"750","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","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"}],"publist_id":"6906","type":"conference"},{"date_published":"2017-07-28T00:00:00Z","article_type":"original","citation":{"ama":"Fulek R, Kynčl J, Pálvölgyi D. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 2017;24(3). doi:10.37236/6663","ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18.","apa":"Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. International Press. https://doi.org/10.37236/6663","ieee":"R. Fulek, J. Kynčl, and D. Pálvölgyi, “Unified Hanani Tutte theorem,” Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, 2017.","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).","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."},"publication":"Electronic Journal of Combinatorics","article_processing_charge":"No","has_accepted_license":"1","day":"28","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":236944,"creator":"dernst","access_level":"open_access","file_name":"2017_ElectrCombi_Fulek.pdf","checksum":"ef320cff0f062051e858f929be6a3581","date_created":"2019-01-18T14:04:08Z","date_updated":"2020-07-14T12:48:06Z","relation":"main_file","file_id":"5853"}],"intvolume":" 24","title":"Unified Hanani Tutte theorem","status":"public","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"795","issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.37236/6663","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa":1,"publication_identifier":{"issn":["10778926"]},"month":"07","volume":24,"date_updated":"2022-03-18T12:58:53Z","date_created":"2018-12-11T11:48:32Z","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek","full_name":"Fulek, Radoslav"},{"last_name":"Kynčl","first_name":"Jan","full_name":"Kynčl, Jan"},{"full_name":"Pálvölgyi, Dömötör","last_name":"Pálvölgyi","first_name":"Dömötör"}],"publisher":"International Press","department":[{"_id":"UlWa"}],"publication_status":"published","year":"2017","ec_funded":1,"publist_id":"6859","file_date_updated":"2020-07-14T12:48:06Z","article_number":"P3.18"},{"language":[{"iso":"eng"}],"date_published":"2017-05-01T00:00:00Z","doi":"10.1002/piuz.201770305","page":"111 - 113","article_type":"original","quality_controlled":"1","citation":{"ama":"Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113. doi:10.1002/piuz.201770305","ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit. Wiley. 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.","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305.","short":"J.M. Fink, Physik in Unserer Zeit 48 (2017) 111–113.","chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit. Wiley, 2017. https://doi.org/10.1002/piuz.201770305."},"publication":"Physik in unserer Zeit","article_processing_charge":"No","day":"01","month":"05","oa_version":"None","volume":48,"date_created":"2018-12-11T11:48:33Z","date_updated":"2022-03-24T09:16:20Z","author":[{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M"}],"department":[{"_id":"JoFi"}],"intvolume":" 48","publisher":"Wiley","status":"public","publication_status":"published","title":"Photonenblockade aufgelöst","year":"2017","_id":"797","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","publist_id":"6856","abstract":[{"lang":"ger","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."}],"type":"journal_article"},{"doi":"10.31263/voebm.v70i2.1898","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"08","publication_identifier":{"issn":["10222588"]},"author":[{"full_name":"Andrae, Magdalena","last_name":"Andrae","first_name":"Magdalena"},{"full_name":"Villányi, Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8126-0426","first_name":"Márton","last_name":"Villányi"}],"date_created":"2018-12-11T11:48:36Z","date_updated":"2021-01-12T08:16:45Z","volume":70,"year":"2017","publication_status":"published","department":[{"_id":"E-Lib"}],"publisher":"VÖB","file_date_updated":"2020-07-14T12:48:09Z","publist_id":"6843","date_published":"2017-08-01T00:00:00Z","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","citation":{"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.","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","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.","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","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.","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"},"page":"274 - 280","day":"01","has_accepted_license":"1","scopus_import":1,"popular_science":"1","oa_version":"Published Version","file":[{"creator":"dernst","file_size":125065,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_VOEB_Andrae.pdf","checksum":"558c18bcf5580d87dd371ec626d52075","date_created":"2019-01-18T13:39:26Z","date_updated":"2020-07-14T12:48:09Z","file_id":"5851","relation":"main_file"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"807","title":"Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung","ddc":["020"],"status":"public","intvolume":" 