[{"doi":"10.1007/s11856-017-1607-7","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1610.09063","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"month":"10","author":[{"first_name":"Xavier","last_name":"Goaoc","full_name":"Goaoc, Xavier"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"full_name":"Paták, Pavel","first_name":"Pavel","last_name":"Paták"},{"full_name":"Patakova, Zuzana","last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tancer, Martin","last_name":"Tancer","first_name":"Martin","orcid":"0000-0002-1191-6714","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1511"}]},"date_created":"2018-12-11T11:47:29Z","date_updated":"2023-02-23T10:02:13Z","volume":222,"year":"2017","acknowledgement":"The work by Z. P. was partially supported by the Israel Science Foundation grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria, supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58).","publication_status":"published","publisher":"Springer","department":[{"_id":"UlWa"}],"ec_funded":1,"publist_id":"7194","date_published":"2017-10-01T00:00:00Z","publication":"Israel Journal of Mathematics","citation":{"short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866.","mla":"Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics, vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:10.1007/s11856-017-1607-7.","chicago":"Goaoc, Xavier, Isaac Mabillard, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics. Springer, 2017. https://doi.org/10.1007/s11856-017-1607-7.","ama":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 2017;222(2):841-866. doi:10.1007/s11856-017-1607-7","ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result,” Israel Journal of Mathematics, vol. 222, no. 2. Springer, pp. 841–866, 2017.","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-017-1607-7","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 222(2), 841–866."},"page":"841 - 866","day":"01","scopus_import":1,"oa_version":"Preprint","_id":"610","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result","status":"public","intvolume":" 222","abstract":[{"lang":"eng","text":"The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition."}],"issue":"2","type":"journal_article"},{"abstract":[{"lang":"eng","text":"Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity."}],"issue":"6365","publist_id":"7193","type":"journal_article","date_updated":"2021-01-12T08:06:10Z","date_created":"2018-12-11T11:47:29Z","volume":358,"oa_version":"None","author":[{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"last_name":"Xu","first_name":"Ping","full_name":"Xu, Ping"},{"first_name":"Irina","last_name":"Mohorianu","full_name":"Mohorianu, Irina"},{"full_name":"Whibley, Annabel","last_name":"Whibley","first_name":"Annabel"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"full_name":"Tavares, Hugo","first_name":"Hugo","last_name":"Tavares"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"full_name":"Carpenter, Rosemary","last_name":"Carpenter","first_name":"Rosemary"},{"full_name":"Li, Miaomiao","last_name":"Li","first_name":"Miaomiao"},{"last_name":"Li","first_name":"Qun","full_name":"Li, Qun"},{"full_name":"Xue, Yongbiao","last_name":"Xue","first_name":"Yongbiao"},{"first_name":"Tamas","last_name":"Dalmay","full_name":"Dalmay, Tamas"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"title":"Evolution of flower color pattern through selection on regulatory small RNAs","publication_status":"published","status":"public","publisher":"American Association for the Advancement of Science","intvolume":" 358","department":[{"_id":"NiBa"}],"_id":"611","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","day":"17","publication_identifier":{"issn":["00368075"]},"scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1126/science.aao3526","date_published":"2017-11-17T00:00:00Z","quality_controlled":"1","page":"925 - 928","publication":"Science","citation":{"ama":"Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 2017;358(6365):925-928. doi:10.1126/science.aao3526","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao3526","ieee":"D. Bradley et al., “Evolution of flower color pattern through selection on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017.","ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","short":"D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928.","mla":"Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:10.1126/science.aao3526.","chicago":"Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aao3526."}},{"article_number":"1535","file_date_updated":"2020-07-14T12:47:20Z","publist_id":"7191","ec_funded":1,"license":"https://creativecommons.org/licenses/by/4.0/","year":"2017","acknowledgement":"We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG).","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"author":[{"orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","last_name":"Chait","first_name":"Remy P","full_name":"Chait, Remy P"},{"full_name":"Ruess, Jakob","first_name":"Jakob","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282"},{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C"}],"date_created":"2018-12-11T11:47:30Z","date_updated":"2021-01-12T08:06:15Z","volume":8,"month":"12","publication_identifier":{"issn":["20411723"]},"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","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"doi":"10.1038/s41467-017-01683-1","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.","lang":"eng"}],"issue":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"613","ddc":["576","579"],"title":"Shaping bacterial population behavior through computer interfaced control of individual cells","status":"public","intvolume":" 8","pubrep_id":"911","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1951699,"creator":"system","access_level":"open_access","file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf","checksum":"44bb5d0229926c23a9955d9fe0f9723f","date_created":"2018-12-12T10:16:05Z","date_updated":"2020-07-14T12:47:20Z","relation":"main_file","file_id":"5190"}],"scopus_import":1,"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Nature Communications","citation":{"ama":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1","ista":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.","ieee":"R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","apa":"Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., & Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01683-1","mla":"Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.","short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).","chicago":"Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01683-1."},"date_published":"2017-12-01T00:00:00Z"},{"scopus_import":1,"day":"01","citation":{"chicago":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2017. https://doi.org/10.1214/16-AIHP765.","mla":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4, Institute of Mathematical Statistics, 2017, pp. 1606–56, doi:10.1214/16-AIHP765.","short":"L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability and Statistics 53 (2017) 1606–1656.","ista":"Erdös L, Schnelli K. 2017. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 53(4), 1606–1656.","ieee":"L. Erdös and K. Schnelli, “Universality for random matrix flows with time dependent density,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656, 2017.","apa":"Erdös, L., & Schnelli, K. (2017). Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AIHP765","ama":"Erdös L, Schnelli K. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2017;53(4):1606-1656. doi:10.1214/16-AIHP765"},"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","page":"1606 - 1656","date_published":"2017-11-01T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"We show that the Dyson Brownian Motion exhibits local universality after a very short time assuming that local rigidity and level repulsion of the eigenvalues hold. These conditions are verified, hence bulk spectral universality is proven, for a large class of Wigner-like matrices, including deformed Wigner ensembles and ensembles with non-stochastic variance matrices whose limiting densities differ from Wigner's semicircle law.","lang":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"615","intvolume":" 53","status":"public","title":"Universality for random matrix flows with time dependent density","oa_version":"Submitted Version","publication_identifier":{"issn":["02460203"]},"month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.00650"}],"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1214/16-AIHP765","language":[{"iso":"eng"}],"publist_id":"7189","ec_funded":1,"year":"2017","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"publication_status":"published","author":[{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"full_name":"Schnelli, Kevin","first_name":"Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231"}],"volume":53,"date_created":"2018-12-11T11:47:30Z","date_updated":"2021-01-12T08:06:22Z"},{"_id":"623","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Extracerebral dysfunction in animal models of autism spectrum disorder","status":"public","intvolume":" 224","oa_version":"None","type":"book_chapter","alternative_title":["ADVSANAT"],"abstract":[{"lang":"eng","text":"Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology."}],"publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","citation":{"ista":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. 2017.Extracerebral dysfunction in animal models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 159–187.","apa":"Hill Yardin, E., Mckeown, S., Novarino, G., & Grabrucker, A. (2017). Extracerebral dysfunction in animal models of autism spectrum disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 159–187). Springer. https://doi.org/10.1007/978-3-319-52498-6_9","ieee":"E. Hill Yardin, S. Mckeown, G. Novarino, and A. Grabrucker, “Extracerebral dysfunction in animal models of autism spectrum disorder,” in Translational Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 159–187.","ama":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. Extracerebral dysfunction in animal models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. Translational Anatomy and Cell Biology of Autism Spectrum Disorder. