[{"day":"17","scopus_import":1,"date_published":"2012-10-17T00:00:00Z","page":"14752 - 14766","publication":"Journal of Neuroscience","citation":{"mla":"Allen, Kevin, et al. “Hippocampal Place Cells Can Encode Multiple Trial-Dependent Features through Rate Remapping.” Journal of Neuroscience, vol. 32, no. 42, Society for Neuroscience, 2012, pp. 14752–66, doi:10.1523/JNEUROSCI.6175-11.2012.","short":"K. Allen, J.N. Rawlins, D. Bannerman, J.L. Csicsvari, Journal of Neuroscience 32 (2012) 14752–14766.","chicago":"Allen, Kevin, J Nick Rawlins, David Bannerman, and Jozsef L Csicsvari. “Hippocampal Place Cells Can Encode Multiple Trial-Dependent Features through Rate Remapping.” Journal of Neuroscience. Society for Neuroscience, 2012. https://doi.org/10.1523/JNEUROSCI.6175-11.2012.","ama":"Allen K, Rawlins JN, Bannerman D, Csicsvari JL. Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. 2012;32(42):14752-14766. doi:10.1523/JNEUROSCI.6175-11.2012","ista":"Allen K, Rawlins JN, Bannerman D, Csicsvari JL. 2012. Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. 32(42), 14752–14766.","apa":"Allen, K., Rawlins, J. N., Bannerman, D., & Csicsvari, J. L. (2012). Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.6175-11.2012","ieee":"K. Allen, J. N. Rawlins, D. Bannerman, and J. L. Csicsvari, “Hippocampal place cells can encode multiple trial-dependent features through rate remapping,” Journal of Neuroscience, vol. 32, no. 42. Society for Neuroscience, pp. 14752–14766, 2012."},"abstract":[{"text":"The activity of hippocampal pyramidal cells reflects both the current position of the animal and information related to its current behavior. Here we investigated whether single hippocampal neurons can encode several independent features defining trials during a memory task. We also tested whether task-related information is represented by partial remapping of the place cell population or, instead, via firing rate modulation of spatially stable place cells. To address these two questions, the activity of hippocampal neurons was recorded in rats performing a conditional discrimination task on a modified T-maze in which the identity of a food reward guided behavior. When the rat was on the central arm of the maze, the firing rate of pyramidal cells changed depending on two independent factors: (1) the identity of the food reward given to the animal and (2) the previous location of the animal on the maze. Importantly, some pyramidal cells encoded information relative to both factors. This trial-type specific and retrospective coding did not interfere with the spatial representation of the maze: hippocampal cells had stable place fields and their theta-phase precession profiles were unaltered during the task, indicating that trial-related information was encoded via rate remapping. During error trials, encoding of both trial-related information and spatial location was impaired. Finally, we found that pyramidal cells also encode trial-related information via rate remapping during the continuous version of the rewarded alternation task without delays. These results suggest that hippocampal neurons can encode several task-related cognitive aspects via rate remapping.","lang":"eng"}],"issue":"42","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Hippocampal place cells can encode multiple trial-dependent features through rate remapping","intvolume":" 32","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2958","month":"10","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.6175-11.2012","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["23077060"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531717/","open_access":"1"}],"oa":1,"ec_funded":1,"publist_id":"3768","date_updated":"2021-01-12T07:40:03Z","date_created":"2018-12-11T12:00:33Z","volume":32,"author":[{"full_name":"Allen, Kevin","last_name":"Allen","first_name":"Kevin"},{"full_name":"Rawlins, J Nick","last_name":"Rawlins","first_name":"J Nick"},{"last_name":"Bannerman","first_name":"David","full_name":"Bannerman, David"},{"first_name":"Jozsef L","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"publication_status":"published","department":[{"_id":"JoCs"}],"publisher":"Society for Neuroscience","year":"2012","acknowledgement":"J.C. was supported by a MRC Intramural Programme Grant (U138197111) and a European Research Council Starter Grant (281511). K.A. held a Wellcome Trust PhD studentship and a Humboldt Research Fellowship for Postdoctoral Researchers. D.M.B. was supported by Wellcome Trust Senior Fellowships (074385 and 087736).","pmid":1},{"page":"238 - 261","publication":"Annals of Statistics","citation":{"mla":"Uhler, Caroline. “Geometry of Maximum Likelihood Estimation in Gaussian Graphical Models.” Annals of Statistics, vol. 40, no. 1, Institute of Mathematical Statistics, 2012, pp. 238–61, doi:10.1214/11-AOS957.","short":"C. Uhler, Annals of Statistics 40 (2012) 238–261.","chicago":"Uhler, Caroline. “Geometry of Maximum Likelihood Estimation in Gaussian Graphical Models.” Annals of Statistics. Institute of Mathematical Statistics, 2012. https://doi.org/10.1214/11-AOS957.","ama":"Uhler C. Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. 2012;40(1):238-261. doi:10.1214/11-AOS957","ista":"Uhler C. 2012. Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. 40(1), 238–261.","apa":"Uhler, C. (2012). Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/11-AOS957","ieee":"C. Uhler, “Geometry of maximum likelihood estimation in Gaussian graphical models,” Annals of Statistics, vol. 40, no. 1. Institute of Mathematical Statistics, pp. 238–261, 2012."},"date_published":"2012-02-01T00:00:00Z","scopus_import":1,"day":"01","status":"public","title":"Geometry of maximum likelihood estimation in Gaussian graphical models","intvolume":" 40","_id":"2959","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"We study maximum likelihood estimation in Gaussian graphical models from a geometric point of view. An algebraic elimination criterion allows us to find exact lower bounds on the number of observations needed to ensure that the maximum likelihood estimator (MLE) exists with probability one. This is applied to bipartite graphs, grids and colored graphs. We also study the ML degree, and we present the first instance of a graph for which the MLE exists with probability one, even when the number of observations equals the treewidth.","lang":"eng"}],"issue":"1","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1012.2643"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1214/11-AOS957","month":"02","publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"CaUh"}],"acknowledgement":"I wish to thank Bernd Sturmfels for many helpful discus- sions and Steffen Lauritzen for introducing me to the problem of the existence of the MLE in Gaussian graphical models. I would also like to thank two referees who provided helpful comments on the original version of this paper.\r\n","year":"2012","date_created":"2018-12-11T12:00:33Z","date_updated":"2021-01-12T07:40:04Z","volume":40,"author":[{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline"}],"publist_id":"3767"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1186/1472-6785-12-7","language":[{"iso":"eng"}],"month":"06","year":"2012","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"SyCr"}],"author":[{"first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"},{"full_name":"Suefuji, Masaki","last_name":"Suefuji","first_name":"Masaki"},{"first_name":"Alexandra","last_name":"Schrempf","full_name":"Schrempf, Alexandra"},{"last_name":"Heinze","first_name":"Jürgen","full_name":"Heinze, Jürgen"}],"date_updated":"2021-01-12T07:40:07Z","date_created":"2018-12-11T12:00:35Z","volume":12,"article_number":"7","file_date_updated":"2020-07-14T12:45:57Z","publist_id":"3753","publication":"BMC Ecology","citation":{"mla":"Cremer, Sylvia, et al. “The Dynamics of Male-Male Competition in Cardiocondyla Obscurior Ants.” BMC Ecology, vol. 12, 7, BioMed Central, 2012, doi:10.1186/1472-6785-12-7.","short":"S. Cremer, M. Suefuji, A. Schrempf, J. Heinze, BMC Ecology 12 (2012).","chicago":"Cremer, Sylvia, Masaki Suefuji, Alexandra Schrempf, and Jürgen Heinze. “The Dynamics of Male-Male Competition in Cardiocondyla Obscurior Ants.” BMC Ecology. BioMed Central, 2012. https://doi.org/10.1186/1472-6785-12-7.","ama":"Cremer S, Suefuji M, Schrempf A, Heinze J. The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. 2012;12. doi:10.1186/1472-6785-12-7","ista":"Cremer S, Suefuji M, Schrempf A, Heinze J. 2012. The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. 12, 7.","apa":"Cremer, S., Suefuji, M., Schrempf, A., & Heinze, J. (2012). The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. BioMed Central. https://doi.org/10.1186/1472-6785-12-7","ieee":"S. Cremer, M. Suefuji, A. Schrempf, and J. Heinze, “The dynamics of male-male competition in Cardiocondyla obscurior ants,” BMC Ecology, vol. 12. BioMed Central, 2012."},"date_published":"2012-06-15T00:00:00Z","scopus_import":1,"day":"15","has_accepted_license":"1","_id":"2966","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The dynamics of male-male competition in Cardiocondyla obscurior ants","ddc":["570"],"intvolume":" 12","pubrep_id":"94","file":[{"relation":"main_file","file_id":"4706","date_updated":"2020-07-14T12:45:57Z","date_created":"2018-12-12T10:08:44Z","checksum":"03d004bdff3724fb1627e3f5004bad80","file_name":"IST-2012-94-v1+1_1472-6785-12-7.pdf","access_level":"open_access","content_type":"application/pdf","file_size":489994,"creator":"system"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Background: The outcome of male-male competition can be predicted from the relative fighting qualities of the opponents, which often depend on their age. In insects, freshly emerged and still sexually inactive males are morphologically indistinct from older, sexually active males. These young inactive males may thus be easy targets for older males if they cannot conceal themselves from their attacks. The ant Cardiocondyla obscurior is characterised by lethal fighting between wingless (" ergatoid" ) males. Here, we analyse for how long young males are defenceless after eclosion, and how early adult males can detect the presence of rival males.Results: We found that old ergatoid males consistently won fights against ergatoid males younger than two days. Old males did not differentiate between different types of unpigmented pupae several days before emergence, but had more frequent contact to ready-to-eclose pupae of female sexuals and winged males than of workers and ergatoid males. In rare cases, old ergatoid males displayed alleviated biting of pigmented ergatoid male pupae shortly before adult eclosion, as well as copulation attempts to dark pupae of female sexuals and winged males. Ergatoid male behaviour may be promoted by a closer similarity of the chemical profile of ready-to-eclose pupae to the profile of adults than that of young pupae several days prior to emergence.Conclusion: Young ergatoid males of C. obscurior would benefit greatly by hiding their identity from older, resident males, as they are highly vulnerable during the first two days of their adult lives. In contrast to the winged males of the same species, which are able to prevent ergatoid male attacks by chemical female mimicry, young ergatoids do not seem to be able to produce a protective chemical profile. Conflicts in male-male competition between ergatoid males of different age thus seem to be resolved in favour of the older males. This might represent selection at the colony level rather than the individual level. © 2012 Cremer et al.; licensee BioMed Central Ltd."}]},{"day":"01","scopus_import":1,"date_published":"2012-11-01T00:00:00Z","page":"1027 - 1047","publication":"Genetics","citation":{"ama":"Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047. doi:10.1534/genetics.112.143164","ista":"Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.","ieee":"S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” Genetics, vol. 192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.","apa":"Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.112.143164","mla":"Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.","short":"S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.","chicago":"Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics. Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164."},"abstract":[{"text":"The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Submitted Version","title":"A novel approach for choosing summary statistics in approximate Bayesian computation","status":"public","intvolume":" 192","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2962","month":"11","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.112.143164","quality_controlled":"1","oa":1,"external_id":{"pmid":["22960215"]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/"}],"publist_id":"3763","date_updated":"2021-01-12T07:40:05Z","date_created":"2018-12-11T12:00:34Z","volume":192,"author":[{"id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Aeschbacher","full_name":"Aeschbacher, Simon"},{"first_name":"Mark","last_name":"Beaumont","full_name":"Beaumont, Mark"},{"full_name":"Futschik, Andreas","first_name":"Andreas","last_name":"Futschik"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2012","pmid":1},{"year":"2012","publication_status":"published","publisher":"VÖB","department":[{"_id":"E-Lib"}],"author":[{"full_name":"Danowski, Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","last_name":"Danowski","first_name":"Patrick"}],"date_created":"2018-12-11T12:00:35Z","date_updated":"2021-01-12T07:40:07Z","volume":65,"file_date_updated":"2020-07-14T12:45:57Z","publist_id":"3754","main_file_link":[{"url":" http://hdl.handle.net/10760/17625","open_access":"1"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"ger"}],"month":"09","_id":"2965","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"title":"Kontext Open Access: Creative Commons","status":"public","intvolume":" 65","popular_science":"1","pubrep_id":"95","file":[{"file_size":503345,"content_type":"application/pdf","creator":"system","file_name":"IST-2012-95-v1+1_sp-beitrag_danowski_kontext_open_access_creative_commons.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:42Z","date_updated":"2020-07-14T12:45:57Z","checksum":"162eea47d9d840c26b496ba6ae4d1c09","relation":"main_file","file_id":"4703"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).","lang":"eng"}],"issue":"2","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","citation":{"chicago":"Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2012.","short":"P. Danowski, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 65 (2012) 200–212.","mla":"Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 65, no. 2, VÖB, 2012, pp. 200–12.","apa":"Danowski, P. (2012). Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.","ieee":"P. Danowski, “Kontext Open Access: Creative Commons,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 65, no. 2. VÖB, pp. 200–212, 2012.","ista":"Danowski P. 2012. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 65(2), 200–212.","ama":"Danowski P. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2012;65(2):200-212."},"page":"200 - 212","date_published":"2012-09-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1"},{"status":"public","title":"Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata","publication_status":"published","intvolume":" 91","department":[{"_id":"JoBo"}],"publisher":"Elsevier","_id":"2963","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","date_created":"2018-12-11T12:00:35Z","date_updated":"2021-01-12T07:40:06Z","volume":91,"oa_version":"None","author":[{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","last_name":"Jesse","first_name":"Fabienne","full_name":"Jesse, Fabienne"},{"full_name":"Riebel, Katharina","first_name":"Katharina","last_name":"Riebel"}],"type":"journal_article","abstract":[{"text":"Zebra finches are an ubiquitous model system for the study of vocal learning in animal communication. Their song has been well described, but its possible function(s) in social communication are only partly understood. The so-called ‘directed song’ is a high-intensity, high-performance song given during courtship in close proximity to the female, which is known to mediate mate choice and mating. However, this singing mode constitutes only a fraction of zebra finch males’ prolific song output. Potential communicative functions of their second, ‘undirected’ singing mode remain unresolved in the face of contradicting reports of both facilitating and inhibiting effects of social company on singing. We addressed this issue by experimentally manipulating social contexts in a within-subject design, comparing a solo versus male or female only company condition, each lasting for 24 hours. Males’ total song output was significantly higher when a conspecific was in audible and visible distance than when they were alone. Male and female company had an equally facilitating effect on song output. Our findings thus indicate that singing motivation is facilitated rather than inhibited by social company, suggesting that singing in zebra finches might function both in inter- and intrasexual communication. ","lang":"eng"}],"publist_id":"3756","issue":"3","quality_controlled":"1","page":"262 - 266","publication":"Behavioural Processes","citation":{"mla":"Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural Processes, vol. 91, no. 3, Elsevier, 2012, pp. 262–66, doi:10.1016/j.beproc.2012.09.006.","short":"F. Jesse, K. Riebel, Behavioural Processes 91 (2012) 262–266.","chicago":"Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural Processes. Elsevier, 2012. https://doi.org/10.1016/j.beproc.2012.09.006.","ama":"Jesse F, Riebel K. Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 2012;91(3):262-266. doi:10.1016/j.beproc.2012.09.006","ista":"Jesse F, Riebel K. 2012. Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 91(3), 262–266.","apa":"Jesse, F., & Riebel, K. (2012). Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. Elsevier. https://doi.org/10.1016/j.beproc.2012.09.006","ieee":"F. Jesse and K. Riebel, “Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata,” Behavioural Processes, vol. 91, no. 3. Elsevier, pp. 262–266, 2012."},"language":[{"iso":"eng"}],"doi":"10.1016/j.beproc.2012.09.006","date_published":"2012-11-01T00:00:00Z","month":"11","day":"01"},{"date_published":"2012-12-01T00:00:00Z","page":"663 - 680","citation":{"ama":"Jain A, Krenn S, Pietrzak KZ, Tentes A. Commitments and efficient zero knowledge proofs from learning parity with noise. In: Wang X, Sako K, eds. Vol 7658. Springer; 2012:663-680. doi:10.1007/978-3-642-34961-4_40","ieee":"A. Jain, S. Krenn, K. Z. Pietrzak, and A. Tentes, “Commitments and efficient zero knowledge proofs from learning parity with noise,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China, 2012, vol. 7658, pp. 663–680.","apa":"Jain, A., Krenn, S., Pietrzak, K. Z., & Tentes, A. (2012). Commitments and efficient zero knowledge proofs from learning parity with noise. In X. Wang & K. Sako (Eds.) (Vol. 7658, pp. 663–680). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China: Springer. https://doi.org/10.1007/978-3-642-34961-4_40","ista":"Jain A, Krenn S, Pietrzak KZ, Tentes A. 2012. Commitments and efficient zero knowledge proofs from learning parity with noise. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 7658, 663–680.","short":"A. Jain, S. Krenn, K.Z. Pietrzak, A. Tentes, in:, X. Wang, K. Sako (Eds.), Springer, 2012, pp. 663–680.","mla":"Jain, Abhishek, et al. Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise. Edited by Xiaoyun Wang and Kazue Sako, vol. 7658, Springer, 2012, pp. 663–80, doi:10.1007/978-3-642-34961-4_40.","chicago":"Jain, Abhishek, Stephan Krenn, Krzysztof Z Pietrzak, and Aris Tentes. “Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise.” edited by Xiaoyun Wang and Kazue Sako, 7658:663–80. Springer, 2012. https://doi.org/10.1007/978-3-642-34961-4_40."},"has_accepted_license":"1","day":"01","scopus_import":1,"oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"IST-2016-721-v1+1_513.pdf","content_type":"application/pdf","file_size":482570,"creator":"system","relation":"main_file","file_id":"5048","checksum":"ab879537385efc4cb4203e7ef0fea17b","date_created":"2018-12-12T10:14:00Z","date_updated":"2020-07-14T12:45:58Z"}],"pubrep_id":"721","intvolume":" 7658","ddc":["004","005"],"status":"public","title":"Commitments and efficient zero knowledge proofs from learning parity with noise","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2974","abstract":[{"lang":"eng","text":"We construct a perfectly binding string commitment scheme whose security is based on the learning parity with noise (LPN) assumption, or equivalently, the hardness of decoding random linear codes. Our scheme not only allows for a simple and efficient zero-knowledge proof of knowledge for committed values (essentially a Σ-protocol), but also for such proofs showing any kind of relation amongst committed values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u) for any circuit C.\r\n\r\nTo get soundness which is exponentially small in a security parameter t, and when the zero-knowledge property relies on the LPN problem with secrets of length l, our 3 round protocol has communication complexity O(t|C|l log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants are small, and the computation consists mostly of computing inner products of bit-vectors."}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-34961-4_40","conference":{"end_date":"2012-12-06","location":"Beijing, China","start_date":"2012-12-02","name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"12","volume":7658,"date_updated":"2021-01-12T07:40:11Z","date_created":"2018-12-11T12:00:38Z","author":[{"first_name":"Abhishek","last_name":"Jain","full_name":"Jain, Abhishek"},{"orcid":"0000-0003-2835-9093","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","last_name":"Krenn","first_name":"Stephan","full_name":"Krenn, Stephan"},{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Tentes, Aris","first_name":"Aris","last_name":"Tentes"}],"editor":[{"full_name":"Wang, Xiaoyun","last_name":"Wang","first_name":"Xiaoyun"},{"full_name":"Sako, Kazue","last_name":"Sako","first_name":"Kazue"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","year":"2012","acknowledgement":"We are grateful to Petros Mol for helpful discussions on the reduction for the hardness of the xLPN problem.\r\n","publist_id":"3730","ec_funded":1,"file_date_updated":"2020-07-14T12:45:58Z"},{"abstract":[{"lang":"eng","text":"The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of exocytosis is a key determinant of synaptic transmission. Evoked release from parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing interneurons is generated by microdomain coupling of N-type channels. Nanodomain coupling has several functional advantages, including speed and efficacy of transmission. One potential disadvantage is that stochastic\r\nopening of presynaptic Ca^(2+) channels may trigger spontaneous transmitter release. We addressed this possibility in rat hippocampal\r\ngranule cells, which receive converging inputs from different inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic Ca^(2+) channels contributes to spontaneous release. Application of the selective P/Q-type Ca^(2+) channel blocker\r\nω-agatoxin IVa had no detectable effects, whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine reduced\r\nmIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM and the slow chelator EGTA-AM reduced the mIPSC frequency,\r\nsuggesting that Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than nanodomain coupling. The CB_(1) receptor\r\nagonist WIN 55212-2 also decreased spontaneous release; this effect was occluded by prior application of ω-conotoxin GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release was generated at the terminals of CCK-expressing interneurons. Tonic inhibition generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels may be important for hippocampal information processing.\r\n"}],"issue":"41","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling","intvolume":" 32","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2969","day":"10","scopus_import":1,"date_published":"2012-10-10T00:00:00Z","page":"14294 - 14304","publication":"Journal of Neuroscience","citation":{"mla":"Goswami, Sarit, et al. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” Journal of Neuroscience, vol. 32, no. 41, Society for Neuroscience, 2012, pp. 14294–304, doi:10.1523/JNEUROSCI.6104-11.2012.","short":"S. Goswami, I. Bucurenciu, P.M. Jonas, Journal of Neuroscience 32 (2012) 14294–14304.","chicago":"Goswami, Sarit, Iancu Bucurenciu, and Peter M Jonas. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” Journal of Neuroscience. Society for Neuroscience, 2012. https://doi.org/10.1523/JNEUROSCI.6104-11.2012.","ama":"Goswami S, Bucurenciu I, Jonas PM. Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. 2012;32(41):14294-14304. doi:10.1523/JNEUROSCI.6104-11.2012","ista":"Goswami S, Bucurenciu I, Jonas PM. 2012. Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. 32(41), 14294–14304.","apa":"Goswami, S., Bucurenciu, I., & Jonas, P. M. (2012). Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.6104-11.2012","ieee":"S. Goswami, I. Bucurenciu, and P. M. Jonas, “Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling,” Journal of Neuroscience, vol. 32, no. 41. Society for Neuroscience, pp. 14294–14304, 2012."},"publist_id":"3744","date_updated":"2021-01-12T07:40:08Z","date_created":"2018-12-11T12:00:36Z","volume":32,"author":[{"id":"3A578F32-F248-11E8-B48F-1D18A9856A87","last_name":"Goswami","first_name":"Sarit","full_name":"Goswami, Sarit"},{"full_name":"Bucurenciu, Iancu","first_name":"Iancu","last_name":"Bucurenciu"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Society for Neuroscience","acknowledgement":"This work was supported by grants from the Deutsche Forschungsgemeinschaft (TR 3/B10, Leibniz program, GSC-4 Spemann Graduate School) and the European Union (European Research Council Advanced Grant).","year":"2012","pmid":1,"month":"10","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.6104-11.2012","quality_controlled":"1","project":[{"_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","grant_number":"SFB-TR3-TP10B","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen"}],"external_id":{"pmid":["23055500"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632771/","open_access":"1"}]},{"publist_id":"3739","issue":"6","abstract":[{"lang":"eng","text":"Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms."}],"type":"journal_article","author":[{"last_name":"Kicheva","first_name":"Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna"},{"full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias"},{"full_name":"Wartlick, Ortrud","last_name":"Wartlick","first_name":"Ortrud"},{"last_name":"Julicher","first_name":"Frank","full_name":"Julicher, Frank"},{"first_name":"Marcos","last_name":"Gonzalez Gaitan","full_name":"Gonzalez Gaitan, Marcos"}],"oa_version":"None","volume":22,"date_created":"2018-12-11T12:00:37Z","date_updated":"2021-01-12T07:40:09Z","_id":"2970","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"AK is currently supported by an MRC CDF. MGG and OW were supported by the Swiss National Science Foundation, grants from the Swiss SystemsX.ch initiative, LipidX-2008/011, an ERC advanced investigator grant and the Polish-Swiss research program.","department":[{"_id":"ToBo"}],"intvolume":" 22","publisher":"Elsevier","title":"Investigating the principles of morphogen gradient formation: from tissues to cells","status":"public","publication_status":"published","day":"01","month":"12","scopus_import":1,"doi":"10.1016/j.gde.2012.08.004","date_published":"2012-12-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ortrud Wartlick, Frank Julicher, and Marcos Gonzalez Gaitan. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.08.004.","short":"A. Kicheva, M.T. Bollenbach, O. Wartlick, F. Julicher, M. Gonzalez Gaitan, Current Opinion in Genetics & Development 22 (2012) 527–532.","mla":"Kicheva, Anna, et al. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development, vol. 22, no. 6, Elsevier, 2012, pp. 527–32, doi:10.1016/j.gde.2012.08.004.","ieee":"A. Kicheva, M. T. Bollenbach, O. Wartlick, F. Julicher, and M. Gonzalez Gaitan, “Investigating the principles of morphogen gradient formation: from tissues to cells,” Current Opinion in Genetics & Development, vol. 22, no. 6. Elsevier, pp. 527–532, 2012.","apa":"Kicheva, A., Bollenbach, M. T., Wartlick, O., Julicher, F., & Gonzalez Gaitan, M. (2012). Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2012.08.004","ista":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. 2012. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 22(6), 527–532.","ama":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 2012;22(6):527-532. doi:10.1016/j.gde.2012.08.004"},"publication":"Current Opinion in Genetics & Development","page":"527 - 532","quality_controlled":"1"},{"date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-3-642-32717-9_2","conference":{"location":"Graz, Austria","start_date":"2012-08-28","end_date":"2012-08-31","name":"Pattern Recognition"},"language":[{"iso":"eng"}],"citation":{"mla":"Zankl, Georg, et al. Interactive Labeling of Image Segmentation Hierarchies. Vol. 7476, Springer, 2012, pp. 11–20, doi:10.1007/978-3-642-32717-9_2.","short":"G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20.","chicago":"Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image Segmentation Hierarchies,” 7476:11–20. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_2.","ama":"Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies. In: Vol 7476. Springer; 2012:11-20. doi:10.1007/978-3-642-32717-9_2","ista":"Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation hierarchies. Pattern Recognition vol. 7476, 11–20.","apa":"Zankl, G., Haxhimusa, Y., & Ion, A. (2012). Interactive labeling of image segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_2","ieee":"G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 11–20."},"page":"11 - 20","quality_controlled":"1","month":"01","day":"01","scopus_import":1,"author":[{"first_name":"Georg","last_name":"Zankl","full_name":"Zankl, Georg"},{"last_name":"Haxhimusa","first_name":"Yll","full_name":"Haxhimusa, Yll"},{"full_name":"Ion, Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87","last_name":"Ion","first_name":"Adrian"}],"volume":7476,"oa_version":"None","date_updated":"2021-01-12T07:40:10Z","date_created":"2018-12-11T12:00:37Z","year":"2012","_id":"2971","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","department":[{"_id":"HeEd"}],"intvolume":" 7476","status":"public","publication_status":"published","title":"Interactive labeling of image segmentation hierarchies","publist_id":"3737","abstract":[{"lang":"eng","text":"We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. "}],"type":"conference"},{"year":"2012","_id":"3105","publication_status":"published","title":"GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses","status":"public","intvolume":" 22","publisher":"Cell Press","author":[{"full_name":"Whitford, Ryan","last_name":"Whitford","first_name":"Ryan"},{"last_name":"Fernandez","first_name":"Ana","full_name":"Fernandez, Ana"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"last_name":"Pérez","first_name":"Amparo","full_name":"Pérez, Amparo Cuéllar"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"first_name":"Andrzej","last_name":"Drozdzecki","full_name":"Drozdzecki, Andrzej"},{"full_name":"Leitner, Johannes","first_name":"Johannes","last_name":"Leitner"},{"first_name":"Lindy","last_name":"Abas","full_name":"Abas, Lindy"},{"full_name":"Aerts, Maarten","last_name":"Aerts","first_name":"Maarten"},{"last_name":"Hoogewijs","first_name":"Kurt","full_name":"Hoogewijs, Kurt"},{"full_name":"Pawel Baster","last_name":"Baster","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Groodt","first_name":"Ruth","full_name":"De Groodt, Ruth"},{"last_name":"Lin","first_name":"Yao","full_name":"Lin, Yao-Cheng"},{"full_name":"Storme, Véronique","first_name":"Véronique","last_name":"Storme"},{"full_name":"Van de Peer, Yves","first_name":"Yves","last_name":"Van De Peer"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"first_name":"Annemieke","last_name":"Madder","full_name":"Madder, Annemieke"},{"full_name":"Devreese, Bart","last_name":"Devreese","first_name":"Bart"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"full_name":"Hilson, Pierre","last_name":"Hilson","first_name":"Pierre"}],"date_created":"2018-12-11T12:01:25Z","date_updated":"2021-01-12T07:41:06Z","volume":22,"type":"journal_article","abstract":[{"lang":"eng","text":"Growth and development are coordinated by an array of intercellular communications. Known plant signaling molecules include phytohormones and hormone peptides. Although both classes can be implicated in the same developmental processes, little is known about the interplay between phytohormone action and peptide signaling within the cellular microenvironment. We show that genes coding for small secretory peptides, designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin. The deregulation of the GLV function impairs the formation of auxin gradients and alters the reorientation of shoots and roots after a gravity stimulus. Specifically, the GLV signal modulates the trafficking dynamics of the auxin efflux carrier PIN-FORMED2 involved in root tropic responses and meristem organization. Our work links the local action of secretory peptides with phytohormone transport. Root growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients, and modulate auxin-dependent root responses to specific stimuli."}],"issue":"3","publist_id":"3594","extern":1,"publication":"Developmental Cell","citation":{"short":"R. Whitford, A. Fernandez, R. Tejos, A. Pérez, J. Kleine Vehn, S. Vanneste, A. Drozdzecki, J. Leitner, L. Abas, M. Aerts, K. Hoogewijs, P. Baster, R. De Groodt, Y. Lin, V. Storme, Y. Van De Peer, T. Beeckman, A. Madder, B. Devreese, C. Luschnig, J. Friml, P. Hilson, Developmental Cell 22 (2012) 678–685.","mla":"Whitford, Ryan, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell, vol. 22, no. 3, Cell Press, 2012, pp. 678–85, doi:10.1016/j.devcel.2012.02.002.","chicago":"Whitford, Ryan, Ana Fernandez, Ricardo Tejos, Amparo Pérez, Jürgen Kleine Vehn, Steffen Vanneste, Andrzej Drozdzecki, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2012.02.002.","ama":"Whitford R, Fernandez A, Tejos R, et al. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 2012;22(3):678-685. doi:10.1016/j.devcel.2012.02.002","apa":"Whitford, R., Fernandez, A., Tejos, R., Pérez, A., Kleine Vehn, J., Vanneste, S., … Hilson, P. (2012). GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2012.02.002","ieee":"R. Whitford et al., “GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses,” Developmental Cell, vol. 22, no. 3. Cell Press, pp. 678–685, 2012.","ista":"Whitford R, Fernandez A, Tejos R, Pérez A, Kleine Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin Y, Storme V, Van De Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson P. 2012. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 22(3), 678–685."