[{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","_id":"2036","abstract":[{"lang":"eng","text":" In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. "}],"volume":281,"author":[{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"},{"last_name":"Neve","first_name":"Paul","full_name":"Neve, Paul"}],"oa":1,"issue":"1794","quality_controlled":"1","department":[{"_id":"CaGu"}],"day":"17","status":"public","date_created":"2018-12-11T11:55:21Z","publisher":"Royal Society, The","scopus_import":1,"date_published":"2014-09-17T00:00:00Z","month":"09","article_number":"20141679","citation":{"ista":"Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2014. https://doi.org/10.1098/rspb.2014.1679.","apa":"Lagator, M., Colegrave, N., & Neve, P. (2014). Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2014.1679","short":"M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. Royal Society, The, 2014.","mla":"Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20141679, Royal Society, The, 2014, doi:10.1098/rspb.2014.1679.","ama":"Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.1679"},"date_updated":"2023-02-23T14:06:44Z","type":"journal_article","oa_version":"Submitted Version","related_material":{"record":[{"status":"public","relation":"research_data","id":"9741"}]},"doi":"10.1098/rspb.2014.1679","publist_id":"5019","intvolume":" 281","title":"Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/"}],"acknowledgement":"The project was supported by Leverhulme Trust.","year":"2014","language":[{"iso":"eng"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences"},{"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:26Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"3356"},{"status":"public","relation":"earlier_version","id":"5385"}]},"article_type":"original","doi":"10.1145/2629686","publist_id":"5013","ec_funded":1,"month":"09","date_published":"2014-09-16T00:00:00Z","ddc":["000","004"],"scopus_import":1,"has_accepted_license":"1","citation":{"apa":"Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2014). Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/2629686","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 15 (2014).","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). 15(4), 27.","chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. “Temporal Specifications with Accumulative Values.” ACM Transactions on Computational Logic (TOCL). ACM, 2014. https://doi.org/10.1145/2629686.","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). 2014;15(4). doi:10.1145/2629686","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications with accumulative values,” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 4. ACM, 2014.","mla":"Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” ACM Transactions on Computational Logic (TOCL), vol. 15, no. 4, 27, ACM, 2014, doi:10.1145/2629686."},"date_updated":"2023-02-23T12:23:54Z","type":"journal_article","article_number":"27","language":[{"iso":"eng"}],"year":"2014","article_processing_charge":"No","publication":"ACM Transactions on Computational Logic (TOCL)","intvolume":" 15","title":"Temporal specifications with accumulative values","pubrep_id":"192","acknowledgement":"The research was supported in part by ERC Starting grant 278410 (QUALITY).","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"volume":15,"author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker","first_name":"Udi","full_name":"Boker, Udi"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"Recently, there has been an effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions. At the heart of quantitative objectives lies the accumulation of values along a computation. It is often the accumulated sum, as with energy objectives, or the accumulated average, as with mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point in time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire infinite computation. We study the border of decidability for such quantitative extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with both prefix-accumulation assertions, or extending LTL with both path-accumulation assertions, results in temporal logics whose model-checking problem is decidable. Moreover, the prefix-accumulation assertions may be generalized with "controlled accumulation," allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that this branching-time logic is, in a sense, the maximal logic with one or both of the prefix-accumulation assertions that permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL, makes the problem undecidable."}],"_id":"2038","status":"public","date_created":"2018-12-11T11:55:21Z","file":[{"date_created":"2018-12-12T10:10:59Z","checksum":"354c41d37500b56320afce94cf9a99c2","access_level":"open_access","file_name":"IST-2014-192-v1+1_AccumulativeValues.pdf","file_id":"4851","relation":"main_file","content_type":"application/pdf","file_size":346184,"creator":"system","date_updated":"2020-07-14T12:45:26Z"}],"publisher":"ACM","quality_controlled":"1","issue":"4","oa":1,"day":"16","department":[{"_id":"ToHe"},{"_id":"KrCh"}]},{"intvolume":" 10","title":"The time scale of evolutionary innovation","pubrep_id":"440","year":"2014","language":[{"iso":"eng"}],"publication":"PLoS Computational Biology","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"month":"09","date_published":"2014-09-11T00:00:00Z","ddc":["510"],"article_number":"7p","has_accepted_license":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology, vol. 10, no. 9, 7p, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003818.","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of evolutionary innovation,” PLoS Computational Biology, vol. 10, no. 9. Public Library of Science, 2014.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary innovation. PLoS Computational Biology. 2014;10(9). doi:10.1371/journal.pcbi.1003818","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak. “The Time Scale of Evolutionary Innovation.” PLoS Computational Biology. Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014).","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., & Nowak, M. (2014). The time scale of evolutionary innovation. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1003818"},"date_updated":"2023-02-23T14:06:36Z","type":"journal_article","file_date_updated":"2020-07-14T12:45:26Z","oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"id":"9739","relation":"research_data","status":"public"}]},"doi":"10.1371/journal.pcbi.1003818","publist_id":"5012","issue":"9","oa":1,"quality_controlled":"1","department":[{"_id":"KrCh"}],"day":"11","status":"public","date_created":"2018-12-11T11:55:22Z","file":[{"access_level":"open_access","file_name":"IST-2016-440-v1+1_journal.pcbi.1003818.pdf","date_created":"2018-12-12T10:11:35Z","checksum":"712d4c5787ddf97809cfc962507f0738","content_type":"application/pdf","file_size":1399093,"date_updated":"2020-07-14T12:45:26Z","creator":"system","file_id":"4890","relation":"main_file"}],"publisher":"Public Library of Science","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","_id":"2039","abstract":[{"lang":"eng","text":"A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time."