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:159-187. doi:10.1007/978-3-319-52498-6_9","chicago":"Hill Yardin, Elisa, Sonja Mckeown, Gaia Novarino, and Andreas Grabrucker. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” In Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, 224:159–87. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_9.","mla":"Hill Yardin, Elisa, et al. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 159–87, doi:10.1007/978-3-319-52498-6_9.","short":"E. Hill Yardin, S. Mckeown, G. Novarino, A. Grabrucker, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 159–187."},"page":"159 - 187","date_published":"2017-05-28T00:00:00Z","scopus_import":1,"series_title":"Advances in Anatomy Embryology and Cell Biology","day":"28","year":"2017","publication_status":"published","editor":[{"last_name":"Schmeisser","first_name":"Michael","full_name":"Schmeisser, Michael"},{"full_name":"Boekers, Tobias","first_name":"Tobias","last_name":"Boekers"}],"publisher":"Springer","department":[{"_id":"GaNo"}],"author":[{"last_name":"Hill Yardin","first_name":"Elisa","full_name":"Hill Yardin, Elisa"},{"first_name":"Sonja","last_name":"Mckeown","full_name":"Mckeown, Sonja"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"first_name":"Andreas","last_name":"Grabrucker","full_name":"Grabrucker, Andreas"}],"date_updated":"2021-01-12T08:06:46Z","date_created":"2018-12-11T11:47:33Z","volume":224,"publist_id":"7177","quality_controlled":"1","doi":"10.1007/978-3-319-52498-6_9","language":[{"iso":"eng"}],"month":"05","publication_identifier":{"issn":["03015556"],"isbn":["978-3-319-52496-2"]}},{"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2017-12-01T00:00:00Z","citation":{"ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” Theoretical Population Biology, vol. 118. Academic Press, pp. 50–73, 2017.","ama":"Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology. Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology, vol. 118, Academic Press, 2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73."},"publication":"Theoretical Population Biology","page":"50 - 73","abstract":[{"text":"Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.","lang":"eng"}],"type":"journal_article","pubrep_id":"908","file":[{"creator":"system","file_size":1133924,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8","date_updated":"2020-07-14T12:47:25Z","date_created":"2018-12-12T10:12:45Z","file_id":"4964","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"626","intvolume":" 118","ddc":["576"],"status":"public","title":"The infinitesimal model: Definition derivation and implications","publication_identifier":{"issn":["00405809"]},"month":"12","doi":"10.1016/j.tpb.2017.06.001","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","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","publist_id":"7169","ec_funded":1,"file_date_updated":"2020-07-14T12:47:25Z","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Alison","last_name":"Etheridge","full_name":"Etheridge, Alison"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"volume":118,"date_updated":"2021-01-12T08:06:50Z","date_created":"2018-12-11T11:47:34Z","year":"2017","department":[{"_id":"NiBa"}],"publisher":"Academic Press","publication_status":"published"},{"file":[{"access_level":"open_access","file_name":"2017_ModelsAlgorithms_Chatterjee.pdf","creator":"dernst","file_size":192826,"content_type":"application/pdf","file_id":"7048","relation":"main_file","checksum":"b2402766ec02c79801aac634bd8f9f6c","date_updated":"2020-07-14T12:47:25Z","date_created":"2019-11-19T08:06:50Z"}],"oa_version":"Submitted Version","intvolume":" 10460","title":"The cost of exactness in quantitative reachability","ddc":["000"],"status":"public","_id":"625","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In the analysis of reactive systems a quantitative objective assigns a real value to every trace of the system. The value decision problem for a quantitative objective requires a trace whose value is at least a given threshold, and the exact value decision problem requires a trace whose value is exactly the threshold. We compare the computational complexity of the value and exact value decision problems for classical quantitative objectives, such as sum, discounted sum, energy, and mean-payoff for two standard models of reactive systems, namely, graphs and graph games."}],"alternative_title":["LNCS"],"type":"book_chapter","date_published":"2017-07-25T00:00:00Z","page":"367 - 381","citation":{"ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “The cost of exactness in quantitative reachability,” in Models, Algorithms, Logics and Tools, vol. 10460, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, and R. Mardare, Eds. Springer, 2017, pp. 367–381.","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2017). The cost of exactness in quantitative reachability. In L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, & R. Mardare (Eds.), Models, Algorithms, Logics and Tools (Vol. 10460, pp. 367–381). Springer. https://doi.org/10.1007/978-3-319-63121-9_18","ista":"Chatterjee K, Doyen L, Henzinger TA. 2017.The cost of exactness in quantitative reachability. In: Models, Algorithms, Logics and Tools. LNCS, vol. 10460, 367–381.","ama":"Chatterjee K, Doyen L, Henzinger TA. The cost of exactness in quantitative reachability. In: Aceto L, Bacci G, Ingólfsdóttir A, Legay A, Mardare R, eds. Models, Algorithms, Logics and Tools. Vol 10460. Theoretical Computer Science and General Issues. Springer; 2017:367-381. doi:10.1007/978-3-319-63121-9_18","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “The Cost of Exactness in Quantitative Reachability.” In Models, Algorithms, Logics and Tools, edited by Luca Aceto, Giorgio Bacci, Anna Ingólfsdóttir, Axel Legay, and Radu Mardare, 10460:367–81. Theoretical Computer Science and General Issues. Springer, 2017. https://doi.org/10.1007/978-3-319-63121-9_18.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, R. Mardare (Eds.), Models, Algorithms, Logics and Tools, Springer, 2017, pp. 367–381.","mla":"Chatterjee, Krishnendu, et al. “The Cost of Exactness in Quantitative Reachability.” Models, Algorithms, Logics and Tools, edited by Luca Aceto et al., vol. 10460, Springer, 2017, pp. 367–81, doi:10.1007/978-3-319-63121-9_18."},"publication":"Models, Algorithms, Logics and Tools","article_processing_charge":"No","has_accepted_license":"1","day":"25","series_title":"Theoretical Computer Science and General Issues","scopus_import":"1","volume":10460,"date_created":"2018-12-11T11:47:34Z","date_updated":"2022-05-23T08:54:02Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"editor":[{"first_name":"Luca","last_name":"Aceto","full_name":"Aceto, Luca"},{"full_name":"Bacci, Giorgio","last_name":"Bacci","first_name":"Giorgio"},{"first_name":"Anna","last_name":"Ingólfsdóttir","full_name":"Ingólfsdóttir, Anna"},{"last_name":"Legay","first_name":"Axel","full_name":"Legay, Axel"},{"last_name":"Mardare","first_name":"Radu","full_name":"Mardare, Radu"}],"publication_status":"published","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23 and S11407-N23 (RiSE/SHiNE), and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003.","year":"2017","ec_funded":1,"publist_id":"7170","file_date_updated":"2020-07-14T12:47:25Z","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-63121-9_18","project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"quality_controlled":"1","oa":1,"publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-319-63120-2"]},"month":"07"},{"publication_identifier":{"issn":["21678359"]},"month":"09","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","doi":"10.7717/peerj.3830","language":[{"iso":"eng"}],"article_number":"3830","publist_id":"7172","file_date_updated":"2020-07-14T12:47:24Z","year":"2017","acknowledgement":"Austrian Science Fund (FWF): M1697, P22249; Swiss National Science Foundation (SNF): 145706; European Commission;FWF Special Research Program: RNA-REG F43","department":[{"_id":"CaGu"}],"publisher":"PeerJ","publication_status":"published","author":[{"full_name":"Nikolic, Nela","last_name":"Nikolic","first_name":"Nela","orcid":"0000-0001-9068-6090","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Didara, Zrinka","first_name":"Zrinka","last_name":"Didara"},{"full_name":"Moll, Isabella","first_name":"Isabella","last_name":"Moll"}],"volume":2017,"date_created":"2018-12-11T11:47:33Z","date_updated":"2021-01-12T08:06:48Z","scopus_import":1,"has_accepted_license":"1","day":"21","citation":{"chicago":"Nikolic, Nela, Zrinka Didara, and Isabella Moll. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ. PeerJ, 2017. https://doi.org/10.7717/peerj.3830.","short":"N. Nikolic, Z. Didara, I. Moll, PeerJ 2017 (2017).","mla":"Nikolic, Nela, et al. “MazF Activation Promotes Translational Heterogeneity of the GrcA MRNA in Escherichia Coli Populations.” PeerJ, vol. 2017, no. 9, 3830, PeerJ, 2017, doi:10.7717/peerj.3830.","ieee":"N. Nikolic, Z. Didara, and I. Moll, “MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations,” PeerJ, vol. 2017, no. 9. PeerJ, 2017.","apa":"Nikolic, N., Didara, Z., & Moll, I. (2017). MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. PeerJ. https://doi.org/10.7717/peerj.3830","ista":"Nikolic N, Didara Z, Moll I. 2017. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017(9), 3830.","ama":"Nikolic N, Didara Z, Moll I. MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. 2017;2017(9). doi:10.7717/peerj.3830"},"publication":"PeerJ","date_published":"2017-09-21T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"lang":"eng","text":"Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein."}],"_id":"624","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2017","title":"MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations","ddc":["579"],"status":"public","pubrep_id":"909","file":[{"access_level":"open_access","file_name":"IST-2017-909-v1+1_peerj-3830.pdf","file_size":682064,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4908","checksum":"3d79ae6b6eabc90b0eaaed82ff3493b0","date_updated":"2020-07-14T12:47:24Z","date_created":"2018-12-12T10:11:51Z"}],"oa_version":"Published Version"},{"doi":"10.1007/978-3-319-63387-9_6","conference":{"end_date":"2017-07-28","location":"Heidelberg, Germany","start_date":"2017-07-24","name":"CAV: Computer Aided Verification"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00314"}],"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-331963386-2"]},"month":"01","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"full_name":"Murhekar, Aniket","last_name":"Murhekar","first_name":"Aniket"}],"volume":10426,"date_created":"2018-12-11T11:47:35Z","date_updated":"2021-01-12T08:06:55Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Springer","editor":[{"full_name":"Majumdar, Rupak","last_name":"Majumdar","first_name":"Rupak"},{"last_name":"Kunčak","first_name":"Viktor","full_name":"Kunčak, Viktor"}],"publication_status":"published","publist_id":"7166","ec_funded":1,"date_published":"2017-01-01T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Aniket Murhekar. “Automated Recurrence Analysis for Almost Linear Expected Runtime Bounds.” edited by Rupak Majumdar and Viktor Kunčak, 10426:118–39. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_6.","short":"K. Chatterjee, H. Fu, A. Murhekar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 118–139.","mla":"Chatterjee, Krishnendu, et al. Automated Recurrence Analysis for Almost Linear Expected Runtime Bounds. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 118–39, doi:10.1007/978-3-319-63387-9_6.","ieee":"K. Chatterjee, H. Fu, and A. Murhekar, “Automated recurrence analysis for almost linear expected runtime bounds,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 118–139.","apa":"Chatterjee, K., Fu, H., & Murhekar, A. (2017). Automated recurrence analysis for almost linear expected runtime bounds. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 118–139). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_6","ista":"Chatterjee K, Fu H, Murhekar A. 2017. Automated recurrence analysis for almost linear expected runtime bounds. CAV: Computer Aided Verification, LNCS, vol. 10426, 118–139.","ama":"Chatterjee K, Fu H, Murhekar A. Automated recurrence analysis for almost linear expected runtime bounds. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:118-139. doi:10.1007/978-3-319-63387-9_6"},"page":"118 - 139","day":"01","scopus_import":1,"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"628","intvolume":" 10426","title":"Automated recurrence analysis for almost linear expected runtime bounds","status":"public","abstract":[{"lang":"eng","text":"We consider the problem of developing automated techniques for solving recurrence relations to aid the expected-runtime analysis of programs. The motivation is that several classical textbook algorithms have quite efficient expected-runtime complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., Quick-Sort), or completely ineffective (e.g., Coupon-Collector). Since the main focus of expected-runtime analysis is to obtain efficient bounds, we consider bounds that are either logarithmic, linear or almost-linear (O(log n), O(n), O(n · log n), respectively, where n represents the input size). Our main contribution is an efficient (simple linear-time algorithm) sound approach for deriving such expected-runtime bounds for the analysis of recurrence relations induced by randomized algorithms. The experimental results show that our approach can efficiently derive asymptotically optimal expected-runtime bounds for recurrences of classical randomized algorithms, including Randomized-Search, Quick-Sort, Quick-Select, Coupon-Collector, where the worst-case bounds are either inefficient (such as linear as compared to logarithmic expected-runtime complexity, or quadratic as compared to linear or almost-linear expected-runtime complexity), or ineffective."}],"type":"conference","alternative_title":["LNCS"]},{"series_title":"Sub-Cellular Biochemistry","scopus_import":1,"day":"13","page":"419 - 444","publication":"Prokaryotic Cytoskeletons","citation":{"chicago":"Loose, Martin, Katja Zieske, and Petra Schwille. “Reconstitution of Protein Dynamics Involved in Bacterial Cell Division.” In Prokaryotic Cytoskeletons, 84:419–44. Sub-Cellular Biochemistry. Springer, 2017. https://doi.org/10.1007/978-3-319-53047-5_15.","short":"M. Loose, K. Zieske, P. Schwille, in:, Prokaryotic Cytoskeletons, Springer, 2017, pp. 419–444.","mla":"Loose, Martin, et al. “Reconstitution of Protein Dynamics Involved in Bacterial Cell Division.” Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp. 419–44, doi:10.1007/978-3-319-53047-5_15.","apa":"Loose, M., Zieske, K., & Schwille, P. (2017). Reconstitution of protein dynamics involved in bacterial cell division. In Prokaryotic Cytoskeletons (Vol. 84, pp. 419–444). Springer. https://doi.org/10.1007/978-3-319-53047-5_15","ieee":"M. Loose, K. Zieske, and P. Schwille, “Reconstitution of protein dynamics involved in bacterial cell division,” in Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp. 419–444.","ista":"Loose M, Zieske K, Schwille P. 2017.Reconstitution of protein dynamics involved in bacterial cell division. In: Prokaryotic Cytoskeletons. vol. 84, 419–444.","ama":"Loose M, Zieske K, Schwille P. Reconstitution of protein dynamics involved in bacterial cell division. In: Prokaryotic Cytoskeletons. Vol 84. Sub-Cellular Biochemistry. Springer; 2017:419-444. doi:10.1007/978-3-319-53047-5_15"},"date_published":"2017-05-13T00:00:00Z","type":"book_chapter","abstract":[{"text":"Even simple cells like bacteria have precisely regulated cellular anatomies, which allow them to grow, divide and to respond to internal or external cues with high fidelity. How spatial and temporal intracellular organization in prokaryotic cells is achieved and maintained on the basis of locally interacting proteins still remains largely a mystery. Bulk biochemical assays with purified components and in vivo experiments help us to approach key cellular processes from two opposite ends, in terms of minimal and maximal complexity. However, to understand how cellular phenomena emerge, that are more than the sum of their parts, we have to assemble cellular subsystems step by step from the bottom up. Here, we review recent in vitro reconstitution experiments with proteins of the bacterial cell division machinery and illustrate how they help to shed light on fundamental cellular mechanisms that constitute spatiotemporal order and regulate cell division.","lang":"eng"}],"title":"Reconstitution of protein dynamics involved in bacterial cell division","status":"public","intvolume":" 84","_id":"629","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","month":"05","publication_identifier":{"eisbn":["978-3-319-53047-5"]},"quality_controlled":"1","external_id":{"pmid":["28500535"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-53047-5_15","publist_id":"7165","publication_status":"published","publisher":"Springer","department":[{"_id":"MaLo"}],"year":"2017","pmid":1,"date_created":"2018-12-11T11:47:35Z","date_updated":"2021-01-12T08:06:57Z","volume":84,"author":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose"},{"first_name":"Katja","last_name":"Zieske","full_name":"Zieske, Katja"},{"full_name":"Schwille, Petra","first_name":"Petra","last_name":"Schwille"}]},{"author":[{"full_name":"Sauermann, Stefan","first_name":"Stefan","last_name":"Sauermann"},{"last_name":"David","first_name":"Veronika","full_name":"David, Veronika"},{"orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","full_name":"Schlögl, Alois"},{"first_name":"Reinhard","last_name":"Egelkraut","full_name":"Egelkraut, Reinhard"},{"full_name":"Frohner, Matthias","first_name":"Matthias","last_name":"Frohner"},{"last_name":"Pohn","first_name":"Birgit","full_name":"Pohn, Birgit"},{"last_name":"Urbauer","first_name":"Philipp","full_name":"Urbauer, Philipp"},{"first_name":"Alexander","last_name":"Mense","full_name":"Mense, Alexander"}],"date_created":"2018-12-11T11:47:36Z","date_updated":"2021-01-12T08:06:59Z","volume":236,"year":"2017","publication_status":"published","publisher":"IOS Press","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"file_date_updated":"2020-07-14T12:47:27Z","publist_id":"7164","license":"https://creativecommons.org/licenses/by-nc/4.0/","conference":{"name":"eHealth: Health Informatics Meets eHealth","start_date":"2017-05-23","location":"Vienna, Austria","end_date":"2017-05-24"},"doi":"10.3233/978-1-61499-759-7-356","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"quality_controlled":"1","month":"01","publication_identifier":{"isbn":["978-161499758-0"]},"pubrep_id":"906","file":[{"creator":"system","file_size":443635,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-906-v1+1_SHTI236-0356.pdf","checksum":"1254dcc5b04a996d97fad9a726b42727","date_created":"2018-12-12T10:11:56Z","date_updated":"2020-07-14T12:47:27Z","file_id":"4913","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"630","ddc":["005"],"title":"Biosignals standards and FHIR: The way to go","status":"public","intvolume":" 236","abstract":[{"lang":"eng","text":"Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years."