},"quality_controlled":0,"page":"678 - 685","date_published":"2012-03-13T00:00:00Z","doi":"10.1016/j.devcel.2012.02.002","month":"03","day":"13"},{"doi":"10.1038/nchembio.958","date_published":"2012-06-01T00:00:00Z","quality_controlled":0,"page":"583 - 589","publication":"Nature Chemical Biology","citation":{"mla":"Irani, Niloufer, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology, vol. 8, no. 6, Nature Publishing Group, 2012, pp. 583–89, doi:10.1038/nchembio.958.","short":"N. Irani, S. Di Rubbo, E. Mylle, J. Van Den Begin, J. Schneider Pizoń, J. Hniliková, M. Šíša, D. Buyst, J. Vilarrasa Blasi, A. Szatmári, D. Van Damme, K. Mishev, M. Codreanu, L. Kohout, M. Strnad, A. Caño Delgado, J. Friml, A. Madder, E. Russinova, Nature Chemical Biology 8 (2012) 583–589.","chicago":"Irani, Niloufer, Simone Di Rubbo, Evelien Mylle, Jos Van Den Begin, Joanna Schneider Pizoń, Jaroslava Hniliková, Miroslav Šíša, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.958.","ama":"Irani N, Di Rubbo S, Mylle E, et al. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 2012;8(6):583-589. doi:10.1038/nchembio.958","ista":"Irani N, Di Rubbo S, Mylle E, Van Den Begin J, Schneider Pizoń J, Hniliková J, Šíša M, Buyst D, Vilarrasa Blasi J, Szatmári A, Van Damme D, Mishev K, Codreanu M, Kohout L, Strnad M, Caño Delgado A, Friml J, Madder A, Russinova E. 2012. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 8(6), 583–589.","apa":"Irani, N., Di Rubbo, S., Mylle, E., Van Den Begin, J., Schneider Pizoń, J., Hniliková, J., … Russinova, E. (2012). Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.958","ieee":"N. Irani et al., “Fluorescent castasterone reveals BRI1 signaling from the plasma membrane,” Nature Chemical Biology, vol. 8, no. 6. Nature Publishing Group, pp. 583–589, 2012."},"day":"01","month":"06","date_created":"2018-12-11T12:01:26Z","date_updated":"2021-01-12T07:41:07Z","volume":8,"author":[{"last_name":"Irani","first_name":"Niloufer","full_name":"Irani, Niloufer G"},{"full_name":"Di Rubbo, Simone","first_name":"Simone","last_name":"Di Rubbo"},{"first_name":"Evelien","last_name":"Mylle","full_name":"Mylle, Evelien"},{"full_name":"Van Den Begin, Jos","first_name":"Jos","last_name":"Van Den Begin"},{"first_name":"Joanna","last_name":"Schneider Pizoń","full_name":"Schneider-Pizoń, Joanna"},{"full_name":"Hniliková, Jaroslava","first_name":"Jaroslava","last_name":"Hniliková"},{"last_name":"Šíša","first_name":"Miroslav","full_name":"Šíša, Miroslav"},{"last_name":"Buyst","first_name":"Dieter","full_name":"Buyst, Dieter"},{"full_name":"Vilarrasa-Blasi, Josep","last_name":"Vilarrasa Blasi","first_name":"Josep"},{"last_name":"Szatmári","first_name":"Anna","full_name":"Szatmári, Anna-Maria"},{"full_name":"Van Damme, Daniël","first_name":"Daniël","last_name":"Van Damme"},{"full_name":"Mishev, Kiril","first_name":"Kiril","last_name":"Mishev"},{"first_name":"Mirela","last_name":"Codreanu","full_name":"Codreanu, Mirela-Corina"},{"last_name":"Kohout","first_name":"Ladislav","full_name":"Kohout, Ladislav"},{"full_name":"Strnad, Miroslav","last_name":"Strnad","first_name":"Miroslav"},{"full_name":"Caño-Delgado, Ana I","first_name":"Ana","last_name":"Caño Delgado"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml"},{"first_name":"Annemieke","last_name":"Madder","full_name":"Madder, Annemieke"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"}],"publication_status":"published","status":"public","title":"Fluorescent castasterone reveals BRI1 signaling from the plasma membrane","intvolume":" 8","publisher":"Nature Publishing Group","year":"2012","_id":"3109","extern":1,"abstract":[{"lang":"eng","text":"Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane."}],"issue":"6","publist_id":"3590","type":"journal_article"},{"publisher":"National Academy of Sciences","intvolume":" 109","status":"public","title":"Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis","publication_status":"published","_id":"3104","year":"2012","volume":109,"date_updated":"2021-01-12T07:41:05Z","date_created":"2018-12-11T12:01:24Z","author":[{"full_name":"Grunewald, Wim","last_name":"Grunewald","first_name":"Wim"},{"first_name":"Ive","last_name":"De Smet","full_name":"De Smet, Ive"},{"last_name":"Lewis","first_name":"Daniel","full_name":"Lewis, Daniel R"},{"full_name":"Löfke, Christian","first_name":"Christian","last_name":"Löfke"},{"full_name":"Jansen, Leentje","last_name":"Jansen","first_name":"Leentje"},{"full_name":"Goeminne, Geert","last_name":"Goeminne","first_name":"Geert"},{"last_name":"Vanden Bossche","first_name":"Robin","full_name":"Vanden Bossche, Robin"},{"last_name":"Karimi","first_name":"Mansour","full_name":"Karimi, Mansour"},{"last_name":"De Rybel","first_name":"Bert","full_name":"De Rybel, Bert"},{"full_name":"Vanholme, Bartel","last_name":"Vanholme","first_name":"Bartel"},{"full_name":"Teichmann, Thomas","last_name":"Teichmann","first_name":"Thomas"},{"last_name":"Boerjan","first_name":"Wout","full_name":"Boerjan, Wout"},{"full_name":"Van Montagu, Marc C","first_name":"Marc","last_name":"Van Montagu"},{"full_name":"Gheysen, Godelieve","last_name":"Gheysen","first_name":"Godelieve"},{"full_name":"Muday, Gloria K","first_name":"Gloria","last_name":"Muday"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"}],"type":"journal_article","extern":1,"issue":"5","publist_id":"3595","abstract":[{"text":"\nGradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis.","lang":"eng"}],"page":"1554 - 1559","quality_controlled":0,"citation":{"chicago":"Grunewald, Wim, Ive De Smet, Daniel Lewis, Christian Löfke, Leentje Jansen, Geert Goeminne, Robin Vanden Bossche, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1121134109.","short":"W. Grunewald, I. De Smet, D. Lewis, C. Löfke, L. Jansen, G. Goeminne, R. Vanden Bossche, M. Karimi, B. De Rybel, B. Vanholme, T. Teichmann, W. Boerjan, M. Van Montagu, G. Gheysen, G. Muday, J. Friml, T. Beeckman, PNAS 109 (2012) 1554–1559.","mla":"Grunewald, Wim, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS, vol. 109, no. 5, National Academy of Sciences, 2012, pp. 1554–59, doi:10.1073/pnas.1121134109.","ieee":"W. Grunewald et al., “Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis,” PNAS, vol. 109, no. 5. National Academy of Sciences, pp. 1554–1559, 2012.","apa":"Grunewald, W., De Smet, I., Lewis, D., Löfke, C., Jansen, L., Goeminne, G., … Beeckman, T. (2012). Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1121134109","ista":"Grunewald W, De Smet I, Lewis D, Löfke C, Jansen L, Goeminne G, Vanden Bossche R, Karimi M, De Rybel B, Vanholme B, Teichmann T, Boerjan W, Van Montagu M, Gheysen G, Muday G, Friml J, Beeckman T. 2012. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 109(5), 1554–1559.","ama":"Grunewald W, De Smet I, Lewis D, et al. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 2012;109(5):1554-1559. doi:10.1073/pnas.1121134109"},"publication":"PNAS","doi":"10.1073/pnas.1121134109","date_published":"2012-01-31T00:00:00Z","month":"01","day":"31"},{"page":"119 - 122","quality_controlled":0,"citation":{"ista":"Barbez E, Kubeš M, Rolčík J, Béziat C, Pěnčík A, Wang B, Rosquete M, Zhu J, Dobrev P, Lee Y, Zašímalová E, Petrášek J, Geisler M, Friml J, Kleine Vehn J. 2012. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 485(7396), 119–122.","ieee":"E. Barbez et al., “A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants,” Nature, vol. 485, no. 7396. Nature Publishing Group, pp. 119–122, 2012.","apa":"Barbez, E., Kubeš, M., Rolčík, J., Béziat, C., Pěnčík, A., Wang, B., … Kleine Vehn, J. (2012). A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11001","ama":"Barbez E, Kubeš M, Rolčík J, et al. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 2012;485(7396):119-122. doi:10.1038/nature11001","chicago":"Barbez, Elke, Martin Kubeš, Jakub Rolčík, Chloe Béziat, Aleš Pěnčík, Bangjun Wang, Michel Rosquete, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11001.","mla":"Barbez, Elke, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature, vol. 485, no. 7396, Nature Publishing Group, 2012, pp. 119–22, doi:10.1038/nature11001.","short":"E. Barbez, M. Kubeš, J. Rolčík, C. Béziat, A. Pěnčík, B. Wang, M. Rosquete, J. Zhu, P. Dobrev, Y. Lee, E. Zašímalová, J. Petrášek, M. Geisler, J. Friml, J. Kleine Vehn, Nature 485 (2012) 119–122."},"publication":"Nature","date_published":"2012-05-03T00:00:00Z","doi":"10.1038/nature11001","day":"03","month":"05","publisher":"Nature Publishing Group","intvolume":" 485","title":"A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants","status":"public","publication_status":"published","_id":"3108","year":"2012","volume":485,"date_updated":"2021-01-12T07:41:07Z","date_created":"2018-12-11T12:01:26Z","author":[{"full_name":"Barbez, Elke","last_name":"Barbez","first_name":"Elke"},{"full_name":"Kubeš, Martin","last_name":"Kubeš","first_name":"Martin"},{"last_name":"Rolčík","first_name":"Jakub","full_name":"Rolčík, Jakub"},{"full_name":"Béziat, Chloe","first_name":"Chloe","last_name":"Béziat"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"last_name":"Wang","first_name":"Bangjun","full_name":"Wang, Bangjun"},{"last_name":"Rosquete","first_name":"Michel","full_name":"Rosquete, Michel Ruiz"},{"last_name":"Zhu","first_name":"Jinsheng","full_name":"Zhu, Jinsheng"},{"full_name":"Dobrev, Petre I","last_name":"Dobrev","first_name":"Petre"},{"full_name":"Lee, Yuree","last_name":"Lee","first_name":"Yuree"},{"first_name":"Eva","last_name":"Zašímalová","full_name":"Zašímalová, Eva"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"}],"type":"journal_article","extern":1,"issue":"7396","publist_id":"3591","abstract":[{"text":"The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-dependent regulation of plant growth by determining the cellular sensitivity to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling. PILS activity affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via intracellular accumulation and metabolism. Our findings reveal that the transport machinery to compartmentalize auxin within the cell is of an unexpected molecular complexity and demonstrate this compartmentalization to be functionally important for a number of developmental processes.","lang":"eng"}]},{"doi":"10.1371/journal.pbio.1001299","date_published":"2012-04-01T00:00:00Z","publication":"PLoS Biology","citation":{"mla":"Nagawa, Shingo, et al. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology, vol. 10, no. 4, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001299.","short":"S. Nagawa, T. Xu, D. Lin, P. Dhonukshe, X. Zhang, J. Friml, B. Scheres, Y. Fu, Z. Yang, PLoS Biology 10 (2012).","chicago":"Nagawa, Shingo, Tongda Xu, Deshu Lin, Pankaj Dhonukshe, Xingxing Zhang, Jiří Friml, Ben Scheres, Ying Fu, and Zhenbiao Yang. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001299.","ama":"Nagawa S, Xu T, Lin D, et al. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001299","ista":"Nagawa S, Xu T, Lin D, Dhonukshe P, Zhang X, Friml J, Scheres B, Fu Y, Yang Z. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 10(4).","ieee":"S. Nagawa et al., “ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012.","apa":"Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., … Yang, Z. (2012). ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001299"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":0,"month":"04","day":"01","author":[{"first_name":"Shingo","last_name":"Nagawa","full_name":"Nagawa, Shingo"},{"last_name":"Xu","first_name":"Tongda","full_name":"Xu, Tongda"},{"first_name":"Deshu","last_name":"Lin","full_name":"Lin, Deshu"},{"full_name":"Dhonukshe, Pankaj","first_name":"Pankaj","last_name":"Dhonukshe"},{"full_name":"Zhang, Xingxing","first_name":"Xingxing","last_name":"Zhang"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Jirí Friml"},{"full_name":"Scheres, Ben","first_name":"Ben","last_name":"Scheres"},{"last_name":"Fu","first_name":"Ying","full_name":"Fu, Ying"},{"first_name":"Zhenbiao","last_name":"Yang","full_name":"Yang, Zhenbiao"}],"date_updated":"2021-01-12T07:41:06Z","date_created":"2018-12-11T12:01:25Z","volume":10,"year":"2012","_id":"3106","title":"ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis","status":"public","publication_status":"published","publisher":"Public Library of Science","intvolume":" 10","abstract":[{"lang":"eng","text":"Cell polarization via asymmetrical distribution of structures or molecules is essential for diverse cellular functions and development of organisms, but how polarity is developmentally controlled has been poorly understood. In plants, the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the cellular efflux of the quintessential phytohormone auxin plays a central role in developmental patterning, morphogenesis, and differential growth. Recently we showed that auxin promotes cell interdigitation by activating the Rho family ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our findings suggest a link between the developmental auxin signal and polar PIN1 distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation of a design principle for cell polarization that is based on Rho GTPase-mediated inhibition of endocytosis."}],"issue":"4","publist_id":"3593","extern":1,"type":"journal_article"},{"status":"public","publication_status":"published","title":"Plant signaling: Deconstructing auxin sensing","publisher":"Nature Publishing Group","intvolume":" 8","_id":"3107","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:01:26Z","date_updated":"2021-01-12T07:41:06Z","volume":8,"oa_version":"None","author":[{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"type":"other_academic_publication","extern":"1","issue":"5","publist_id":"3592","quality_controlled":"1","page":"415 - 416","publication":"Nature Chemical Biology","citation":{"short":"S. Vanneste, J. Friml, Plant Signaling: Deconstructing Auxin Sensing, Nature Publishing Group, 2012.","mla":"Vanneste, Steffen, and Jiří Friml. “Plant Signaling: Deconstructing Auxin Sensing.” Nature Chemical Biology, vol. 8, no. 5, Nature Publishing Group, 2012, pp. 415–16, doi:10.1038/nchembio.943.","chicago":"Vanneste, Steffen, and Jiří Friml. Plant Signaling: Deconstructing Auxin Sensing. Nature Chemical Biology. Vol. 8. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.943.","ama":"Vanneste S, Friml J. Plant Signaling: Deconstructing Auxin Sensing. Vol 8. Nature Publishing Group; 2012:415-416. doi:10.1038/nchembio.943","apa":"Vanneste, S., & Friml, J. (2012). Plant signaling: Deconstructing auxin sensing. Nature Chemical Biology (Vol. 8, pp. 415–416). Nature Publishing Group. https://doi.org/10.1038/nchembio.943","ieee":"S. Vanneste and J. Friml, Plant signaling: Deconstructing auxin sensing, vol. 8, no. 5. Nature Publishing Group, 2012, pp. 415–416.","ista":"Vanneste S, Friml J. 2012. Plant signaling: Deconstructing auxin sensing, Nature Publishing Group,p."},"language":[{"iso":"eng"}],"doi":"10.1038/nchembio.943","date_published":"2012-05-01T00:00:00Z","day":"01","month":"05"},{"file":[{"creator":"system","file_size":4939370,"content_type":"application/pdf","file_name":"IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf","access_level":"open_access","date_created":"2018-12-12T10:11:23Z","date_updated":"2020-07-14T12:46:00Z","checksum":"babda64c24cf90a4d05ae86d712bed08","file_id":"4877","relation":"main_file"}],"oa_version":"Submitted Version","pubrep_id":"600","ddc":["000"],"title":"Controlling liquids using meshes","status":"public","_id":"3119","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.\r\n","lang":"eng"}],"type":"conference","date_published":"2012-07-29T00:00:00Z","page":"255 - 264","publication":"Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation","citation":{"ama":"Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. ACM; 2012:255-264.","ista":"Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264.","ieee":"K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using meshes,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Aire-la-Ville, Switzerland, 2012, pp. 255–264.","apa":"Raveendran, K., Thuerey, N., Wojtan, C., & Turk, G. (2012). Controlling liquids using meshes. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation (pp. 255–264). Aire-la-Ville, Switzerland: ACM.","mla":"Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–64.","short":"K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264.","chicago":"Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling Liquids Using Meshes.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 255–64. ACM, 2012."},"day":"29","has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T12:01:30Z","date_updated":"2023-02-23T11:13:07Z","author":[{"full_name":"Raveendran, Karthik","first_name":"Karthik","last_name":"Raveendran"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"},{"full_name":"Turk, Greg","first_name":"Greg","last_name":"Turk"}],"related_material":{"link":[{"relation":"table_of_contents","url":"http://dl.acm.org/citation.cfm?id=2422393"}]},"publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"acknowledgement":"This work was partially funded by NSF grants CCF-0811485 and IIS-1130934. We would like to thank Scanline VFX for additional funding. We would like to thank Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback.","year":"2012","file_date_updated":"2020-07-14T12:46:00Z","publist_id":"3580","language":[{"iso":"eng"}],"conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","end_date":"2012-07-31","start_date":"2012-07-29","location":"Aire-la-Ville, Switzerland"},"quality_controlled":"1","oa":1,"month":"07"},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"ista":"Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53.","apa":"Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549","ieee":"M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012.","ama":"Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549","chicago":"Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549.","mla":"Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549.","short":"M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012)."