70","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"}],"issue":"2","type":"journal_article"},{"language":[{"iso":"eng"}],"doi":"10.31263/voebm.v70i2.1678","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["10222588"]},"month":"08","volume":70,"date_updated":"2021-01-12T08:17:44Z","date_created":"2018-12-11T11:48:42Z","author":[{"full_name":"Petritsch, Barbara","first_name":"Barbara","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614"}],"department":[{"_id":"E-Lib"}],"publisher":"VÖB","publication_status":"published","year":"2017","publist_id":"6823","file_date_updated":"2020-07-14T12:48:11Z","date_published":"2017-08-01T00:00:00Z","page":"200 - 207","citation":{"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.","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.","ieee":"B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","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","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.","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"},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","has_accepted_license":"1","day":"01","scopus_import":1,"file":[{"file_id":"5850","relation":"main_file","checksum":"7c4544d07efa2c2add8612b489abb4e2","date_updated":"2020-07-14T12:48:11Z","date_created":"2019-01-18T13:32:17Z","access_level":"open_access","file_name":"2017_VOEB_Petritsch.pdf","creator":"dernst","content_type":"application/pdf","file_size":7843975}],"oa_version":"Published Version","intvolume":" 70","status":"public","ddc":["020"],"title":"Metadata for research data in practice","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"825","issue":"2","abstract":[{"text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.","lang":"eng"}],"type":"journal_article"},{"publist_id":"6451","publisher":"Springer","department":[{"_id":"HaJa"}],"editor":[{"full_name":"Stein, Viktor","last_name":"Stein","first_name":"Viktor"}],"publication_status":"published","year":"2017","volume":1596,"date_created":"2018-12-11T11:49:24Z","date_updated":"2021-01-12T08:22:13Z","author":[{"first_name":"Ben","last_name":"Clifton","full_name":"Clifton, Ben"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"full_name":"Sanchez Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","last_name":"Sanchez Romero"},{"first_name":"Michel","last_name":"Herde","full_name":"Herde, Michel"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"},{"last_name":"Jackson","first_name":"Colin","full_name":"Jackson, Colin"}],"publication_identifier":{"issn":["10643745"]},"month":"03","project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","grant_number":"RGY0084/2012"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6940-1_5","alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","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"}],"intvolume":" 1596","status":"public","title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","_id":"957","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"None","series_title":"Synthetic Protein Switches","scopus_import":1,"day":"15","page":"71 - 87","citation":{"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","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.","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.","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","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.","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.","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."},"publication":"Synthetic Protein Switches","date_published":"2017-03-15T00:00:00Z"},{"quality_controlled":"1","project":[{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","end_date":"2017-08-25","location":"Aalborg, Denmark","start_date":"2017-08-21"},"doi":"10.4230/LIPIcs.MFCS.2017.37","month":"06","publication_identifier":{"issn":["18688969"]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"year":"2017","date_updated":"2023-02-23T12:35:50Z","date_created":"2018-12-11T11:49:26Z","volume":83,"author":[{"full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy","last_name":"Avni"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"related_material":{"record":[{"id":"6005","status":"public","relation":"later_version"}]},"article_number":"37","file_date_updated":"2020-07-14T12:48:18Z","publist_id":"6438","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.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.","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.","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","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37"},"date_published":"2017-06-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","title":"Timed network games with clocks","ddc":["004"],"status":"public","intvolume":" 83","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"963","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":369730,"access_level":"open_access","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf","checksum":"f55eaf7f3c36ea07801112acfedd17d5","date_updated":"2020-07-14T12:48:18Z","date_created":"2018-12-12T10:14:10Z","file_id":"5059","relation":"main_file"}],"pubrep_id":"829","alternative_title":["LIPIcs"],"type":"conference","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. "}]},{"article_processing_charge":"No","day":"18","month":"10","doi":"10.5061/dryad.1f1rc","date_published":"2017-10-18T00:00:00Z","citation":{"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.