[{"publication_status":"published","type":"dissertation","department":[{"_id":"ChLa"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","file":[{"date_updated":"2018-12-12T10:14:07Z","file_name":"IST-2017-776-v1+1_Pentina_Thesis_2016.pdf","creator":"system","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:14:07Z","content_type":"application/pdf","file_size":2140062,"file_id":"5056"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","OA_place":"publisher","ddc":["006"],"page":"127","file_date_updated":"2018-12-12T10:14:07Z","day":"01","publist_id":"6234","citation":{"short":"A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute of Science and Technology Austria, 2016.","ieee":"A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute of Science and Technology Austria, 2016.","chicago":"Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>.","ista":"Pentina A. 2016. Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria.","apa":"Pentina, A. (2016). <i>Theoretical foundations of multi-task lifelong learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>","ama":"Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>","mla":"Pentina, Anastasia. <i>Theoretical Foundations of Multi-Task Lifelong Learning</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>."},"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:TH_776","acknowledgement":"First and foremost I would like to express my gratitude to my supervisor, Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of doing research\r\n(including English grammar), for your trust in my capabilities and endless support. Thank\r\nyou for granting me freedom in my research and, at the same time, having time and\r\nhelping me cope with the consequences whenever I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it was a great pleasure and honor to be a part of\r\nit. There could not have been a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming me into his group at the University of Waterloo,\r\nfor inspiring discussions and support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful collaboration and for taking care of me during that not-so-sunny month of May.\r\nI thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding me with insightful comments.\r\nI would like to thank my colleagues for their support, entertaining conversations and\r\nendless table soccer games we shared together: Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas, Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo. Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible without funding from the European\r\nResearch Council under the European Union's Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036.","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:50:17Z","author":[{"full_name":"Pentina, Anastasia","last_name":"Pentina","first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-09T10:49:34Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"abstract":[{"lang":"eng","text":"Traditionally machine learning has been focusing on the problem of solving a single\r\ntask in isolation. While being quite well understood, this approach disregards an\r\nimportant aspect of human learning: when facing a new problem, humans are able to\r\nexploit knowledge acquired from previously learned tasks. Intuitively, access to several\r\nproblems simultaneously or sequentially could also be advantageous for a machine\r\nlearning system, especially if these tasks are closely related. Indeed, results of many\r\nempirical studies have provided justification for this intuition. However, theoretical\r\njustifications of this idea are rather limited.\r\nThe focus of this thesis is to expand the understanding of potential benefits of information\r\ntransfer between several related learning problems. We provide theoretical\r\nanalysis for three scenarios of multi-task learning - multiple kernel learning, sequential\r\nlearning and active task selection. We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate how the task generation process influences the generalization\r\nguarantees in this scenario. In addition, we show how some of the obtained\r\ntheoretical results can be used to derive principled multi-task and lifelong learning\r\nalgorithms and illustrate their performance on various synthetic and real-world datasets."}],"oa_version":"Published Version","status":"public","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","degree_awarded":"PhD","year":"2016","_id":"1126","pubrep_id":"776","date_published":"2016-11-01T00:00:00Z","month":"11","title":"Theoretical foundations of multi-task lifelong learning"},{"file_date_updated":"2021-02-22T11:51:13Z","page":"75","supervisor":[{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","publist_id":"6239","day":"01","citation":{"mla":"Acar, Hande. <i>Selective Barriers to Horizontal Gene Transfer</i>. Institute of Science and Technology Austria, 2016.","apa":"Acar, H. (2016). <i>Selective barriers to horizontal gene transfer</i>. Institute of Science and Technology Austria.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016."},"department":[{"_id":"JoBo"}],"alternative_title":["ISTA Thesis"],"file":[{"file_id":"6814","file_size":3682711,"content_type":"application/pdf","relation":"main_file","date_created":"2019-08-13T11:17:50Z","date_updated":"2019-08-13T11:17:50Z","file_name":"PhDThesis_HandeAcar_1230.pdf","access_level":"closed","creator":"dernst","checksum":"94bbbc754c36115bf37f8fc11fad43c4"},{"access_level":"open_access","creator":"dernst","checksum":"94bbbc754c36115bf37f8fc11fad43c4","file_name":"2016_Thesis_HandeAcar.pdf","date_updated":"2021-02-22T11:51:13Z","date_created":"2021-02-22T11:51:13Z","relation":"main_file","file_size":3682711,"content_type":"application/pdf","success":1,"file_id":"9184"}],"corr_author":"1","publication_status":"published","type":"dissertation","ddc":["570"],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","OA_place":"publisher","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","ec_funded":1,"date_published":"2016-12-01T00:00:00Z","month":"12","title":"Selective barriers to horizontal gene transfer","degree_awarded":"PhD","_id":"1121","year":"2016","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-09T10:51:38Z","project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"date_created":"2018-12-11T11:50:16Z","author":[{"id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","first_name":"Hande","last_name":"Acar","orcid":"0000-0003-1986-9753","full_name":"Acar, Hande"}],"abstract":[{"lang":"eng","text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments."}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1},{"author":[{"orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis"}],"date_created":"2018-12-11T11:51:47Z","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-09T10:52:07Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"abstract":[{"text":"Hybrid zones represent evolutionary laboratories, where recombination brings together alleles in combinations which have not previously been tested by selection. This provides an excellent opportunity to test the effect of molecular variation on fitness, and how this variation is able to spread through populations in a natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for two loci controlling the distribution of yellow and magenta floral pigments. Where the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine to give striking transgressive variation for flower colour. The sharp transition in phenotype over ~1km implies strong selection maintaining the hybrid zone. An indirect assay of pollinator visitation in the field found that pollinators forage in a positive-frequency dependent manner on Antirrhinum, matching previous data on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds demonstrated assortative mating for pigmentation alleles, and that pollinator behaviour alone is sufficient to explain this pattern. Selection by pollinators should be sufficiently strong to maintain the hybrid