}],"volume":10,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Adlam","first_name":"Ben","full_name":"Adlam, Ben"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}]},{"day":"26","department":[{"_id":"ToBo"}],"quality_controlled":"1","title":"Coordination of progenitor specification and growth in mouse and chick spinal cord","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/","open_access":"1"}],"intvolume":" 345","oa":1,"issue":"6204","publication":"Science","publisher":"American Association for the Advancement of Science","date_created":"2018-12-11T11:55:22Z","status":"public","language":[{"iso":"eng"}],"year":"2014","type":"journal_article","citation":{"ista":"Kicheva A, Bollenbach MT, Ribeiro A, Pérez Valle H, Lovell Badge R, Episkopou V, Briscoe J. 2014. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 345(6204), 1254927.","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ana Ribeiro, Helena Pérez Valle, Robin Lovell Badge, Vasso Episkopou, and James Briscoe. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1254927.","apa":"Kicheva, A., Bollenbach, M. T., Ribeiro, A., Pérez Valle, H., Lovell Badge, R., Episkopou, V., & Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1254927","short":"A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014).","ieee":"A. Kicheva et al., “Coordination of progenitor specification and growth in mouse and chick spinal cord,” Science, vol. 345, no. 6204. American Association for the Advancement of Science, 2014.","mla":"Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” Science, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:10.1126/science.1254927.","ama":"Kicheva A, Bollenbach MT, Ribeiro A, et al. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 2014;345(6204). doi:10.1126/science.1254927"},"date_updated":"2021-01-12T06:54:55Z","abstract":[{"text":"Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. ","lang":"eng"}],"_id":"2040","article_number":"1254927","publication_status":"published","date_published":"2014-09-26T00:00:00Z","month":"09","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"doi":"10.1126/science.1254927","publist_id":"5011","author":[{"last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias"},{"full_name":"Ribeiro, Ana","first_name":"Ana","last_name":"Ribeiro"},{"last_name":"Pérez Valle","first_name":"Helena","full_name":"Pérez Valle, Helena"},{"last_name":"Lovell Badge","first_name":"Robin","full_name":"Lovell Badge, Robin"},{"last_name":"Episkopou","first_name":"Vasso","full_name":"Episkopou, Vasso"},{"last_name":"Briscoe","first_name":"James","full_name":"Briscoe, James"}],"oa_version":"Submitted Version","volume":345},{"author":[{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M"},{"last_name":"Lisman","first_name":"John","full_name":"Lisman, John"}],"volume":8,"abstract":[{"lang":"eng","text":"The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time."}],"_id":"2041","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file":[{"checksum":"3ca57b164045523f876407e9f13a9fb8","date_created":"2018-12-12T10:17:38Z","file_name":"IST-2016-424-v1+1_fncir-08-00107.pdf","access_level":"open_access","relation":"main_file","file_id":"5294","date_updated":"2020-07-14T12:45:26Z","creator":"system","file_size":201110,"content_type":"application/pdf"}],"publisher":"Frontiers Research Foundation","status":"public","date_created":"2018-12-11T11:55:22Z","day":"10","department":[{"_id":"PeJo"}],"quality_controlled":"1","oa":1,"publist_id":"5010","doi":"10.3389/fncir.2014.00107","oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:26Z","citation":{"mla":"Jonas, Peter M., and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits, vol. 8, 2p, Frontiers Research Foundation, 2014, doi:10.3389/fncir.2014.00107.","ieee":"P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” Frontiers in Neural Circuits, vol. 8. Frontiers Research Foundation, 2014.","ama":"Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 2014;8. doi:10.3389/fncir.2014.00107","chicago":"Jonas, Peter M, and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” Frontiers in Neural Circuits. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncir.2014.00107.","ista":"Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p.","short":"P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014).","apa":"Jonas, P. M., & Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. Frontiers Research Foundation. https://doi.org/10.3389/fncir.2014.00107"},"has_accepted_license":"1","date_updated":"2021-01-12T06:54:55Z","type":"journal_article","article_number":"2p","date_published":"2014-09-10T00:00:00Z","month":"09","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"publication":"Frontiers in Neural Circuits","language":[{"iso":"eng"}],"year":"2014","pubrep_id":"424","intvolume":" 8","title":"Structure, function and plasticity of hippocampal dentate gyrus microcircuits"},{"doi":"10.1186/1471-2164-15-663","publist_id":"5009","oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:26Z","citation":{"chicago":"Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics. BioMed Central, 2014. https://doi.org/10.1186/1471-2164-15-663.","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663.","short":"A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).","apa":"Kupczok, A., & Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-15-663","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” BMC Genomics, vol. 15, no. 1, 663, BioMed Central, 2014, doi:10.1186/1471-2164-15-663.","ieee":"A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” BMC Genomics, vol. 15, no. 1. BioMed Central, 2014.","ama":"Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 2014;15(1). doi:10.1186/1471-2164-15-663"},"date_updated":"2021-01-12T06:54:56Z","has_accepted_license":"1","type":"journal_article","article_number":"663","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2014-08-08T00:00:00Z","month":"08","ddc":["570"],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"scopus_import":1,"publication":"BMC Genomics","year":"2014","language":[{"iso":"eng"}],"pubrep_id":"396","intvolume":" 