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","mla":"Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","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.","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"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.1f1rc","open_access":"1"}],"abstract":[{"lang":"eng","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."}],"type":"research_data_reference","related_material":{"record":[{"id":"1197","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Prentice","first_name":"Jason","full_name":"Prentice, Jason"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"last_name":"Ioffe","first_name":"Mark","full_name":"Ioffe, Mark"},{"last_name":"Loback","first_name":"Adrianna","full_name":"Loback, Adrianna"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"full_name":"Berry, Michael","last_name":"Berry","first_name":"Michael"}],"oa_version":"Published Version","date_created":"2021-07-23T11:34:34Z","date_updated":"2023-02-21T16:34:41Z","year":"2017","_id":"9709","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"GaTk"}],"title":"Data from: Error-robust modes of the retinal population code","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"541","ddc":["576","579"],"status":"public","title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","intvolume":" 13","pubrep_id":"959","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","creator":"system","file_size":1308475,"content_type":"application/pdf","file_id":"5088","relation":"main_file","checksum":"22426d9382f21554bad5fa5967afcfd0","date_created":"2018-12-12T10:14:35Z","date_updated":"2020-07-14T12:46:46Z"}],"type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"12","publication":"PLoS Genetics","citation":{"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","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.","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. 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Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004","ama":"Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004"},"article_processing_charge":"No","day":"18","month":"07"},{"article_processing_charge":"No","month":"06","day":"01","doi":"10.1371/journal.pcbi.1005582.s001","date_published":"2017-06-01T00:00:00Z","citation":{"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","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017.","ista":"Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public Library of Science, 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","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.","short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).","mla":"Chalk, Matthew J., et al. Supplementary Appendix. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005582.s001."},"abstract":[{"lang":"eng","text":"Includes derivation of optimal estimation algorithm, generalisation to non-poisson noise statistics, correlated input noise, and implementation of in a multi-layer neural network."}],"type":"research_data_reference","related_material":{"record":[{"id":"680","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Chalk, Matthew J","last_name":"Chalk","first_name":"Matthew J","orcid":"0000-0001-7782-4436","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paul","last_name":"Masset","full_name":"Masset, Paul"},{"full_name":"Gutkin, Boris","last_name":"Gutkin","first_name":"Boris"},{"full_name":"Denève, Sophie","last_name":"Denève","first_name":"Sophie"}],"oa_version":"Published Version","date_created":"2021-08-10T07:05:10Z","date_updated":"2023-02-23T12:52:17Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9855","year":"2017","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"title":"Supplementary appendix","status":"public"},{"publist_id":"6478","abstract":[{"lang":"eng","text":"Recently there has been a proliferation of automated program repair (APR) techniques, targeting various programming languages. Such techniques can be generally classified into two families: syntactic- and semantics-based. Semantics-based APR, on which we focus, typically uses symbolic execution to infer semantic constraints and then program synthesis to construct repairs conforming to them. While syntactic-based APR techniques have been shown successful on bugs in real-world programs written in both C and Java, semantics-based APR techniques mostly target C programs. This leaves empirical comparisons of the APR families not fully explored, and developers without a Java-based semantics APR technique. We present JFix, a semantics-based APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs. It extends one particular APR technique (Angelix), and is designed to be sufficiently generic to support a variety of such techniques. We demonstrate that semantics-based APR can indeed efficiently and effectively repair a variety of classes of bugs in large real-world Java programs. This supports our claim that the framework can both support developers seeking semantics-based repair of bugs in Java programs, as well as enable larger scale empirical studies comparing syntactic- and semantics-based APR targeting