},"date_published":"2012-07-01T00:00:00Z","alternative_title":["SIGGRAPH"],"type":"journal_article","abstract":[{"lang":"eng","text":"We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process."}],"issue":"4","status":"public","ddc":["000"],"title":"Tracking surfaces with evolving topology","intvolume":" 31","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3118","oa_version":"Submitted Version","file":[{"file_name":"IST-2016-602-v1+1_topoReg.pdf","access_level":"open_access","creator":"system","file_size":44538518,"content_type":"application/pdf","file_id":"5359","relation":"main_file","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:18:37Z","checksum":"1e219c5bf4e5552c1290c62eefa5cd60"}],"pubrep_id":"602","month":"07","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2185520.2185549","article_number":"53","file_date_updated":"2020-07-14T12:46:00Z","publist_id":"3581","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","acknowledgement":"This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. ","year":"2012","date_created":"2018-12-11T12:01:29Z","date_updated":"2022-05-24T08:21:11Z","volume":31,"author":[{"last_name":"Bojsen-Hansen","first_name":"Morten","orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","full_name":"Bojsen-Hansen, Morten"},{"last_name":"Li","first_name":"Hao","full_name":"Li, Hao"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}]},{"month":"08","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2012-08-01T00:00:00Z","doi":"10.1111/j.1365-294X.2012.05643.x","page":"3640 - 3643","quality_controlled":"1","citation":{"mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","apa":"Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x"},"publication":"Molecular Ecology","publist_id":"3577","issue":"15","abstract":[{"text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ","lang":"eng"}],"type":"journal_article","oa_version":"None","volume":21,"date_created":"2018-12-11T12:01:31Z","date_updated":"2021-01-12T07:41:13Z","author":[{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"last_name":"Barrett","first_name":"Spencer","full_name":"Barrett, Spencer"}],"publisher":"Wiley-Blackwell","intvolume":" 21","department":[{"_id":"NiBa"}],"status":"public","publication_status":"published","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","year":"2012","_id":"3122","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"day":"01","scopus_import":1,"date_published":"2012-09-01T00:00:00Z","page":"1195 - 1197","citation":{"mla":"Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:10.1038/nn.3162.","short":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197.","chicago":"Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3162.","ama":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 2012;15(9):1195-1197. doi:10.1038/nn.3162","ista":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197.","ieee":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” Nature Neuroscience, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012.","apa":"Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., & Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3162"},"publication":"Nature Neuroscience","issue":"9","abstract":[{"lang":"eng","text":"Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type."}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 15","status":"public","title":"Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA","_id":"3121","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"09","language":[{"iso":"eng"}],"doi":"10.1038/nn.3162","quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/","open_access":"1"}],"oa":1,"external_id":{"pmid":["22842148"]},"publist_id":"3578","volume":15,"date_created":"2018-12-11T12:01:30Z","date_updated":"2021-01-12T07:41:12Z","author":[{"last_name":"Williams","first_name":"Courtney","full_name":"Williams, Courtney"},{"full_name":"Chen, Wenyan","last_name":"Chen","first_name":"Wenyan"},{"first_name":"Chia","last_name":"Lee","full_name":"Lee, Chia"},{"first_name":"Daniel","last_name":"Yaeger","full_name":"Yaeger, Daniel"},{"first_name":"Nicholas","last_name":"Vyleta","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Nicholas"},{"last_name":"Smith","first_name":"Stephen","full_name":"Smith, Stephen"}],"department":[{"_id":"PeJo"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"acknowledgement":"The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. ","year":"2012"},{"day":"01","scopus_import":1,"date_published":"2012-07-01T00:00:00Z","citation":{"ama":"Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 2012;148(4):1171-1194. doi:10.1112/S0010437X11007226","ista":"Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194.","apa":"Brown, G., Kerber, M., & Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X11007226","ieee":"G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” Compositio Mathematica, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012.","mla":"Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:10.1112/S0010437X11007226.","short":"G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194.","chicago":"Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica. Cambridge University Press, 2012. https://doi.org/10.1112/S0010437X11007226."},"publication":"Compositio Mathematica","page":"1171 - 1194","issue":"4","abstract":[{"lang":"eng","text":"We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica."}],"type":"journal_article","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3120","intvolume":" 148","status":"public","title":"Fano 3 folds in codimension 4 Tom and Jerry Part I","month":"07","doi":"10.1112/S0010437X11007226","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1009.4313"}],"quality_controlled":"1","publist_id":"3579","author":[{"full_name":"Brown, Gavin","last_name":"Brown","first_name":"Gavin"},{"orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","first_name":"Michael","full_name":"Kerber, Michael"},{"first_name":"Miles","last_name":"Reid","full_name":"Reid, Miles"}],"volume":148,"date_created":"2018-12-11T12:01:30Z","date_updated":"2021-01-12T07:41:12Z","acknowledgement":"This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.","year":"2012","department":[{"_id":"HeEd"}],"publisher":"Cambridge University Press","publication_status":"published"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms."}],"issue":"15","publist_id":"3582","year":"2012","_id":"3117","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Minimizing a sum of submodular functions","department":[{"_id":"VlKo"}],"intvolume":" 160","publisher":"Elsevier","author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T12:01:29Z","date_updated":"2021-01-12T07:41:11Z","volume":160,"oa_version":"Preprint","scopus_import":1,"month":"10","day":"01","publication":"Discrete Applied Mathematics","oa":1,"citation":{"mla":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258.","chicago":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025.","ama":"Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025","ista":"Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258.","ieee":"V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.","apa":"Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025"},"main_file_link":[{"url":"http://arxiv.org/abs/1006.1990","open_access":"1"}],"quality_controlled":"1","page":"2246 - 2258","doi":"10.1016/j.dam.2012.05.025","date_published":"2012-10-01T00:00:00Z","language":[{"iso":"eng"}]},{"month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","doi":"10.1371/journal.pgen.1002740","language":[{"iso":"eng"}],"article_number":"e1002740","ec_funded":1,"publist_id":"3566","file_date_updated":"2020-07-14T12:46:01Z","acknowledgement":"The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions.","year":"2012","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"Weissman, Daniel","first_name":"Daniel","last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"volume":8,"date_updated":"2021-01-12T07:41:17Z","date_created":"2018-12-11T12:01:34Z","scopus_import":1,"has_accepted_license":"1","day":"07","citation":{"short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740.","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740.","ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740","apa":"Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740","ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740."},"publication":"PLoS Genetics","date_published":"2012-06-07T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3131","intvolume":" 8","title":"Limits to the rate of adaptive substitution in sexual populations","ddc":["570","576"],"status":"public","pubrep_id":"114","oa_version":"Published Version","file":[{"file_id":"4659","relation":"main_file","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:08:00Z","checksum":"729a4becda7d786c4c3db8f9a1f77953","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1284801}]},{"scopus_import":1,"day":"28","has_accepted_license":"1","publication":"PLoS Genetics","citation":{"short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803.","chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803.","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002803","apa":"Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803","ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803."},"date_published":"2012-06-28T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes."}],"issue":"6","title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","ddc":["576"],"status":"public","intvolume":" 8","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3130","oa_version":"Published Version","file":[{"file_id":"4973","relation":"main_file","date_created":"2018-12-12T10:12:52Z","date_updated":"2020-07-14T12:46:01Z","checksum":"f8506fb579eda6fc5613ba9bf421b86a","file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","access_level":"open_access","creator":"system","file_size":2674138,"content_type":"application/pdf"}],"pubrep_id":"386","month":"06","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1002803","article_number":"e1002803","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"3567","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"year":"2012","acknowledgement":"We thank Alex Boehm for discussions and comments.","date_updated":"2021-01-12T07:41:16Z","date_created":"2018-12-11T12:01:34Z","volume":8,"author":[{"full_name":"Bergmiller, Tobias","first_name":"Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"},{"full_name":"Silander, Olin","last_name":"Silander","first_name":"Olin"}]},{"oa_version":"None","volume":"7358 ","date_updated":"2021-01-12T07:41:18Z","date_created":"2018-12-11T12:01:36Z","author":[{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Mateescu","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","full_name":"Mateescu, Maria"},{"id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali","full_name":"Sezgin, Ali"}],"publisher":"Springer","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"status":"public","title":"Delayed continuous time Markov chains for genetic regulatory circuits","publication_status":"published","_id":"3136","acknowledgement":"This work was supported by the ERC Advanced Investigator grant on Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3561","ec_funded":1,"abstract":[{"text":"Continuous-time Markov chains (CTMC) with their rich theory and efficient simulation algorithms have been successfully used in modeling stochastic processes in diverse areas such as computer science, physics, and biology. However, systems that comprise non-instantaneous events cannot be accurately and efficiently modeled with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that allows for the specification of a lower bound on the time interval between an event's initiation and its completion, and we propose an algorithm for the computation of their behavior. Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times. Furthermore, from the nature of delayed CTMCs, we obtain a parallelized version of our algorithm. We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster. We compare performance and accuracy of our results with results obtained by using pure CTMCs. © 2012 Springer-Verlag.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-31424-7_24","date_published":"2012-07-01T00:00:00Z","conference":{"end_date":"2012-07-13","location":"Berkeley, CA, USA","start_date":"2012-07-07","name":"CAV: Computer Aided Verification"},"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"page":"294 - 309","quality_controlled":"1","citation":{"ama":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309. doi:10.1007/978-3-642-31424-7_24","ieee":"C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed continuous time Markov chains for genetic regulatory circuits,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.","apa":"Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., & Sezgin, A. (2012). Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358, pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_24","ista":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification, LNCS, vol. 7358, 294–309.","short":"C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309.","mla":"Guet, Calin C., et al. Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits. Vol. 7358, Springer, 2012, pp. 294–309, doi:10.1007/978-3-642-31424-7_24.","chicago":"Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,” 7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24."},"month":"07","day":"01","scopus_import":1},{"ec_funded":1,"publist_id":"3562","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"Tomas Brazdil, Antonin Kucera, and Petr Novotny are supported by the Czech Science Foundation, grant No. P202/10/1469. Krishnendu Chatterjee is supported by the FWF (Austrian Science Fund) NFN Grant No S11407-N23 (RiSE) and ERC Start grant (279307: Graph Games).","year":"2012","volume":7358,"date_created":"2018-12-11T12:01:35Z","date_updated":"2021-01-12T07:41:18Z","author":[{"full_name":"Brázdil, Brázdil","last_name":"Brázdil","first_name":"Brázdil"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"}],"month":"07","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.0796"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-31424-7_8","conference":{"name":"CAV: Computer Aided Verification","location":"Berkeley, CA, USA","start_date":"2012-07-07","end_date":"2012-07-13"},"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. ","lang":"eng"}],"intvolume":" 7358","title":"Efficient controller synthesis for consumption games with multiple resource types","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3135","oa_version":"Preprint","scopus_import":1,"day":"01","page":"23 - 38","citation":{"chicago":"Brázdil, Brázdil, Krishnendu Chatterjee, Antonín Kučera, and Petr Novotný. “Efficient Controller Synthesis for Consumption Games with Multiple Resource Types,” 7358:23–38. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_8.","short":"B. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, in:, Springer, 2012, pp. 23–38.","mla":"Brázdil, Brázdil, et al. Efficient Controller Synthesis for Consumption Games with Multiple Resource Types. Vol. 7358, Springer, 2012, pp. 23–38, doi:10.1007/978-3-642-31424-7_8.","ieee":"B. Brázdil, K. Chatterjee, A. Kučera, and P. Novotný, “Efficient controller synthesis for consumption games with multiple resource types,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 23–38.","apa":"Brázdil, B., Chatterjee, K., Kučera, A., & Novotný, P. (2012). Efficient controller synthesis for consumption games with multiple resource types (Vol. 7358, pp. 23–38). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_8","ista":"Brázdil B, Chatterjee K, Kučera A, Novotný P. 2012. Efficient controller synthesis for consumption games with multiple resource types. CAV: Computer Aided Verification, LNCS, vol. 7358, 23–38.","ama":"Brázdil B, Chatterjee K, Kučera A, Novotný P. Efficient controller synthesis for consumption games with multiple resource types. In: Vol 7358. Springer; 2012:23-38. doi:10.1007/978-3-642-31424-7_8"},"date_published":"2012-07-01T00:00:00Z"},{"citation":{"short":"H. Edelsbrunner, M. Kerber, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–258.","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–58, doi:10.1145/2261250.2261287.","chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 249–58. ACM, 2012. https://doi.org/10.1145/2261250.2261287.","ama":"Edelsbrunner H, Kerber M. Alexander duality for functions: The persistent behavior of land and water and shore. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:249-258. doi:10.1145/2261250.2261287","apa":"Edelsbrunner, H., & Kerber, M. (2012). Alexander duality for functions: The persistent behavior of land and water and shore. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 249–258). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261287","ieee":"H. Edelsbrunner and M. Kerber, “Alexander duality for functions: The persistent behavior of land and water and shore,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 249–258.","ista":"Edelsbrunner H, Kerber M. 2012. Alexander duality for functions: The persistent behavior of land and water and shore. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 249–258."