15","title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","author":[{"full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Kupczok"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"volume":15,"abstract":[{"text":"Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here.","lang":"eng"}],"_id":"2042","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","file":[{"date_created":"2018-12-12T10:11:24Z","checksum":"3f6d2776b90a842a28359cc957d3d04b","access_level":"open_access","file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf","file_id":"4878","relation":"main_file","date_updated":"2020-07-14T12:45:26Z","creator":"system","content_type":"application/pdf","file_size":1489769}],"publisher":"BioMed Central","status":"public","date_created":"2018-12-11T11:55:23Z","day":"08","department":[{"_id":"JoBo"}],"quality_controlled":"1","issue":"1","oa":1},{"doi":"10.1137/1.9781611973198.4","publist_id":"5008","conference":{"end_date":"2014-01-05","name":"ALENEX: Algorithm Engineering and Experiments","start_date":"2014-01-05","location":"Portland, USA"},"editor":[{"full_name":" McGeoch, Catherine","last_name":" McGeoch","first_name":"Catherine"},{"last_name":"Meyer","first_name":"Ulrich","full_name":"Meyer, Ulrich"}],"ec_funded":1,"oa_version":"Submitted Version","date_updated":"2021-01-12T06:54:56Z","citation":{"chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Distributed Computation of Persistent Homology.” In Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, 31–38. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973198.4.","ista":"Bauer U, Kerber M, Reininghaus J. 2014. Distributed computation of persistent homology. Proceedings of the Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, 31–38.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, C. McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2014, pp. 31–38.","apa":"Bauer, U., Kerber, M., & Reininghaus, J. (2014). Distributed computation of persistent homology. In C. McGeoch & U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments (pp. 31–38). Portland, USA: Society of Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973198.4","mla":"Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” Proceedings of the Workshop on Algorithm Engineering and Experiments, edited by Catherine McGeoch and Ulrich Meyer, Society of Industrial and Applied Mathematics, 2014, pp. 31–38, doi:10.1137/1.9781611973198.4.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Distributed computation of persistent homology,” in Proceedings of the Workshop on Algorithm Engineering and Experiments, Portland, USA, 2014, pp. 31–38.","ama":"Bauer U, Kerber M, Reininghaus J. Distributed computation of persistent homology. In: McGeoch C, Meyer U, eds. Proceedings of the Workshop on Algorithm Engineering and Experiments. Society of Industrial and Applied Mathematics; 2014:31-38. doi:10.1137/1.9781611973198.4"},"type":"conference","date_published":"2014-01-01T00:00:00Z","month":"01","scopus_import":1,"publication":"Proceedings of the Workshop on Algorithm Engineering and Experiments","year":"2014","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1310.0710","open_access":"1"}],"title":"Distributed computation of persistent homology","author":[{"full_name":"Bauer, Ulrich","last_name":"Bauer","orcid":"0000-0002-9683-0724","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kerber, Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299","first_name":"Michael"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"}],"project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"abstract":[{"lang":"eng","text":"Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node."}],"_id":"2043","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","page":"31 - 38","publisher":"Society of Industrial and Applied Mathematics","status":"public","date_created":"2018-12-11T11:55:23Z","day":"01","department":[{"_id":"HeEd"}],"quality_controlled":"1","oa":1},{"oa_version":"Submitted Version","doi":"10.1007/978-3-319-04099-8_7","publist_id":"5007","editor":[{"full_name":"Bremer, Peer-Timo","last_name":"Bremer","first_name":"Peer-Timo"},{"last_name":"Hotz","first_name":"Ingrid","full_name":"Hotz, Ingrid"},{"first_name":"Valerio","last_name":"Pascucci","full_name":"Pascucci, Valerio"},{"full_name":"Peikert, Ronald","last_name":"Peikert","first_name":"Ronald"}],"ec_funded":1,"month":"03","date_published":"2014-03-19T00:00:00Z","scopus_import":1,"citation":{"ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in Topological Methods in Data Analysis and Visualization III, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.","mla":"Bauer, Ulrich, et al. “Clear and Compress: Computing Persistent Homology in Chunks.” Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer et al., Springer, 2014, pp. 103–17, doi:10.1007/978-3-319-04099-8_7.","ama":"Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III. Mathematics and Visualization. Springer; 2014:103-117. doi:10.1007/978-3-319-04099-8_7","ista":"Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Clear and Compress: Computing Persistent Homology in Chunks.” In Topological Methods in Data Analysis and Visualization III, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 103–17. Mathematics and Visualization. Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_7.","apa":"Bauer, U., Kerber, M., & Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (pp. 103–117). Springer. https://doi.org/10.1007/978-3-319-04099-8_7","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III, Springer, 2014, pp. 103–117."},"date_updated":"2021-01-12T06:54:56Z","type":"book_chapter","year":"2014","language":[{"iso":"eng"}],"publication":"Topological Methods in Data Analysis and Visualization III","title":"Clear and Compress: Computing Persistent Homology in Chunks","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.0477"}],"project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"author":[{"orcid":"0000-0002-9683-0724","last_name":"Bauer","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"first_name":"Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael"},{"last_name":"Reininghaus","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","full_name":"Reininghaus, Jan"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation.","lang":"eng"}],"_id":"2044","status":"public","date_created":"2018-12-11T11:55:23Z","page":"103 - 117","publisher":"Springer","quality_controlled":"1","oa":1,"series_title":"Mathematics and Visualization","day":"19","department":[{"_id":"HeEd"}]},{"intvolume":" 8383","title":"Enhanced chosen-ciphertext security and applications","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2012/543"}],"acknowledgement":"The second author was supported by EPSRC grant EP/H043454/1.","year":"2014","language":[{"iso":"eng"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","month":"01","date_published":"2014-01-01T00:00:00Z","scopus_import":1,"citation":{"short":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344.","apa":"Dachman Soled, D., Fuchsbauer, G., Mohassel, P., & O’Neill, A. (2014). Enhanced chosen-ciphertext security and applications. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 329–344). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_19","chicago":"Dachman Soled, Dana, Georg Fuchsbauer, Payman Mohassel, and Adam O’Neill. “Enhanced Chosen-Ciphertext Security and Applications.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:329–44. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_19.","ista":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. 2014. Enhanced chosen-ciphertext security and applications. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 329–344.","ama":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. Enhanced chosen-ciphertext security and applications. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:329-344. doi:10.1007/978-3-642-54631-0_19","mla":"Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:10.1007/978-3-642-54631-0_19.","ieee":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, and A. O’Neill, “Enhanced chosen-ciphertext security and applications,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 329–344."},"date_updated":"2021-01-12T06:54:57Z","type":"conference","oa_version":"Submitted Version","alternative_title":["LNCS"],"doi":"10.1007/978-3-642-54631-0_19","conference":{"location":"Buenos Aires, Argentina","name":"PKC: Public Key Crypography","start_date":"2014-03-26","end_date":"2014-03-28"},"publist_id":"5006","editor":[{"full_name":"Krawczyk, Hugo","last_name":"Krawczyk","first_name":"Hugo"}],"ec_funded":1,"quality_controlled":"1","oa":1,"day":"01","department":[{"_id":"KrPi"}],"status":"public","date_created":"2018-12-11T11:55:24Z","publisher":"Springer","page":"329 - 344","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest.","lang":"eng"}],"_id":"2045","project":[{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"259668"}],"volume":8383,"author":[{"full_name":"Dachman Soled, Dana","last_name":"Dachman Soled","first_name":"Dana"},{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","last_name":"Fuchsbauer","first_name":"Georg"},{"last_name":"Mohassel","first_name":"Payman","full_name":"Mohassel, Payman"},{"full_name":"O’Neill, Adam","last_name":"O’Neill","first_name":"Adam"}]},{"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","language":[{"iso":"eng"}],"acknowledgement":"Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1.","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2013/413"}],"title":"Policy-based signatures","intvolume":" 8383","ec_funded":1,"editor":[{"first_name":"Hugo","last_name":"Krawczyk","full_name":"Krawczyk, Hugo"}],"doi":"10.1007/978-3-642-54631-0_30","publist_id":"5005","conference":{"end_date":"2014-05-28","name":"PKC: Public Key Crypography","start_date":"2014-05-26","location":"Buenos Aires, Argentina"},"alternative_title":["LNCS"],"oa_version":"Submitted Version","type":"conference","date_updated":"2021-01-12T06:54:57Z","citation":{"apa":"Bellare, M., & Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. https://doi.org/10.1007/978-3-642-54631-0_30","short":"M. Bellare, G. Fuchsbauer, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 520–537.","ista":"Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537.","chicago":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, 8383:520–37. Springer, 2014. https://doi.org/10.1007/978-3-642-54631-0_30.","ama":"Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8383. Springer; 2014:520-537. doi:10.1007/978-3-642-54631-0_30","ieee":"M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537.","mla":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 520–37, doi:10.1007/978-3-642-54631-0_30."},"scopus_import":1,"date_published":"2014-01-01T00:00:00Z","month":"01","publisher":"Springer","page":"520 - 537","date_created":"2018-12-11T11:55:24Z","status":"public","department":[{"_id":"KrPi"}],"day":"01","oa":1,"quality_controlled":"1","author":[{"first_name":"Mihir","last_name":"Bellare","full_name":"Bellare, Mihir"},{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"}],"volume":8383,"project":[{"call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"_id":"2046","abstract":[{"lang":"eng","text":"We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications."}],"publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","main_file_link":[{"url":"http://arxiv.org/abs/1407.8067","open_access":"1"}],"intvolume":" 8744","acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","year":"2014","language":[{"iso":"eng"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","month":"01","date_published":"2014-01-01T00:00:00Z","scopus_import":1,"type":"conference","date_updated":"2021-01-12T06:54:57Z","citation":{"mla":"Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:10.1007/978-3-319-11257-2_14.","ieee":"F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Ibiza, Spain, 2014, vol. 8744, pp. 170–184.","ama":"Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8744. Springer; 2014:170-184. doi:10.1007/978-3-319-11257-2_14","chicago":"Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. https://doi.org/10.1007/978-3-319-11257-2_14.","ista":"Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.","short":"F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184.","apa":"Yu, F., Rybar, M., Uhler, C., & Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. https://doi.org/10.1007/978-3-319-11257-2_14"},"oa_version":"Submitted Version","editor":[{"first_name":"Josep","last_name":"Domingo Ferrer","full_name":"Domingo Ferrer, Josep"}],"conference":{"end_date":"2014-09-19","start_date":"2014-09-17","name":"PSD: Privacy in Statistical Databases","location":"Ibiza, Spain"},"doi":"10.1007/978-3-319-11257-2_14","publist_id":"5004","alternative_title":["LNCS"],"quality_controlled":"1","oa":1,"arxiv":1,"day":"01","department":[{"_id":"KrPi"},{"_id":"CaUh"}],"date_created":"2018-12-11T11:55:24Z","status":"public","publisher":"Springer","page":"170 - 184","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance.","lang":"eng"}],"_id":"2047","project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070"}],"volume":8744,"external_id":{"arxiv":["1407.8067"]},"author":[{"full_name":"Yu, Fei","first_name":"Fei","last_name":"Yu"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar","full_name":"Rybar, Michal"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","orcid":"0000-0002-7008-0216","first_name":"Caroline","full_name":"Uhler, Caroline"},{"last_name":"Fienberg","first_name":"Stephen","full_name":"Fienberg, Stephen"}]},{"quality_controlled":"1","arxiv":1,"oa":1,"day":"10","department":[{"_id":"BjHo"}],"status":"public","date_created":"2018-12-11T11:55:25Z","publisher":"Cambridge