Java. The demonstration of our tool is available via the project website at: https://xuanbachle.github.io/semanticsrepair/ "}],"type":"conference","oa_version":"None","date_created":"2018-12-11T11:49:19Z","date_updated":"2021-01-12T08:22:05Z","author":[{"full_name":"Le, Xuan","first_name":"Xuan","last_name":"Le"},{"id":"3598E630-F248-11E8-B48F-1D18A9856A87","last_name":"Chu","first_name":"Duc Hiep","full_name":"Chu, Duc Hiep"},{"full_name":"Lo, David","first_name":"David","last_name":"Lo"},{"full_name":"Le Goues, Claire","first_name":"Claire","last_name":"Le Goues"},{"full_name":"Visser, Willem","first_name":"Willem","last_name":"Visser"}],"publisher":"ACM","department":[{"_id":"ToHe"}],"publication_status":"published","status":"public","title":"JFIX: Semantics-based repair of Java programs via symbolic PathFinder","_id":"941","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","month":"07","day":"10","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2017-07-10T00:00:00Z","doi":"10.1145/3092703.3098225","conference":{"location":"Santa Barbara, CA, United States","start_date":"2017-07-10","end_date":"2017-07-14","name":"ISSTA: International Symposium on Software Testing and Analysis"},"page":"376 - 379 ","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","citation":{"ama":"Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ACM; 2017:376-379. doi:10.1145/3092703.3098225","ista":"Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis. ISSTA: International Symposium on Software Testing and Analysis, 376–379.","ieee":"X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa Barbara, CA, United States, 2017, pp. 376–379.","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","mla":"Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.","short":"X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017, pp. 376–379.","chicago":"Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser. “JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis, 376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225."},"publication":"Proceedings of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis"},{"day":"15","series_title":"Synthetic Protein Switches","scopus_import":1,"date_published":"2017-05-15T00:00:00Z","page":"89 - 99","publication":"Synthetic Protein Switches","citation":{"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.","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.","chicago":"Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.","ama":"Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6","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.","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","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."},"abstract":[{"text":"Biosensors that exploit Forster resonance energy transfer (FRET) can be used to visualize biological and physiological processes and are capable of providing detailed information in both spatial and temporal dimensions. In a FRET-based biosensor, substrate binding is associated with a change in the relative positions of two fluorophores, leading to a change in FRET efficiency that may be observed in the fluorescence spectrum. As a result, their design requires a ligand-binding protein that exhibits a conformational change upon binding. However, not all ligand-binding proteins produce responsive sensors upon conjugation to fluorescent proteins or dyes, and identifying the optimum locations for the fluorophores often involves labor-intensive iterative design or high-throughput screening. Combining the genetic fusion of a fluorescent protein to the ligand-binding protein with site-specific covalent attachment of a fluorescent dye can allow fine control over the positions of the two fluorophores, allowing the construction of very sensitive sensors. This relies upon the accurate prediction of the locations of the two fluorophores in bound and unbound states. In this chapter, we describe a method for computational identification of dye-attachment sites that allows the use of cysteine modification to attach synthetic dyes that can be paired with a fluorescent protein for the purposes of creating FRET sensors.","lang":"eng"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","oa_version":"None","status":"public","title":"Method for developing optical sensors using a synthetic dye fluorescent protein FRET pair and computational modeling and assessment","intvolume":" 