[{"volume":93,"external_id":{"arxiv":["1507.02562"],"isi":["000369439100005"]},"fulldoi":"https://doi.org/10.1103/PhysRevE.93.022404","oa_version":"Preprint","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.02562"}],"isi":1,"date_created":"2018-12-11T11:50:54Z","_id":"1242","doi":"10.1103/PhysRevE.93.022404","article_processing_charge":"No","date_updated":"2026-08-12T14:28:33Z","scopus_import":"1","status":"public","article_number":"022404","department":[{"_id":"GaTk"}],"month":"02","title":"Extending the dynamic range of transcription factor action by translational regulation","date_published":"2016-02-04T00:00:00Z","acknowledgement":"We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S.","year":"2016","type":"journal_article","intvolume":"        93","issue":"2","publication":"Physical Review E","day":"04","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"arxiv":1,"oa":1,"quality_controlled":"1","publication_status":"published","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6088","abstract":[{"text":"A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression.","lang":"eng"}],"citation":{"apa":"Sokolowski, T. R., Walczak, A., Bialek, W., &#38; Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>","ieee":"T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” <i>Physical Review E</i>, vol. 93, no. 2. American Physical Society, 2016.","chicago":"Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>.","mla":"Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E</i>, vol. 93, no. 2, 022404, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>.","ama":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E</i>. 2016;93(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E 93 (2016).","ista":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E. 93(2), 022404."},"author":[{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R"},{"first_name":"Aleksandra","full_name":"Walczak, Aleksandra","last_name":"Walczak"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"}]},{"publist_id":"6220","abstract":[{"text":"Automata with monitor counters, where the transitions do not depend on counter values, and nested weighted automata are two expressive automata-theoretic frameworks for quantitative properties. For a well-studied and wide class of quantitative functions, we establish that automata with monitor counters and nested weighted automata are equivalent. We study for the first time such quantitative automata under probabilistic semantics. We show that several problems that are undecidable for the classical questions of emptiness and universality become decidable under the probabilistic semantics. We present a complete picture of decidability for such automata, and even an almost-complete picture of computational complexity, for the probabilistic questions we consider.","lang":"eng"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Quantitative Automata under Probabilistic Semantics.” <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, IEEE, 2016, pp. 76–85, doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Quantitative automata under probabilistic semantics,” in <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, New York, NY, USA, 2016, pp. 76–85.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Quantitative Automata under Probabilistic Semantics.” In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>, 76–85. IEEE, 2016. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2016). Quantitative automata under probabilistic semantics. In <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i> (pp. 76–85). New York, NY, USA: IEEE. <a href=\"https://doi.org/10.1145/2933575.2933588\">https://doi.org/10.1145/2933575.2933588</a>","ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Quantitative automata under probabilistic semantics. Proceedings of the 31st Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 76–85.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Proceedings of the 31st Annual ACM/IEEE Symposium, IEEE, 2016, pp. 76–85.","ama":"Chatterjee K, Henzinger TA, Otop J. Quantitative automata under probabilistic semantics. In: <i>Proceedings of the 31st Annual ACM/IEEE Symposium</i>. IEEE; 2016:76-85. doi:<a href=\"https://doi.org/10.1145/2933575.2933588\">10.1145/2933575.2933588</a>"},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"oa":1,"publication":"Proceedings of the 31st Annual ACM/IEEE Symposium","day":"05","type":"conference","year":"2016","month":"07","title":"Quantitative automata under probabilistic semantics","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499- N23, FWF NFN Grant No S114","date_published":"2016-07-05T00:00:00Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"status":"public","scopus_import":"1","date_updated":"2026-08-19T09:35:52Z","page":"76 - 85","doi":"10.1145/2933575.2933588","_id":"1138","article_processing_charge":"No","ec_funded":1,"conference":{"end_date":"2016-07-08","start_date":"2016-07-05","location":"New York, NY, USA","name":"LICS: Logic in Computer Science"},"isi":1,"date_created":"2018-12-11T11:50:21Z","oa_version":"Preprint","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.06764"}],"external_id":{"arxiv":["1604.06764"],"isi":["000387609200008"]},"fulldoi":"https://doi.org/10.1145/2933575.2933588"},{"date_updated":"2026-08-19T09:31:46Z","scopus_import":"1","page":"26 - 48","_id":"1529","doi":"10.1016/j.artint.2016.01.007","ec_funded":1,"article_processing_charge":"No","department":[{"_id":"KrCh"}],"status":"public","volume":234,"external_id":{"arxiv":["1411.3880"],"isi":["000372683700002"]},"fulldoi":"https://doi.org/10.1016/j.artint.2016.01.007","isi":1,"date_created":"2018-12-11T11:52:33Z","oa_version":"Preprint","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"quality_controlled":"1","publication_status":"published","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"arxiv":1,"oa":1,"publist_id":"5642","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and an integer cost associated with every transition. The optimization objective we study asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest.","lang":"eng"}],"corr_author":"1","citation":{"ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 234, 26–48.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. <i>Artificial Intelligence</i>. 2016;234:26-48. doi:<a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">10.1016/j.artint.2016.01.007</a>","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence 234 (2016) 26–48.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Artificial Intelligence</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">https://doi.org/10.1016/j.artint.2016.01.007</a>.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” <i>Artificial Intelligence</i>, vol. 234. Elsevier, pp. 26–48, 2016.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Artificial Intelligence</i>, vol. 234, Elsevier, 2016, pp. 26–48, doi:<a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">10.1016/j.artint.2016.01.007</a>.