University Press","page":"463 - 491","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"The flow instability and further transition to turbulence in a toroidal pipe (torus) with curvature ratio (tube-to-coiling diameter) 0.049 is investigated experimentally. The flow inside the toroidal pipe is driven by a steel sphere fitted to the inner pipe diameter. The sphere is moved with constant azimuthal velocity from outside the torus by a moving magnet. The experiment is designed to investigate curved pipe flow by optical measurement techniques. Using stereoscopic particle image velocimetry, laser Doppler velocimetry and pressure drop measurements, the flow is measured for Reynolds numbers ranging from 1000 to 15 000. Time- and space-resolved velocity fields are obtained and analysed. The steady axisymmetric basic flow is strongly influenced by centrifugal effects. On an increase of the Reynolds number we find a sequence of bifurcations. For Re=4075±2% a supercritical bifurcation to an oscillatory flow is found in which waves travel in the streamwise direction with a phase velocity slightly faster than the mean flow. The oscillatory flow is superseded by a presumably quasi-periodic flow at a further increase of the Reynolds number before turbulence sets in. The results are found to be compatible, in general, with earlier experimental and numerical investigations on transition to turbulence in helical and curved pipes. However, important aspects of the bifurcation scenario differ considerably.","lang":"eng"}],"_id":"2050","volume":738,"author":[{"full_name":"Kühnen, Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4312-0179","last_name":"Kühnen","first_name":"Jakob"},{"last_name":"Holzner","first_name":"Markus","full_name":"Holzner, Markus"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hendrik","last_name":"Kuhlmann","full_name":"Kuhlmann, Hendrik"}],"external_id":{"arxiv":["1508.06546"]},"intvolume":" 738","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.06546"}],"title":"Experimental investigation of transitional flow in a toroidal pipe","language":[{"iso":"eng"}],"year":"2014","publication":"Journal of Fluid Mechanics","article_processing_charge":"No","month":"01","date_published":"2014-01-10T00:00:00Z","scopus_import":1,"date_updated":"2021-01-12T06:54:59Z","citation":{"mla":"Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics, vol. 738, Cambridge University Press, 2014, pp. 463–91, doi:10.1017/jfm.2013.603.","ieee":"J. Kühnen, M. Holzner, B. Hof, and H. Kuhlmann, “Experimental investigation of transitional flow in a toroidal pipe,” Journal of Fluid Mechanics, vol. 738. Cambridge University Press, pp. 463–491, 2014.","ama":"Kühnen J, Holzner M, Hof B, Kuhlmann H. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 2014;738:463-491. doi:10.1017/jfm.2013.603","chicago":"Kühnen, Jakob, Markus Holzner, Björn Hof, and Hendrik Kuhlmann. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” Journal of Fluid Mechanics. Cambridge University Press, 2014. https://doi.org/10.1017/jfm.2013.603.","ista":"Kühnen J, Holzner M, Hof B, Kuhlmann H. 2014. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 738, 463–491.","short":"J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491.","apa":"Kühnen, J., Holzner, M., Hof, B., & Kuhlmann, H. (2014). Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2013.603"},"type":"journal_article","oa_version":"Submitted Version","publist_id":"5001","doi":"10.1017/jfm.2013.603"},{"date_created":"2018-12-11T11:55:26Z","status":"public","year":"2014","extern":1,"publisher":"Neural Information Processing Systems","title":"Multilabel structured output learning with random spanning trees of max-margin Markov networks","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01065586","open_access":"1"}],"quality_controlled":0,"oa":1,"day":"01","publist_id":"4996","conference":{"name":"NIPS: Neural Information Processing Systems"},"author":[{"full_name":"Marchand, Mario","first_name":"Mario","last_name":"Marchand"},{"last_name":"Hongyu","first_name":"Su","full_name":"Hongyu, Su"},{"id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","first_name":"Emilie","orcid":"0000-0002-8301-7240","last_name":"Morvant","full_name":"Emilie Morvant"},{"first_name":"Juho","last_name":"Rousu","full_name":"Rousu, Juho"},{"last_name":"Shawe Taylor","first_name":"John","full_name":"Shawe-Taylor, John"}],"publication_status":"published","month":"01","date_published":"2014-01-01T00:00:00Z","type":"conference","citation":{"short":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Neural Information Processing Systems, 2014.","apa":"Marchand, M., Hongyu, S., Morvant, E., Rousu, J., & Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. Presented at the NIPS: Neural Information Processing Systems, Neural Information Processing Systems.","chicago":"Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” Neural Information Processing Systems, 2014.","ista":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. NIPS: Neural Information Processing Systems.","ama":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: Neural Information Processing Systems; 2014.","mla":"Marchand, Mario, et al. Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks. Neural Information Processing Systems, 2014.","ieee":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” presented at the NIPS: Neural Information Processing Systems, 2014."},"date_updated":"2021-01-12T06:54:59Z","abstract":[{"text":"We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach.","lang":"eng"}],"_id":"2051"},{"intvolume":" 8704","title":"Parameterized model checking of rendezvous systems","quality_controlled":"1","day":"01","acknowledgement":"The second, third, fourth and fifth authors were supported by the Austrian National Research Network S11403-N23 (RiSE) of the Austrian Science Fund (FWF) and by the Vienna Science and Technology Fund (WWTF) through grants PROSEED, ICT12-059, and VRG11-005.","department":[{"_id":"KrCh"}],"status":"public","date_created":"2018-12-11T11:55:26Z","language":[{"iso":"eng"}],"year":"2014","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","page":"109 - 124","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","month":"09","date_published":"2014-09-01T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"A standard technique for solving the parameterized model checking problem is to reduce it to the classic model checking problem of finitely many finite-state systems. This work considers some of the theoretical power and limitations of this technique. We focus