}],"type":"conference","alternative_title":["Studies in Health Technology and Informatics"],"date_published":"2017-01-01T00:00:00Z","citation":{"mla":"Sauermann, Stefan, et al. Biosignals Standards and FHIR: The Way to Go. Vol. 236, IOS Press, 2017, pp. 356–62, doi:10.3233/978-1-61499-759-7-356.","short":"S. Sauermann, V. David, A. Schlögl, R. Egelkraut, M. Frohner, B. Pohn, P. Urbauer, A. Mense, in:, IOS Press, 2017, pp. 356–362.","chicago":"Sauermann, Stefan, Veronika David, Alois Schlögl, Reinhard Egelkraut, Matthias Frohner, Birgit Pohn, Philipp Urbauer, and Alexander Mense. “Biosignals Standards and FHIR: The Way to Go,” 236:356–62. IOS Press, 2017. https://doi.org/10.3233/978-1-61499-759-7-356.","ama":"Sauermann S, David V, Schlögl A, et al. Biosignals standards and FHIR: The way to go. In: Vol 236. IOS Press; 2017:356-362. doi:10.3233/978-1-61499-759-7-356","ista":"Sauermann S, David V, Schlögl A, Egelkraut R, Frohner M, Pohn B, Urbauer P, Mense A. 2017. Biosignals standards and FHIR: The way to go. eHealth: Health Informatics Meets eHealth, Studies in Health Technology and Informatics, vol. 236, 356–362.","ieee":"S. Sauermann et al., “Biosignals standards and FHIR: The way to go,” presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria, 2017, vol. 236, pp. 356–362.","apa":"Sauermann, S., David, V., Schlögl, A., Egelkraut, R., Frohner, M., Pohn, B., … Mense, A. (2017). Biosignals standards and FHIR: The way to go (Vol. 236, pp. 356–362). Presented at the eHealth: Health Informatics Meets eHealth, Vienna, Austria: IOS Press. https://doi.org/10.3233/978-1-61499-759-7-356"},"page":"356 - 362","day":"01","has_accepted_license":"1","scopus_import":1},{"month":"01","doi":"10.1090/proc/13468","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1509.09045","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"publist_id":"7160","ec_funded":1,"author":[{"full_name":"Lewin, Mathieu","first_name":"Mathieu","last_name":"Lewin"},{"full_name":"Nam, Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam","first_name":"Phan"},{"full_name":"Rougerie, Nicolas","last_name":"Rougerie","first_name":"Nicolas"}],"date_updated":"2021-01-12T08:07:03Z","date_created":"2018-12-11T11:47:36Z","volume":145,"year":"2017","publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"RoSe"}],"day":"01","scopus_import":1,"date_published":"2017-01-01T00:00:00Z","publication":"Proceedings of the American Mathematical Society","citation":{"mla":"Lewin, Mathieu, et al. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society, vol. 145, no. 6, American Mathematical Society, 2017, pp. 2441–54, doi:10.1090/proc/13468.","short":"M. Lewin, P. Nam, N. Rougerie, Proceedings of the American Mathematical Society 145 (2017) 2441–2454.","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/proc/13468.","ama":"Lewin M, Nam P, Rougerie N. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 2017;145(6):2441-2454. doi:10.1090/proc/13468","ista":"Lewin M, Nam P, Rougerie N. 2017. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 145(6), 2441–2454.","apa":"Lewin, M., Nam, P., & Rougerie, N. (2017). A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/13468","ieee":"M. Lewin, P. Nam, and N. Rougerie, “A note on 2D focusing many boson systems,” Proceedings of the American Mathematical Society, vol. 145, no. 6. American Mathematical Society, pp. 2441–2454, 2017."},"page":"2441 - 2454","abstract":[{"lang":"eng","text":"We consider a 2D quantum system of N bosons in a trapping potential |x|s, interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all 0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of the many-body system is described in the large N limit by the corresponding cubic nonlinear Schrödinger energy functional. Our result covers the focusing case (w < 0) where even the stability of the many-body system is not obvious. This answers an open question mentioned by X. Chen and J. Holmer for harmonic traps (s = 2). Together with the BBGKY hierarchy approach used by these authors, our result implies the convergence of the many-body quantum dynamics to the focusing NLS equation with harmonic trap for all 0 < β < 3/4. "}],"issue":"6","type":"journal_article","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"632","title":"A note on 2D focusing many boson systems","status":"public","intvolume":" 145"},{"page":"189 - 211","publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","citation":{"chicago":"Schroeder, Jan, Elena Deliu, Gaia Novarino, and Michael Schmeisser. “Genetic and Pharmacological Reversibility of Phenotypes in Mouse Models of Autism Spectrum Disorder.” In Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, 224:189–211. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_10.","short":"J. Schroeder, E. Deliu, G. Novarino, M. Schmeisser, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 189–211.","mla":"Schroeder, Jan, et al. “Genetic and Pharmacological Reversibility of Phenotypes in Mouse Models of Autism Spectrum Disorder.” Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 189–211, doi:10.1007/978-3-319-52498-6_10.","apa":"Schroeder, J., Deliu, E., Novarino, G., & Schmeisser, M. (2017). Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 189–211). Springer. https://doi.org/10.1007/978-3-319-52498-6_10","ieee":"J. Schroeder, E. Deliu, G. Novarino, and M. Schmeisser, “Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder,” in Translational Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 189–211.","ista":"Schroeder J, Deliu E, Novarino G, Schmeisser M. 2017.Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 189–211.","ama":"Schroeder J, Deliu E, Novarino G, Schmeisser M. Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. Translational Anatomy and Cell Biology of Autism Spectrum Disorder. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:189-211. doi:10.1007/978-3-319-52498-6_10"},"date_published":"2017-05-28T00:00:00Z","series_title":"Advances in Anatomy Embryology and Cell Biology","scopus_import":1,"day":"28","title":"Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder","status":"public","intvolume":" 224","_id":"634","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","alternative_title":["ADVSANAT"],"type":"book_chapter","abstract":[{"text":"As autism spectrum disorder (ASD) is largely regarded as a neurodevelopmental condition, long-time consensus was that its hallmark features are irreversible. However, several studies from recent years using defined mouse models of ASD have provided clear evidence that in mice neurobiological and behavioural alterations can be ameliorated or even reversed by genetic restoration or pharmacological treatment either before or after symptom onset. Here, we review findings on genetic and pharmacological reversibility of phenotypes in mouse models of ASD. Our review should give a comprehensive overview on both aspects and encourage future studies to better understand the underlying molecular mechanisms that might be translatable from animals to humans.","lang":"eng"}],"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Transmembrane Transporters in Health and Disease","_id":"25473368-B435-11E9-9278-68D0E5697425","grant_number":"F03523"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-52498-6_10","month":"05","publication_identifier":{"eisbn":["978-3-319-52498-6"]},"publication_status":"published","editor":[{"last_name":"Schmeisser","first_name":"Michael","full_name":"Schmeisser, Michael"},{"last_name":"Boekers","first_name":"Tobias","full_name":"Boekers, Tobias"}],"publisher":"Springer","department":[{"_id":"GaNo"}],"year":"2017","date_created":"2018-12-11T11:47:37Z","date_updated":"2021-01-12T08:07:08Z","volume":224,"author":[{"full_name":"Schroeder, Jan","first_name":"Jan","last_name":"Schroeder"},{"full_name":"Deliu, Elena","last_name":"Deliu","first_name":"Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"},{"full_name":"Schmeisser, Michael","first_name":"Michael","last_name":"Schmeisser"}],"publist_id":"7156"},{"project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"}],"quality_controlled":"1","doi":"10.1007/978-3-319-63501-9_6","conference":{"location":"Heidelberg, Germany","start_date":"2017-07-22","end_date":"2017-07-23","name":"NSV: Numerical Software Verification"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331963500-2"]},"month":"01","year":"2017","publisher":"Springer","editor":[{"last_name":"Abate","first_name":"Alessandro","full_name":"Abate, Alessandro"},{"full_name":"Bodo, Sylvie","last_name":"Bodo","first_name":"Sylvie"}],"department":[{"_id":"ToHe"}],"publication_status":"published","author":[{"full_name":"Bak, Stanley","last_name":"Bak","first_name":"Stanley"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"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":"Aviral","last_name":"Kumar","full_name":"Kumar, Aviral"}],"volume":10381,"date_created":"2018-12-11T11:47:37Z","date_updated":"2021-01-12T08:07:06Z","publist_id":"7159","citation":{"ieee":"S. Bak, S. Bogomolov, T. A. Henzinger, and A. Kumar, “Challenges and tool implementation of hybrid rapidly exploring random trees,” presented at the NSV: Numerical Software Verification, Heidelberg, Germany, 2017, vol. 10381, pp. 83–89.","apa":"Bak, S., Bogomolov, S., Henzinger, T. A., & Kumar, A. (2017). Challenges and tool implementation of hybrid rapidly exploring random trees. In A. Abate & S. Bodo (Eds.) (Vol. 10381, pp. 83–89). Presented at the NSV: Numerical Software Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63501-9_6","ista":"Bak S, Bogomolov S, Henzinger TA, Kumar A. 2017. Challenges and tool implementation of hybrid rapidly exploring random trees. NSV: Numerical Software Verification, LNCS, vol. 10381, 83–89.","ama":"Bak S, Bogomolov S, Henzinger TA, Kumar A. Challenges and tool implementation of hybrid rapidly exploring random trees. In: Abate A, Bodo S, eds. Vol 10381. Springer; 2017:83-89. doi:10.1007/978-3-319-63501-9_6","chicago":"Bak, Stanley, Sergiy Bogomolov, Thomas A Henzinger, and Aviral Kumar. “Challenges and Tool Implementation of Hybrid Rapidly Exploring Random Trees.” edited by Alessandro Abate and Sylvie Bodo, 10381:83–89. Springer, 2017. https://doi.org/10.1007/978-3-319-63501-9_6.