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2016). Optimal cost almost-sure reachability in POMDPs. <i>Artificial Intelligence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.artint.2016.01.007\">https://doi.org/10.1016/j.artint.2016.01.007</a>"},"related_material":{"record":[{"status":"public","id":"5425","relation":"earlier_version"},{"id":"1820","status":"public","relation":"earlier_version"}]},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"last_name":"Gupta","full_name":"Gupta, Raghav","first_name":"Raghav"},{"first_name":"Ayush","full_name":"Kanodia, Ayush","last_name":"Kanodia"}],"publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2016","title":"Optimal cost almost-sure reachability in POMDPs","month":"05","date_published":"2016-05-01T00:00:00Z","acknowledgement":"We thank Blai Bonet for helping us with RTDP-Bel. The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publication":"Artificial Intelligence","day":"01","type":"journal_article","intvolume":"       234"},{"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"author":[{"full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793","first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"full_name":"de Vladar, Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold"},{"first_name":"Tomasz","last_name":"Włodarski","full_name":"Włodarski, Tomasz"},{"first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1077"}]},"citation":{"apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>."},"abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","publisher":"The Royal Society","date_updated":"2026-08-27T12:09:34Z","oa":1,"article_processing_charge":"No","_id":"9864","doi":"10.6084/m9.figshare.4315652.v1","day":"14","date_created":"2021-08-10T08:29:47Z","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"type":"research_data_reference","oa_version":"Published Version","year":"2016","fulldoi":"https://doi.org/10.6084/m9.figshare.4315652.v1","date_published":"2016-12-14T00:00:00Z","month":"12","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family"},{"author":[{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"first_name":"Myrsini","full_name":"Natsopoulou, Myrsini","last_name":"Natsopoulou"},{"first_name":"Vincent","last_name":"Doublet","full_name":"Doublet, Vincent"},{"last_name":"Fürst","full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Weging, Silvio","last_name":"Weging","first_name":"Silvio"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"},{"first_name":"Andreas","last_name":"Gogol Döring","full_name":"Gogol Döring, Andreas"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"}],"related_material":{"record":[{"relation":"research_data","id":"9704","status":"public"}]},"citation":{"ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2016;283(1833). doi:<a href=\"https://doi.org/10.1098/rspb.2016.0811\">10.1098/rspb.2016.0811</a>","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016).","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1833), 20160811.","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Elevated virulence of an emerging viral genotype as a driver of honeybee loss. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2016.0811\">https://doi.org/10.1098/rspb.2016.0811</a>","ieee":"D. Mcmahon <i>et al.</i>, “Elevated virulence of an emerging viral genotype as a driver of honeybee loss,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1833. Royal Society, 2016.","mla":"Mcmahon, Dino, et al. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 283, no. 1833, 20160811, Royal Society, 2016, doi:<a href=\"https://doi.org/10.1098/rspb.2016.0811\">10.1098/rspb.2016.0811</a>.","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2016. <a href=\"https://doi.org/10.1098/rspb.2016.0811\">https://doi.org/10.1098/rspb.2016.0811</a>."},"file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6060","abstract":[{"lang":"eng","text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society","publication_status":"published","quality_controlled":"1","oa":1,"day":"29","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","ddc":["576","592"],"issue":"1833","intvolume":"       283","type":"journal_article","year":"2016","date_published":"2016-06-29T00:00:00Z","acknowledgement":"This work was supported by the Federal Ministry of Food, Agriculture and Consumer Protection (Germany): Fit Bee project (grant 511-06.01-28-1-71.007-10), the EU: BeeDoc (grant 244956), iDiv (2013 NGS-Fast Track grant W47004118) and the Insect Pollinators Initiative (IPI grant BB/I000100/1 and BB/I000151/1). The IPI is funded jointly by the Biotechnology and Biological Sciences Research Council, the Department for Environment, Food and Rural Affairs, the Natural Environment Research Council, the Scottish Government and the Wellcome Trust, under the Living with Environmental Change Partnership. We thank A. Abrahams, M. Husemann and A. Soro\r\nfor support in obtaining\r\nV.  destructor\r\n-free honeybees; and BBKA\r\nPresident D. Aston for access to records of colony overwinter\r\n2011–2012 mortality in the UK. We also thank the anonymous refe-\r\nrees and Stephen Martin for comments that led to substantial\r\nimprovement of the manuscript.","file":[{"date_updated":"2020-07-14T12:44:42Z","file_id":"4708","file_name":"IST-2016-701-v1+1_20160811.full.pdf","checksum":"0b0d1be38b497d004064650acb3baced","content_type":"application/pdf","file_size":796872,"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:08:46Z","relation":"main_file"}],"title":"Elevated virulence of an emerging viral genotype as a driver of honeybee loss","month":"06","department":[{"_id":"SyCr"}],"article_number":"20160811","pubrep_id":"701","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","date_updated":"2026-08-27T12:13:27Z","scopus_import":"1","article_processing_charge":"No","doi":"10.1098/rspb.2016.0811","_id":"1262","date_created":"2018-12-11T11:51:00Z","isi":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1098/rspb.2016.0811","external_id":{"isi":["000381247300009"]},"volume":283},{"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cq7t1"}],"type":"research_data_reference","day":"06","date_created":"2021-07-23T08:30:38Z","title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","month":"05","date_published":"2016-05-06T00:00:00Z","year":"2016","fulldoi":"https://doi.org/10.5061/dryad.cq7t1","status":"public","publisher":"Dryad","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.","lang":"eng"}],"department":[{"_id":"SyCr"}],"author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini","first_name":"Myrsini"},{"last_name":"Doublet","full_name":"Doublet, Vincent","first_name":"Vincent"},{"full_name":"Fürst, Matthias","last_name":"Fürst","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X","first_name":"Matthias"},{"first_name":"Silvio","last_name":"Weging","full_name":"Weging, Silvio"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"},{"full_name":"Gogol Döring, Andreas","last_name":"Gogol Döring","first_name":"Andreas"},{"last_name":"Paxton","full_name":"Paxton, Robert","first_name":"Robert"}],"citation":{"ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>"},"related_material":{"record":[{"relation":"used_in_publication","id":"1262","status":"public"}]},"_id":"9704","doi":"10.5061/dryad.cq7t1","article_processing_charge":"No","oa":1,"date_updated":"2026-08-27T12:13:28Z"},{"conference":{"start_date":"2016-12-05","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","location":"Barcelona, Spain"},"ec_funded":1,"article_processing_charge":"No","_id":"948","page":"4285 - 4293","scopus_import":"1","date_updated":"2026-09-17T13:00:27Z","status":"public","department":[{"_id":"GaTk"}],"alternative_title":["Advances in Neural Information Processing Systems"],"volume":29,"main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}],"oa_version":"None","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:21Z","oa":1,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems Foundation","citation":{"apa":"Monk, T., Savin, C., &#38; Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 4285–4293.","mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 4285–93.