on concurrent systems in which processes communicate via pairwise rendezvous, as well as the special cases of disjunctive guards and token passing; specifications are expressed in indexed temporal logic without the next operator; and the underlying network topologies are generated by suitable Monadic Second Order Logic formulas and graph operations. First, we settle the exact computational complexity of the parameterized model checking problem for some of our concurrent systems, and establish new decidability results for others. Second, we consider the cases that model checking the parameterized system can be reduced to model checking some fixed number of processes, the number is known as a cutoff. We provide many cases for when such cutoffs can be computed, establish lower bounds on the size of such cutoffs, and identify cases where no cutoff exists. Third, we consider cases for which the parameterized system is equivalent to a single finite-state system (more precisely a Büchi word automaton), and establish tight bounds on the sizes of such automata."}],"citation":{"mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Rendezvous Systems.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–24, doi:10.1007/978-3-662-44584-6_9.","ieee":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model checking of rendezvous systems,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 109–124.","ama":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. Parameterized model checking of rendezvous systems. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:109-124. doi:10.1007/978-3-662-44584-6_9","chicago":"Aminof, Benjamin, Tomer Kotek, Sacha Rubin, Francesco Spegni, and Helmut Veith. “Parameterized Model Checking of Rendezvous Systems.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:109–24. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_9.","ista":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model checking of rendezvous systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124.","short":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, H. Veith, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–124.","apa":"Aminof, B., Kotek, T., Rubin, S., Spegni, F., & Veith, H. (2014). Parameterized model checking of rendezvous systems. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 109–124). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_9"},"date_updated":"2021-01-12T06:54:59Z","type":"conference","_id":"2052","oa_version":"None","volume":8704,"alternative_title":["LNCS"],"author":[{"id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","first_name":"Benjamin","last_name":"Aminof","full_name":"Aminof, Benjamin"},{"full_name":"Kotek, Tomer","first_name":"Tomer","last_name":"Kotek"},{"full_name":"Rubin, Sacha","last_name":"Rubin","first_name":"Sacha"},{"full_name":"Spegni, Francesco","first_name":"Francesco","last_name":"Spegni"},{"full_name":"Veith, Helmut","last_name":"Veith","first_name":"Helmut"}],"conference":{"start_date":"2014-09-02","name":"CONCUR: Concurrency Theory","end_date":"2014-09-05","location":"Rome, Italy"},"editor":[{"full_name":"Baldan, Paolo","last_name":"Baldan","first_name":"Paolo"},{"full_name":"Gorla, Daniele","first_name":"Daniele","last_name":"Gorla"}],"doi":"10.1007/978-3-662-44584-6_9","publist_id":"4994"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","page":"249 - 265","date_created":"2018-12-11T11:55:27Z","status":"public","day":"01","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"oa":1,"author":[{"first_name":"Holger","last_name":"Hermanns","full_name":"Hermanns, Holger"},{"last_name":"Krčál","first_name":"Jan","full_name":"Krčál, Jan"},{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan"}],"project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}],"volume":8704,"abstract":[{"text":"In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems.","lang":"eng"}],"_id":"2053","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","language":[{"iso":"eng"}],"acknowledgement":"This work is supported by the EU 7th Framework Programme under grant agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative Research Teams.","title":"Probabilistic bisimulation: Naturally on distributions","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5084"}],"intvolume":" 8704","doi":"10.1007/978-3-662-44584-6_18","conference":{"end_date":"2014-09-05","start_date":"2014-09-02","name":"CONCUR: Concurrency Theory","location":"Rome, Italy"},"publist_id":"4993","editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"last_name":"Gorla","first_name":"Daniele","full_name":"Gorla, Daniele"}],"alternative_title":["LNCS"],"ec_funded":1,"oa_version":"Submitted Version","type":"conference","citation":{"apa":"Hermanns, H., Krčál, J., & Kretinsky, J. (2014). Probabilistic bisimulation: Naturally on distributions. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 249–265). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_18","short":"H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–265.","ista":"Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally on distributions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 249–265.","chicago":"Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation: Naturally on Distributions.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_18.","ama":"Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on distributions. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:249-265. doi:10.1007/978-3-662-44584-6_18","ieee":"H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally on distributions,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 249–265.","mla":"Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–65, doi:10.1007/978-3-662-44584-6_18."