1596","_id":"958","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"05","publication_identifier":{"issn":["10643745"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-6940-1_6","quality_controlled":"1","publist_id":"6450","date_created":"2018-12-11T11:49:24Z","date_updated":"2021-01-12T08:22:13Z","volume":1596,"author":[{"full_name":"Mitchell, Joshua","first_name":"Joshua","last_name":"Mitchell"},{"first_name":"William","last_name":"Zhang","full_name":"Zhang, William"},{"last_name":"Herde","first_name":"Michel","full_name":"Herde, Michel"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"full_name":"Jackson, Colin","first_name":"Colin","last_name":"Jackson"}],"publication_status":"published","publisher":"Springer","editor":[{"first_name":"Viktor","last_name":"Stein","full_name":"Stein, Viktor"}],"department":[{"_id":"HaJa"}],"year":"2017"},{"abstract":[{"text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2022-08-25T13:34:55Z","date_created":"2021-07-23T09:39:34Z","related_material":{"record":[{"id":"9702","relation":"used_in_publication","status":"deleted"}]},"author":[{"full_name":"Riccio, Paul","first_name":"Paul","last_name":"Riccio"},{"full_name":"Cebrián, Christina","last_name":"Cebrián","first_name":"Christina"},{"first_name":"Hui","last_name":"Zong","full_name":"Zong, Hui"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"last_name":"Costantini","first_name":"Frank","full_name":"Costantini, Frank"}],"department":[{"_id":"SiHi"}],"publisher":"Dryad","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","status":"public","_id":"9707","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"14","month":"01","doi":"10.5061/dryad.pk16b","date_published":"2017-01-14T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.pk16b","open_access":"1"}],"oa":1,"citation":{"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.","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.","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.","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.","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"}},{"oa_version":"Published Version","date_updated":"2023-02-23T12:25:04Z","date_created":"2021-08-09T13:27:16Z","related_material":{"record":[{"id":"541","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","full_name":"Nikolic, Nela"},{"last_name":"Schreiber","first_name":"Frank","full_name":"Schreiber, Frank"},{"first_name":"Alma","last_name":"Dal Co","full_name":"Dal Co, Alma"},{"first_name":"Daniel","last_name":"Kiviet","full_name":"Kiviet, Daniel"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller","full_name":"Bergmiller, Tobias"},{"last_name":"Littmann","first_name":"Sten","full_name":"Littmann, Sten"},{"full_name":"Kuypers, Marcel","first_name":"Marcel","last_name":"Kuypers"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","status":"public","title":"Source data for figures and tables","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9844","year":"2017","type":"research_data_reference","date_published":"2017-12-18T00:00:00Z","doi":"10.1371/journal.pgen.1007122.s018","citation":{"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.","mla":"Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122.s018.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, (2017).","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.","ieee":"N. Nikolic et al., “Source data for figures and tables.” Public Library of Science, 2017.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Source data for figures and tables. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s018","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables. 2017. doi:10.1371/journal.pgen.1007122.s018"},"article_processing_charge":"No","month":"12","day":"18"},{"type":"conference_abstract","file_date_updated":"2023-05-16T07:20:50Z","publication_status":"published","ddc":["000"],"status":"public","title":"Scientific Computing at IST Austria","publisher":"FSP Scientific Computing","department":[{"_id":"ScienComp"}],"year":"2017","_id":"12905","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-05-05T12:58:53Z","date_updated":"2023-05-16T07:22:23Z","oa_version":"Published Version","file":[{"file_id":"12969","relation":"main_file","success":1,"checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","date_created":"2023-05-16T07:20:50Z","date_updated":"2023-05-16T07:20:50Z","access_level":"open_access","file_name":"2017_AHPC_Schloegl.pdf","creator":"dernst","file_size":1005486,"content_type":"application/pdf"}],"author":[{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss","first_name":"Janos","full_name":"Kiss, Janos"}],"day":"03","month":"03","has_accepted_license":"1","article_processing_charge":"No","page":"28","publication":"AHPC17 – Austrian HPC Meeting 2017","oa":1,"citation":{"mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","chicago":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In AHPC17 – Austrian HPC Meeting 2017, 28. FSP Scientific Computing, 2017.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: AHPC17 – Austrian HPC Meeting 2017. FSP Scientific Computing; 2017:28.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 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.","ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in AHPC17 – Austrian HPC Meeting 2017, Grundlsee, Austria, 2017, p. 28."},"main_file_link":[{"open_access":"1","url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf"}],"language":[{"iso":"eng"}],"conference":{"name":"AHPC: Austrian HPC Meeting","end_date":"2017-03-03","location":"Grundlsee, Austria","start_date":"2017-03-01"},"date_published":"2017-03-03T00:00:00Z"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13160","intvolume":" 10205","title":"Index appearance record for transforming Rabin automata into parity automata","status":"public","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."