zone, although other mechanisms may be at work. At a broader scale I examined evolutionary transitions between yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection has acted strate that pollinators are a major determinant of reproductive success and mating patterns in wild Antirrhinum.","lang":"eng"}],"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","degree_awarded":"PhD","_id":"1398","pubrep_id":"526","year":"2016","date_published":"2016-02-18T00:00:00Z","title":"The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone","month":"02","type":"dissertation","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"file":[{"file_id":"19957","file_size":7590862,"content_type":"application/pdf","relation":"main_file","date_created":"2025-07-03T06:24:17Z","date_updated":"2025-07-03T06:24:17Z","file_name":"2016_Thesis_Ellis_noSignatures.pdf","creator":"dernst","checksum":"f0f7c260e19ec1416824b165afe2d5fd","access_level":"open_access"},{"content_type":"application/pdf","file_size":11928241,"file_id":"5106","file_name":"IST-2016-526-v1+1_Ellis_signed_thesis.pdf","date_updated":"2025-07-03T06:24:39Z","access_level":"closed","checksum":"a89b17ff27cf92c9a15f6b3d46bd7e53","creator":"system","relation":"main_file","date_created":"2018-12-12T10:14:51Z"}],"corr_author":"1","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"id":"5553","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","status":"public","id":"5551"},{"status":"public","id":"5552","relation":"dissertation_contains"}]},"has_accepted_license":"1","OA_place":"publisher","ddc":["576"],"page":"130","file_date_updated":"2025-07-03T06:24:39Z","citation":{"mla":"Ellis, Thomas. <i>The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>.","chicago":"Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>.","ista":"Ellis T. 2016. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute of Science and Technology Austria.","ama":"Ellis T. The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">10.15479/AT:ISTA:TH_526 </a>","apa":"Ellis, T. (2016). <i>The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_526 \">https://doi.org/10.15479/AT:ISTA:TH_526 </a>","short":"T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of Science and Technology Austria, 2016.","ieee":"T. Ellis, “The role of pollinator-mediated selection in the maintenance of a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of Science and Technology Austria, 2016."},"publist_id":"5809","day":"18","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"acknowledgement":"I am indebted to many people for their support during my PhD, but I particularly wish to thank Nick Barton for his guidance and intuition, and for encouraging me to take the time to look beyond the immediate topic of my PhD to understand the broader context. I am also especially grateful to David Field his bottomless patience, invaluable advice on experimental design, analysis and scientific writing, and for tireless work on the population surveys and genomic work without most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work with the combined strengths of the groups at The John Innes Centre, University of Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections, as well as Monique Burrus and Christophe Andalo and a large number of volunteers for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski for providing seeds and for her input into the design of the experimental arrays, and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous reviewers for their insightful comments on sections of this manuscript. I also thank Jana Porsche for her e ff orts in tracking down the more obscure references for chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer and Magnus Nordborg for taking the time to read and evaluate the thesis given a shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been the supportive atmosphere of IST. In particular, I have come to appreciate the enormous support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for their enthusiasm and readiness to help where possible in setting up our greenhouse and experiments. ","doi":"10.15479/AT:ISTA:TH_526 "},{"publisher":"Nature Publishing Group","has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"1396","status":"public"}]},"ddc":["570"],"publication":"Nature Communications","type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"PeJo"}],"file":[{"file_size":4510512,"content_type":"application/pdf","file_id":"5355","access_level":"open_access","checksum":"7e84d0392348c874d473b62f1042de22","creator":"system","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","date_updated":"2020-07-14T12:44:53Z","date_created":"2018-12-12T10:18:33Z","relation":"main_file"}],"corr_author":"1","citation":{"ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>, vol. 7, 11552, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>.","apa":"Mishra, R. K., Kim, S., Guzmán, J., &#38; Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>","ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>","chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>.","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552."},"publist_id":"5766","isi":1,"day":"13","article_number":"11552","acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/ncomms11552","file_date_updated":"2020-07-14T12:44:53Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000375938200001"]},"oa":1,"volume":7,"abstract":[{"lang":"eng","text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network."}],"oa_version":"Published Version","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Mishra, Rajiv Kumar","last_name":"Mishra","first_name":"Rajiv Kumar","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kim, Sooyun","id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","first_name":"Sooyun","last_name":"Kim"},{"orcid":"0000-0003-2209-5242","full_name":"Guzmán, José","first_name":"José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"date_created":"2018-12-11T11:51:59Z","date_updated":"2026-04-09T10:52:26Z","intvolume":"         7","_id":"1432","pubrep_id":"582","year":"2016","date_published":"2016-05-13T00:00:00Z","title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","scopus_import":"1","month":"05","ec_funded":1,"status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"type":"dissertation","publication_status":"published","department":[{"_id":"PeJo"}],"alternative_title":["ISTA Thesis"],"corr_author":"1","file":[{"file_name":"Thesis_Mishra_Rajiv (Final).pdf","date_updated":"2020-07-14T12:44:48Z","access_level":"closed","creator":"dernst","checksum":"5a010a838faf040f7064f3cfb802f743","relation":"main_file","date_created":"2019-08-09T12:14:46Z","file_size":2407572,"content_type":"application/pdf","file_id":"6782"},{"date_updated":"2021-02-22T11:48:44Z","file_name":"2016_RajivMishra_Thesis.pdf","creator":"dernst","checksum":"81b26d9ede92c99f1d8cc6fa1d04cbbb","access_level":"open_access","relation":"main_file","date_created":"2021-02-22T11:48:44Z","file_size":2407572,"content_type":"application/pdf","success":1,"file_id":"9183"}],"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"1432","relation":"part_of_dissertation"}]},"ddc":["570"],"page":"83","file_date_updated":"2021-02-22T11:48:44Z","citation":{"ieee":"R. K. Mishra, “Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus,” Institute of Science and Technology Austria, 2016.","short":"R.K. Mishra, Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus, Institute of Science and Technology Austria, 2016.","mla":"Mishra, Rajiv Kumar. <i>Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus</i>. Institute of Science and Technology Austria, 2016.","ama":"Mishra RK. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. 2016.","apa":"Mishra, R. K. (2016). <i>Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus</i>. Institute of Science and Technology Austria.","chicago":"Mishra, Rajiv Kumar. “Synaptic Plasticity Rules at CA3-CA3 Recurrent Synapses in Hippocampus.” Institute of Science and Technology Austria, 2016.","ista":"Mishra RK. 2016. Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus. Institute of Science and Technology Austria."},"day":"01","publist_id":"5811","supervisor":[{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"author":[{"full_name":"Mishra, Rajiv Kumar","first_name":"Rajiv Kumar","last_name":"Mishra","id":"46CB58F2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:51:46Z","publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-09T10:52:26Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"abstract":[{"lang":"eng","text":"CA3 pyramidal neurons are thought to pay a key role in memory storage and pattern completion by activity-dependent synaptic plasticity between CA3-CA3 recurrent excitatory synapses. To examine the induction rules of synaptic plasticity at CA3-CA3 synapses, we performed whole-cell patch-clamp recordings in acute hippocampal slices from rats (postnatal 21-24 days) at room temperature. Compound excitatory postsynaptic potentials (ESPSs) were recorded by tract stimulation in stratum oriens in the presence of 10 µM gabazine. High-frequency stimulation (HFS) induced N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP). Although LTP by HFS did not requier postsynaptic spikes, it was blocked by Na+-channel blockers suggesting that local active processes (e.g.) dendritic spikes) may contribute to LTP induction without requirement of a somatic action potential (AP). We next examined the properties of spike timing-dependent plasticity (STDP) at CA3-CA3 synapses. Unexpectedly, low-frequency pairing of EPSPs and backpropagated action potentialy (bAPs) induced LTP, independent of temporal order. The STDP curve was symmetric and broad, with a half-width of ~150 ms. Consistent with these specific STDP induction properties, post-presynaptic sequences led to a supralinear summation of spine [Ca2+] transients. Furthermore, in autoassociative network models, storage and recall was substantially more robust with symmetric than with asymmetric STDP rules. In conclusion, we found associative forms of LTP at CA3-CA3 recurrent collateral synapses with distinct induction rules. LTP induced by HFS may be associated with dendritic spikes. In contrast, low frequency pairing of pre- and postsynaptic activity induced LTP only if EPSP-AP were temporally very close. Together, these induction mechanisms of synaptiic plasticity may contribute to memory storage in the CA3-CA3 microcircuit at different ranges of activity."}],"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","degree_awarded":"PhD","_id":"1396","year":"2016","date_published":"2016-03-01T00:00:00Z","title":"Synaptic plasticity rules at CA3-CA3 recurrent synapses in hippocampus","month":"03"},{"status":"public","article_processing_charge":"No","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"file_date_updated":"2020-07-14T12:47:01Z","day":"19","_id":"5553","citation":{"ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>.","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>","apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","short":"D. Field, T. Ellis, (2016).","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016."},"datarep_id":"37","year":"2016","month":"02","doi":"10.15479/AT:ISTA:37","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2016-02-19T00:00:00Z","date_created":"2018-12-12T12:31:30Z","author":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas"}],"type":"research_data","file":[{"content_type":"application/zip","file_size":132808,"file_id":"5620","checksum":"4ae751b1fa4897fa216241f975a57313","access_level":"open_access","creator":"system","file_name":"IST-2016-37-v1+1_paternity_archive.zip","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:02Z","relation":"main_file"}],"contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","contributor_type":"project_manager","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"date_updated":"2026-04-09T10:52:06Z","department":[{"_id":"NiBa"}],"oa":1,"has_accepted_license":"1","related_material":{"record":[{"id":"1398","status":"public","relation":"part_of_dissertation"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","ddc":["576"],"abstract":[{"lang":"eng","text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org."}]},{"abstract":[{"text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1398"}]},"has_accepted_license":"1","department":[{"_id":"NiBa"}],"date_updated":"2026-04-09T10:52:07Z","contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"file":[{"content_type":"application/zip","file_size":32775,"file_id":"5640","access_level":"open_access","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","creator":"system","file_name":"IST-2016-35-v1+1_array_data.zip","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:05:12Z","relation":"main_file"}],"type":"research_data","author":[{"first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"date_created":"2018-12-12T12:31:29Z","date_published":"2016-02-19T00:00:00Z","title":"Data on pollinator observations and offpsring phenotypes","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"month":"02","doi":"10.15479/AT:ISTA:35","datarep_id":"35","_id":"5551","citation":{"ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>.","ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>","mla":"Ellis, Thomas. <i>Data on Pollinator Observations and Offpsring Phenotypes</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","short":"T. Ellis, (2016).","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016."},"year":"2016","day":"19","file_date_updated":"2020-07-14T12:47:01Z","article_processing_charge":"No","status":"public"},{"date_updated":"2026-04-09T10:52:07Z","file":[{"content_type":"application/zip","file_size":44905,"file_id":"5625","file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_updated":"2020-07-14T12:47:01Z","access_level":"open_access","checksum":"cbc61b523d4d475a04a737d50dc470ef","creator":"system","relation":"main_file","date_created":"2018-12-12T13:03:07Z"}],"contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"author":[{"full_name":"Ellis, Thomas","orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas"}],"date_created":"2018-12-12T12:31:30Z","type":"research_data","oa_version":"Published Version","abstract":[{"text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1398","status":"public"}]},"has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:01Z","status":"public","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","doi":"10.15479/AT:ISTA:36","month":"02","date_published":"2016-02-19T00:00:00Z","datarep_id":"36","_id":"5552","year":"2016","citation":{"short":"T. Ellis, (2016).","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>.","ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>","mla":"Ellis, Thomas. <i>Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>."},"day":"19"},{"ddc":["000"],"OA_place":"publisher","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","id":"2218","status":"public"},{"status":"public","id":"2445","relation":"part_of_dissertation"},{"id":"1729","status":"public","relation":"part_of_dissertation"}]},"publisher":"Institute of Science and Technology Austria","corr_author":"1","file":[{"date_created":"2021-02-22T11:39:32Z","relation":"main_file","access_level":"open_access","checksum":"319a506831650327e85376db41fc1094","creator":"dernst","date_updated":"2021-02-22T11:39:32Z","file_name":"2016_Tarrach_Thesis.pdf","file_id":"9179","success":1,"content_type":"application/pdf","file_size":1523935},{"content_type":"application/pdf","file_size":1306068,"file_id":"10296","access_level":"closed","checksum":"39efcd789f0ad859ff15652cb7afc412","creator":"cchlebak","file_name":"2016_Tarrach_Thesispdfa.pdf","date_updated":"2021-11-17T13:46:55Z","date_created":"2021-11-16T14:14:38Z","relation":"main_file"}],"alternative_title":["ISTA Thesis"],"department":[{"_id":"ToHe"},{"_id":"GradSch"}],"type":"dissertation","publication_status":"published","doi":"10.15479/at:ista:1130","supervisor":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"url":"http://thorstent.github.io/theses/phd_thorsten_tarrach.pdf","open_access":"1"}],"citation":{"short":"T. Tarrach, Automatic Synthesis of Synchronisation Primitives for Concurrent Programs, Institute of Science and Technology Austria, 2016.","ieee":"T. Tarrach, “Automatic synthesis of synchronisation primitives for concurrent programs,” Institute of Science and Technology Austria, 2016.","mla":"Tarrach, Thorsten. <i>Automatic Synthesis of Synchronisation Primitives for Concurrent Programs</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>.","chicago":"Tarrach, Thorsten. “Automatic Synthesis of Synchronisation Primitives for Concurrent Programs.