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, A. Kumar, in:, A. Abate, S. Bodo (Eds.), Springer, 2017, pp. 83–89.","mla":"Bak, Stanley, et al. Challenges and Tool Implementation of Hybrid Rapidly Exploring Random Trees. Edited by Alessandro Abate and Sylvie Bodo, vol. 10381, Springer, 2017, pp. 83–89, doi:10.1007/978-3-319-63501-9_6."},"page":"83 - 89","date_published":"2017-01-01T00:00:00Z","scopus_import":1,"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"633","intvolume":" 10381","title":"Challenges and tool implementation of hybrid rapidly exploring random trees","status":"public","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"A Rapidly-exploring Random Tree (RRT) is an algorithm which can search a non-convex region of space by incrementally building a space-filling tree. The tree is constructed from random points drawn from system’s state space and is biased to grow towards large unexplored areas in the system. RRT can provide better coverage of a system’s possible behaviors compared with random simulations, but is more lightweight than full reachability analysis. In this paper, we explore some of the design decisions encountered while implementing a hybrid extension of the RRT algorithm, which have not been elaborated on before. In particular, we focus on handling non-determinism, which arises due to discrete transitions. We introduce the notion of important points to account for this phenomena. We showcase our ideas using heater and navigation benchmarks.","lang":"eng"}]},{"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"635","intvolume":" 10212","title":"Scrypt is maximally memory hard","status":"public","abstract":[{"lang":"eng","text":"Memory-hard functions (MHFs) are hash algorithms whose evaluation cost is dominated by memory cost. As memory, unlike computation, costs about the same across different platforms, MHFs cannot be evaluated at significantly lower cost on dedicated hardware like ASICs. MHFs have found widespread applications including password hashing, key derivation, and proofs-of-work. This paper focuses on scrypt, a simple candidate MHF designed by Percival, and described in RFC 7914. It has been used within a number of cryptocurrencies (e.g., Litecoin and Dogecoin) and has been an inspiration for Argon2d, one of the winners of the recent password-hashing competition. Despite its popularity, no rigorous lower bounds on its memory complexity are known. We prove that scrypt is optimally memory-hard, i.e., its cumulative memory complexity (cmc) in the parallel random oracle model is Ω(n2w), where w and n are the output length and number of invocations of the underlying hash function, respectively. High cmc is a strong security target for MHFs introduced by Alwen and Serbinenko (STOC’15) which implies high memory cost even for adversaries who can amortize the cost over many evaluations and evaluate the underlying hash functions many times in parallel. Our proof is the first showing optimal memory-hardness for any MHF. Our result improves both quantitatively and qualitatively upon the recent work by Alwen et al. (EUROCRYPT’16) who proved a weaker lower bound of Ω(n2w/ log2 n) for a restricted class of adversaries."}],"type":"conference","alternative_title":["LNCS"],"date_published":"2017-01-01T00:00:00Z","citation":{"short":"J.F. Alwen, B. Chen, K.Z. Pietrzak, L. Reyzin, S. Tessaro, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 33–62.","mla":"Alwen, Joel F., et al. Scrypt Is Maximally Memory Hard. Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 33–62, doi:10.1007/978-3-319-56617-7_2.","chicago":"Alwen, Joel F, Binchi Chen, Krzysztof Z Pietrzak, Leonid Reyzin, and Stefano Tessaro. “Scrypt Is Maximally Memory Hard.” edited by Jean-Sébastien Coron and Jesper Buus Nielsen, 10212:33–62. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_2.","ama":"Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. Scrypt is maximally memory hard. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:33-62. doi:10.1007/978-3-319-56617-7_2","ieee":"J. F. Alwen, B. Chen, K. Z. Pietrzak, L. Reyzin, and S. Tessaro, “Scrypt is maximally memory hard,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 33–62.","apa":"Alwen, J. F., Chen, B., Pietrzak, K. Z., Reyzin, L., & Tessaro, S. (2017). Scrypt is maximally memory hard. In J.-S. Coron & J. Buus Nielsen (Eds.) (Vol. 10212, pp. 33–62). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_2","ista":"Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. 2017. Scrypt is maximally memory hard. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 10212, 33–62."},"page":"33 - 62","day":"01","scopus_import":1,"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen","full_name":"Alwen, Joel F"},{"last_name":"Chen","first_name":"Binchi","full_name":"Chen, Binchi"},{"full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"full_name":"Reyzin, Leonid","last_name":"Reyzin","first_name":"Leonid"},{"last_name":"Tessaro","first_name":"Stefano","full_name":"Tessaro, Stefano"}],"volume":10212,"date_created":"2018-12-11T11:47:37Z","date_updated":"2021-01-12T08:07:10Z","year":"2017","editor":[{"last_name":"Coron","first_name":"Jean-Sébastien","full_name":"Coron, Jean-Sébastien"},{"full_name":"Buus Nielsen, Jesper","first_name":"Jesper","last_name":"Buus Nielsen"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"publication_status":"published","publist_id":"7154","ec_funded":1,"doi":"10.1007/978-3-319-56617-7_2","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","location":"Paris, France","start_date":"2017-04-30","end_date":"2017-05-04"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/989"}],"oa":1,"project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-331956616-0"]},"month":"01"},{"publist_id":"7152","publisher":"Springer","department":[{"_id":"ToHe"}],"editor":[{"full_name":"Abate, Alessandro","first_name":"Alessandro","last_name":"Abate"},{"last_name":"Geeraerts","first_name":"Gilles","full_name":"Geeraerts, Gilles"}],"publication_status":"published","year":"2017","volume":10419,"date_created":"2018-12-11T11:47:38Z","date_updated":"2021-01-12T08:07:14Z","author":[{"last_name":"Bakhirkin","first_name":"Alexey","full_name":"Bakhirkin, Alexey"},{"full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","first_name":"Thomas","last_name":"Ferrere"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"last_name":"Ulus","first_name":"Dogan","full_name":"Ulus, Dogan"}],"publication_identifier":{"isbn":["978-331965764-6"]},"month":"08","project":[{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01552132"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-65765-3_11","conference":{"end_date":"2017-09-07","start_date":"2017-09-05","location":"Berlin, Germany","name":"FORMATS: Formal Modelling and Analysis of Timed Systems"},"alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Signal regular expressions can specify sequential properties of real-valued signals based on threshold conditions, regular operations, and duration constraints. In this paper we endow them with a quantitative semantics which indicates how robustly a signal matches or does not match a given expression. First, we show that this semantics is a safe approximation of a distance between the signal and the language defined by the expression. Then, we consider the robust matching problem, that is, computing the quantitative semantics of every segment of a given signal relative to an expression. We present an algorithm that solves this problem for piecewise-constant and piecewise-linear signals and show that for such signals the robustness map is a piecewise-linear function. The availability of an indicator describing how robustly a signal segment matches some regular pattern provides a general framework for quantitative monitoring of cyber-physical systems.","lang":"eng"}],"intvolume":" 10419","title":"On the quantitative semantics of regular expressions over real-valued signals","status":"public","_id":"636","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":1,"day":"03","page":"189 - 206","citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Oded Maler, and Dogan Ulus. “On the Quantitative Semantics of Regular Expressions over Real-Valued Signals.” edited by Alessandro Abate and Gilles Geeraerts, 10419:189–206. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_11.","short":"A. Bakhirkin, T. Ferrere, O. Maler, D. Ulus, in:, A. Abate, G. Geeraerts (Eds.), Springer, 2017, pp. 189–206.","mla":"Bakhirkin, Alexey, et al. On the Quantitative Semantics of Regular Expressions over Real-Valued Signals. Edited by Alessandro Abate and Gilles Geeraerts, vol. 10419, Springer, 2017, pp. 189–206, doi:10.1007/978-3-319-65765-3_11.","ieee":"A. Bakhirkin, T. Ferrere, O. Maler, and D. Ulus, “On the quantitative semantics of regular expressions over real-valued signals,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 189–206.","apa":"Bakhirkin, A., Ferrere, T., Maler, O., & Ulus, D. (2017). On the quantitative semantics of regular expressions over real-valued signals. In A. Abate & G. Geeraerts (Eds.) (Vol. 10419, pp. 189–206). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. https://doi.org/10.1007/978-3-319-65765-3_11","ista":"Bakhirkin A, Ferrere T, Maler O, Ulus D. 2017. On the quantitative semantics of regular expressions over real-valued signals. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 189–206.","ama":"Bakhirkin A, Ferrere T, Maler O, Ulus D. On the quantitative semantics of regular expressions over real-valued signals. In: Abate A, Geeraerts G, eds. Vol 10419. Springer; 2017:189-206. doi:10.1007/978-3-319-65765-3_11"},"date_published":"2017-08-03T00:00:00Z"},{"status":"public","publication_status":"published","title":"Numerical Software Verification","department":[{"_id":"ToHe"}],"editor":[{"full_name":"Bogomolov, Sergiy","first_name":"Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0686-0365"},{"first_name":"Matthieu","last_name":"Martel","full_name":"Martel, Matthieu"},{"full_name":"Prabhakar, Pavithra","first_name":"Pavithra","last_name":"Prabhakar"}],"intvolume":" 10152","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"638","year":"2017","date_created":"2018-12-11T11:47:38Z","date_updated":"2022-05-24T07:09:52Z","oa_version":"None","volume":10152,"type":"conference_editor","abstract":[{"lang":"eng","text":"This book constitutes the refereed proceedings of the 9th InternationalWorkshop on Numerical Software Verification, NSV 2016, held in Toronto, ON, Canada in July 2011 - colocated with CAV 2016, the 28th International Conference on Computer Aided Verification.