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2017-03-31T00:00:00Z","citation":{"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.","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.","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.","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","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.","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.","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"},"publication":"Tools and Algorithms for the Construction and Analysis of Systems","page":"443-460","article_processing_charge":"No","day":"31","author":[{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan"},{"full_name":"Meggendorfer, Tobias","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","first_name":"Tobias","last_name":"Meggendorfer"},{"first_name":"Clara","last_name":"Waldmann","full_name":"Waldmann, Clara"},{"full_name":"Weininger, Maximilian","last_name":"Weininger","first_name":"Maximilian"}],"volume":10205,"date_created":"2023-06-21T13:21:14Z","date_updated":"2023-06-21T13:29:46Z","year":"2017","acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","doi":"10.1007/978-3-662-54577-5_26","conference":{"location":"Uppsala, Sweden","start_date":"2017-04-22","end_date":"2017-04-29","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1701.05738","open_access":"1"}],"external_id":{"arxiv":["1701.05738"]},"quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783662545775"],"eissn":["1611-3349"],"isbn":["9783662545768"]},"month":"03"},{"publication_identifier":{"issn":["1868-8969"]},"month":"09","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1705.01433"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.CONCUR.2017.21","conference":{"end_date":"2017-09-07","start_date":"2017-09-05","location":"Berlin, Germany","name":"CONCUR: Concurrency Theory"},"article_number":"17","publist_id":"6466","file_date_updated":"2020-07-14T12:48:16Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_status":"published","year":"2017","volume":85,"date_created":"2018-12-11T11:49:22Z","date_updated":"2023-08-29T07:02:13Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"6752"}]},"author":[{"last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev","first_name":"Ventsislav K","full_name":"Chonev, Ventsislav K"}],"scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"short":"G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","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.","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.","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","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.","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","ista":"Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR: Concurrency Theory, LIPIcs, vol. 85, 17."},"date_published":"2017-09-01T00:00:00Z","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","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"}],"intvolume":" 85","ddc":["000"],"title":"Infinite-duration bidding games","status":"public","_id":"950","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-844-v1+1_concur-cr.pdf","content_type":"application/pdf","file_size":335170,"creator":"system","relation":"main_file","file_id":"5318","checksum":"6d5cccf755207b91ccbef95d8275b013","date_created":"2018-12-12T10:18:00Z","date_updated":"2020-07-14T12:48:16Z"}],"pubrep_id":"844"},{"file":[{"file_name":"IST-2017-896-v1+1_LIPIcs-SoCG-2017-49.pdf","access_level":"open_access","creator":"system","file_size":710007,"content_type":"application/pdf","file_id":"5265","relation":"main_file","date_updated":"2020-07-14T12:47:41Z","date_created":"2018-12-12T10:17:12Z","checksum":"24fdde981cc513352a78dcf9b0660ae9"}],"oa_version":"Published Version","pubrep_id":"896","ddc":["514","516"],"title":"A proof of the orbit conjecture for flipping edge labelled triangulations","status":"public","intvolume":" 77","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"683","abstract":[{"text":"Given a triangulation of a point set in the plane, a flip deletes an edge e whose removal leaves a convex quadrilateral, and replaces e by the opposite diagonal of the quadrilateral. It is well known that any triangulation of a point set can be reconfigured to any other triangulation by some sequence of flips. We explore this question in the setting where each edge of a triangulation has a label, and a flip transfers the label of the removed edge to the new edge. It is not true that every labelled triangulation of a point set can be reconfigured to every other labelled triangulation via a sequence of flips, but we characterize when this is possible. There is an obvious necessary condition: for each label l, if edge e has label l in the first triangulation and edge f has label l in the second triangulation, then there must be some sequence of flips that moves label l from e to f, ignoring all other labels. Bose, Lubiw, Pathak and Verdonschot formulated the Orbit Conjecture, which states that this necessary condition is also sufficient, i.e. that all labels can be simultaneously mapped to their destination if and only if each label individually can be mapped to its destination. We prove this conjecture. Furthermore, we give a polynomial-time algorithm to find a sequence of flips to reconfigure one labelled triangulation to another, if such a sequence exists, and we prove an upper bound of O(n7) on the length of the flip sequence. Our proof uses the topological result that the sets of pairwise non-crossing edges on a planar point set form a simplicial complex that is homeomorphic to a high-dimensional ball (this follows from a result of Orden and Santos; we give a different proof based on a shelling argument). The dual cell complex of this simplicial ball, called the flip complex, has the usual flip graph as its 1-skeleton. We use properties of the 2-skeleton of the flip complex to prove the Orbit Conjecture.