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems Foundation, 2016.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems Foundation, 2016, pp. 4285–4293.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems Foundation; 2016:4285-4293.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293."},"author":[{"first_name":"Travis","last_name":"Monk","full_name":"Monk, Travis"},{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina"},{"first_name":"Jörg","last_name":"Lücke","full_name":"Lücke, Jörg"}],"abstract":[{"text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations.","lang":"eng"}],"publist_id":"6469","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and  LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","date_published":"2016-01-01T00:00:00Z","month":"01","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","year":"2016","type":"conference","intvolume":"        29","day":"01"},{"publication_status":"published","quality_controlled":"1","oa":1,"project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17","call_identifier":"FWF"},{"_id":"2527D5CC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I812-B12","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation"},{"_id":"25548C20-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"961","status":"public"},{"status":"public","id":"50","relation":"dissertation_contains"}]},"file_date_updated":"2018-12-12T10:11:04Z","citation":{"ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. 2016;16(3):866-877. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>","short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877.","ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>","ieee":"K. Sako <i>et al.</i>, “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” <i>Cell Reports</i>, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>.","mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>."},"author":[{"full_name":"Sako, Keisuke","last_name":"Sako","orcid":"0000-0002-6453-8075","first_name":"Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pradhan","full_name":"Pradhan, Saurabh","first_name":"Saurabh"},{"first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","last_name":"Barone"},{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro"},{"first_name":"Patrick","last_name":"Mueller","full_name":"Mueller, Patrick"},{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","full_name":"Ruprecht, Verena"},{"last_name":"Capek","full_name":"Capek, Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0001-5199-9940"},{"first_name":"Sanjeev","last_name":"Galande","full_name":"Galande, Sanjeev"},{"full_name":"Janovjak, Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"abstract":[{"text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.","lang":"eng"}],"publist_id":"6275","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Cell Press","year":"2016","file":[{"access_level":"open_access","creator":"system","date_created":"2018-12-12T10:11:04Z","relation":"main_file","file_id":"4857","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","date_updated":"2018-12-12T10:11:04Z","content_type":"application/pdf","file_size":3921947}],"acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","date_published":"2016-07-19T00:00:00Z","title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","month":"07","publication":"Cell Reports","day":"19","ddc":["570","576"],"issue":"3","type":"journal_article","intvolume":"        16","page":"866 - 877","date_updated":"2026-10-01T22:30:40Z","scopus_import":"1","article_processing_charge":"No","ec_funded":1,"_id":"1100","doi":"10.1016/j.celrep.2016.06.036","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"pubrep_id":"754","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"SSU"}],"status":"public","external_id":{"isi":["000380264200024"]},"fulldoi":"https://doi.org/10.1016/j.celrep.2016.06.036","volume":16,"date_created":"2018-12-11T11:50:08Z","has_accepted_license":"1","isi":1,"oa_version":"Published Version","language":[{"iso":"eng"}]},{"ddc":["576","616"],"issue":"6","publication":"Cell","day":"01","type":"journal_article","intvolume":"       167","article_type":"original","year":"2016","title":"Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder","month":"12","acknowledgement":"This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu, and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900 to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.), the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility","file":[{"relation":"main_file","date_created":"2018-12-12T10:13:44Z","access_level":"open_access","creator":"system","file_size":73907957,"content_type":"application/pdf","date_updated":"2020-07-14T12:44:37Z","checksum":"7fe01ab12a6610d3db421e0136db2f77","file_name":"IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf","file_id":"5030"}],"date_published":"2016-12-01T00:00:00Z","publist_id":"6170","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. We previously described abnormalities in the branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation, and severe neurological abnormalities. Furthermore, we identified several patients with autistic traits and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for the BCAA in human brain function."}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"395"}]},"file_date_updated":"2020-07-14T12:44:37Z","citation":{"ama":"Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. 2016;167(6):1481-1494. doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>","short":"D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise, M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai, A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri, K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.","ista":"Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A, Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.","apa":"Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise, M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>","chicago":"Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">https://doi.org/10.1016/j.cell.2016.11.013</a>.","mla":"Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.” <i>Cell</i>, vol. 167, no. 6, Cell Press, 2016, pp. 1481–94, doi:<a href=\"https://doi.org/10.1016/j.cell.2016.11.013\">10.1016/j.cell.2016.11.013</a>.","ieee":"D.-C. Tarlungeanu <i>et al.</i>, “Impaired amino acid transport at the blood brain barrier is a cause of autism spectrum disorder,” <i>Cell</i>, vol. 167, no. 6. Cell Press, pp. 1481–1494, 2016."