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.5052"}],"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","page":"249 - 258","quality_controlled":"1","date_published":"2012-06-20T00:00:00Z","doi":"10.1145/2261250.2261287","conference":{"name":"SCG: Symposium on Computational Geometry","end_date":"2012-06-20","start_date":"2012-06-17","location":"Chapel Hill, NC, USA"},"language":[{"iso":"eng"}],"scopus_import":1,"month":"06","day":"20","_id":"3133","acknowledgement":"his research is partially supported by the National Science Foundation (NSF) under grant DBI-0820624, the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.\r\nThe authors thank an anonymous referee for suggesting the simplified proof of the Contravariant PE Theorem given in this paper. They also thank Frederick Cohen, Yuriy Mileyko and Amit Patel for helpful discussions.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","department":[{"_id":"HeEd"}],"publisher":"ACM","title":"Alexander duality for functions: The persistent behavior of land and water and shore","status":"public","publication_status":"published","author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael"}],"oa_version":"Preprint","date_updated":"2021-01-12T07:41:17Z","date_created":"2018-12-11T12:01:35Z","type":"conference","publist_id":"3564","abstract":[{"text":"This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. ","lang":"eng"}]},{"type":"conference","publist_id":"3563","abstract":[{"text":"It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. ","lang":"eng"}],"department":[{"_id":"HeEd"}],"publisher":"ACM","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","status":"public","publication_status":"published","_id":"3134","year":"2012","acknowledgement":"This research is partially supported by the National Science Foun- dation (NSF) under grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_created":"2018-12-11T12:01:35Z","date_updated":"2023-02-23T10:59:27Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"2815"}]},"author":[{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"first_name":"Brittany","last_name":"Fasy","full_name":"Fasy, Brittany"},{"last_name":"Rote","first_name":"Günter","full_name":"Rote, Günter"}],"scopus_import":1,"day":"20","month":"06","page":"91 - 100","quality_controlled":"1","citation":{"ama":"Edelsbrunner H, Fasy B, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:91-100. doi:10.1145/2261250.2261265","ista":"Edelsbrunner H, Fasy B, Rote G. 2012. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 91–100.","apa":"Edelsbrunner, H., Fasy, B., & Rote, G. (2012). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 91–100). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261265","ieee":"H. Edelsbrunner, B. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 91–100.","mla":"Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100, doi:10.1145/2261250.2261265.","short":"H. Edelsbrunner, B. Fasy, G. Rote, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100.","chicago":"Edelsbrunner, Herbert, Brittany Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 91–100. ACM, 2012. https://doi.org/10.1145/2261250.2261265."},"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","language":[{"iso":"eng"}],"doi":"10.1145/2261250.2261265","date_published":"2012-06-20T00:00:00Z","conference":{"name":"SCG: Symposium on Computational Geometry","end_date":"2012-06-20","start_date":"2012-06-17","location":"Chapel Hill, NC, USA"}},{"month":"08","day":"01","scopus_import":1,"date_published":"2012-08-01T00:00:00Z","doi":"10.1007/s00114-012-0943-z","language":[{"iso":"eng"}],"citation":{"short":"M. Konrad, T. Pamminger, S. Foitzik, Naturwissenschaften 99 (2012) 627–636.","mla":"Konrad, Matthias, et al. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften, vol. 99, no. 8, Springer, 2012, pp. 627–36, doi:10.1007/s00114-012-0943-z.","chicago":"Konrad, Matthias, Tobias Pamminger, and Susanne Foitzik. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften. Springer, 2012. https://doi.org/10.1007/s00114-012-0943-z.","ama":"Konrad M, Pamminger T, Foitzik S. Two pathways ensuring social harmony. Naturwissenschaften. 2012;99(8):627-636. doi:10.1007/s00114-012-0943-z","apa":"Konrad, M., Pamminger, T., & Foitzik, S. (2012). Two pathways ensuring social harmony. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-012-0943-z","ieee":"M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,” Naturwissenschaften, vol. 99, no. 8. Springer, pp. 627–636, 2012.","ista":"Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony. Naturwissenschaften. 99(8), 627–636."},"publication":"Naturwissenschaften","page":"627 - 636","quality_controlled":"1","publist_id":"3565","issue":"8","abstract":[{"text":"Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony.","lang":"eng"}],"type":"journal_article","author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","first_name":"Matthias"},{"last_name":"Pamminger","first_name":"Tobias","full_name":"Pamminger, Tobias"},{"first_name":"Susanne","last_name":"Foitzik","full_name":"Foitzik, Susanne"}],"oa_version":"None","volume":99,"date_created":"2018-12-11T12:01:34Z","date_updated":"2021-01-12T07:41:17Z","year":"2012","_id":"3132","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We like to thank the editor and three anonymous reviewers for their time and constructive criticism and Inon Scharf, Volker Witte and Andreas Modlmeier for helpful comments on earlier versions of the manuscript. The first and second authors appear in alphabetical order and contributed equally to this paper.","department":[{"_id":"SyCr"}],"intvolume":" 99","publisher":"Springer","publication_status":"published","status":"public","title":"Two pathways ensuring social harmony"},{"month":"05","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0036044","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publist_id":"3526","file_date_updated":"2020-07-14T12:46:01Z","article_number":"e36044","volume":7,"date_updated":"2021-01-12T07:41:29Z","date_created":"2018-12-11T12:01:45Z","author":[{"full_name":"Vyleta, Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87","first_name":"Meghan","last_name":"Vyleta"},{"full_name":"Wong, John","last_name":"Wong","first_name":"John"},{"first_name":"Bruce","last_name":"Magun","full_name":"Magun, Bruce"}],"department":[{"_id":"SyCr"}],"publisher":"Public Library of Science","publication_status":"published","acknowledgement":"Supported by National Institutes of Health grants GM071338 (ML) and AI059355 (BM).\r\nWe acknowledge the expertise of Dr. Martina Ralle in Department of Biochemistry and Molecular Biology at OHSU for measurements of potassium using inductively coupled plasma mass spectrometry.","year":"2012","has_accepted_license":"1","day":"14","scopus_import":1,"date_published":"2012-05-14T00:00:00Z","citation":{"ieee":"M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome,” PLoS One, vol. 7, no. 5. Public Library of Science, 2012.","apa":"Vyleta, M., Wong, J., & Magun, B. (2012). Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036044","ista":"Vyleta M, Wong J, Magun B. 2012. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 7(5), e36044.","ama":"Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 2012;7(5). doi:10.1371/journal.pone.0036044","chicago":"Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036044.","short":"M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).","mla":"Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One, vol. 7, no. 5, e36044, Public Library of Science, 2012, doi:10.1371/journal.pone.0036044."},"publication":"PLoS One","issue":"5","abstract":[{"lang":"eng","text":"Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by inducing efflux of cellular potassium. Loss of cellular potassium is known to potently suppress protein synthesis, leading us to test whether the inhibition of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome. Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide, puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin, ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of IL-1ß from cells in response to these agents was detected by immunoblotting and ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition of translation by each of the tested translation inhibitors led to processing of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger efflux of intracellular potassium, the addition of high extracellular potassium suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA, which are known to activate the NLRP3 inflammasome, also substantially inhibited protein translation, supporting a close association between inhibition of translation and inflammasome activation. These data demonstrate that translational inhibition itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent inflammatory signaling and that other physical, chemical, or pathogen-associated agents that impair translation may lead to IL-1ß-dependent inflammation through activation of the NLRP3 inflammasome. For agents that inhibit translation through decreased cellular potassium, the application of high extracellular potassium restores protein translation and suppresses activation of the NLRP inflammasome. For agents that inhibit translation through mechanisms that do not involve loss of potassium, high extracellular potassium suppresses IL-1ß processing through a mechanism that remains undefined."}],"type":"journal_article","file":[{"file_id":"5082","relation":"main_file","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:14:30Z","checksum":"30cef37e27eaa467f6571b3640282010","file_name":"IST-2012-97-v1+1_journal.pone.0036044.pdf","access_level":"open_access","creator":"system","file_size":2984012,"content_type":"application/pdf"}],"oa_version":"Published Version","pubrep_id":"97","intvolume":" 7","title":"Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome","status":"public","ddc":["610"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3161"},{"oa":1,"quality_controlled":"1","doi":"10.1007/978-3-642-29860-8_12","conference":{"end_date":"2011-09-30","location":"San Francisco, CA, United States","start_date":"2011-09-27","name":"RV: Runtime Verification"},"language":[{"iso":"eng"}],"month":"01","year":"2012","publisher":"Springer","department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Asarin, Eugene","first_name":"Eugene","last_name":"Asarin"},{"last_name":"Donzé","first_name":"Alexandre","full_name":"Donzé, Alexandre"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan"}],"volume":7186,"date_updated":"2021-01-12T07:41:29Z","date_created":"2018-12-11T12:01:45Z","publist_id":"3525","file_date_updated":"2020-07-14T12:46:01Z","citation":{"ieee":"E. Asarin, A. Donzé, O. Maler, and D. Nickovic, “Parametric identification of temporal properties,” presented at the RV: Runtime Verification, San Francisco, CA, United States, 2012, vol. 7186, pp. 147–160.","apa":"Asarin, E., Donzé, A., Maler, O., & Nickovic, D. (2012). Parametric identification of temporal properties (Vol. 7186, pp. 147–160). Presented at the RV: Runtime Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-642-29860-8_12","ista":"Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.","ama":"Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal properties. In: Vol 7186. Springer; 2012:147-160. doi:10.1007/978-3-642-29860-8_12","chicago":"Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric Identification of Temporal Properties,” 7186:147–60. Springer, 2012. https://doi.org/10.1007/978-3-642-29860-8_12.","short":"E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 147–160.","mla":"Asarin, Eugene, et al. Parametric Identification of Temporal Properties. Vol. 7186, Springer, 2012, pp. 147–60, doi:10.1007/978-3-642-29860-8_12."},"page":"147 - 160","date_published":"2012-01-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","_id":"3162","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7186","status":"public","ddc":["000"],"title":"Parametric identification of temporal properties","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":374726,"creator":"dernst","access_level":"open_access","file_name":"2012_RV_Asarin.pdf","checksum":"ba4a75287008fc64b8fbf78a7476ec32","date_updated":"2020-07-14T12:46:01Z","date_created":"2020-05-15T12:50:15Z","relation":"main_file","file_id":"7862"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Given a dense-time real-valued signal and a parameterized temporal logic formula with both magnitude and timing parameters, we compute the subset of the parameter space that renders the formula satisfied by the trace. We provide two preliminary implementations, one which follows the exact semantics and attempts to compute the validity domain by quantifier elimination in linear arithmetics and one which conducts adaptive search in the parameter space."}]},{"scopus_import":1,"day":"01","month":"06","page":"2055 - 2058","quality_controlled":"1","citation":{"ama":"Pantazis P, Bollenbach MT. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 2012;11(11):2055-2058. doi:10.4161/cc.20118","ista":"Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058.","ieee":"P. Pantazis and M. T. Bollenbach, “Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo,” Cell Cycle, vol. 11, no. 11. Taylor and Francis, pp. 2055–2058, 2012.","apa":"Pantazis, P., & Bollenbach, M. T. (2012). Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. Taylor and Francis. https://doi.org/10.4161/cc.20118","mla":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle, vol. 11, no. 11, Taylor and Francis, 2012, pp. 2055–58, doi:10.4161/cc.20118.","short":"P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058.","chicago":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle. Taylor and Francis, 2012. https://doi.org/10.4161/cc.20118."},"publication":"Cell Cycle","language":[{"iso":"eng"}],"date_published":"2012-06-01T00:00:00Z","doi":"10.4161/cc.20118","type":"journal_article","publist_id":"3531","issue":"11","abstract":[{"lang":"eng","text":"There is a long-running controversy about how early cell fate decisions are made in the developing mammalian embryo. 1,2 In particular, it is controversial when the first events that can predict the establishment of the pluripotent and extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur. It has long been proposed that the position and polarity of cells at the 16- to 32-cell stage embryo influence their decision to either give rise to the pluripotent cell lineage that eventually contributes to the inner cell mass (ICM), comprising the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm (TE) surrounding the blastocoel. The positioning of cells in the embryo at this developmental stage could largely be the result of random events, making this a stochastic model of cell lineage allocation. Contrary to such a stochastic model, some studies have detected putative differences in the lineage potential of individual blastomeres before compaction, indicating that the first cell fate decisions may occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a key transcription factor (TF) controlling pre-implantation development in the mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications of such molecular heterogeneities in early development and offer potential avenues toward a mechanistic understanding of these observations, contributing to the resolution of the controversy of developmental cell lineage allocation."}],"intvolume":" 11","department":[{"_id":"ToBo"}],"publisher":"Taylor and Francis","publication_status":"published","title":"Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo","status":"public","year":"2012","_id":"3160","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":11,"date_created":"2018-12-11T12:01:44Z","date_updated":"2021-01-12T07:41:28Z","author":[{"full_name":"Pantazis, Periklis","last_name":"Pantazis","first_name":"Periklis"},{"full_name":"Bollenbach, Tobias","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3164","year":"2012","title":"Guest editorial: Special issue on structured prediction and inference","publication_status":"published","status":"public","intvolume":" 99","department":[{"_id":"ChLa"}],"publisher":"Springer","author":[{"full_name":"Blaschko, Matthew","first_name":"Matthew","last_name":"Blaschko"},{"last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"date_updated":"2021-01-12T07:41:30Z","date_created":"2018-12-11T12:01:46Z","oa_version":"None","volume":99,"type":"journal_article","abstract":[{"text":"Overview of the Special Issue on structured prediction and inference.","lang":"eng"}],"issue":"3","publist_id":"3521","publication":"International Journal of Computer Vision","citation":{"ama":"Blaschko M, Lampert C. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 2012;99(3):257-258. doi:10.1007/s11263-012-0530-y","ieee":"M. Blaschko and C. Lampert, “Guest editorial: Special issue on structured prediction and inference,” International Journal of Computer Vision, vol. 99, no. 3. Springer, pp. 257–258, 2012.","apa":"Blaschko, M., & Lampert, C. (2012). Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. Springer. https://doi.org/10.1007/s11263-012-0530-y","ista":"Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 99(3), 257–258.","short":"M. Blaschko, C. Lampert, International Journal of Computer Vision 99 (2012) 257–258.","mla":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision, vol. 99, no. 3, Springer, 2012, pp. 257–58, doi:10.1007/s11263-012-0530-y.","chicago":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision. Springer, 2012. https://doi.org/10.1007/s11263-012-0530-y."