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>.","ista":"Tarrach T. 2016. Automatic synthesis of synchronisation primitives for concurrent programs. Institute of Science and Technology Austria.","ama":"Tarrach T. Automatic synthesis of synchronisation primitives for concurrent programs. 2016. doi:<a href=\"https://doi.org/10.15479/at:ista:1130\">10.15479/at:ista:1130</a>","apa":"Tarrach, T. (2016). <i>Automatic synthesis of synchronisation primitives for concurrent programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1130\">https://doi.org/10.15479/at:ista:1130</a>"},"publist_id":"6230","day":"07","file_date_updated":"2021-11-17T13:46:55Z","page":"151","oa_version":"Published Version","abstract":[{"text":"In this thesis we present a computer-aided programming approach to concurrency. Our approach helps the programmer by automatically fixing concurrency-related bugs, i.e. bugs that occur when the program is executed using an aggressive preemptive scheduler, but not when using a non-preemptive (cooperative) scheduler. Bugs are program behaviours that are incorrect w.r.t. a specification. We consider both user-provided explicit specifications in the form of assertion\r\nstatements in the code as well as an implicit specification. The implicit specification is inferred from the non-preemptive behaviour. Let us consider sequences of calls that the program makes to an external interface. The implicit specification requires that any such sequence produced under a preemptive scheduler should be included in the set of sequences produced under a non-preemptive scheduler. We consider several semantics-preserving fixes that go beyond atomic sections typically explored in the synchronisation synthesis literature. Our synthesis is able to place locks, barriers and wait-signal statements and last, but not least reorder independent statements. The latter may be useful if a thread is released to early, e.g., before some initialisation is completed. We guarantee that our synthesis does not introduce deadlocks and that the synchronisation inserted is optimal w.r.t. a given objective function. We dub our solution trace-based synchronisation synthesis and it is loosely based on counterexample-guided inductive synthesis (CEGIS). The synthesis works by discovering a trace that is incorrect w.r.t. the specification and identifying ordering constraints crucial to trigger the specification violation. Synchronisation may be placed immediately (greedy approach) or delayed until all incorrect traces are found (non-greedy approach). For the non-greedy approach we construct a set of global constraints over synchronisation placements. Each model of the global constraints set corresponds to a correctness-ensuring synchronisation placement. The placement that is optimal w.r.t. the given objective function is chosen as the synchronisation solution. We evaluate our approach on a number of realistic (albeit simplified) Linux device-driver\r\nbenchmarks. The benchmarks are versions of the drivers with known concurrency-related bugs. For the experiments with an explicit specification we added assertions that would detect the bugs in the experiments. Device drivers lend themselves to implicit specification, where the device and the operating system are the external interfaces. Our experiments demonstrate that our synthesis method is precise and efficient. We implemented objective functions for coarse-grained and fine-grained locking and observed that different synchronisation placements are produced for our experiments, favouring e.g. a minimal number of synchronisation operations or maximum concurrency.","lang":"eng"}],"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-09T10:54:01Z","publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Thorsten","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten"}],"date_created":"2018-12-11T11:50:19Z","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"}],"title":"Automatic synthesis of synchronisation primitives for concurrent programs","month":"07","date_published":"2016-07-07T00:00:00Z","_id":"1130","year":"2016","degree_awarded":"PhD","article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"status":"public"},{"acknowledgement":"This PhD thesis may not have been completed without the help and care I received from some peo- ple during my PhD life. I am especially grateful to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices but also for their patience and support. I thank Calin Guet and Jonathan Bollback for allowing me to “play around” in their labs and get some experience on experimental evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and sharing their experimental data with me. I thank Johannes Jaeger for reviewing my thesis. I thank all members of Barton group (aka bartonians) for their feedback, and all workers of IST Austria for making the best working conditions. Lastly, I thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous support and encouragement. I truly had a great chance of having right people around me.","supervisor":[{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"day":"01","publist_id":"6229","citation":{"mla":"Tugrul, Murat. <i>Evolution of Transcriptional Regulatory Sequences</i>. Institute of Science and Technology Austria, 2016.","ama":"Tugrul M. Evolution of transcriptional regulatory sequences. 2016.","apa":"Tugrul, M. (2016). <i>Evolution of transcriptional regulatory sequences</i>. Institute of Science and Technology Austria.","ista":"Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute of Science and Technology Austria.","chicago":"Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute of Science and Technology Austria, 2016.","ieee":"M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute of Science and Technology Austria, 2016.","short":"M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of Science and Technology Austria, 2016."},"file_date_updated":"2021-02-22T11:45:20Z","page":"89","ddc":["576"],"OA_place":"publisher","related_material":{"record":[{"relation":"research_data","id":"5554","status":"public"},{"relation":"part_of_dissertation","id":"1666","status":"public"}]},"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","corr_author":"1","alternative_title":["ISTA Thesis"],"file":[{"relation":"main_file","date_created":"2019-08-13T08:53:52Z","file_name":"Tugrul_thesis_w_signature_page.pdf","date_updated":"2019-08-13T08:53:52Z","creator":"dernst","checksum":"66cb61a59943e4fb7447c6a86be5ef51","access_level":"closed","file_id":"6810","file_size":3695257,"content_type":"application/pdf"},{"file_id":"9182","success":1,"content_type":"application/pdf","file_size":3880811,"date_created":"2021-02-22T11:45:20Z","relation":"main_file","creator":"dernst","checksum":"293e388d70563760f6b24c3e66283dda","access_level":"open_access","file_name":"2016_Tugrul_Thesis.pdf","date_updated":"2021-02-22T11:45:20Z"}],"department":[{"_id":"NiBa"}],"publication_status":"published","type":"dissertation","month":"07","title":"Evolution of transcriptional regulatory sequences","date_published":"2016-07-01T00:00:00Z","year":"2016","_id":"1131","degree_awarded":"PhD","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","oa_version":"Published Version","abstract":[{"text":"Evolution of gene regulation is important for phenotypic evolution and diversity. Sequence-specific binding of regulatory proteins is one of the key regulatory mechanisms determining gene expression. Although there has been intense interest in evolution of regulatory binding sites in the last decades, a theoretical understanding is far from being complete. In this thesis, I aim at a better understanding of the evolution of transcriptional regulatory binding sequences by using biophysical and population genetic models.