},"author":[{"full_name":"Tarlungeanu, Dora-Clara","last_name":"Tarlungeanu","first_name":"Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Deliu","full_name":"Deliu, Elena","first_name":"Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9033-9096","first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","last_name":"Dotter","full_name":"Dotter, Christoph"},{"first_name":"Majdi","last_name":"Kara","full_name":"Kara, Majdi"},{"last_name":"Janiesch","full_name":"Janiesch, Philipp","first_name":"Philipp"},{"first_name":"Mariafrancesca","full_name":"Scalise, Mariafrancesca","last_name":"Scalise"},{"first_name":"Michele","last_name":"Galluccio","full_name":"Galluccio, Michele"},{"first_name":"Mateja","last_name":"Tesulov","full_name":"Tesulov, Mateja"},{"full_name":"Morelli, Emanuela","last_name":"Morelli","first_name":"Emanuela","id":"3F4D1282-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sönmez","full_name":"Sönmez, Fatma","first_name":"Fatma"},{"last_name":"Bilgüvar","full_name":"Bilgüvar, Kaya","first_name":"Kaya"},{"first_name":"Ryuichi","last_name":"Ohgaki","full_name":"Ohgaki, Ryuichi"},{"full_name":"Kanai, Yoshikatsu","last_name":"Kanai","first_name":"Yoshikatsu"},{"last_name":"Johansen","full_name":"Johansen, Anide","first_name":"Anide"},{"full_name":"Esharif, Seham","last_name":"Esharif","first_name":"Seham"},{"last_name":"Ben Omran","full_name":"Ben Omran, Tawfeg","first_name":"Tawfeg"},{"first_name":"Meral","last_name":"Topcu","full_name":"Topcu, Meral"},{"last_name":"Schlessinger","full_name":"Schlessinger, Avner","first_name":"Avner"},{"first_name":"Cesare","full_name":"Indiveri, Cesare","last_name":"Indiveri"},{"first_name":"Kent","full_name":"Duncan, Kent","last_name":"Duncan"},{"first_name":"Ahmet","full_name":"Caglayan, Ahmet","last_name":"Caglayan"},{"last_name":"Günel","full_name":"Günel, Murat","first_name":"Murat"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph"},{"first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","last_name":"Novarino"}],"publisher":"Cell Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"F03523","_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease"}],"oa":1,"has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:50:35Z","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":167,"external_id":{"isi":["000389470500012"]},"fulldoi":"https://doi.org/10.1016/j.cell.2016.11.013","pubrep_id":"771","department":[{"_id":"GaNo"}],"status":"public","scopus_import":"1","date_updated":"2026-10-01T22:30:46Z","page":"1481 - 1494","doi":"10.1016/j.cell.2016.11.013","_id":"1183","article_processing_charge":"No"},{"ec_funded":1,"article_processing_charge":"No","doi":"10.1038/ncb3426","_id":"1321","page":"1253 - 1259","scopus_import":"1","date_updated":"2026-10-01T22:30:48Z","tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"acknowledged_ssus":[{"_id":"SSU"}],"status":"public","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"external_id":{"isi":["000387165600018"]},"fulldoi":"https://doi.org/10.1038/ncb3426","volume":18,"oa_version":"Submitted Version","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:21Z","has_accepted_license":"1","isi":1,"oa":1,"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"}],"publication_status":"published","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:44:43Z","citation":{"short":"A.F. Leithner, A. Eichner, J. Müller, A. Reversat, M. Brown, J. Schwarz, J. Merrin, D. De Gorter, F.K. Schur, J. Bayerl, I. de Vries, S. Wieser, R. Hauschild, F. Lai, M. Moser, D. Kerjaschki, K. Rottner, V. Small, T. Stradal, M.K. Sixt, Nature Cell Biology 18 (2016) 1253–1259.","ama":"Leithner AF, Eichner A, Müller J, et al. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. 2016;18:1253-1259. doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>","ista":"Leithner AF, Eichner A, Müller J, Reversat A, Brown M, Schwarz J, Merrin J, De Gorter D, Schur FK, Bayerl J, de Vries I, Wieser S, Hauschild R, Lai F, Moser M, Kerjaschki D, Rottner K, Small V, Stradal T, Sixt MK. 2016. Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. Nature Cell Biology. 18, 1253–1259.","apa":"Leithner, A. F., Eichner, A., Müller, J., Reversat, A., Brown, M., Schwarz, J., … Sixt, M. K. (2016). Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>","chicago":"Leithner, Alexander F, Alexander Eichner, Jan Müller, Anne Reversat, Markus Brown, Jan Schwarz, Jack Merrin, et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncb3426\">https://doi.org/10.1038/ncb3426</a>.","mla":"Leithner, Alexander F., et al. “Diversified Actin Protrusions Promote Environmental Exploration but Are Dispensable for Locomotion of Leukocytes.” <i>Nature Cell Biology</i>, vol. 18, Nature Publishing Group, 2016, pp. 1253–59, doi:<a href=\"https://doi.org/10.1038/ncb3426\">10.1038/ncb3426</a>.","ieee":"A. F. Leithner <i>et al.</i>, “Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes,” <i>Nature Cell Biology</i>, vol. 18. Nature Publishing Group, pp. 1253–1259, 2016."},"related_material":{"record":[{"relation":"dissertation_contains","id":"323","status":"public"}]},"author":[{"last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1073-744X"},{"first_name":"Alexander","id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","full_name":"Eichner, Alexander","last_name":"Eichner"},{"first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","full_name":"Müller, Jan","last_name":"Müller"},{"full_name":"Reversat, Anne","last_name":"Reversat","id":"35B76592-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0666-8928","first_name":"Anne"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan","last_name":"Schwarz"},{"full_name":"Merrin, Jack","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"last_name":"De Gorter","full_name":"De Gorter, David","first_name":"David"},{"full_name":"Schur, Florian","last_name":"Schur","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian"},{"first_name":"Jonathan","full_name":"Bayerl, Jonathan","last_name":"Bayerl"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Wieser","full_name":"Wieser, Stefan"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"last_name":"Lai","full_name":"Lai, Frank","first_name":"Frank"},{"first_name":"Markus","last_name":"Moser","full_name":"Moser, Markus"},{"first_name":"Dontscho","last_name":"Kerjaschki","full_name":"Kerjaschki, Dontscho"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"first_name":"Victor","last_name":"Small","full_name":"Small, Victor"},{"last_name":"Stradal","full_name":"Stradal, Theresia","first_name":"Theresia"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"publist_id":"5949","abstract":[{"text":"Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion.","lang":"eng"}],"corr_author":"1","acknowledgement":"This work was supported by the German Research Foundation (DFG) Priority Program SP 1464 to T.E.B.S. and M.S., and European Research Council (ERC GA 281556) and Human Frontiers Program grants to M.S.\r\nService Units of IST Austria for excellent technical support.","file":[{"relation":"main_file","date_created":"2020-05-14T16:33:46Z","creator":"dernst","access_level":"open_access","file_size":4433280,"content_type":"application/pdf","checksum":"e1411cb7c99a2d9089c178a6abef25e7","file_name":"2018_NatureCell_Leithner.pdf","file_id":"7844","date_updated":"2020-07-14T12:44:43Z"}],"date_published":"2016-10-24T00:00:00Z","title":"Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes","month":"10","year":"2016","type":"journal_article","intvolume":"        18","article_type":"original","publication":"Nature Cell Biology","day":"24","ddc":["570"]},{"external_id":{"arxiv":["1510.07565"]},"fulldoi":"https://doi.org/10.1145/2837614.2837624","alternative_title":["POPL"],"volume":"20-22","main_file_link":[{"url":"http://arxiv.org/abs/1510.07565","open_access":"1"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:52:01Z","conference":{"start_date":"2016-01-20","end_date":"2016-01-22","name":"POPL: Principles of Programming Languages","location":"St. Petersburg, FL, USA"},"ec_funded":1,"_id":"1437","doi":"10.1145/2837614.2837624","page":"733 - 747","scopus_import":1,"date_updated":"2026-10-01T22:30:57Z","status":"public","department":[{"_id":"KrCh"}],"date_published":"2016-01-11T00:00:00Z","month":"01","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","year":"2016","type":"conference","day":"11","arxiv":1,"oa":1,"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"publication_status":"published","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","citation":{"short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747."