},"quality_controlled":"1","page":"257 - 258","date_published":"2012-09-01T00:00:00Z","doi":"10.1007/s11263-012-0530-y","language":[{"iso":"eng"}],"scopus_import":1,"month":"09","day":"01"},{"doi":"10.1186/1745-6150-7-6","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"02","author":[{"full_name":"Vladar, Harold","last_name":"Vladar","first_name":"Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87"}],"volume":7,"date_created":"2018-12-11T12:01:46Z","date_updated":"2021-01-12T07:41:31Z","year":"2012","acknowledgement":"The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ","department":[{"_id":"NiBa"}],"publisher":"BioMed Central","publication_status":"published","ec_funded":1,"publist_id":"3518","file_date_updated":"2020-07-14T12:46:02Z","article_number":"6","date_published":"2012-02-10T00:00:00Z","citation":{"mla":"de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.","short":"H. de Vladar, Biology Direct 7 (2012).","chicago":"Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.","ama":"de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-6","ista":"de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6.","ieee":"H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012.","apa":"de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6"},"publication":"Biology Direct","has_accepted_license":"1","day":"10","pubrep_id":"99","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5166","date_created":"2018-12-12T10:15:44Z","date_updated":"2020-07-14T12:46:02Z","checksum":"e511e401e239ef608a7fd79b21a06d78","file_name":"IST-2012-99-v1+1_1745-6150-7-6.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4099536,"creator":"system"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3166","intvolume":" 7","status":"public","ddc":["570","576"],"title":"Amino acid fermentation at the origin of the genetic code","abstract":[{"lang":"eng","text":"There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)"}],"type":"journal_article"},{"doi":"10.1126/science.336.6077.32","date_published":"2012-04-06T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"pmid":["22491839"]},"citation":{"mla":"Weber, Michele. “NextGen Speaks 13 .” Science, vol. 336, no. 6077, American Association for the Advancement of Science, 2012, pp. 32–34, doi:10.1126/science.336.6077.32.","short":"M. Weber, Science 336 (2012) 32–34.","chicago":"Weber, Michele. “NextGen Speaks 13 .” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.336.6077.32.","ama":"Weber M. NextGen speaks 13 . Science. 2012;336(6077):32-34. doi:10.1126/science.336.6077.32","ista":"Weber M. 2012. NextGen speaks 13 . Science. 336(6077), 32–34.","apa":"Weber, M. (2012). NextGen speaks 13 . Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.336.6077.32","ieee":"M. Weber, “NextGen speaks 13 ,” Science, vol. 336, no. 6077. American Association for the Advancement of Science, pp. 32–34, 2012."},"publication":"Science","page":"32-34","article_type":"letter_note","day":"06","month":"04","popular_science":"1","author":[{"full_name":"Weber, Michele","last_name":"Weber","first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","volume":336,"date_updated":"2021-01-12T07:41:32Z","date_created":"2018-12-11T12:01:47Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3167","year":"2012","intvolume":" 336","publisher":"American Association for the Advancement of Science","department":[{"_id":"MiSi"}],"title":"NextGen speaks 13 ","status":"public","publication_status":"published","issue":"6077","publist_id":"3516","type":"journal_article"},{"day":"01","month":"11","page":"116 - 135","quality_controlled":0,"citation":{"chicago":"Pietrzak, Krzysztof Z, and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology. Springer, 2012. https://doi.org/10.1007/s00145-010-9090-x.","short":"K.Z. Pietrzak, D. Wikström, Journal of Cryptology 25 (2012) 116–135.","mla":"Pietrzak, Krzysztof Z., and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology, vol. 25, no. 1, Springer, 2012, pp. 116–35, doi:10.1007/s00145-010-9090-x.","ieee":"K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound protocols revisited,” Journal of Cryptology, vol. 25, no. 1. Springer, pp. 116–135, 2012.","apa":"Pietrzak, K. Z., & Wikström, D. (2012). Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-010-9090-x","ista":"Pietrzak KZ, Wikström D. 2012. Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. 25(1), 116–135.","ama":"Pietrzak KZ, Wikström D. Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. 2012;25(1):116-135. doi:10.1007/s00145-010-9090-x"},"publication":"Journal of Cryptology","doi":"10.1007/s00145-010-9090-x","date_published":"2012-11-01T00:00:00Z","type":"journal_article","extern":1,"publist_id":"3439","issue":"1","abstract":[{"lang":"eng","text":"We prove a negative result concerning error reduction by parallel repetition for computationally sound protocols, e.g., interactive arguments. Our main result is a complete and computationally sound eight round interactive argument for which k-fold parallel repetition does not reduce the error below a constant for any polynomial k. The starting point for our construction is the work of Bellare, Impagliazzo and Naor (FOCS'97). For any fixed k, they construct a four round protocol for which k-fold parallel repetition does not lower the soundness error. The communication complexity of this protocol is linear in k. By using universal arguments due to Barak and Goldreich (CCC 2002), we turn this protocol into an eight-round protocol whose complexity is basically independent of k. "}],"intvolume":" 25","publisher":"Springer","status":"public","title":"Parallel repetition of computationally sound protocols revisited","publication_status":"published","_id":"3241","year":"2012","volume":25,"date_updated":"2021-01-12T07:42:03Z","date_created":"2018-12-11T12:02:12Z","author":[{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak"},{"first_name":"Douglas","last_name":"Wikström","full_name":"Wikström, Douglas"}]},{"month":"01","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1004.2697","open_access":"1"}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1007/978-3-642-27940-9_11","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2012-01-22","location":"Philadelphia, PA, USA","end_date":"2012-01-24"},"language":[{"iso":"eng"}],"publist_id":"3405","ec_funded":1,"year":"2012","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 (Modern Graph Algorithmic Techniques in Formal Verification), FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nThe authors would like to thank Avik Chaudhuri for his invaluable help and feedback.","publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Raman","first_name":"Vishwanath","full_name":"Raman, Vishwanath"}],"volume":7148,"date_created":"2018-12-11T12:02:16Z","date_updated":"2021-01-12T07:42:08Z","scopus_import":1,"day":"20","citation":{"ama":"Chatterjee K, Raman V. Synthesizing protocols for digital contract signing. In: Vol 7148. Springer; 2012:152-168. doi:10.1007/978-3-642-27940-9_11","apa":"Chatterjee, K., & Raman, V. (2012). Synthesizing protocols for digital contract signing (Vol. 7148, pp. 152–168). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_11","ieee":"K. Chatterjee and V. Raman, “Synthesizing protocols for digital contract signing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 152–168.","ista":"Chatterjee K, Raman V. 2012. Synthesizing protocols for digital contract signing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 152–168.","short":"K. Chatterjee, V. Raman, in:, Springer, 2012, pp. 152–168.","mla":"Chatterjee, Krishnendu, and Vishwanath Raman. Synthesizing Protocols for Digital Contract Signing. Vol. 7148, Springer, 2012, pp. 152–68, doi:10.1007/978-3-642-27940-9_11.","chicago":"Chatterjee, Krishnendu, and Vishwanath Raman. “Synthesizing Protocols for Digital Contract Signing,” 7148:152–68. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_11."},"page":"152 - 168","date_published":"2012-01-20T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents, the trusted third party (TTP) and the protocols as path formulas in Linear Temporal Logic (LTL) and prove that the satisfaction of the objectives of the agents and the TTP imply satisfaction of the protocol objectives. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail in synthesizing these protocols, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of assume-guarantee synthesis as follows: (a) any solution of assume-guarantee synthesis is attack-free; no subset of participants can violate the objectives of the other participants without violating their own objectives; (b) the Asokan-Shoup-Waidner (ASW) certified mail protocol that has known vulnerabilities is not a solution of AGS; and (c) the Kremer-Markowitch (KM) non-repudiation protocol is a solution of AGS. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can generate correct protocols and automatically discover vulnerabilities. The solution to assume-guarantee synthesis can be computed efficiently as the secure equilibrium solution of three-player graph games. © 2012 Springer-Verlag.","lang":"eng"}],"_id":"3252","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 7148","title":"Synthesizing protocols for digital contract signing","status":"public","oa_version":"Preprint"},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2012-01-01T00:00:00Z","page":"37 - 46","citation":{"chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives,” 7119:37–46. Springer, 2012. https://doi.org/10.1007/978-3-642-25929-6_3.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives. Vol. 7119, Springer, 2012, pp. 37–46, doi:10.1007/978-3-642-25929-6_3.","short":"K. Chatterjee, L. Doyen, in:, Springer, 2012, pp. 37–46.","ista":"Chatterjee K, Doyen L. 2012. Games and Markov decision processes with mean payoff parity and energy parity objectives. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7119, 37–46.","ieee":"K. Chatterjee and L. Doyen, “Games and Markov decision processes with mean payoff parity and energy parity objectives,” presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic, 2012, vol. 7119, pp. 37–46.","apa":"Chatterjee, K., & Doyen, L. (2012). Games and Markov decision processes with mean payoff parity and energy parity objectives (Vol. 7119, pp. 37–46). Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-25929-6_3","ama":"Chatterjee K, Doyen L. Games and Markov decision processes with mean payoff parity and energy parity objectives. In: Vol 7119. Springer; 2012:37-46. doi:10.1007/978-3-642-25929-6_3"},"abstract":[{"text":"In this paper we survey results of two-player games on graphs and Markov decision processes with parity, mean-payoff and energy objectives, and the combination of mean-payoff and energy objectives with parity objectives. These problems have applications in verification and synthesis of reactive systems in resource-constrained environments.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_name":"2012_MEMICS_Chatterjee.pdf","file_size":114060,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7863","checksum":"eed2cc1e76b160418c977e76e8899a60","date_updated":"2020-07-14T12:46:05Z","date_created":"2020-05-15T12:53:12Z"}],"intvolume":" 7119","title":"Games and Markov decision processes with mean payoff parity and energy parity objectives","ddc":["000"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3255","month":"01","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-25929-6_3","conference":{"end_date":"2011-10-16","start_date":"2011-10-14","location":"Lednice, Czech Republic","name":"MEMICS: Mathematical and Engineering Methods in Computer Science"},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"quality_controlled":"1","oa":1,"publist_id":"3400","file_date_updated":"2020-07-14T12:46:05Z","volume":7119,"date_updated":"2021-01-12T07:42:10Z","date_created":"2018-12-11T12:02:17Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","year":"2012","acknowledgement":"This work was partially supported by FWF NFN Grant S11407-N23 (RiSE) and a Microsoft faculty fellowship."},{"abstract":[{"text":"The Learning Parity with Noise (LPN) problem has recently found many applications in cryptography as the hardness assumption underlying the constructions of "provably secure" cryptographic schemes like encryption or authentication protocols. Being provably secure means that the scheme comes with a proof showing that the existence of an efficient adversary against the scheme implies that the underlying hardness assumption is wrong. LPN based schemes are appealing for theoretical and practical reasons. On the theoretical side, LPN based schemes offer a very strong security guarantee. The LPN problem is equivalent to the problem of decoding random linear codes, a problem that has been extensively studied in the last half century. The fastest known algorithms run in exponential time and unlike most number-theoretic problems used in cryptography, the LPN problem does not succumb to known quantum algorithms. On the practical side, LPN based schemes are often extremely simple and efficient in terms of code-size as well as time and space requirements. This makes them prime candidates for light-weight devices like RFID tags, which are too weak to implement standard cryptographic primitives like the AES block-cipher. This talk will be a gentle introduction to provable security using simple LPN based schemes as examples. Starting from pseudorandom generators and symmetric key encryption, over secret-key authentication protocols, and, if time admits, touching on recent constructions of public-key identification, commitments and zero-knowledge proofs.","lang":"eng"}],"publist_id":"3407","alternative_title":["LNCS"],"type":"conference","date_created":"2018-12-11T12:02:15Z","date_updated":"2021-01-12T07:42:07Z","volume":7147,"oa_version":"None","author":[{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"}],"title":"Cryptography from learning parity with noise","publication_status":"published","status":"public","department":[{"_id":"KrPi"}],"intvolume":" 7147","publisher":"Springer","year":"2012","_id":"3250","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"02","day":"19","scopus_import":1,"language":[{"iso":"eng"}],"conference":{"end_date":"2012-01-27","location":"Špindlerův Mlýn, Czech Republic","start_date":"2012-01-21","name":"SOFSEM: Current Trends in Theory and Practice of Computer Science"},"date_published":"2012-02-19T00:00:00Z","doi":"10.1007/978-3-642-27660-6_9","quality_controlled":"1","page":"99 - 114","citation":{"apa":"Pietrzak, K. Z. (2012). Cryptography from learning parity with noise (Vol. 7147, pp. 99–114). Presented at the SOFSEM: Current Trends in Theory and Practice of Computer Science, Špindlerův Mlýn, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-27660-6_9","ieee":"K. Z. Pietrzak, “Cryptography from learning parity with noise,” presented at the SOFSEM: Current Trends in Theory and Practice of Computer Science, Špindlerův Mlýn, Czech Republic, 2012, vol. 7147, pp. 99–114.","ista":"Pietrzak KZ. 2012. Cryptography from learning parity with noise. SOFSEM: Current Trends in Theory and Practice of Computer Science, LNCS, vol. 7147, 99–114.","ama":"Pietrzak KZ. Cryptography from learning parity with noise. In: Vol 7147. Springer; 2012:99-114. doi:10.1007/978-3-642-27660-6_9","chicago":"Pietrzak, Krzysztof Z. “Cryptography from Learning Parity with Noise,” 7147:99–114. Springer, 2012. https://doi.org/10.1007/978-3-642-27660-6_9.","short":"K.Z. Pietrzak, in:, Springer, 2012, pp. 99–114.","mla":"Pietrzak, Krzysztof Z. Cryptography from Learning Parity with Noise. Vol. 7147, Springer, 2012, pp. 99–114, doi:10.1007/978-3-642-27660-6_9."}},{"publist_id":"3398","file_date_updated":"2020-07-14T12:46:05Z","volume":47,"date_created":"2018-12-11T12:02:17Z","date_updated":"2021-01-12T07:42:10Z","author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael"}],"department":[{"_id":"HeEd"}],"publisher":"Springer","publication_status":"published","acknowledgement":"This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0057 and HR0011-09-0065 as well as the National Science Foundation (NSF) under grant DBI-0820624.","year":"2012","month":"03","language":[{"iso":"eng"}],"doi":"10.1007/s00454-011-9382-4","quality_controlled":"1","oa":1,"issue":"2","abstract":[{"lang":"eng","text":"We use a distortion to define the dual complex of a cubical subdivision of ℝ n as an n-dimensional subcomplex of the nerve of the set of n-cubes. Motivated by the topological analysis of high-dimensional digital image data, we consider such subdivisions defined by generalizations of quad- and oct-trees to n dimensions. Assuming the subdivision is balanced, we show that mapping each vertex to the center of the corresponding n-cube gives a geometric realization of the dual complex in ℝ n."}],"type":"journal_article","oa_version":"Submitted Version","file":[{"date_created":"2018-12-12T10:08:15Z","date_updated":"2020-07-14T12:46:05Z","checksum":"76486f3b2c9e7fd81342f3832ca387e7","file_id":"4675","relation":"main_file","creator":"system","file_size":203636,"content_type":"application/pdf","file_name":"IST-2016-543-v1+1_2012-J-08-HierarchyCubeComplex.pdf","access_level":"open_access"}],"pubrep_id":"543","intvolume":" 47","ddc":["000"],"title":"Dual complexes of cubical subdivisions of ℝn","status":"public","_id":"3256","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2012-03-01T00:00:00Z","page":"393 - 414","citation":{"ista":"Edelsbrunner H, Kerber M. 2012. Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. 47(2), 393–414.","ieee":"H. Edelsbrunner and M. Kerber, “Dual complexes of cubical subdivisions of ℝn,” Discrete & Computational Geometry, vol. 47, no. 2. Springer, pp. 393–414, 2012.","apa":"Edelsbrunner, H., & Kerber, M. (2012). Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-011-9382-4","ama":"Edelsbrunner H, Kerber M. Dual complexes of cubical subdivisions of ℝn. Discrete & Computational Geometry. 2012;47(2):393-414. doi:10.1007/s00454-011-9382-4","chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Dual Complexes of Cubical Subdivisions of ℝn.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-011-9382-4.","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Dual Complexes of Cubical Subdivisions of ℝn.” Discrete & Computational Geometry, vol. 47, no. 2, Springer, 2012, pp. 393–414, doi:10.1007/s00454-011-9382-4.","short":"H. Edelsbrunner, M. Kerber, Discrete & Computational Geometry 47 (2012) 393–414."},"publication":"Discrete & Computational Geometry"},{"oa_version":"None","_id":"3254","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"The complexity of stochastic Müller games","intvolume":" 211","abstract":[{"lang":"eng","text":"The theory of graph games with ω-regular winning conditions is the foundation for modeling and synthesizing reactive processes. In the case of stochastic reactive processes, the corresponding stochastic graph games have three players, two of them (System and Environment) behaving adversarially, and the third (Uncertainty) behaving probabilistically. We consider two problems for stochastic graph games: the qualitative problem asks for the set of states from which a player can win with probability 1 (almost-sure winning); and the quantitative problem asks for the maximal probability of winning (optimal winning) from each state. We consider ω-regular winning conditions formalized as Müller winning conditions. We present optimal memory bounds for pure (deterministic) almost-sure winning and optimal winning strategies in stochastic graph games with Müller winning conditions. We also study the complexity of stochastic Müller games and show that both the qualitative and quantitative analysis problems are PSPACE-complete. Our results are relevant in synthesis of stochastic reactive processes."}],"type":"journal_article","date_published":"2012-02-01T00:00:00Z","publication":"Information and Computation","citation":{"mla":"Chatterjee, Krishnendu. “The Complexity of Stochastic Müller Games.” Information and Computation, vol. 211, Elsevier, 2012, pp. 29–48, doi:10.1016/j.ic.2011.11.004.","short":"K. Chatterjee, Information and Computation 211 (2012) 29–48.","chicago":"Chatterjee, Krishnendu. “The Complexity of Stochastic Müller Games.” Information and Computation. Elsevier, 2012. https://doi.org/10.1016/j.ic.2011.11.004.","ama":"Chatterjee K. The complexity of stochastic Müller games. Information and Computation. 2012;211:29-48. doi:10.1016/j.ic.2011.11.004","ista":"Chatterjee K. 2012. The complexity of stochastic Müller games. Information and Computation. 211, 29–48.","apa":"Chatterjee, K. (2012). The complexity of stochastic Müller games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2011.11.004","ieee":"K. Chatterjee, “The complexity of stochastic Müller games,” Information and Computation, vol. 211. Elsevier, pp. 29–48, 2012."},"page":"29 - 48","day":"01","scopus_import":1,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"date_updated":"2021-01-12T07:42:09Z","date_created":"2018-12-11T12:02:17Z","volume":211,"year":"2012","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"ec_funded":1,"publist_id":"3403","doi":"10.1016/j.ic.2011.11.004","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://arise.or.at/pubpdf/The_complexity_of_stochastic_M___u_ller_games.pdf"}],"quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"02"},{"date_updated":"2021-01-12T07:42:09Z","date_created":"2018-12-11T12:02:17Z","volume":7148,"oa_version":"None","author":[{"first_name":"Ahmed","last_name":"Bouajjani","full_name":"Bouajjani, Ahmed"},{"id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","last_name":"Dragoi","first_name":"Cezara","full_name":"Dragoi, Cezara"},{"full_name":"Enea, Constantin","first_name":"Constantin","last_name":"Enea"},{"full_name":"Sighireanu, Mihaela","first_name":"Mihaela","last_name":"Sighireanu"}],"status":"public","publication_status":"published","title":"Abstract domains for automated reasoning about list manipulating programs with infinite data","department":[{"_id":"ToHe"}],"intvolume":" 7148","publisher":"Springer","year":"2012","_id":"3253","acknowledgement":"This work was partly supported by the French National Research Agency (ANR) project Veridyc (ANR-09-SEGI-016).","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We describe a framework for reasoning about programs with lists carrying integer numerical data. We use abstract domains to describe and manipulate complex constraints on configurations of these programs mixing constraints on the shape of the heap, sizes of the lists, on the multisets of data stored in these lists, and on the data at their different positions. Moreover, we provide powerful techniques for automatic validation of Hoare-triples and invariant checking, as well as for automatic synthesis of invariants and procedure summaries using modular inter-procedural analysis. The approach has been implemented in a tool called Celia and experimented successfully on a large benchmark of programs."}],"publist_id":"3404","alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","end_date":"2012-01-24","location":"Philadelphia, PA, USA","start_date":"2012-01-22"},"doi":"10.1007/978-3-642-27940-9_1","date_published":"2012-02-26T00:00:00Z","quality_controlled":"1","page":"1 - 22","citation":{"chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Abstract Domains for Automated Reasoning about List Manipulating Programs with Infinite Data,” 7148:1–22. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_1.","short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Springer, 2012, pp. 1–22.","mla":"Bouajjani, Ahmed, et al. Abstract Domains for Automated Reasoning about List Manipulating Programs with Infinite Data. Vol. 7148, Springer, 2012, pp. 1–22, doi:10.1007/978-3-642-27940-9_1.","ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Abstract domains for automated reasoning about list manipulating programs with infinite data,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 1–22.","apa":"Bouajjani, A., Dragoi, C., Enea, C., & Sighireanu, M. (2012). Abstract domains for automated reasoning about list manipulating programs with infinite data (Vol. 7148, pp. 1–22). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_1","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Abstract domains for automated reasoning about list manipulating programs with infinite data. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 1–22.","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Abstract domains for automated reasoning about list manipulating programs with infinite data. In: Vol 7148. Springer; 2012:1-22. doi:10.1007/978-3-642-27940-9_1"},"day":"26","month":"02"},{"conference":{"end_date":"2011-11-13","location":"Barcelona, Spain","start_date":"2011-11-06","name":"ICCV: International Conference on Computer Vision"},"date_published":"2012-01-12T00:00:00Z","doi":"10.1109/ICCV.2011.6126486","language":[{"iso":"eng"}],"citation":{"ieee":"A. Ion, J. Carreira, and C. Sminchisescu, “Image segmentation by figure-ground composition into maximal cliques,” presented at the ICCV: International Conference on Computer Vision, Barcelona, Spain, 2012.","apa":"Ion, A., Carreira, J., & Sminchisescu, C. (2012). Image segmentation by figure-ground composition into maximal cliques. Presented at the ICCV: International Conference on Computer Vision, Barcelona, Spain: IEEE. https://doi.org/10.1109/ICCV.2011.6126486","ista":"Ion A, Carreira J, Sminchisescu C. 2012. Image segmentation by figure-ground composition into maximal cliques. ICCV: International Conference on Computer Vision, 6126486.","ama":"Ion A, Carreira J, Sminchisescu C. Image segmentation by figure-ground composition into maximal cliques. In: IEEE; 2012. doi:10.1109/ICCV.2011.6126486","chicago":"Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Image Segmentation by Figure-Ground Composition into Maximal Cliques.” IEEE, 2012. https://doi.org/10.1109/ICCV.2011.6126486.","short":"A. Ion, J. Carreira, C. Sminchisescu, in:, IEEE, 2012.","mla":"Ion, Adrian, et al. Image Segmentation by Figure-Ground Composition into Maximal Cliques. 6126486, IEEE, 2012, doi:10.1109/ICCV.2011.6126486."},"quality_controlled":"1","day":"12","month":"01","author":[{"id":"29F89302-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian","last_name":"Ion","full_name":"Ion, Adrian"},{"first_name":"Joao","last_name":"Carreira","full_name":"Carreira, Joao"},{"first_name":"Cristian","last_name":"Sminchisescu","full_name":"Sminchisescu, Cristian"}],"date_created":"2018-12-11T12:02:21Z","date_updated":"2021-01-12T07:42:15Z","oa_version":"None","year":"2012","_id":"3265","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Image segmentation by figure-ground composition into maximal cliques","publication_status":"published","status":"public","department":[{"_id":"HeEd"}],"publisher":"IEEE","abstract":[{"lang":"eng","text":"We propose a mid-level statistical model for image segmentation that composes multiple figure-ground hypotheses (FG) obtained by applying constraints at different locations and scales, into larger interpretations (tilings) of the entire image. Inference is cast as optimization over sets of maximal cliques sampled from a graph connecting all non-overlapping figure-ground segment hypotheses. Potential functions over cliques combine unary, Gestalt-based figure qualities, and pairwise compatibilities among spatially neighboring segments, constrained by T-junctions and the boundary interface statistics of real scenes. Learning the model parameters is based on maximum likelihood, alternating between sampling image tilings and optimizing their potential function parameters. State of the art results are reported on the Berkeley and Stanford segmentation datasets, as well as VOC2009, where a 28% improvement was achieved."}],"publist_id":"3382","article_number":"6126486","type":"conference"},{"author":[{"first_name":"Yevgeniy","last_name":"Dodis","full_name":"Dodis, Yevgeniy"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Kiltz, Eike","first_name":"Eike","last_name":"Kiltz"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}],"date_created":"2018-12-11T12:02:27Z","date_updated":"2021-01-12T07:42:22Z","volume":7237,"year":"2012","acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC)","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:46:06Z","ec_funded":1,"publist_id":"3364","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","start_date":"2012-04-15","location":"Cambridge, UK","end_date":"2012-04-19"},"doi":"10.1007/978-3-642-29011-4_22","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"month":"03","pubrep_id":"686","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":372292,"access_level":"open_access","file_name":"IST-2016-686-v1+1_059.pdf","checksum":"8557c17a8c2586d06ebfe62d934f5c5f","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:14:23Z","file_id":"5074","relation":"main_file"}],"_id":"3282","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Message authentication, revisited","ddc":["000","004"],"intvolume":" 7237","abstract":[{"lang":"eng","text":"Traditionally, symmetric-key message authentication codes (MACs) are easily built from pseudorandom functions (PRFs). In this work we propose a wide variety of other approaches to building efficient MACs, without going through a PRF first. In particular, unlike deterministic PRF-based MACs, where each message has a unique valid tag, we give a number of probabilistic MAC constructions from various other primitives/assumptions. Our main results are summarized as follows: We show several new probabilistic MAC constructions from a variety of general assumptions, including CCA-secure encryption, Hash Proof Systems and key-homomorphic weak PRFs. By instantiating these frameworks under concrete number theoretic assumptions, we get several schemes which are more efficient than just using a state-of-the-art PRF instantiation under the corresponding assumption. For probabilistic MACs, unlike deterministic ones, unforgeability against a chosen message attack (uf-cma ) alone does not imply security if the adversary can additionally make verification queries (uf-cmva ). We give an efficient generic transformation from any uf-cma secure MAC which is "message-hiding" into a uf-cmva secure MAC. This resolves the main open problem of Kiltz et al. from Eurocrypt'11; By using our transformation on their constructions, we get the first efficient MACs from the LPN assumption. While all our new MAC constructions immediately give efficient actively secure, two-round symmetric-key identification schemes, we also show a very simple, three-round actively secure identification protocol from any weak PRF. In particular, the resulting protocol is much more efficient than the trivial approach of building a regular PRF from a weak PRF. © 2012 International Association for Cryptologic Research."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2012-03-10T00:00:00Z","citation":{"ista":"Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. 2012. Message authentication, revisited. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 7237, 355–374.","ieee":"Y. Dodis, K. Z. Pietrzak, E. Kiltz, and D. Wichs, “Message authentication, revisited,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK, 2012, vol. 7237, pp. 355–374.","apa":"Dodis, Y., Pietrzak, K. Z., Kiltz, E., & Wichs, D. (2012). Message authentication, revisited (Vol. 7237, pp. 355–374). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Cambridge, UK: Springer. https://doi.org/10.1007/978-3-642-29011-4_22","ama":"Dodis Y, Pietrzak KZ, Kiltz E, Wichs D. Message authentication, revisited. In: Vol 7237. Springer; 2012:355-374. doi:10.1007/978-3-642-29011-4_22","chicago":"Dodis, Yevgeniy, Krzysztof Z Pietrzak, Eike Kiltz, and Daniel Wichs. “Message Authentication, Revisited,” 7237:355–74. Springer, 2012. https://doi.org/10.1007/978-3-642-29011-4_22.","mla":"Dodis, Yevgeniy, et al. Message Authentication, Revisited. Vol. 7237, Springer, 2012, pp. 355–74, doi:10.1007/978-3-642-29011-4_22.","short":"Y. Dodis, K.Z. Pietrzak, E. Kiltz, D. Wichs, in:, Springer, 2012, pp. 355–374."},"page":"355 - 374","day":"10","has_accepted_license":"1"},{"doi":"10.1007/978-3-642-28914-9_31","conference":{"start_date":"2012-03-19","location":"Taormina, Sicily, Italy","end_date":"2012-03-21","name":"TCC: Theory of Cryptography Conference"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.iacr.org/archive/tcc2012/71940166/71940166.pdf"}],"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"05","author":[{"orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z"}],"volume":7194,"date_updated":"2021-01-12T07:42:21Z","date_created":"2018-12-11T12:02:26Z","year":"2012","acknowledgement":"Supported by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC Starting Grant (259668-PSPC).","publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","publist_id":"3366","ec_funded":1,"date_published":"2012-05-04T00:00:00Z","citation":{"mla":"Pietrzak, Krzysztof Z. Subspace LWE. Vol. 7194, Springer, 2012, pp. 548–63, doi:10.1007/978-3-642-28914-9_31.","short":"K.Z. Pietrzak, in:, Springer, 2012, pp. 548–563.","chicago":"Pietrzak, Krzysztof Z. “Subspace LWE,” 7194:548–63. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_31.","ama":"Pietrzak KZ. Subspace LWE. In: Vol 7194. Springer; 2012:548-563. doi:10.1007/978-3-642-28914-9_31","ista":"Pietrzak KZ. 2012. Subspace LWE. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 548–563.","ieee":"K. Z. Pietrzak, “Subspace LWE,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 548–563.","apa":"Pietrzak, K. Z. (2012). Subspace LWE (Vol. 7194, pp. 548–563). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_31"},"page":"548 - 563","day":"04","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3280","intvolume":" 7194","title":"Subspace LWE","status":"public","abstract":[{"lang":"eng","text":"The (decisional) learning with errors problem (LWE) asks to distinguish "noisy" inner products of a secret vector with random vectors from uniform. The learning parities with noise problem (LPN) is the special case where the elements of the vectors are bits. In recent years, the LWE and LPN problems have found many applications in cryptography. In this paper we introduce a (seemingly) much stronger adaptive assumption, called "subspace LWE" (SLWE), where the adversary can learn the inner product of the secret and random vectors after they were projected into an adaptively and adversarially chosen subspace. We prove that, surprisingly, the SLWE problem mapping into subspaces of dimension d is almost as hard as LWE using secrets of length d (the other direction is trivial.) This result immediately implies that several existing cryptosystems whose security is based on the hardness of the LWE/LPN problems are provably secure in a much stronger sense than anticipated. As an illustrative example we show that the standard way of using LPN for symmetric CPA secure encryption is even secure against a very powerful class of related key attacks. "}],"type":"conference","alternative_title":["LNCS"]},{"alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We consider the problem of amplifying the "lossiness" of functions. We say that an oracle circuit C*: {0,1} m → {0,1}* amplifies relative lossiness from ℓ/n to L/m if for every function f:{0,1} n → {0,1} n it holds that 1 If f is injective then so is C f. 2 If f has image size of at most 2 n-ℓ, then C f has image size at most 2 m-L. The question is whether such C* exists for L/m ≫ ℓ/n. This problem arises naturally in the context of cryptographic "lossy functions," where the relative lossiness is the key parameter. We show that for every circuit C* that makes at most t queries to f, the relative lossiness of C f is at most L/m ≤ ℓ/n + O(log t)/n. In particular, no black-box method making a polynomial t = poly(n) number of queries can amplify relative lossiness by more than an O(logn)/n additive term. We show that this is tight by giving a simple construction (cascading with some randomization) that achieves such amplification."