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2017-06-01T00:00:00Z","citation":{"chicago":"Lubiw, Anna, Zuzana Masárová, and Uli Wagner. “A Proof of the Orbit Conjecture for Flipping Edge Labelled Triangulations,” Vol. 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.49.","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.","short":"A. Lubiw, Z. Masárová, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","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.","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.","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","ama":"Lubiw A, Masárová Z, Wagner U. A proof of the orbit conjecture for flipping edge labelled triangulations. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.SoCG.2017.49"},"day":"01","has_accepted_license":"1","scopus_import":1,"date_updated":"2023-09-05T15:01:43Z","date_created":"2018-12-11T11:47:54Z","volume":77,"author":[{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"full_name":"Masárová, Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6660-1322","first_name":"Zuzana","last_name":"Masárová"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"related_material":{"record":[{"id":"5986","relation":"later_version","status":"public"}]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"year":"2017","file_date_updated":"2020-07-14T12:47:41Z","publist_id":"7033","article_number":"49","language":[{"iso":"eng"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Brisbane, Australia","start_date":"2017-07-04","end_date":"2017-07-07"},"doi":"10.4230/LIPIcs.SoCG.2017.49","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"06"},{"month":"01","publication_identifier":{"issn":["2663-337X"]},"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"oa":1,"supervisor":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:TH_730","file_date_updated":"2020-07-14T12:44:34Z","ec_funded":1,"publist_id":"6203","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"acknowledgement":" First of all, I want to thank my advisor, prof. Thomas A. Henzinger, for his guidance during my PhD program. I am grateful for the freedom I was given to pursue my research interests, and his continuous support. Working with prof. Henzinger was a truly inspiring experience and taught me what it means to be a scientist. I want to express my gratitude to my collaborators: Nikola Beneš, Krishnendu Chatterjee, Martin Chmelík, Ashutosh Gupta, Willibald Krenn, Jan Kˇretínský, Dejan Nickovic, Andrey Kupriyanov, and Tatjana Petrov. I have learned a great deal from my collaborators, and without their help this thesis would not be possible. In addition, I want to thank the members of my thesis committee: Dirk Beyer, Dejan Nickovic, and Georg Weissenbacher for their advice and reviewing this dissertation. I would especially like to acknowledge the late Helmut Veith, who was a member of my committee. I will remember Helmut for his kindness, enthusiasm, and wit, as well as for being an inspiring scientist. Finally, I would like to thank my colleagues for making my stay at IST such a pleasant experience: Guy Avni, Sergiy Bogomolov, Ventsislav Chonev, Rasmus Ibsen-Jensen, Mirco Giacobbe, Bernhard Kragl, Hui Kong, Petr Novotný, Jan Otop, Andreas Pavlogiannis, Tantjana Petrov, Arjun Radhakrishna, Jakob Ruess, Thorsten Tarrach, as well as other members of groups Henzinger and Chatterjee. ","year":"2017","date_updated":"2023-09-07T11:58:34Z","date_created":"2018-12-11T11:50:27Z","author":[{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1093"},{"status":"public","relation":"part_of_dissertation","id":"1230"},{"status":"public","relation":"part_of_dissertation","id":"1234"},{"id":"1391","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1501"},{"relation":"part_of_dissertation","status":"public","id":"1502"},{"id":"2063","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"2167"}]},"day":"02","has_accepted_license":"1","article_processing_charge":"No","page":"163","citation":{"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","ieee":"P. Daca, “Statistical and logical methods for property checking,” Institute of Science and Technology Austria, 2017.","ista":"Daca P. 2017. Statistical and logical methods for property checking. Institute of Science and Technology Austria.","ama":"Daca P. Statistical and logical methods for property checking. 2017. doi:10.15479/AT:ISTA:TH_730","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.","short":"P. Daca, Statistical and Logical Methods for Property Checking, Institute of Science and Technology Austria, 2017.","mla":"Daca, Przemyslaw. Statistical and Logical Methods for Property Checking. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:TH_730."},"date_published":"2017-01-02T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","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"}],"ddc":["004","005"],"status":"public","title":"Statistical and logical methods for property checking","_id":"1155","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1028586,"creator":"system","access_level":"open_access","file_name":"IST-2017-730-v1+1_Statistical_and_Logical_Methods_for_Property_Checking.pdf","checksum":"1406a681cb737508234fde34766be2c2","date_created":"2018-12-12T10:11:26Z","date_updated":"2020-07-14T12:44:34Z","relation":"main_file","file_id":"4880"}],"pubrep_id":"730"},{"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"has_accepted_license":"1","day":"01","month":"02","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2017-02-01T00:00:00Z","page":"83","oa":1,"citation":{"mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017.","chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","apa":"Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria."},"file_date_updated":"2021-02-22T13:45:59Z","abstract":[{"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.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","file":[{"checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","date_updated":"2020-07-14T12:47:27Z","date_created":"2019-04-09T15:15:32Z","relation":"main_file","file_id":"6292","file_size":3025175,"content_type":"application/pdf","creator":"dernst","access_level":"closed","file_name":"thesis_pavel_payne_final_w_signature_page.pdf"},{"creator":"dernst","file_size":3111536,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_Payne_Thesis.pdf","success":1,"checksum":"af531e921a7f64a9e0af4cd8783b2226","date_updated":"2021-02-22T13:45:59Z","date_created":"2021-02-22T13:45:59Z","file_id":"9187","relation":"main_file"}],"oa_version":"Published Version","date_updated":"2023-09-07T12:00:00Z","date_created":"2019-04-09T15:16:45Z","author":[{"full_name":"Payne, Pavel","last_name":"Payne","first_name":"Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Bacterial herd and social immunity to phages","publication_status":"published","status":"public","ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6291","year":"2017"},{"_id":"561","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Effects of mutations in phage restriction sites during escape from restriction–modification","status":"public","intvolume":" 13","oa_version":"Published Version","type":"journal_article","abstract":[{"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.","lang":"eng"}],"issue":"12","publication":"Biology Letters","citation":{"ama":"Pleska M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 2017;13(12). doi:10.1098/rsbl.2017.0646","apa":"Pleska, M., & Guet, C. C. (2017). Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. The Royal Society. https://doi.org/10.1098/rsbl.2017.0646","ieee":"M. Pleska and C. C. Guet, “Effects of mutations in phage restriction sites during escape from restriction–modification,” Biology Letters, vol. 13, no. 12. The Royal Society, 2017.","ista":"Pleska M, Guet CC. 2017. Effects of mutations in phage restriction sites during escape from restriction–modification. Biology Letters. 13(12), 20170646.","short":"M. Pleska, C.C. Guet, Biology Letters 13 (2017).","mla":"Pleska, Maros, and Calin C. Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters, vol. 13, no. 12, 20170646, The Royal Society, 2017, doi:10.1098/rsbl.2017.0646.","chicago":"Pleska, Maros, and Calin C Guet. “Effects of Mutations in Phage Restriction Sites during Escape from Restriction–Modification.” Biology Letters. The Royal Society, 2017. https://doi.org/10.1098/rsbl.2017.0646."},"article_type":"original","date_published":"2017-12-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2017","acknowledgement":"This work was funded by an HFSP Young Investigators' grant RGY0079/2011 (C.C.G.). M.P. is a recipient of a DOC Fellowship of the Austrian Academy of Science at the Institute of Science and Technology Austria.","pmid":1,"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"The Royal Society","author":[{"orcid":"0000-0001-7460-7479","id":"4569785E-F248-11E8-B48F-1D18A9856A87","last_name":"Pleska","first_name":"Maros","full_name":"Pleska, Maros"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9847"},{"id":"202","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:47:11Z","date_updated":"2023-09-07T11:59:32Z","volume":13,"article_number":"20170646","publist_id":"7253","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2017.0646"}],"external_id":{"pmid":["29237814"]},"quality_controlled":"1","project":[{"name":"Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant)","_id":"251BCBEC-B435-11E9-9278-68D0E5697425","grant_number":"RGY0079/2011"},{"name":"Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship)","grant_number":"24210","_id":"251D65D8-B435-11E9-9278-68D0E5697425"}],"doi":"10.1098/rsbl.2017.0646","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["1744-9561"]}}]