\r\nThe NSV workshop is dedicated to the development of logical and mathematical techniques for the reasoning about programmability and reliability."}],"publist_id":"7150","quality_controlled":"1","citation":{"chicago":"Bogomolov, Sergiy, Matthieu Martel, and Pavithra Prabhakar, eds. Numerical Software Verification. Vol. 10152. LNCS. Springer, 2017. https://doi.org/10.1007/978-3-319-54292-8.","short":"S. Bogomolov, M. Martel, P. Prabhakar, eds., Numerical Software Verification, Springer, 2017.","mla":"Bogomolov, Sergiy, et al., editors. Numerical Software Verification. Vol. 10152, Springer, 2017, doi:10.1007/978-3-319-54292-8.","apa":"Bogomolov, S., Martel, M., & Prabhakar, P. (Eds.). (2017). Numerical Software Verification (Vol. 10152). Presented at the NSV: Numerical Software Verification, Toronto, ON, Canada: Springer. https://doi.org/10.1007/978-3-319-54292-8","ieee":"S. Bogomolov, M. Martel, and P. Prabhakar, Eds., Numerical Software Verification, vol. 10152. Springer, 2017.","ista":"Bogomolov S, Martel M, Prabhakar P eds. 2017. Numerical Software Verification, Springer,p.","ama":"Bogomolov S, Martel M, Prabhakar P, eds. Numerical Software Verification. Vol 10152. Springer; 2017. doi:10.1007/978-3-319-54292-8"},"language":[{"iso":"eng"}],"conference":{"end_date":"2016-07-18","start_date":"2016-07-17","location":"Toronto, ON, Canada","name":"NSV: Numerical Software Verification"},"date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-54292-8","series_title":"LNCS","month":"01","day":"01","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-54292-8"]},"article_processing_charge":"No"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Data-independent Memory Hard Functions (iMHFS) are finding a growing number of applications in security; especially in the domain of password hashing. An important property of a concrete iMHF is specified by fixing a directed acyclic graph (DAG) Gn on n nodes. The quality of that iMHF is then captured by the following two pebbling complexities of Gn: – The parallel cumulative pebbling complexity Π∥cc(Gn) must be as high as possible (to ensure that the amortized cost of computing the function on dedicated hardware is dominated by the cost of memory). – The sequential space-time pebbling complexity Πst(Gn) should be as close as possible to Π∥cc(Gn) (to ensure that using many cores in parallel and amortizing over many instances does not give much of an advantage). In this paper we construct a family of DAGs with best possible parameters in an asymptotic sense, i.e., where Π∥cc(Gn) = Ω(n2/ log(n)) (which matches a known upper bound) and Πst(Gn) is within a constant factor of Π∥cc(Gn). Our analysis relies on a new connection between the pebbling complexity of a DAG and its depth-robustness (DR) – a well studied combinatorial property. We show that high DR is sufficient for high Π∥cc. Alwen and Blocki (CRYPTO’16) showed that high DR is necessary and so, together, these results fully characterize DAGs with high Π∥cc in terms of DR. Complementing these results, we provide new upper and lower bounds on the Π∥cc of several important candidate iMHFs from the literature. We give the first lower bounds on the memory hardness of the Catena and Balloon Hashing functions in a parallel model of computation and we give the first lower bounds of any kind for (a version) of Argon2i. Finally we describe a new class of pebbling attacks improving on those of Alwen and Blocki (CRYPTO’16). By instantiating these attacks we upperbound the Π∥cc of the Password Hashing Competition winner Argon2i and one of the Balloon Hashing functions by O (n1.71). We also show an upper bound of O(n1.625) for the Catena functions and the two remaining Balloon Hashing functions.","lang":"eng"}],"_id":"640","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 10212","title":"Depth-robust graphs and their cumulative memory complexity","status":"public","oa_version":"Submitted Version","scopus_import":1,"day":"01","citation":{"mla":"Alwen, Joel F., et al. Depth-Robust Graphs and Their Cumulative Memory Complexity. Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 3–32, doi:10.1007/978-3-319-56617-7_1.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 3–32.","chicago":"Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Depth-Robust Graphs and Their Cumulative Memory Complexity.” edited by Jean-Sébastien Coron and Jesper Buus Nielsen, 10212:3–32. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_1.","ama":"Alwen JF, Blocki J, Pietrzak KZ. Depth-robust graphs and their cumulative memory complexity. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:3-32. doi:10.1007/978-3-319-56617-7_1","ista":"Alwen JF, Blocki J, Pietrzak KZ. 2017. Depth-robust graphs and their cumulative memory complexity. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 10212, 3–32.","ieee":"J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Depth-robust graphs and their cumulative memory complexity,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France, 2017, vol. 10212, pp. 3–32.","apa":"Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2017). Depth-robust graphs and their cumulative memory complexity. In J.-S. Coron & J. Buus Nielsen (Eds.) (Vol. 10212, pp. 3–32). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Paris, France: Springer. https://doi.org/10.1007/978-3-319-56617-7_1"},"page":"3 - 32","date_published":"2017-04-01T00:00:00Z","ec_funded":1,"publist_id":"7148","year":"2017","department":[{"_id":"KrPi"}],"publisher":"Springer","editor":[{"full_name":"Coron, Jean-Sébastien","last_name":"Coron","first_name":"Jean-Sébastien"},{"last_name":"Buus Nielsen","first_name":"Jesper","full_name":"Buus Nielsen, Jesper"}],"publication_status":"published","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"volume":10212,"date_updated":"2021-01-12T08:07:22Z","date_created":"2018-12-11T11:47:39Z","publication_identifier":{"isbn":["978-331956616-0"]},"month":"04","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/875"}],"oa":1,"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"quality_controlled":"1","doi":"10.1007/978-3-319-56617-7_1","conference":{"location":"Paris, France","start_date":"2017-04-30","end_date":"2017-05-04","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"language":[{"iso":"eng"}]},{"scopus_import":1,"publication_identifier":{"isbn":["978-331958770-7"]},"month":"01","day":"01","page":"323 - 334","quality_controlled":"1","citation":{"chicago":"Trajkovska, Vera, Paul Swoboda, Freddie Åström, and Stefanie Petra. “Graphical Model Parameter Learning by Inverse Linear Programming.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:323–34. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_26.","short":"V. Trajkovska, P. Swoboda, F. Åström, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 323–334.","mla":"Trajkovska, Vera, et al. Graphical Model Parameter Learning by Inverse Linear Programming. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 323–34, doi:10.1007/978-3-319-58771-4_26.","ieee":"V. Trajkovska, P. Swoboda, F. Åström, and S. Petra, “Graphical model parameter learning by inverse linear programming,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 323–334.","apa":"Trajkovska, V., Swoboda, P., Åström, F., & Petra, S. (2017). Graphical model parameter learning by inverse linear programming. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 323–334). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_26","ista":"Trajkovska V, Swoboda P, Åström F, Petra S. 2017. Graphical model parameter learning by inverse linear programming. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 323–334.","ama":"Trajkovska V, Swoboda P, Åström F, Petra S. Graphical model parameter learning by inverse linear programming. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:323-334. doi:10.1007/978-3-319-58771-4_26"},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-58771-4_26","date_published":"2017-01-01T00:00:00Z","conference":{"name":"SSVM: Scale Space and Variational Methods in Computer Vision","location":"Kolding, Denmark","start_date":"2017-06-04","end_date":"2017-06-08"},"alternative_title":["LNCS"],"type":"conference","publist_id":"7147","abstract":[{"lang":"eng","text":"We introduce two novel methods for learning parameters of graphical models for image labelling. The following two tasks underline both methods: (i) perturb model parameters based on given features and ground truth labelings, so as to exactly reproduce these labelings as optima of the local polytope relaxation of the labelling problem; (ii) train a predictor for the perturbed model parameters so that improved model parameters can be applied to the labelling of novel data. Our first method implements task (i) by inverse linear programming and task (ii) using a regressor e.g. a Gaussian process. Our second approach simultaneously solves tasks (i) and (ii) in a joint manner, while being restricted to linearly parameterised predictors. Experiments demonstrate the merits of both approaches."