}],"publist_id":"3365","title":"Lossy functions do not amplify well","status":"public","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"intvolume":" 7194","acknowledgement":"We would like to thank Oded Goldreich and Omer Rein- gold for discussions at an early stage of this project, and Scott Aaronson for clarifications regarding the collision problem.\r\n","_id":"3281","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:02:26Z","date_updated":"2021-01-12T07:42:22Z","oa_version":"None","volume":7194,"author":[{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alon","last_name":"Rosen","full_name":"Rosen, Alon"},{"last_name":"Segev","first_name":"Gil","full_name":"Segev, Gil"}],"day":"04","month":"05","quality_controlled":"1","page":"458 - 475","citation":{"ista":"Pietrzak KZ, Rosen A, Segev G. 2012. Lossy functions do not amplify well. TCC: Theory of Cryptography Conference, LNCS, vol. 7194, 458–475.","ieee":"K. Z. Pietrzak, A. Rosen, and G. Segev, “Lossy functions do not amplify well,” presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy, 2012, vol. 7194, pp. 458–475.","apa":"Pietrzak, K. Z., Rosen, A., & Segev, G. (2012). Lossy functions do not amplify well (Vol. 7194, pp. 458–475). Presented at the TCC: Theory of Cryptography Conference, Taormina, Sicily, Italy: Springer. https://doi.org/10.1007/978-3-642-28914-9_26","ama":"Pietrzak KZ, Rosen A, Segev G. Lossy functions do not amplify well. In: Vol 7194. Springer; 2012:458-475. doi:10.1007/978-3-642-28914-9_26","chicago":"Pietrzak, Krzysztof Z, Alon Rosen, and Gil Segev. “Lossy Functions Do Not Amplify Well,” 7194:458–75. Springer, 2012. https://doi.org/10.1007/978-3-642-28914-9_26.","mla":"Pietrzak, Krzysztof Z., et al. Lossy Functions Do Not Amplify Well. Vol. 7194, Springer, 2012, pp. 458–75, doi:10.1007/978-3-642-28914-9_26.","short":"K.Z. Pietrzak, A. Rosen, G. Segev, in:, Springer, 2012, pp. 458–475."},"main_file_link":[{"url":"http://www.iacr.org/archive/tcc2012/tcc2012-index.html"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2012-03-19","location":"Taormina, Sicily, Italy","end_date":"2012-03-21","name":"TCC: Theory of Cryptography Conference"},"doi":"10.1007/978-3-642-28914-9_26","date_published":"2012-05-04T00:00:00Z"},{"day":"01","month":"01","citation":{"ama":"Kolmogorov V, Živný S. The complexity of conservative valued CSPs. In: SIAM; 2012:750-759.","ieee":"V. Kolmogorov and S. Živný, “The complexity of conservative valued CSPs,” presented at the SODA: Symposium on Discrete Algorithms, 2012, pp. 750–759.","apa":"Kolmogorov, V., & Živný, S. (2012). The complexity of conservative valued CSPs (pp. 750–759). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.","ista":"Kolmogorov V, Živný S. 2012. The complexity of conservative valued CSPs. SODA: Symposium on Discrete Algorithms, 750–759.","short":"V. Kolmogorov, S. Živný, in:, SIAM, 2012, pp. 750–759.","mla":"Kolmogorov, Vladimir, and Stanislav Živný. The Complexity of Conservative Valued CSPs. SIAM, 2012, pp. 750–59.","chicago":"Kolmogorov, Vladimir, and Stanislav Živný. “The Complexity of Conservative Valued CSPs,” 750–59. SIAM, 2012."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1008.1555"}],"oa":1,"quality_controlled":0,"page":"750 - 759","conference":{"name":"SODA: Symposium on Discrete Algorithms"},"date_published":"2012-01-01T00:00:00Z","type":"conference","abstract":[{"text":"We study the complexity of valued constraint satisfaction problems (VCSP). A problem from VCSP is characterised by a constraint language, a fixed set of cost functions over a finite domain. An instance of the problem is specified by a sum of cost functions from the language and the goal is to minimise the sum. Under the unique games conjecture, the approximability of finite-valued VCSPs is well-understood, see Raghavendra [FOCS’08]. However, there is no characterisation of finite-valued VCSPs, let alone general-valued VCSPs, that can be solved exactly in polynomial time, thus giving insights from a combinatorial optimisation perspective.\nWe consider the case of languages containing all possible unary cost functions. In the case of languages consisting of only {0, ∞}-valued cost functions (i.e. relations), such languages have been called conservative and studied by Bulatov [LICS’03] and recently by Barto [LICS’11]. Since we study valued languages, we call a language conservative if it contains all finite-valued unary cost functions. The computational complexity of conservative valued languages has been studied by Cohen et al. [AIJ’06] for languages over Boolean domains, by Deineko et al. [JACM’08] for {0,1}-valued languages (a.k.a Max-CSP), and by Takhanov [STACS’10] for {0,∞}-valued languages containing all finite- valued unary cost functions (a.k.a. Min-Cost-Hom).\nWe prove a Schaefer-like dichotomy theorem for conservative valued languages: if all cost functions in the language satisfy a certain condition (specified by a complementary combination of STP and MJN multimorphisms), then any instance can be solved in polynomial time (via a new algorithm developed in this paper), otherwise the language is NP-hard. This is the first complete complexity classification of general-valued constraint languages over non-Boolean domains. It is a common phenomenon that complexity classifications of problems over non-Boolean domains is significantly harder than the Boolean case. The polynomial-time algorithm we present for the tractable cases is a generalisation of the submodular minimisation problem and a result of Cohen et al. [TCS’08].\nOur results generalise previous results by Takhanov [STACS’10] and (a subset of results) by Cohen et al. [AIJ’06] and Deineko et al. [JACM’08]. Moreover, our results do not rely on any computer-assisted search as in Deineko et al. [JACM’08], and provide a powerful tool for proving hardness of finite-valued and general-valued languages.","lang":"eng"}],"publist_id":"3362","extern":1,"_id":"3284","year":"2012","acknowledgement":"Vladimir Kolmogorov is supported by the Royal Academy of Eng ineering/EPSRC.","title":"The complexity of conservative valued CSPs","publication_status":"published","status":"public","publisher":"SIAM","author":[{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"first_name":"Stanislav","last_name":"Živný","full_name":"Živný, Stanislav"}],"date_created":"2018-12-11T12:02:27Z","date_updated":"2021-01-12T07:42:23Z"},{"article_processing_charge":"No","month":"01","day":"02","language":[{"iso":"eng"}],"date_published":"2012-01-02T00:00:00Z","doi":"10.1021/ja209688a","page":"1438 - 1441","quality_controlled":"1","article_type":"original","citation":{"short":"A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, A. Cabot, Journal of the American Chemical Society 134 (2012) 1438–1441.","mla":"Shavel, Alexey, et al. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society, vol. 134, no. 3, ACS, 2012, pp. 1438–41, doi:10.1021/ja209688a.","chicago":"Shavel, Alexey, Doris Cadavid, Maria Ibáñez, Alex Carrete, and Andreu Cabot. “Continuous Production of Cu Inf 2 Inf ZnSnS Inf 4 Inf Nanocrystals in a Flow Reactor.” Journal of the American Chemical Society. ACS, 2012. https://doi.org/10.1021/ja209688a.","ama":"Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 2012;134(3):1438-1441. doi:10.1021/ja209688a","ieee":"A. Shavel, D. Cadavid, M. Ibáñez, A. Carrete, and A. Cabot, “Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor,” Journal of the American Chemical Society, vol. 134, no. 3. ACS, pp. 1438–1441, 2012.","apa":"Shavel, A., Cadavid, D., Ibáñez, M., Carrete, A., & Cabot, A. (2012). Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. ACS. https://doi.org/10.1021/ja209688a","ista":"Shavel A, Cadavid D, Ibáñez M, Carrete A, Cabot A. 2012. Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor. Journal of the American Chemical Society. 134(3), 1438–1441."},"publication":"Journal of the American Chemical Society","extern":"1","issue":"3","publist_id":"7531","abstract":[{"lang":"eng","text":"A procedure for the continuous production of Cu 2ZnSnS 4 (CZTS) nanoparticles with controlled composition is presented. CZTS nanoparticles were prepared through the reaction of the metals' amino complexes with elemental sulfur in a continuous-flow reactor at moderate temperatures (300-330 °C). High-resolution transmission electron microscopy and X-ray diffraction analysis showed the nanocrystals to have a crystallographic structure compatible with that of the kesterite. Chemical characterization of the materials showed the presence of the four elements in each individual nanocrystal. Composition control was achieved by adjusting the solution flow rate through the reactor and the proper choice of the nominal precursor concentration within the flowing solution. Single-particle analysis revealed a composition distribution within each sample, which was optimized at the highest synthesis temperatures used. "}],"type":"journal_article","oa_version":"None","volume":134,"date_updated":"2021-01-12T07:42:29Z","date_created":"2018-12-11T11:45:51Z","author":[{"full_name":"Shavel, Alexey","first_name":"Alexey","last_name":"Shavel"},{"full_name":"Cadavid, Doris","first_name":"Doris","last_name":"Cadavid"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria"},{"full_name":"Carrete, Alex","last_name":"Carrete","first_name":"Alex"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"publisher":"ACS","intvolume":" 134","status":"public","publication_status":"published","title":"Continuous production of Cu inf 2 inf ZnSnS inf 4 inf nanocrystals in a flow reactor","_id":"330","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_published":"2012-01-01T00:00:00Z","page":"7 - 21","publication":"Nature Reviews Neuroscience","citation":{"mla":"Eggermann, Emmanuel, et al. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience, vol. 13, no. 1, Nature Publishing Group, 2012, pp. 7–21, doi:10.1038/nrn3125.","short":"E. Eggermann, I. Bucurenciu, S. Goswami, P.M. Jonas, Nature Reviews Neuroscience 13 (2012) 7–21.","chicago":"Eggermann, Emmanuel, Iancu Bucurenciu, Sarit Goswami, and Peter M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Sensors of Exocytosis at Fast Mammalian Synapses.” Nature Reviews Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nrn3125.","ama":"Eggermann E, Bucurenciu I, Goswami S, Jonas PM. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 2012;13(1):7-21. doi:10.1038/nrn3125","ista":"Eggermann E, Bucurenciu I, Goswami S, Jonas PM. 2012. Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. 13(1), 7–21.","ieee":"E. Eggermann, I. Bucurenciu, S. Goswami, and P. M. Jonas, “Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses,” Nature Reviews Neuroscience, vol. 13, no. 1. Nature Publishing Group, pp. 7–21, 2012.","apa":"Eggermann, E., Bucurenciu, I., Goswami, S., & Jonas, P. M. (2012). Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses. Nature Reviews Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nrn3125"},"day":"01","has_accepted_license":"1","scopus_import":1,"oa_version":"Submitted Version","file":[{"checksum":"4c1c86b2f6e4e1562f5bb800b457ea9f","date_updated":"2020-07-14T12:46:07Z","date_created":"2018-12-12T10:12:13Z","file_id":"4931","relation":"main_file","creator":"system","file_size":314246,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-820-v1+1_17463_3_art_file_109404_ltmxbw.pdf"},{"relation":"main_file","file_id":"4932","checksum":"bceb2efdd49d115f4dde8486bc1be3f2","date_updated":"2020-07-14T12:46:07Z","date_created":"2018-12-12T10:12:14Z","access_level":"open_access","file_name":"IST-2017-820-v1+2_17463_3_figure_109402_ltmwlp.pdf","content_type":"application/pdf","file_size":1840216,"creator":"system"}],"pubrep_id":"820","ddc":["570"],"status":"public","title":"Nanodomain coupling between Ca(2+) channels and sensors of exocytosis at fast mammalian synapses","intvolume":" 13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3317","abstract":[{"lang":"eng","text":"The physical distance between presynaptic Ca2+ channels and the Ca2+ sensors that trigger exocytosis of neurotransmitter-containing vesicles is a key determinant of the signalling properties of synapses in the nervous system. Recent functional analysis indicates that in some fast central synapses, transmitter release is triggered by a small number of Ca2+ channels that are coupled to Ca2+ sensors at the nanometre scale. Molecular analysis suggests that this tight coupling is generated by protein–protein interactions involving Ca2+ channels, Ca2+ sensors and various other synaptic proteins. Nanodomain coupling has several functional advantages, as it increases the efficacy, speed and energy efficiency of synaptic transmission."}],"issue":"1","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/nrn3125","quality_controlled":"1","project":[{"grant_number":"JO_780/A5","_id":"25BC64A8-B435-11E9-9278-68D0E5697425","name":"Synaptic Mechanisms of Neuronal Network Function"},{"grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen"}],"oa":1,"month":"01","date_updated":"2021-01-12T07:42:36Z","date_created":"2018-12-11T12:02:38Z","volume":13,"author":[{"first_name":"Emmanuel","last_name":"Eggermann","id":"34DACA34-E9AE-11E9-849C-D35BD8ADC20C","full_name":"Eggermann, Emmanuel"},{"full_name":"Bucurenciu, Iancu","last_name":"Bucurenciu","first_name":"Iancu","id":"4BD1D872-E9AE-11E9-9EE9-8BF4597A9E2A"},{"full_name":"Goswami, Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","first_name":"Sarit","last_name":"Goswami"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M"}],"publication_status":"published","department":[{"_id":"PeJo"}],"publisher":"Nature Publishing Group","acknowledgement":"Work of the authors was funded by grants of the Deutsche Forschungsgemeinschaft to P.J. (grants SFB 780/A5, TR 3/B10 and the Leibniz programme), a European Research Council Advanced grant to P.J. and a Swiss National Foundation fellowship to E.E.\r\nWe thank D. Tsien and E. Neher for their comments on this Review, J. Guzmán and A. Pernía-Andrade for reading earlier versions and E. Kramberger for perfect editorial support. We apologize that owing to space constraints, not all relevant papers could be cited.\r\n","year":"2012","file_date_updated":"2020-07-14T12:46:07Z","publist_id":"3322"},{"scopus_import":1,"day":"01","month":"04","publication":"International Journal of Foundations of Computer Science","citation":{"chicago":"Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2012. https://doi.org/10.1142/S0129054112400308.","short":"K. Chatterjee, R. Majumdar, International Journal of Foundations of Computer Science 23 (2012) 609–625.","mla":"Chatterjee, Krishnendu, and Ritankar Majumdar. “Discounting and Averaging in Games across Time Scales.” International Journal of Foundations of Computer Science, vol. 23, no. 3, World Scientific Publishing, 2012, pp. 609–25, doi:10.1142/S0129054112400308.","apa":"Chatterjee, K., & Majumdar, R. (2012). Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S0129054112400308","ieee":"K. Chatterjee and R. Majumdar, “Discounting and averaging in games across time scales,” International Journal of Foundations of Computer Science, vol. 23, no. 3. World Scientific Publishing, pp. 609–625, 2012.","ista":"Chatterjee K, Majumdar R. 2012. Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. 23(3), 609–625.","ama":"Chatterjee K, Majumdar R. Discounting and averaging in games across time scales. International Journal of Foundations of Computer Science. 2012;23(3):609-625. doi:10.1142/S0129054112400308"},"quality_controlled":"1","page":"609 - 625","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"date_published":"2012-04-01T00:00:00Z","doi":"10.1142/S0129054112400308","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We introduce two-level discounted and mean-payoff games played by two players on a perfect-information stochastic game graph. The upper level game is a discounted or mean-payoff game and the lower level game is a (undiscounted) reachability game. Two-level games model hierarchical and sequential decision making under uncertainty across different time scales. For both discounted and mean-payoff two-level games, we show the existence of pure memoryless optimal strategies for both players and an ordered field property. We show that if there is only one player (Markov decision processes), then the values can be computed in polynomial time. It follows that whether the value of a player is equal to a given rational constant in two-level discounted or mean-payoff games can be decided in NP ∩ coNP. We also give an alternate strategy improvement algorithm to compute the value. © 2012 World Scientific Publishing Company.","lang":"eng"}],"issue":"3","publist_id":"3326","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3314","year":"2012","publication_status":"published","status":"public","title":"Discounting and averaging in games across time scales","publisher":"World Scientific Publishing","department":[{"_id":"KrCh"}],"intvolume":" 23","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Majumdar, Ritankar","last_name":"Majumdar","first_name":"Ritankar"}],"date_updated":"2021-01-12T07:42:35Z","date_created":"2018-12-11T12:02:37Z","volume":23,"oa_version":"None"}]