\r\nIn the first part of the thesis, I discuss how to formulate the evolutionary dynamics of binding se- quences in a single isolated binding site and in promoter/enhancer regions. I develop a theoretical framework bridging between a thermodynamical model for transcription and a mutation-selection-drift model for monomorphic populations. I mainly address the typical evolutionary rates, and how they de- pend on biophysical parameters (e.g. binding length and specificity) and population genetic parameters (e.g. population size and selection strength).\r\nIn the second part of the thesis, I analyse empirical data for a better evolutionary and biophysical understanding of sequence-specific binding of bacterial RNA polymerase. First, I infer selection on regulatory and non-regulatory binding sites of RNA polymerase in the E. coli K12 genome. Second, I infer the chemical potential of RNA polymerase, an important but unknown physical parameter defining the threshold energy for strong binding. Furthermore, I try to understand the relation between the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial isolates by constructing a simple but biophysically motivated gene expression model. Lastly, I lay out a statistical framework to predict adaptive point mutations in de novo promoter evolution in a selection experiment.","lang":"eng"}],"oa":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-09T10:52:40Z","publication_identifier":{"issn":["2663-337X"]},"date_created":"2018-12-11T11:50:19Z","author":[{"full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","first_name":"Murat"}]},{"has_accepted_license":"1","oa":1,"related_material":{"record":[{"status":"public","id":"1131","relation":"used_in_publication"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution."}],"author":[{"first_name":"Murat","last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","full_name":"Tugrul, Murat"}],"date_created":"2018-12-12T12:31:30Z","type":"research_data","date_updated":"2026-04-09T10:52:40Z","file":[{"file_id":"5626","content_type":"application/zip","file_size":1123495,"date_created":"2018-12-12T13:03:08Z","relation":"main_file","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","creator":"system","access_level":"open_access","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","date_updated":"2020-07-14T12:47:01Z"}],"contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","contributor_type":"researcher","first_name":"Magdalena"},{"first_name":"Fabienne","last_name":"Jesse","contributor_type":"researcher","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"_id":"5554","datarep_id":"43","citation":{"ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>.","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>","mla":"Tugrul, Murat. <i>Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","short":"M. Tugrul, (2016).","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016."},"year":"2016","day":"12","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"month":"05","doi":"10.15479/AT:ISTA:43","date_published":"2016-05-12T00:00:00Z","status":"public","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:01Z","keyword":["RNAP binding","de novo promoter evolution","lac promoter"]},{"ddc":["576"],"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","id":"2023","relation":"part_of_dissertation"}]},"OA_place":"publisher","has_accepted_license":"1","department":[{"_id":"NiBa"}],"corr_author":"1","file":[{"file_id":"6811","content_type":"application/pdf","file_size":3564901,"date_created":"2019-08-13T09:01:00Z","relation":"main_file","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","creator":"dernst","access_level":"closed","file_name":"Novak_thesis.pdf","date_updated":"2019-08-13T09:01:00Z"},{"success":1,"file_id":"9186","content_type":"application/pdf","file_size":2814384,"date_created":"2021-02-22T13:42:47Z","relation":"main_file","checksum":"30808d2f7ca920e09f63a95cdc49bffd","creator":"dernst","access_level":"open_access","date_updated":"2021-02-22T13:42:47Z","file_name":"2016_Novak_Thesis.pdf"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","type":"dissertation","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"day":"01","publist_id":"6235","citation":{"mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016."},"file_date_updated":"2021-02-22T13:42:47Z","page":"124","abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2026-04-09T14:25:34Z","date_created":"2018-12-11T11:50:17Z","author":[{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"}],"date_published":"2016-07-01T00:00:00Z","month":"07","title":"Evolutionary proccesses in variable emvironments","degree_awarded":"PhD","year":"2016","_id":"1125","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public"},{"project":[{"grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:53:20Z","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Pausinger"}],"date_updated":"2026-04-09T14:26:05Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000375634100016"]},"volume":287,"oa":1,"abstract":[{"lang":"eng","text":"We introduce a modification of the classic notion of intrinsic volume using persistence moments of height functions. Evaluating the modified first intrinsic volume on digital approximations of a compact body with smoothly embedded boundary in Rn, we prove convergence to the first intrinsic volume of the body as the resolution of the approximation improves. We have weaker results for the other modified intrinsic volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional unit ball."}],"oa_version":"Published Version","status":"public","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"       287","_id":"1662","pubrep_id":"774","year":"2016","date_published":"2016-01-10T00:00:00Z","scopus_import":"1","month":"01","title":"Approximation and convergence of the intrinsic volume","publication_status":"published","type":"journal_article","quality_controlled":"1","department":[{"_id":"HeEd"}],"corr_author":"1","file":[{"content_type":"application/pdf","file_size":248985,"file_id":"4928","creator":"system","access_level":"open_access","checksum":"f8869ec110c35c852ef6a37425374af7","date_updated":"2020-07-14T12:45:10Z","file_name":"IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf","date_created":"2018-12-12T10:12:10Z","relation":"main_file"}],"publisher":"Academic Press","has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"1399","relation":"dissertation_contains"}]},"publication":"Advances in Mathematics","ddc":["004"],"page":"674 - 703","file_date_updated":"2020-07-14T12:45:10Z","day":"10","isi":1,"publist_id":"5488","citation":{"short":"H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.","ieee":"H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic volume,” <i>Advances in Mathematics</i>, vol. 287. Academic Press, pp. 674–703, 2016.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” <i>Advances in Mathematics</i>, vol. 287, Academic Press, 2016, pp. 674–703, doi:<a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">10.1016/j.aim.2015.10.004</a>.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” <i>Advances in Mathematics</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">https://doi.org/10.1016/j.aim.2015.10.004</a>.","ista":"Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 287, 674–703.","apa":"Edelsbrunner, H., &#38; Pausinger, F. (2016). Approximation and convergence of the intrinsic volume. <i>Advances in Mathematics</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">https://doi.org/10.1016/j.aim.2015.10.004</a>","ama":"Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic volume. <i>Advances in Mathematics</i>. 