},"date_updated":"2021-01-12T06:55:00Z","month":"09","date_published":"2014-09-01T00:00:00Z"},{"quality_controlled":"1","department":[{"_id":"KrCh"}],"day":"01","date_created":"2018-12-11T11:55:27Z","status":"public","page":"544 - 559","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"2054","abstract":[{"lang":"eng","text":"We study two-player concurrent games on finite-state graphs played for an infinite number of rounds, where in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine the successor state. The objectives are ω-regular winning conditions specified as parity objectives. We consider the qualitative analysis problems: the computation of the almost-sure and limit-sure winning set of states, where player 1 can ensure to win with probability 1 and with probability arbitrarily close to 1, respectively. In general the almost-sure and limit-sure winning strategies require both infinite-memory as well as infinite-precision (to describe probabilities). While the qualitative analysis problem for concurrent parity games with infinite-memory, infinite-precision randomized strategies was studied before, we study the bounded-rationality problem for qualitative analysis of concurrent parity games, where the strategy set for player 1 is restricted to bounded-resource strategies. In terms of precision, strategies can be deterministic, uniform, finite-precision, or infinite-precision; and in terms of memory, strategies can be memoryless, finite-memory, or infinite-memory. We present a precise and complete characterization of the qualitative winning sets for all combinations of classes of strategies. In particular, we show that uniform memoryless strategies are as powerful as finite-precision infinite-memory strategies, and infinite-precision memoryless strategies are as powerful as infinite-precision finite-memory strategies. We show that the winning sets can be computed in (n2d+3) time, where n is the size of the game structure and 2d is the number of priorities (or colors), and our algorithms are symbolic. The membership problem of whether a state belongs to a winning set can be decided in NP ∩ coNP. Our symbolic algorithms are based on a characterization of the winning sets as μ-calculus formulas, however, our μ-calculus formulas are crucially different from the ones for concurrent parity games (without bounded rationality); and our memoryless witness strategy constructions are significantly different from the infinite-memory witness strategy constructions for concurrent parity games."}],"volume":8704,"project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"title":"Qualitative concurrent parity games: Bounded rationality","intvolume":" 8704","year":"2014","language":[{"iso":"eng"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","month":"09","date_published":"2014-09-01T00:00:00Z","type":"conference","date_updated":"2023-02-23T11:23:36Z","citation":{"short":"K. Chatterjee, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 544–559.","apa":"Chatterjee, K. (2014). Qualitative concurrent parity games: Bounded rationality. In P. Baldan & D. Gorla (Eds.), Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8704, pp. 544–559). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-662-44584-6_37","chicago":"Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded Rationality.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, 8704:544–59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.1007/978-3-662-44584-6_37.","ista":"Chatterjee K. 2014. Qualitative concurrent parity games: Bounded rationality. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 544–559.","ama":"Chatterjee K. Qualitative concurrent parity games: Bounded rationality. In: Baldan P, Gorla D, eds. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:544-559. doi:10.1007/978-3-662-44584-6_37","mla":"Chatterjee, Krishnendu. “Qualitative Concurrent Parity Games: Bounded Rationality.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 544–59, doi:10.1007/978-3-662-44584-6_37.","ieee":"K. Chatterjee, “Qualitative concurrent parity games: Bounded rationality,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Rome, Italy, 2014, vol. 8704, pp. 544–559."},"oa_version":"None","ec_funded":1,"publist_id":"4992","editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"first_name":"Daniele","last_name":"Gorla","full_name":"Gorla, Daniele"}],"conference":{"start_date":"2014-09-02","name":"CONCUR: Concurrency Theory","end_date":"2014-09-05","location":"Rome, Italy"},"doi":"10.1007/978-3-662-44584-6_37","alternative_title":["LNCS"],"related_material":{"record":[{"relation":"earlier_version","id":"3354","status":"public"}]}},{"publisher":"Springer","page":"767 - 797","date_created":"2018-12-11T11:55:28Z","status":"public","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"day":"20","oa":1,"issue":"3","quality_controlled":"1","author":[{"full_name":"Ganguly, Arnab","last_name":"Ganguly","first_name":"Arnab"},{"first_name":"Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"},{"full_name":"Koeppl, Heinz","first_name":"Heinz","last_name":"Koeppl"}],"volume":69,"_id":"2056","abstract":[{"lang":"eng","text":"We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk."}],"publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Mathematical Biology","year":"2014","language":[{"iso":"eng"}],"acknowledgement":"T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology.","main_file_link":[{"url":"http://arxiv.org/abs/1303.4532","open_access":"1"}],"title":"Markov chain aggregation and its applications to combinatorial reaction networks","intvolume":" 69","doi":"10.1007/s00285-013-0738-7","publist_id":"4990","oa_version":"Submitted Version","type":"journal_article","citation":{"apa":"Ganguly, A., Petrov, T., & Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-013-0738-7","short":"A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797.","ista":"Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.","chicago":"Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology. Springer, 2014. https://doi.org/10.1007/s00285-013-0738-7.","ama":"Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 2014;69(3):767-797. doi:10.1007/s00285-013-0738-7","ieee":"A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” Journal of Mathematical Biology, vol. 69, no. 3. Springer, pp. 767–797, 2014.","mla":"Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” Journal of Mathematical Biology, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:10.1007/s00285-013-0738-7."},"date_updated":"2021-01-12T06:55:01Z","scopus_import":1,"date_published":"2014-11-20T00:00:00Z","month":"11"},{"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","year":"2014","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arxiv.org/abs/1404.7796","open_access":"1"}],"title":"Majority vote of diverse classifiers for late fusion","intvolume":" 8621","ec_funded":1,"conference":{"end_date":"2014-08-22","start_date":"2014-08-20","name":"IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition","location":"Joensuu, Finland"},"publist_id":"4989","doi":"10.1007/978-3-662-44415-3_16","alternative_title":["LNCS"],"oa_version":"Preprint","type":"conference","date_updated":"2021-01-12T06:55:01Z","citation":{"chicago":"Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of Diverse Classifiers for Late Fusion.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8621:153–62. Springer, 2014. https://doi.org/10.1007/978-3-662-44415-3_16.","ista":"Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers for late fusion. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS, vol. 8621, 153–162.","short":"E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 153–162.","apa":"Morvant, E., Habrard, A., & Ayache, S. (2014). Majority vote of diverse classifiers for late fusion. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. https://doi.org/10.1007/978-3-662-44415-3_16","mla":"Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8621, Springer, 2014, pp. 153–62, doi:10.1007/978-3-662-44415-3_16.","ieee":"E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers for late fusion,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Joensuu, Finland, 2014, vol. 8621, pp. 153–162.","ama":"Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late fusion. In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 8621. Springer; 2014:153-162. doi:10.1007/978-3-662-44415-3_16"},"scopus_import":1,"month":"01","date_published":"2014-01-01T00:00:00Z","page":"153 - 162","publisher":"Springer","date_created":"2018-12-11T11:55:28Z","status":"public","department":[{"_id":"ChLa"}],"day":"01","oa":1,"arxiv":1,"quality_controlled":"1","author":[{"id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","first_name":"Emilie","orcid":"0000-0002-8301-7240","last_name":"Morvant","full_name":"Morvant, Emilie"},{"full_name":"Habrard, Amaury","first_name":"Amaury","last_name":"Habrard"},{"last_name":"Ayache","first_name":"Stéphane","full_name":"Ayache, Stéphane"}],"external_id":{"arxiv":["1404.7796"]},"volume":8621,"project":[{"grant_number":"308036","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"_id":"2057","abstract":[{"text":"In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"pubrep_id":"606","intvolume":" 33","title":"Blending liquids","article_processing_charge":"No","publication":"ACM Transactions on Graphics","year":"2014","language":[{"iso":"eng"}],"article_number":"137","date_updated":"2022-08-25T14:02:46Z","has_accepted_license":"1","citation":{"short":"K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014.","apa":"Raveendran, K., Wojtan, C., Thuerey, N., & Türk, G. (2014). Blending liquids. In ACM Transactions on Graphics (Vol. 33). Vancouver, Canada: ACM. https://doi.org/10.1145/2601097.2601126","chicago":"Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending Liquids.” In ACM Transactions on Graphics, Vol. 33. ACM, 2014. https://doi.org/10.1145/2601097.2601126.","ista":"Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33, 137.","ama":"Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: ACM Transactions on Graphics. Vol 33. ACM; 2014. doi:10.1145/2601097.2601126","mla":"Raveendran, Karthik, et al. “Blending Liquids.” ACM Transactions on Graphics, vol. 33, no. 4, 137, ACM, 2014, doi:10.1145/2601097.2601126.","ieee":"K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in ACM Transactions on Graphics, Vancouver, Canada, 2014, vol. 33, no. 4."},"type":"conference","scopus_import":"1","month":"07","date_published":"2014-07-01T00:00:00Z","ddc":["000"],"conference":{"end_date":"2014-08-14","start_date":"2014-08-10","name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","location":"Vancouver, Canada"},"publist_id":"4988","doi":"10.1145/2601097.2601126","file_date_updated":"2020-07-14T12:45:27Z","oa_version":"Submitted Version","department":[{"_id":"ChWo"}],"day":"01","oa":1,"issue":"4","quality_controlled":"1","file":[{"creator":"system","date_updated":"2020-07-14T12:45:27Z","file_size":8387384,"content_type":"application/pdf","relation":"main_file","file_id":"4688","file_name":"IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf","access_level":"open_access","checksum":"1752760a2e71e254537f31c0d10d9c6c","date_created":"2018-12-12T10:08:27Z"}],"publisher":"ACM","status":"public","date_created":"2018-12-11T11:55:28Z","_id":"2058","abstract":[{"lang":"eng","text":"We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","author":[{"first_name":"Karthik","last_name":"Raveendran","full_name":"Raveendran, Karthik"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"full_name":"Türk, Greg","last_name":"Türk","first_name":"Greg"}],"volume":33,"project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070"}]},{"publist_id":"4987","doi":"10.1007/s00709-014-0616-1","oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:27Z","type":"journal_article","citation":{"mla":"Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:10.1007/s00709-014-0616-1.","ieee":"E. Dubas et al., “The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos,” Protoplasma, vol. 251, no. 5. Springer, pp. 1077–1087, 2014.","ama":"Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 2014;251(5):1077-1087. doi:10.1007/s00709-014-0616-1","chicago":"Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková, Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” Protoplasma. Springer, 2014. https://doi.org/10.1007/s00709-014-0616-1.","ista":"Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska M. 2014. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087.","apa":"Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur, I., & Krzewska, M. (2014). The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. Springer. https://doi.org/10.1007/s00709-014-0616-1"},"date_updated":"2021-01-12T06:55:02Z","has_accepted_license":"1","ddc":["580"],"month":"02","date_published":"2014-02-20T00:00:00Z","scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication":"Protoplasma","language":[{"iso":"eng"}],"year":"2014","pubrep_id":"394","acknowledgement":"The research was supported by the IPP PAS-IPGB SAS bilateral project (“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547, and VEGA 2-0090-14.","title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos","intvolume":" 251","author":[{"full_name":"Dubas, Ewa","first_name":"Ewa","last_name":"Dubas"},{"last_name":"Moravčíková","first_name":"Jana","full_name":"Moravčíková, Jana"},{"full_name":"Libantová, Jana","first_name":"Jana","last_name":"Libantová"},{"full_name":"Matušíková, Ildikó","last_name":"Matušíková","first_name":"Ildikó"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"full_name":"Zur, Iwona","last_name":"Zur","first_name":"Iwona"},{"full_name":"Krzewska, Monika","first_name":"Monika","last_name":"Krzewska"}],"volume":251,"abstract":[{"lang":"eng","text":"Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant."}],"_id":"2059","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","page":"1077 - 1087","file":[{"checksum":"d570a6073765118fc0bb83c31d96fa53","date_created":"2018-12-12T10:18:31Z","file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf","access_level":"open_access","relation":"main_file","file_id":"5353","creator":"system","date_updated":"2020-07-14T12:45:27Z","file_size":6377990,"content_type":"application/pdf"}],"date_created":"2018-12-11T11:55:29Z","status":"public","day":"20","department":[{"_id":"EvBe"}],"quality_controlled":"1","oa":1,"issue":"5"}]