},"related_material":{"record":[{"id":"5441","status":"public","relation":"earlier_version"},{"status":"public","id":"5442","relation":"earlier_version"},{"id":"6009","status":"public","relation":"later_version"},{"status":"public","id":"821","relation":"dissertation_contains"},{"id":"8934","status":"public","relation":"dissertation_contains"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722"}],"abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks.","lang":"eng"}],"publist_id":"5761","corr_author":"1"},{"conference":{"end_date":"2016-07-23","start_date":"2016-07-17","location":"Toronto, Canada","name":"CAV: Computer Aided Verification"},"ec_funded":1,"article_processing_charge":"No","_id":"1386","doi":"10.1007/978-3-319-41528-4_1","page":"3 - 22","scopus_import":"1","date_updated":"2026-10-01T22:30:58Z","status":"public","department":[{"_id":"KrCh"}],"fulldoi":"https://doi.org/10.1007/978-3-319-41528-4_1","external_id":{"arxiv":["1604.07169"],"isi":["000387731200001"]},"volume":9779,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1604.07169"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","date_created":"2018-12-11T11:51:43Z","isi":1,"oa":1,"arxiv":1,"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Fu","full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongfei"},{"first_name":"Amir","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir","last_name":"Goharshady"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Termination Analysis of Probabilistic Programs through Positivstellensatz’s</i>. Vol. 9779, Springer, 2016, pp. 3–22, doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Termination Analysis of Probabilistic Programs through Positivstellensatz’s,” 9779:3–22. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Termination analysis of probabilistic programs through Positivstellensatz’s,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9779, pp. 3–22.","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2016). Termination analysis of probabilistic programs through Positivstellensatz’s (Vol. 9779, pp. 3–22). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">https://doi.org/10.1007/978-3-319-41528-4_1</a>","ista":"Chatterjee K, Fu H, Goharshady AK. 2016. Termination analysis of probabilistic programs through Positivstellensatz’s. CAV: Computer Aided Verification, LNCS, vol. 9779, 3–22.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, in:, Springer, 2016, pp. 3–22.","ama":"Chatterjee K, Fu H, Goharshady AK. Termination analysis of probabilistic programs through Positivstellensatz’s. In: Vol 9779. Springer; 2016:3-22. doi:<a href=\"https://doi.org/10.1007/978-3-319-41528-4_1\">10.1007/978-3-319-41528-4_1</a>"},"related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"corr_author":"1","publist_id":"5824","abstract":[{"text":"We consider nondeterministic probabilistic programs with the most basic liveness property of termination. We present efficient methods for termination analysis of nondeterministic probabilistic programs with polynomial guards and assignments. Our approach is through synthesis of polynomial ranking supermartingales, that on one hand significantly generalizes linear ranking supermartingales and on the other hand is a counterpart of polynomial ranking-functions for proving termination of nonprobabilistic programs. The approach synthesizes polynomial ranking-supermartingales through Positivstellensatz's, yielding an efficient method which is not only sound, but also semi-complete over a large subclass of programs. We show experimental results to demonstrate that our approach can handle several classical programs with complex polynomial guards and assignments, and can synthesize efficient quadratic ranking-supermartingales when a linear one does not exist even for simple affine programs.","lang":"eng"}],"date_published":"2016-07-01T00:00:00Z","title":"Termination analysis of probabilistic programs through Positivstellensatz's","month":"07","year":"2016","intvolume":"      9779","type":"conference","day":"01"},{"publist_id":"4673","abstract":[{"text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. Finite-valued constraint languages contain functions that take on rational costs and general-valued constraint languages contain functions that take on rational or infinite costs. An instance of the problem is specified by a sum of functions from the language with the goal to minimise the sum. This framework includes and generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint satisfaction problems (Max-CSPs).\r\nOur main result is a precise algebraic characterisation of valued constraint languages whose instances can be solved exactly by the basic linear programming relaxation (BLP). For a general-valued constraint language Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional polymorphism of every arity. For a finite-valued constraint language Γ, BLP is a decision procedure if and only if Γ admits a symmetric fractional polymorphism of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism of arity 2.\r\nUsing these results, we obtain tractability of several novel and previously widely-open classes of VCSPs, including problems over valued constraint languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly) tree-submodular on arbitrary trees. ","lang":"eng"}],"citation":{"chicago":"Kolmogorov, Vladimir, Johan Thapper, and Stanislav Živný. “The Power of Linear Programming for General-Valued CSPs.” <i>SIAM Journal on Computing</i>. SIAM, 2015. <a href=\"https://doi.org/10.1137/130945648\">https://doi.org/10.1137/130945648</a>.","ieee":"V. Kolmogorov, J. Thapper, and S. Živný, “The power of linear programming for general-valued CSPs,” <i>SIAM Journal on Computing</i>, vol. 44, no. 1. SIAM, pp. 1–36, 2015.","mla":"Kolmogorov, Vladimir, et al. “The Power of Linear Programming for General-Valued CSPs.” <i>SIAM Journal on Computing</i>, vol. 44, no. 1, SIAM, 2015, pp. 1–36, doi:<a href=\"https://doi.org/10.1137/130945648\">10.1137/130945648</a>.","apa":"Kolmogorov, V., Thapper, J., &#38; Živný, S. (2015). The power of linear programming for general-valued CSPs. <i>SIAM Journal on Computing</i>. SIAM. <a href=\"https://doi.org/10.1137/130945648\">https://doi.org/10.1137/130945648</a>","ista":"Kolmogorov V, Thapper J, Živný S. 2015. The power of linear programming for general-valued CSPs. SIAM Journal on Computing. 44(1), 1–36.","ama":"Kolmogorov V, Thapper J, Živný S. The power of linear programming for general-valued CSPs. <i>SIAM Journal on Computing</i>. 2015;44(1):1-36. doi:<a href=\"https://doi.org/10.1137/130945648\">10.1137/130945648</a>","short":"V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015) 1–36."