2016;287:674-703. doi:<a href=\"https://doi.org/10.1016/j.aim.2015.10.004\">10.1016/j.aim.2015.10.004</a>"},"doi":"10.1016/j.aim.2015.10.004","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne Marie Svane for her comments on an early version of this paper. The second author wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for enlightening discussions and their kind hospitality during a visit of their department in 2014.","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"}},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":59,"oa":1,"abstract":[{"text":"We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. ","lang":"eng"}],"oa_version":"Published Version","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211"}],"date_created":"2018-12-11T11:50:06Z","author":[{"first_name":"Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Kretinsky"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana"}],"date_updated":"2026-04-15T10:02:12Z","intvolume":"        59","_id":"1093","year":"2016","pubrep_id":"794","date_published":"2016-08-01T00:00:00Z","month":"08","scopus_import":1,"title":"Linear distances between Markov chains","status":"public","ec_funded":1,"language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","related_material":{"record":[{"relation":"dissertation_contains","id":"1155","status":"public"}]},"has_accepted_license":"1","ddc":["004"],"publication_status":"published","type":"conference","quality_controlled":"1","department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"file":[{"creator":"system","access_level":"open_access","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","date_updated":"2018-12-12T10:11:39Z","date_created":"2018-12-12T10:11:39Z","relation":"main_file","file_size":501827,"content_type":"application/pdf","file_id":"4895"}],"alternative_title":["LIPIcs"],"publist_id":"6283","day":"01","citation":{"short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59.","mla":"Daca, Przemyslaw, et al. <i>Linear Distances between Markov Chains</i>. Vol. 59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">10.4230/LIPIcs.CONCUR.2016.20</a>.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.20</a>.","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">10.4230/LIPIcs.CONCUR.2016.20</a>","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.20</a>"},"article_number":"20","doi":"10.4230/LIPIcs.CONCUR.2016.20","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF) under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award), by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced Postdoc. Mobility Fellowship – grant number P300P2_161067.","conference":{"start_date":"2016-08-23","location":"Quebec City; Canada","name":"CONCUR: Concurrency Theory","end_date":"2016-08-26"},"file_date_updated":"2018-12-12T10:11:39Z"},{"publication_status":"published","type":"conference","quality_controlled":"1","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"alternative_title":["LNCS"],"publisher":"Springer","related_material":{"record":[{"relation":"later_version","id":"471","status":"public"},{"id":"1155","status":"public","relation":"dissertation_contains"}]},"page":"112 - 129","conference":{"end_date":"2016-04-08","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","location":"Eindhoven, The Netherlands","start_date":"2016-04-02"},"day":"01","publist_id":"6099","isi":1,"citation":{"mla":"Daca, Przemyslaw, et al. <i>Faster Statistical Model Checking for Unbounded Temporal Properties</i>. Vol. 9636, Springer, 2016, pp. 112–29, doi:<a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">10.1007/978-3-662-49674-9_7</a>.","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Faster statistical model checking for unbounded temporal properties. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 9636, 112–129.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties,” 9636:112–29. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">https://doi.org/10.1007/978-3-662-49674-9_7</a>.","ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. In: Vol 9636. Springer; 2016:112-129. doi:<a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">10.1007/978-3-662-49674-9_7</a>","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Petrov, T. (2016). Faster statistical model checking for unbounded temporal properties (Vol. 9636, pp. 112–129). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49674-9_7\">https://doi.org/10.1007/978-3-662-49674-9_7</a>","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Springer, 2016, pp. 112–129.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Eindhoven, The Netherlands, 2016, vol. 9636, pp. 112–129."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.05739"}],"doi":"10.1007/978-3-662-49674-9_7","acknowledgement":"This research was funded in part by the European Research Council (ERC) under\r\ngrant  agreement  267989  (QUAREM),  the  Austrian  Science  Fund  (FWF)  under\r\ngrants project S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), the Peo-\r\nple Programme (Marie Curie Actions) of the European Union’s Seventh Framework\r\nProgramme (FP7/2007-2013) REA Grant No 291734, the SNSF Advanced Postdoc.\r\nMobility Fellowship – grant number P300P2\r\n161067, and the Czech Science Foun-\r\ndation under grant agreement P202/12/G061.","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:50:51Z","author":[{"first_name":"Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881"},{"last_name":"Petrov","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"}],"date_updated":"2026-04-15T10:02:12Z","external_id":{"isi":["000406428000007"],"arxiv":["1504.05739"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":9636,"abstract":[{"lang":"eng","text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds."}],"oa_version":"Preprint","arxiv":1,"status":"public","ec_funded":1,"language":[{"iso":"eng"}],"article_processing_charge":"No","intvolume":"      9636","year":"2016","_id":"1234","date_published":"2016-01-01T00:00:00Z","scopus_import":"1","month":"01","title":"Faster statistical model checking for unbounded temporal properties"},{"page":"230 - 248","conference":{"name":"CAV: Computer Aided Verification","end_date":"2016-07-23","location":"Toronto, Canada","start_date":"2016-07-17"},"doi":"10.1007/978-3-319-41540-6_13","citation":{"ieee":"P. Daca, T. A. Henzinger, and A. Kupriyanov, “Array folds logic,” presented at the CAV: Computer Aided Verification, Toronto, Canada, 2016, vol. 9780, pp. 230–248.","short":"P. Daca, T.A. Henzinger, A. Kupriyanov, in:, Springer, 2016, pp. 230–248.","apa":"Daca, P., Henzinger, T. A., &#38; Kupriyanov, A. (2016). Array folds logic (Vol. 9780, pp. 230–248). Presented at the CAV: Computer Aided Verification, Toronto, Canada: Springer. <a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">https://doi.org/10.1007/978-3-319-41540-6_13</a>","ama":"Daca P, Henzinger TA, Kupriyanov A. Array folds logic. In: Vol 9780. Springer; 2016:230-248. doi:<a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">10.1007/978-3-319-41540-6_13</a>","ista":"Daca P, Henzinger TA, Kupriyanov A. 2016. Array folds logic. CAV: Computer Aided Verification, LNCS, vol. 9780, 230–248.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, and Andrey Kupriyanov. “Array Folds Logic,” 9780:230–48. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">https://doi.org/10.1007/978-3-319-41540-6_13</a>.","mla":"Daca, Przemyslaw, et al. <i>Array Folds Logic</i>. Vol. 9780, Springer, 2016, pp. 230–48, doi:<a href=\"https://doi.org/10.1007/978-3-319-41540-6_13\">10.1007/978-3-319-41540-6_13</a>."