},"related_material":{"record":[{"id":"2518","status":"public","relation":"earlier_version"}]},"author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johan","last_name":"Thapper","full_name":"Thapper, Johan"},{"last_name":"Živný","full_name":"Živný, Stanislav","first_name":"Stanislav"}],"publisher":"SIAM","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publication_status":"published","arxiv":1,"oa":1,"issue":"1","publication":"SIAM Journal on Computing","day":"01","type":"journal_article","intvolume":"        44","year":"2015","month":"02","title":"The power of linear programming for general-valued CSPs","date_published":"2015-02-01T00:00:00Z","department":[{"_id":"VlKo"}],"status":"public","date_updated":"2025-09-23T14:14:57Z","scopus_import":"1","page":"1 - 36","_id":"2271","doi":"10.1137/130945648","article_processing_charge":"No","isi":1,"date_created":"2018-12-11T11:56:41Z","oa_version":"Preprint","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.4219"}],"volume":44,"external_id":{"arxiv":["1311.4219"],"isi":["000353967100001"]},"fulldoi":"https://doi.org/10.1137/130945648"},{"department":[{"_id":"XiFe"}],"extern":"1","status":"public","keyword":["Cell Biology","Plant Science","Physiology","General Medicine"],"page":"1616-1623","date_updated":"2023-05-08T11:03:23Z","scopus_import":"1","article_processing_charge":"No","doi":"10.1093/pcp/pcv087","_id":"12196","date_created":"2023-01-16T09:20:22Z","oa_version":"None","language":[{"iso":"eng"}],"external_id":{"pmid":["26063389"]},"fulldoi":"https://doi.org/10.1093/pcp/pcv087","volume":56,"citation":{"chicago":"Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” <i>Plant and Cell Physiology</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/pcp/pcv087\">https://doi.org/10.1093/pcp/pcv087</a>.","mla":"Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” <i>Plant and Cell Physiology</i>, vol. 56, no. 8, Oxford University Press, 2015, pp. 1616–23, doi:<a href=\"https://doi.org/10.1093/pcp/pcv087\">10.1093/pcp/pcv087</a>.","ieee":"K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity,” <i>Plant and Cell Physiology</i>, vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.","apa":"Johnson, K. C. M., Xia, S., Feng, X., &#38; Li, X. (2015). The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. <i>Plant and Cell Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/pcp/pcv087\">https://doi.org/10.1093/pcp/pcv087</a>","ista":"Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.","ama":"Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity. <i>Plant and Cell Physiology</i>. 2015;56(8):1616-1623. doi:<a href=\"https://doi.org/10.1093/pcp/pcv087\">10.1093/pcp/pcv087</a>","short":"K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015) 1616–1623."},"author":[{"first_name":"Kaeli C.M.","last_name":"Johnson","full_name":"Johnson, Kaeli C.M."},{"first_name":"Shitou","last_name":"Xia","full_name":"Xia, Shitou"},{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng"},{"full_name":"Li, Xin","last_name":"Li","first_name":"Xin"}],"abstract":[{"text":"SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity.","lang":"eng"}],"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","publication_status":"published","quality_controlled":"1","publication_identifier":{"issn":["0032-0781","1471-9053"]},"publication":"Plant and Cell Physiology","issue":"8","type":"journal_article","intvolume":"        56","article_type":"original","year":"2015","acknowledgement":"This work was supported by the National Sciences and Engineering Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles Copeland for critical reading of the manuscript.","date_published":"2015-08-01T00:00:00Z","title":"The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity","month":"08"},{"publication_identifier":{"isbn":["9780262330275"]},"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"oa":1,"quality_controlled":"1","publication_status":"published","publisher":"MIT Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","citation":{"apa":"Martius, G. S., &#38; Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In <i>Proceedings of the 13th European Conference on Artificial Life</i> (p. 78). York, United Kingdom: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">https://doi.org/10.7551/978-0-262-33027-5-ch018</a>","mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” <i>Proceedings of the 13th European Conference on Artificial Life</i>, MIT Press, 2015, p. 78, doi:<a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">10.7551/978-0-262-33027-5-ch018</a>.","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In <i>Proceedings of the 13th European Conference on Artificial Life</i>, 78. MIT Press, 2015. <a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">https://doi.org/10.7551/978-0-262-33027-5-ch018</a>.","ieee":"G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in <i>Proceedings of the 13th European Conference on Artificial Life</i>, York, United Kingdom, 2015, p. 78.","ama":"Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: <i>Proceedings of the 13th European Conference on Artificial Life</i>. MIT Press; 2015:78. doi:<a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">10.7551/978-0-262-33027-5-ch018</a>","short":"G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78.","ista":"Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78."},"file_date_updated":"2023-05-02T07:02:59Z","author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"},{"full_name":"Olbrich, Eckehard","last_name":"Olbrich","first_name":"Eckehard"}],"month":"07","title":"Quantifying self-organizing behavior of autonomous robots","acknowledgement":"This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734).","file":[{"relation":"main_file","success":1,"date_created":"2023-05-02T07:02:59Z","access_level":"open_access","creator":"dernst","file_size":1674241,"content_type":"application/pdf","checksum":"880eabe59c9df12f06a882aa1bc4e600","file_name":"2015_ECAL_Martius.pdf","file_id":"12882","date_updated":"2023-05-02T07:02:59Z"}],"date_published":"2015-07-01T00:00:00Z","year":"2015","type":"conference","ddc":["000"],"publication":"Proceedings of the 13th European Conference on Artificial Life","day":"01","doi":"10.7551/978-0-262-33027-5-ch018","_id":"12881","conference":{"location":"York, United Kingdom","name":"ECAL: European Conference on Artificial Life","start_date":"2015-07-20","end_date":"2015-07-24"},"article_processing_charge":"No","ec_funded":1,"scopus_import":"1","date_updated":"2025-09-29T11:08:17Z","page":"78","status":"public","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"ChLa"}],"external_id":{"isi":["000510147800018"]},"fulldoi":"https://doi.org/10.7551/978-0-262-33027-5-ch018","oa_version":"Published Version","language":[{"iso":"eng"}],"has_accepted_license":"1","isi":1,"date_created":"2023-04-30T22:01:07Z"},{"citation":{"ama":"Nam P, Seiringer R. Collective excitations of Bose gases in the mean-field regime. <i>Archive for Rational Mechanics and Analysis</i>. 2015;215(2):381-417. doi:<a href=\"https://doi.org/10.1007/s00205-014-0781-6\">10.1007/s00205-014-0781-6</a>","short":"P. Nam, R. Seiringer, Archive for Rational Mechanics and Analysis 215 (2015) 381–417.","ista":"Nam P, Seiringer R. 2015. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 215(2), 381–417.","apa":"Nam, P., &#38; Seiringer, R. (2015). Collective excitations of Bose gases in the mean-field regime. <i>Archive for Rational Mechanics and Analysis</i>. Springer. <a href=\"https://doi.org/10.1007/s00205-014-0781-6\">https://doi.org/10.1007/s00205-014-0781-6</a>","chicago":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” <i>Archive for Rational Mechanics and Analysis</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00205-014-0781-6\">https://doi.org/10.1007/s00205-014-0781-6</a>.","mla":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 215, no. 2, Springer, 2015, pp. 381–417, doi:<a href=\"https://doi.org/10.1007/s00205-014-0781-6\">10.1007/s00205-014-0781-6</a>.","ieee":"P. Nam and R. Seiringer, “Collective excitations of Bose gases in the mean-field regime,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 215, no. 2. Springer, pp. 381–417, 2015."