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1603.06850"}],"day":"13","publist_id":"5818","isi":1,"department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"corr_author":"1","type":"conference","publication_status":"published","quality_controlled":"1","publisher":"Springer","related_material":{"record":[{"id":"1155","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"article_processing_charge":"No","ec_funded":1,"status":"public","date_published":"2016-07-13T00:00:00Z","title":"Array folds logic","month":"07","scopus_import":"1","intvolume":"      9780","_id":"1391","year":"2016","date_updated":"2026-04-15T10:02:12Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"id":"2C311BF8-F248-11E8-B48F-1D18A9856A87","last_name":"Kupriyanov","first_name":"Andrey","full_name":"Kupriyanov, Andrey"}],"date_created":"2018-12-11T11:51:45Z","abstract":[{"text":"We present an extension to the quantifier-free theory of integer arrays which allows us to express counting. The properties expressible in Array Folds Logic (AFL) include statements such as &quot;the first array cell contains the array length,&quot; and &quot;the array contains equally many minimal and maximal elements.&quot; These properties cannot be expressed in quantified fragments of the theory of arrays, nor in the theory of concatenation. Using reduction to counter machines, we show that the satisfiability problem of AFL is PSPACE-complete, and with a natural restriction the complexity decreases to NP. We also show that adding either universal quantifiers or concatenation leads to undecidability.\r\nAFL contains terms that fold a function over an array. We demonstrate that folding, a well-known concept from functional languages, allows us to concisely summarize loops that count over arrays, which occurs frequently in real-life programs. We provide a tool that can discharge proof obligations in AFL, and we demonstrate on practical examples that our decision procedure can solve a broad range of problems in symbolic testing and program verification.","lang":"eng"}],"oa_version":"Preprint","arxiv":1,"external_id":{"isi":["000387731400013"],"arxiv":["1603.06850"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"volume":9780},{"date_published":"2016-01-01T00:00:00Z","month":"01","scopus_import":"1","title":"Abstraction-driven concolic testing","intvolume":"      9583","year":"2016","_id":"1230","language":[{"iso":"eng"}],"article_processing_charge":"No","status":"public","ec_funded":1,"abstract":[{"text":"Concolic testing is a promising method for generating test suites for large programs. However, it suffers from the path-explosion problem and often fails to find tests that cover difficult-to-reach parts of programs. In contrast, model checkers based on counterexample-guided abstraction refinement explore programs exhaustively, while failing to scale on large programs with precision. In this paper, we present a novel method that iteratively combines concolic testing and model checking to find a test suite for a given coverage criterion. If concolic testing fails to cover some test goals, then the model checker refines its program abstraction to prove more paths infeasible, which reduces the search space for concolic testing. We have implemented our method on top of the concolictesting tool Crest and the model checker CpaChecker. We evaluated our tool on a collection of programs and a category of SvComp benchmarks. In our experiments, we observed an improvement in branch coverage compared to Crest from 48% to 63% in the best case, and from 66% to 71% on average.","lang":"eng"}],"arxiv":1,"oa_version":"Preprint","external_id":{"isi":["000375148800016"],"arxiv":["1511.02615"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":9583,"oa":1,"date_updated":"2026-04-15T10:02:12Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"date_created":"2018-12-11T11:50:50Z","author":[{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","last_name":"Daca"},{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1007/978-3-662-49122-5_16","acknowledgement":"We thank Andrey Kupriyanov for feedback on the manuscript,\r\nand Michael Tautschnig for help with preparing the experiments. This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","day":"01","isi":1,"publist_id":"6104","citation":{"ieee":"P. Daca, A. Gupta, and T. A. Henzinger, “Abstraction-driven concolic testing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 328–347.","short":"P. Daca, A. Gupta, T.A. Henzinger, in:, Springer, 2016, pp. 328–347.","mla":"Daca, Przemyslaw, et al. <i>Abstraction-Driven Concolic Testing</i>. Vol. 9583, Springer, 2016, pp. 328–47, doi:<a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">10.1007/978-3-662-49122-5_16</a>.","ama":"Daca P, Gupta A, Henzinger TA. Abstraction-driven concolic testing. In: Vol 9583. Springer; 2016:328-347. doi:<a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">10.1007/978-3-662-49122-5_16</a>","apa":"Daca, P., Gupta, A., &#38; Henzinger, T. A. (2016). Abstraction-driven concolic testing (Vol. 9583, pp. 328–347). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">https://doi.org/10.1007/978-3-662-49122-5_16</a>","ista":"Daca P, Gupta A, Henzinger TA. 2016. Abstraction-driven concolic testing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583, 328–347.","chicago":"Daca, Przemyslaw, Ashutosh Gupta, and Thomas A Henzinger. “Abstraction-Driven Concolic Testing,” 9583:328–47. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-49122-5_16\">https://doi.org/10.1007/978-3-662-49122-5_16</a>."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.02615"}],"page":"328 - 347","conference":{"end_date":"2016-01-19","name":"VMCAI: Verification, Model Checking and Abstract Interpretation","location":"St. Petersburg, FL, USA","start_date":"2016-01-17"},"publisher":"Springer","related_material":{"record":[{"status":"public","id":"1155","relation":"dissertation_contains"}]},"department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"publication_status":"published","type":"conference","quality_controlled":"1"},{"title":"Dynamic resource allocation games","month":"09","scopus_import":"1","date_published":"2016-09-01T00:00:00Z","_id":"1341","pubrep_id":"645","year":"2016","intvolume":"      9928","article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","oa_version":"Preprint","abstract":[{"text":"In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability.","lang":"eng"}],"oa":1,"volume":9928,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000389020400013"]},"date_updated":"2026-04-16T09:35:14Z","author":[{"full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"date_created":"2018-12-11T11:51:28Z","project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"This research was supported in part by the European Research Council (ERC) under grants 267989 (QUAREM) and 278410 (QUALITY), and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award).","doi":"10.1007/978-3-662-53354-3_13","citation":{"ieee":"G. Avni, T. A. Henzinger, and O. Kupferman, “Dynamic resource allocation games,” presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom, 2016, vol. 9928, pp. 153–166.","short":"G. Avni, T.A. Henzinger, O. Kupferman, in:, Springer, 2016, pp. 153–166.","ama":"Avni G, Henzinger TA, Kupferman O. Dynamic resource allocation games. In: Vol 9928. Springer; 2016:153-166. doi:<a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">10.1007/978-3-662-53354-3_13</a>","apa":"Avni, G., Henzinger, T. A., &#38; Kupferman, O. (2016). Dynamic resource allocation games (Vol. 9928, pp. 153–166). Presented at the SAGT: Symposium on Algorithmic Game Theory, Liverpool, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">https://doi.org/10.1007/978-3-662-53354-3_13</a>","chicago":"Avni, Guy, Thomas A Henzinger, and Orna Kupferman. “Dynamic Resource Allocation Games,” 9928:153–66. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">https://doi.org/10.1007/978-3-662-53354-3_13</a>.","ista":"Avni G, Henzinger TA, Kupferman O. 2016. Dynamic resource allocation games. SAGT: Symposium on Algorithmic Game Theory, LNCS, vol. 9928, 153–166.","mla":"Avni, Guy, et al. <i>Dynamic Resource Allocation Games</i>. Vol. 9928, Springer, 2016, pp. 153–66, doi:<a href=\"https://doi.org/10.1007/978-3-662-53354-3_13\">10.1007/978-3-662-53354-3_13</a>."},"isi":1,"day":"01","publist_id":"5926","file_date_updated":"2020-07-14T12:44:45Z","conference":{"start_date":"2016-09-19","end_date":"2016-09-21","name":"SAGT: Symposium on Algorithmic Game Theory","location":"Liverpool, United Kingdom"},"page":"153 - 166","ddc":["000"],"related_material":{"record":[{"id":"6761","status":"public","relation":"later_version"}]},"has_accepted_license":"1","publisher":"Springer","corr_author":"1","alternative_title":["LNCS"],"file":[{"file_size":243458,"content_type":"application/pdf","file_id":"5073","checksum":"0825eefd4e22774f6f62cb7d7389b05a","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:44:45Z","file_name":"IST-2016-645-v1+1_sagt-cr.pdf","date_created":"2018-12-12T10:14:22Z","relation":"main_file"}],"department":[{"_id":"ToHe"}],"quality_controlled":"1","type":"conference","publication_status":"published"},{"article_processing_charge":"No","language":[{"iso":"eng"}],"ec_funded":1,"status":"public","title":"Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity","scopus_import":"1","month":"11","date_published":"2016-11-21T00:00:00Z","year":"2016","_id":"1212","pubrep_id":"1008","intvolume":"        26","date_updated":"2026-04-28T08:29:26Z","author":[{"first_name":"Hana","last_name":"Rakusová","full_name":"Rakusová, Hana"},{"full_name":"Abbas, Mohamad","first_name":"Mohamad","last_name":"Abbas","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Han","first_name":"Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","full_name":"Han, Huibin"},{"first_name":"Siyuan","last_name":"Song","full_name":"Song, Siyuan"},{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí"}],"date_created":"2018-12-11T11:50:44Z","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Plants adjust their growth according to gravity. Gravitropism involves gravity perception, signal transduction, and asymmetric growth response, with organ bending as a consequence [1]. Asymmetric growth results from the asymmetric distribution of the plant-specific signaling molecule auxin [2] that is generated by lateral transport, mediated in the hypocotyl predominantly by the auxin transporter PIN-FORMED3 (PIN3) [3–5]. Gravity stimulation polarizes PIN3 to the bottom sides of endodermal cells, correlating with increased auxin accumulation in adjacent tissues at the lower side of the stimulated organ, where auxin induces cell elongation and, hence, organ bending. A curvature response allows the hypocotyl to resume straight growth at a defined angle [6], implying that at some point auxin symmetry is restored to prevent overbending. Here, we present initial insights into cellular and molecular mechanisms that lead to the termination of the tropic response. We identified an auxin feedback on PIN3 polarization as underlying mechanism that restores symmetry of the PIN3-dependent auxin flow. Thus, two mechanistically distinct PIN3 polarization events redirect auxin fluxes at different time points of the gravity response: first, gravity-mediated redirection of PIN3-mediated auxin flow toward the lower hypocotyl side, where auxin gradually accumulates and promotes growth, and later PIN3 polarization to the opposite cell side, depleting this auxin maximum to end the bending. Accordingly, genetic or pharmacological interference with the late PIN3 polarization prevents termination of the response and leads to hypocotyl overbending. This observation reveals a role of auxin feedback on PIN polarity in the termination of the tropic response. © 2016 Elsevier Ltd"}],"volume":26,"oa":1,"external_id":{"isi":["000388545900020"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:44:39Z","page":"3026 - 3032","acknowledgement":"We thank Dr. Jie Li (Key Laboratory of Plant Molecular Physiology, Chinese Academy of Science, China) for the pPIN3::PIN3-GFP/DII::VENUS line and Martine De Cock for help in preparing the manuscript. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP), by the Czech Science Foundation GAČR (GA13-40637S) to J.F., and by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601) to H.S.R. H.R. is indebted to the Agency for Innovation by Science and Technology (IWT) for a predoctoral fellowship.\r\n","issue":"22","doi":"10.1016/j.cub.2016.08.067","citation":{"ieee":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, and J. Friml, “Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity,” <i>Current Biology</i>, vol. 26, no. 22. Cell Press, pp. 3026–3032, 2016.","short":"H. Rakusová, M. Abbas, H. Han, S. Song, H. Robert, J. Friml, Current Biology 26 (2016) 3026–3032.","apa":"Rakusová, H., Abbas, M., Han, H., Song, S., Robert, H., &#38; Friml, J. (2016). Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2016.08.067\">https://doi.org/10.1016/j.cub.2016.08.067</a>","ama":"Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. <i>Current Biology</i>. 2016;26(22):3026-3032. doi:<a href=\"https://doi.org/10.1016/j.cub.2016.08.067\">10.1016/j.cub.2016.08.067</a>","ista":"Rakusová H, Abbas M, Han H, Song S, Robert H, Friml J. 2016. Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity. Current Biology. 26(22), 3026–3032.","chicago":"Rakusová, Hana, Mohamad Abbas, Huibin Han, Siyuan Song, Hélène Robert, and Jiří Friml. “Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity.” <i>Current Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.cub.2016.08.067\">https://doi.org/10.1016/j.cub.2016.08.067</a>.","mla":"Rakusová, Hana, et al. “Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity.” <i>Current Biology</i>, vol. 26, no. 22, Cell Press, 2016, pp. 3026–32, doi:<a href=\"https://doi.org/10.1016/j.cub.2016.08.067\">10.1016/j.cub.2016.08.067</a>."},"day":"21","isi":1,"publist_id":"6138","file":[{"checksum":"79ed2498185a027cf51a8f88100379e6","creator":"system","access_level":"open_access","file_name":"IST-2018-1008-v1+1_Rakusova_CurrBiol_2016_proof.pdf","date_updated":"2020-07-14T12:44:39Z","date_created":"2018-12-12T10:09:33Z","relation":"main_file","file_size":5391923,"content_type":"application/pdf","file_id":"4757"}],"department":[{"_id":"JiFr"}],"quality_controlled":"1","type":"journal_article","publication_status":"published","ddc":["581"],"publication":"Current Biology","has_accepted_license":"1","publisher":"Cell Press"},{"DOAJ_listed":"1","status":"public","language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","intvolume":"        33","_id":"5749","pubrep_id":"587","year":"2016","date_published":"2016-03-01T00:00:00Z","title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","month":"03","scopus_import":"1","author":[{"last_name":"Wielgoss","first_name":"Sébastien","full_name":"Wielgoss, Sébastien"},{"last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"full_name":"Bischofberger, Anna M.","last_name":"Bischofberger","first_name":"Anna M."},{"first_name":"Alex R.","last_name":"Hall","full_name":"Hall, Alex R."}],"date_created":"2018-12-18T13:18:10Z","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"date_updated":"2026-04-29T05:57:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000371219500015"],"pmid":["26609077"]},"pmid":1,"oa":1,"OA_type":"gold","volume":33,"abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"oa_version":"Published Version","page":"770-782","file_date_updated":"2020-07-14T12:47:10Z","citation":{"ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016."},"isi":1,"day":"01","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"doi":"10.1093/molbev/msv270","issue":"3","type":"journal_article","publication_status":"published","quality_controlled":"1","department":[{"_id":"CaGu"}],"file":[{"file_id":"5750","content_type":"application/pdf","file_size":634037,"relation":"main_file","date_created":"2018-12-18T13:21:45Z","file_name":"2016_MolBiolEvol_Wielgoss.pdf","date_updated":"2020-07-14T12:47:10Z","checksum":"47d9010690b6c5c17f2ac830cc63ac5c","access_level":"open_access","creator":"dernst"}],"publisher":"Oxford University Press","OA_place":"publisher","related_material":{"record":[{"status":"public","id":"9719","relation":"research_data"}]},"has_accepted_license":"1","ddc":["576"],"publication":"Molecular Biology and Evolution"}]