},"author":[{"first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","full_name":"Nam, Phan"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521"}],"abstract":[{"lang":"eng","text":"We study the spectrum of a large system of N identical bosons interacting via a two-body potential with strength 1/N. In this mean-field regime, Bogoliubov's theory predicts that the spectrum of the N-particle Hamiltonian can be approximated by that of an effective quadratic Hamiltonian acting on Fock space, which describes the fluctuations around a condensed state. Recently, Bogoliubov's theory has been justified rigorously in the case that the low-energy eigenvectors of the N-particle Hamiltonian display complete condensation in the unique minimizer of the corresponding Hartree functional. In this paper, we shall justify Bogoliubov's theory for the high-energy part of the spectrum of the N-particle Hamiltonian corresponding to (non-linear) excited states of the Hartree functional. Moreover, we shall extend the existing results on the excitation spectrum to the case of non-uniqueness and/or degeneracy of the Hartree minimizer. In particular, the latter covers the case of rotating Bose gases, when the rotation speed is large enough to break the symmetry and to produce multiple quantized vortices in the Hartree minimizer. "}],"publist_id":"4951","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer","publication_status":"published","quality_controlled":"1","arxiv":1,"oa":1,"publication":"Archive for Rational Mechanics and Analysis","day":"01","issue":"2","type":"journal_article","intvolume":"       215","year":"2015","date_published":"2015-02-01T00:00:00Z","title":"Collective excitations of Bose gases in the mean-field regime","month":"02","department":[{"_id":"RoSe"}],"status":"public","page":"381 - 417","scopus_import":"1","date_updated":"2025-09-23T08:17:14Z","article_processing_charge":"No","doi":"10.1007/s00205-014-0781-6","_id":"2085","date_created":"2018-12-11T11:55:37Z","isi":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.1153"}],"oa_version":"Preprint","language":[{"iso":"eng"}],"external_id":{"arxiv":["1402.1153"],"isi":["000347150400002"]},"fulldoi":"https://doi.org/10.1007/s00205-014-0781-6","volume":215},{"isi":1,"date_created":"2018-12-11T11:56:05Z","language":[{"iso":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.5106"}],"volume":333,"fulldoi":"https://doi.org/10.1007/s00220-014-2119-5","external_id":{"isi":["000348303100008"],"arxiv":["1309.5106"]},"department":[{"_id":"LaEr"}],"status":"public","date_updated":"2025-09-23T13:39:37Z","scopus_import":"1","page":"1365 - 1416","doi":"10.1007/s00220-014-2119-5","_id":"2166","article_processing_charge":"No","issue":"3","day":"01","publication":"Communications in Mathematical Physics","intvolume":"       333","type":"journal_article","year":"2015","title":"The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case","month":"02","date_published":"2015-02-01T00:00:00Z","abstract":[{"text":"We consider the spectral statistics of large random band matrices on mesoscopic energy scales. We show that the correlation function of the local eigenvalue density exhibits a universal power law behaviour that differs from the Wigner-Dyson- Mehta statistics. This law had been predicted in the physics literature by Altshuler and Shklovskii in (Zh Eksp Teor Fiz (Sov Phys JETP) 91(64):220(127), 1986); it describes the correlations of the eigenvalue density in general metallic sampleswith weak disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas for band matrices. In two dimensions, where the leading term vanishes owing to an algebraic cancellation, we identify the first non-vanishing term and show that it differs substantially from the prediction of Kravtsov and Lerner in (Phys Rev Lett 74:2563-2566, 1995). The proof is given in the current paper and its companion (Ann. H. Poincaré. arXiv:1309.5107, 2014). ","lang":"eng"}],"publist_id":"4818","author":[{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","last_name":"Erdös","full_name":"Erdös, László"},{"full_name":"Knowles, Antti","last_name":"Knowles","first_name":"Antti"}],"citation":{"ista":"Erdös L, Knowles A. 2015. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 333(3), 1365–1416.","ama":"Erdös L, Knowles A. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. <i>Communications in Mathematical Physics</i>. 2015;333(3):1365-1416. doi:<a href=\"https://doi.org/10.1007/s00220-014-2119-5\">10.1007/s00220-014-2119-5</a>","short":"L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416.","mla":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” <i>Communications in Mathematical Physics</i>, vol. 333, no. 3, Springer, 2015, pp. 1365–416, doi:<a href=\"https://doi.org/10.1007/s00220-014-2119-5\">10.1007/s00220-014-2119-5</a>.","chicago":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” <i>Communications in Mathematical Physics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00220-014-2119-5\">https://doi.org/10.1007/s00220-014-2119-5</a>.","ieee":"L. Erdös and A. Knowles, “The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case,” <i>Communications in Mathematical Physics</i>, vol. 333, no. 3. Springer, pp. 1365–1416, 2015.","apa":"Erdös, L., &#38; Knowles, A. (2015). The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-014-2119-5\">https://doi.org/10.1007/s00220-014-2119-5</a>"},"publisher":"Springer","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","publication_status":"published","oa":1,"arxiv":1},{"volume":1,"fulldoi":"https://doi.org/10.1038/nplants.2015.94","external_id":{"pmid":["27250258"],"isi":["000364407200001"]},"isi":1,"date_created":"2018-12-11T11:51:42Z","language":[{"iso":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/","open_access":"1"}],"date_updated":"2025-09-29T11:04:05Z","scopus_import":"1","_id":"1383","doi":"10.1038/nplants.2015.94","article_processing_charge":"No","department":[{"_id":"JiFr"}],"article_number":"15094","status":"public","year":"2015","title":"V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis","month":"07","date_published":"2015-07-06T00:00:00Z","issue":"7","day":"06","publication":"Nature Plants","article_type":"original","intvolume":"         1","type":"journal_article","quality_controlled":"1","publication_status":"published","oa":1,"pmid":1,"abstract":[{"lang":"eng","text":"In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants."}],"publist_id":"5827","author":[{"first_name":"Luo","last_name":"Yu","full_name":"Yu, Luo"},{"full_name":"Scholl, Stefan","last_name":"Scholl","first_name":"Stefan"},{"full_name":"Doering, Anett","last_name":"Doering","first_name":"Anett"},{"first_name":"Zhang","full_name":"Yi, Zhang","last_name":"Yi"},{"first_name":"Niloufer","last_name":"Irani","full_name":"Irani, Niloufer"},{"last_name":"Di Rubbo","full_name":"Di Rubbo, Simone","first_name":"Simone"},{"first_name":"Lutz","last_name":"Neumetzler","full_name":"Neumetzler, Lutz"},{"first_name":"Praveen","full_name":"Krishnamoorthy, Praveen","last_name":"Krishnamoorthy"},{"first_name":"Isabelle","full_name":"Van Houtte, Isabelle","last_name":"Van Houtte"},{"first_name":"Evelien","last_name":"Mylle","full_name":"Mylle, Evelien"},{"first_name":"Volker","full_name":"Bischoff, Volker","last_name":"Bischoff"},{"first_name":"Samantha","last_name":"Vernhettes","full_name":"Vernhettes, Samantha"},{"full_name":"Winne, Johan","last_name":"Winne","first_name":"Johan"},{"last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stierhof","full_name":"Stierhof, York","first_name":"York"},{"full_name":"Schumacher, Karin","last_name":"Schumacher","first_name":"Karin"},{"last_name":"Persson","full_name":"Persson, Staffan","first_name":"Staffan"},{"last_name":"Russinova","full_name":"Russinova, Eugenia","first_name":"Eugenia"}],"citation":{"ista":"Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7), 15094.","ama":"Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. 2015;1(7). doi:<a href=\"https://doi.org/10.1038/nplants.2015.94\">10.1038/nplants.2015.94</a>","short":"L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler, P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne, J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants 1 (2015).","ieee":"L. Yu <i>et al.</i>, “V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis,” <i>Nature Plants</i>, vol. 1, no. 7. Nature Publishing Group, 2015.","chicago":"Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nplants.2015.94\">https://doi.org/10.1038/nplants.2015.94</a>.","mla":"Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis and Recycling in Arabidopsis.” <i>Nature Plants</i>, vol. 1, no. 7, 15094, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/nplants.2015.94\">10.1038/nplants.2015.94</a>.","apa":"Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova, E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nplants.2015.94\">https://doi.org/10.1038/nplants.2015.94</a>"},"publisher":"Nature Publishing Group","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"ddc":["000"],"day":"01","type":"dissertation","year":"2015","supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"title":"Learning with attributes for object recognition: Parametric and non-parametrics views","month":"04","acknowledgement":"I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. ","date_published":"2015-04-01T00:00:00Z","file":[{"success":1,"relation":"main_file","date_created":"2021-02-22T11:33:17Z","access_level":"open_access","creator":"dernst","file_size":7964342,"content_type":"application/pdf","date_updated":"2021-02-22T11:33:17Z","file_name":"2015_Thesis_Sharmanska.pdf","checksum":"3605b402bb6934e09ae4cf672c84baf7","file_id":"9177"},{"content_type":"application/pdf","file_size":7372241,"date_updated":"2021-11-17T13:47:24Z","file_id":"10297","checksum":"e37593b3ee75bf3180629df2d6ca8f4e","file_name":"2015_Thesis_Sharmanska_pdfa.pdf","relation":"main_file","access_level":"closed","creator":"cchlebak","date_created":"2021-11-16T14:40:45Z"}],"publist_id":"5806","abstract":[{"lang":"eng","text":"The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views."}],"corr_author":"1","citation":{"mla":"Sharmanska, Viktoriia. <i>Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views</i>. Institute of Science and Technology Austria, 2015, doi:<a href=\"https://doi.org/10.15479/at:ista:1401\">10.15479/at:ista:1401</a>.","ieee":"V. Sharmanska, “Learning with attributes for object recognition: Parametric and non-parametrics views,” Institute of Science and Technology Austria, 2015.","chicago":"Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria, 2015. <a href=\"https://doi.org/10.15479/at:ista:1401\">https://doi.org/10.15479/at:ista:1401</a>.","apa":"Sharmanska, V. (2015). <i>Learning with attributes for object recognition: Parametric and non-parametrics views</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1401\">https://doi.org/10.15479/at:ista:1401</a>","ista":"Sharmanska V. 2015. Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria.","short":"V. Sharmanska, Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.","ama":"Sharmanska V. Learning with attributes for object recognition: Parametric and non-parametrics views. 2015. doi:<a href=\"https://doi.org/10.15479/at:ista:1401\">10.15479/at:ista:1401</a>"},"file_date_updated":"2021-11-17T13:47:24Z","author":[{"first_name":"Viktoriia","orcid":"0000-0003-0192-9308","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"oa":1,"has_accepted_license":"1","date_created":"2018-12-11T11:51:48Z","oa_version":"Published Version","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}],"alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:1401","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"OA_place":"publisher","status":"public","date_updated":"2026-04-09T14:25:49Z","page":"144","_id":"1401","doi":"10.15479/at:ista:1401","article_processing_charge":"No"},{"date_updated":"2025-06-03T11:41:36Z","quality_controlled":"1","publication_status":"published","page":"3070 - 3078","_id":"1424","conference":{"start_date":"2015-12-07","end_date":"2015-12-12","name":"NIPS: Neural Information Processing Systems","location":"Montreal, Canada"},"article_processing_charge":"No","oa":1,"abstract":[{"text":"We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data.","lang":"eng"}],"publist_id":"5782","citation":{"short":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information Processing Systems Foundation, 2015, pp. 3070–3078.","ama":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems Foundation; 2015:3070-3078.","ista":"Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological data analysis-A kernel perspective. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 28, 3070–3078.","apa":"Kwitt, R., Huber, S., Niethammer, M., Lin, W., &#38; Bauer, U. (2015). Statistical topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological data analysis-A kernel perspective,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.","chicago":"Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer. “Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural Information Processing Systems Foundation, 2015.","mla":"Kwitt, Roland, et al. <i>Statistical Topological Data Analysis-A Kernel Perspective</i>. Vol. 28, Neural Information Processing Systems Foundation, 2015, pp. 3070–78."},"department":[{"_id":"HeEd"}],"author":[{"full_name":"Kwitt, Roland","last_name":"Kwitt","first_name":"Roland"},{"full_name":"Huber, Stefan","last_name":"Huber","orcid":"0000-0002-8871-5814","first_name":"Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Niethammer, Marc","last_name":"Niethammer","first_name":"Marc"},{"first_name":"Weili","full_name":"Lin, Weili","last_name":"Lin"},{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","last_name":"Bauer"}],"publisher":"Neural Information Processing Systems Foundation","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Advances in Neural Information Processing Systems"],"volume":28,"year":"2015","month":"12","title":"Statistical topological data analysis-A kernel perspective","acknowledgement":"This work was partially supported by the Austrian Science FUnd, project no. KLI 00012.","date_published":"2015-12-01T00:00:00Z","date_created":"2018-12-11T11:51:56Z","day":"01","oa_version":"Submitted Version","language":[{"iso":"eng"}],"type":"conference","intvolume":"        28","main_file_link":[{"url":"https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective","open_access":"1"}]}]