}],"publisher":"Springer","intvolume":" 10302","department":[{"_id":"VlKo"}],"editor":[{"last_name":"Lauze","first_name":"François","full_name":"Lauze, François"},{"first_name":"Yiqiu","last_name":"Dong","full_name":"Dong, Yiqiu"},{"last_name":"Bjorholm Dahl","first_name":"Anders","full_name":"Bjorholm Dahl, Anders"}],"status":"public","publication_status":"published","title":"Graphical model parameter learning by inverse linear programming","_id":"641","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","volume":10302,"oa_version":"None","date_created":"2018-12-11T11:47:39Z","date_updated":"2021-01-12T08:07:23Z","author":[{"full_name":"Trajkovska, Vera","first_name":"Vera","last_name":"Trajkovska"},{"full_name":"Swoboda, Paul","first_name":"Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Åström, Freddie","first_name":"Freddie","last_name":"Åström"},{"first_name":"Stefanie","last_name":"Petra","full_name":"Petra, Stefanie"}]},{"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","month":"08","day":"04","citation":{"ama":"Henzinger TA, Kragl B, Qadeer S. Synchronizing the Asynchronous. IST Austria; 2017. doi:10.15479/AT:IST-2018-853-v2-2","ista":"Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST Austria, 28p.","ieee":"T. A. Henzinger, B. Kragl, and S. Qadeer, Synchronizing the asynchronous. IST Austria, 2017.","apa":"Henzinger, T. A., Kragl, B., & Qadeer, S. (2017). Synchronizing the asynchronous. IST Austria. https://doi.org/10.15479/AT:IST-2018-853-v2-2","mla":"Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria, 2017, doi:10.15479/AT:IST-2018-853-v2-2.","short":"T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST Austria, 2017.","chicago":"Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. Synchronizing the Asynchronous. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2018-853-v2-2."},"oa":1,"page":"28","doi":"10.15479/AT:IST-2018-853-v2-2","date_published":"2017-08-04T00:00:00Z","language":[{"iso":"eng"}],"type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent asynchronous computation threads. We show that specifications and correctness proofs for asynchronous programs can be structured by introducing the fiction, for proof purposes, that intermediate, non-quiescent states of asynchronous operations can be ignored. Then, the task of specification becomes relatively simple and the task of verification can be naturally decomposed into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure of an asynchronous program, the atomic effect of non-atomic operations and the synchronous effect of asynchronous operations. This structuring of specifications and proofs corresponds to the introduction of multiple layers of stepwise refinement for asynchronous programs. We present the first proof rule, called synchronization, to reduce asynchronous invocations on a lower layer to synchronous invocations on a higher layer. We implemented our proof method in CIVL and evaluated it on a collection of benchmark programs."}],"file_date_updated":"2020-07-14T12:47:30Z","_id":"6426","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"publisher":"IST Austria","publication_status":"published","status":"public","ddc":["000"],"title":"Synchronizing the asynchronous","related_material":{"record":[{"id":"133","relation":"later_version","status":"public"}]},"author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","first_name":"Bernhard","full_name":"Kragl, Bernhard"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"oa_version":"Published Version","file":[{"checksum":"b48d42725182d7ca10107a118815f4cf","date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-13T08:14:44Z","file_id":"6431","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":971347,"access_level":"open_access","file_name":"main(1).pdf"}],"date_updated":"2023-02-21T16:59:21Z","date_created":"2019-05-13T08:15:55Z"},{"date_published":"2017-08-31T00:00:00Z","publication":"Chinese Journal of Physiology","citation":{"mla":"Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology, vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:10.4077/CJP.2017.BAF469.","short":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology 60 (2017) 207–214.","chicago":"Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469.","ama":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469","ista":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 60(4), 207–214.","apa":"Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469","ieee":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp. 207–214, 2017."},"article_type":"original","page":"207 - 214","day":"31","article_processing_charge":"No","scopus_import":1,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"643","title":"Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats","status":"public","ddc":["570"],"intvolume":" 60","abstract":[{"text":"It has been reported that nicotinamide-overload induces oxidative stress associated with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT) were also carried out in adult Sprague-Dawley rats treated with or without cumulative doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration significantly increased the plasma H2O2 levels associated with high insulin levels. Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration of nicotinic acid, another form of Vitamin B3, also significantly increased plasma insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic acid or nicotinamide impaired glucose metabolism. This study suggested that excess Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance.","lang":"eng"}],"issue":"4","type":"journal_article","doi":"10.4077/CJP.2017.BAF469","language":[{"iso":"eng"}],"external_id":{"pmid":["28847140"]},"quality_controlled":"1","month":"08","publication_identifier":{"issn":["03044920"]},"author":[{"last_name":"Sun","first_name":"Wuping","full_name":"Sun, Wuping"},{"full_name":"Zhai, Ming-Zhu","first_name":"Ming-Zhu","last_name":"Zhai","id":"34009CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhou","first_name":"Qian","full_name":"Zhou, Qian"},{"full_name":"Qian, Chengrui","last_name":"Qian","first_name":"Chengrui"},{"full_name":"Jiang, Changyu","last_name":"Jiang","first_name":"Changyu"}],"date_created":"2018-12-11T11:47:40Z","date_updated":"2021-01-12T08:07:28Z","volume":60,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"RySh"}],"publisher":"Chinese Physiological Society","publist_id":"7142"},{"publist_id":"7144","author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","first_name":"Mate","full_name":"Gerencser, Mate"},{"full_name":"Gyöngy, István","last_name":"Gyöngy","first_name":"István"}],"volume":86,"date_updated":"2021-01-12T08:07:26Z","date_created":"2018-12-11T11:47:40Z","year":"2017","department":[{"_id":"JaMa"}],"publisher":"American Mathematical Society","publication_status":"published","publication_identifier":{"issn":["00255718"]},"month":"01","doi":"10.1090/mcom/3201","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.05535"}],"oa":1,"quality_controlled":"1","issue":"307","abstract":[{"lang":"eng","text":"Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"642","intvolume":" 86","status":"public","title":"Localization errors in solving stochastic partial differential equations in the whole space","day":"01","scopus_import":1,"date_published":"2017-01-01T00:00:00Z","citation":{"ama":"Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397. doi:10.1090/mcom/3201","ista":"Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 86(307), 2373–2397.","apa":"Gerencser, M., & Gyöngy, I. (2017). Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. American Mathematical Society. https://doi.org/10.1090/mcom/3201","ieee":"M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial differential equations in the whole space,” Mathematics of Computation, vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017.","mla":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation, vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201.","short":"M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.","chicago":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation. American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201."},"publication":"Mathematics of Computation","page":"2373 - 2397"},{"publist_id":"7135","ec_funded":1,"author":[{"last_name":"Ashok","first_name":"Pranav","full_name":"Ashok, Pranav"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","full_name":"Daca, Przemyslaw"},{"full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky"},{"last_name":"Meggendorfer","first_name":"Tobias","full_name":"Meggendorfer, Tobias"}],"volume":10426,"date_created":"2018-12-11T11:47:41Z","date_updated":"2021-01-12T08:07:32Z","year":"2017","editor":[{"full_name":"Majumdar, Rupak","first_name":"Rupak","last_name":"Majumdar"},{"full_name":"Kunčak, Viktor","first_name":"Viktor","last_name":"Kunčak"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","publication_identifier":{"isbn":["978-331963386-2"]},"month":"07","doi":"10.1007/978-3-319-63387-9_10","conference":{"name":"CAV: Computer Aided Verification","end_date":"2017-07-28","location":"Heidelberg, Germany","start_date":"2017-07-24"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02326"}],"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","abstract":[{"text":"Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"645","intvolume":" 10426","title":"Value iteration for long run average reward in markov decision processes","status":"public","day":"13","scopus_import":1,"date_published":"2017-07-13T00:00:00Z","citation":{"chicago":"Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_10.","mla":"Ashok, Pranav, et al. Value Iteration for Long Run Average Reward in Markov Decision Processes. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 201–21, doi:10.1007/978-3-319-63387-9_10.","short":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221.","ista":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration for long run average reward in markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 10426, 201–221.","ieee":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, and T. Meggendorfer, “Value iteration for long run average reward in markov decision processes,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 201–221.","apa":"Ashok, P., Chatterjee, K., Daca, P., Kretinsky, J., & Meggendorfer, T. (2017). Value iteration for long run average reward in markov decision processes. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10426, pp. 201–221). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63387-9_10","ama":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration for long run average reward in markov decision processes. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:201-221. doi:10.1007/978-3-319-63387-9_10"},"page":"201 - 221"},{"day":"29","scopus_import":1,"date_published":"2017-06-29T00:00:00Z","page":"1087 - 1110","citation":{"short":"V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017) 1087–1110.","mla":"Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:10.1137/16M1091836.","chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2017. https://doi.org/10.1137/16M1091836.","ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. SIAM Journal on Computing. 2017;46(3):1087-1110. doi:10.1137/16M1091836","apa":"Kolmogorov, V., Krokhin, A., & Rolinek, M. (2017). The complexity of general-valued CSPs. SIAM Journal on Computing. SIAM. https://doi.org/10.1137/16M1091836","ieee":"V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” SIAM Journal on Computing, vol. 46, no. 3. SIAM, pp. 1087–1110, 2017.","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued CSPs. SIAM Journal on Computing. 46(3), 1087–1110."},"publication":"SIAM Journal on Computing","issue":"3","abstract":[{"lang":"eng","text":"An instance of the valued constraint satisfaction problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P 6= NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in f0;1g corresponds to ordinary CSPs, where one deals only with the feasibility issue, and there is no optimization. This case is the subject of the algebraic CSP dichotomy conjecture predicting for which constraint languages CSPs are tractable (i.e., solvable in polynomial time) and for which they are NP-hard. The case when all allowed functions take only finite values corresponds to a finitevalued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Živný. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e., the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 46","status":"public","title":"The complexity of general-valued CSPs","_id":"644","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","language":[{"iso":"eng"}],"doi":"10.1137/16M1091836","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1502.07327","open_access":"1"}],"ec_funded":1,"publist_id":"7138","volume":46,"date_updated":"2023-02-23T10:07:49Z","date_created":"2018-12-11T11:47:40Z","related_material":{"record":[{"relation":"other","status":"public","id":"1637"}]},"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"last_name":"Krokhin","first_name":"Andrei","full_name":"Krokhin, Andrei"},{"first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal"}],"publisher":"SIAM","department":[{"_id":"VlKo"}],"publication_status":"published","year":"2017"},{"publication_status":"published","department":[{"_id":"VlKo"}],"publisher":"Springer","editor":[{"first_name":"François","last_name":"Lauze","full_name":"Lauze, François"},{"first_name":"Yiqiu","last_name":"Dong","full_name":"Dong, Yiqiu"},{"first_name":"Anders","last_name":"Bjorholm Dahl","full_name":"Bjorholm Dahl, Anders"}],"year":"2017","date_created":"2018-12-11T11:47:41Z","date_updated":"2021-01-12T08:07:34Z","volume":10302,"author":[{"last_name":"Kuske","first_name":"Jan","full_name":"Kuske, Jan"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"first_name":"Stefanie","last_name":"Petra","full_name":"Petra, Stefanie"}],"publist_id":"7132","ec_funded":1,"quality_controlled":"1","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://arxiv.org/abs/1703.03769","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SSVM: Scale Space and Variational Methods in Computer Vision","start_date":"2017-06-04","location":"Kolding, Denmark","end_date":"2017-06-08"},"doi":"10.1007/978-3-319-58771-4_19","month":"06","publication_identifier":{"isbn":["978-331958770-7"]},"status":"public","title":"A novel convex relaxation for non binary discrete tomography","intvolume":" 10302","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"646","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations."}],"page":"235 - 246","citation":{"mla":"Kuske, Jan, et al. A Novel Convex Relaxation for Non Binary Discrete Tomography. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:10.1007/978-3-319-58771-4_19.","short":"J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 235–246.","chicago":"Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. https://doi.org/10.1007/978-3-319-58771-4_19.","ama":"Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246. doi:10.1007/978-3-319-58771-4_19","ista":"Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 235–246.","apa":"Kuske, J., Swoboda, P., & Petra, S. (2017). A novel convex relaxation for non binary discrete tomography. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_19","ieee":"J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary discrete tomography,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246."},"date_published":"2017-06-01T00:00:00Z","scopus_import":1,"day":"01"},{"scopus_import":1,"day":"01","citation":{"mla":"Skórski, Maciej. On the Complexity of Breaking Pseudoentropy. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:10.1007/978-3-319-55911-7_43.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.","chicago":"Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_43.","ama":"Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:600-613. doi:10.1007/978-3-319-55911-7_43","ista":"Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 600–613.","apa":"Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_43","ieee":"M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 600–613."},"page":"600 - 613","date_published":"2017-04-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) differs from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"648","intvolume":" 10185","title":"On the complexity of breaking pseudoentropy","status":"public","oa_version":"Submitted Version","publication_identifier":{"isbn":["978-331955910-0"]},"month":"04","main_file_link":[{"url":"https://eprint.iacr.org/2016/1186.pdf","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1007/978-3-319-55911-7_43","conference":{"end_date":"2017-04-22","location":"Bern, Switzerland","start_date":"2017-04-20","name":"TAMC: Theory and Applications of Models of Computation"},"language":[{"iso":"eng"}],"publist_id":"7125","year":"2017","publisher":"Springer","editor":[{"full_name":"Jäger, Gerhard","last_name":"Jäger","first_name":"Gerhard"},{"full_name":"Steila, Silvia","last_name":"Steila","first_name":"Silvia"}],"department":[{"_id":"KrPi"}],"publication_status":"published","author":[{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski"}],"volume":10185,"date_created":"2018-12-11T11:47:42Z","date_updated":"2021-01-12T08:07:39Z"},{"page":"159 - 174","citation":{"mla":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:10.1007/978-3-319-58002-9_5.","short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174.","chicago":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In Modern Approaches to Discrete Curvature, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. https://doi.org/10.1007/978-3-319-58002-9_5.","ama":"Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. Modern Approaches to Discrete Curvature. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:10.1007/978-3-319-58002-9_5","ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.","apa":"Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman & P. Romon (Eds.), Modern Approaches to Discrete Curvature (Vol. 2184, pp. 159–174). Springer. https://doi.org/10.1007/978-3-319-58002-9_5","ieee":"J. Maas, “Entropic Ricci curvature for discrete spaces,” in Modern Approaches to Discrete Curvature, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174."},"publication":"Modern Approaches to Discrete Curvature","date_published":"2017-10-05T00:00:00Z","series_title":"Lecture Notes in Mathematics","scopus_import":"1","article_processing_charge":"No","day":"05","intvolume":" 2184","status":"public","title":"Entropic Ricci curvature for discrete spaces","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"649","oa_version":"None","type":"book_chapter","abstract":[{"text":"We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani.","lang":"eng"}],"quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-58002-9_5","publication_identifier":{"eissn":["978-3-319-58002-9"],"isbn":["978-3-319-58001-2"]},"month":"10","editor":[{"first_name":"Laurent","last_name":"Najman","full_name":"Najman, Laurent"},{"full_name":"Romon, Pascal","last_name":"Romon","first_name":"Pascal"}],"publisher":"Springer","department":[{"_id":"JaMa"}],"publication_status":"published","year":"2017","volume":2184,"date_created":"2018-12-11T11:47:42Z","date_updated":"2022-05-24T07:01:33Z","author":[{"full_name":"Maas, Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan"}],"publist_id":"7123"},{"scopus_import":1,"day":"01","page":"586 - 599","citation":{"ieee":"M. Skórski, “A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 586–599.","apa":"Skórski, M. (2017). A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 586–599). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_42","ista":"Skórski M. 2017. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 586–599.","ama":"Skórski M. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:586-599. doi:10.1007/978-3-319-55911-7_42","chicago":"Skórski, Maciej. “A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds.” edited by Gerhard Jäger and Silvia Steila, 10185:586–99. Springer, 2017. https://doi.org/10.1007/978-3-319-55911-7_42.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599.","mla":"Skórski, Maciej. A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 586–99, doi:10.1007/978-3-319-55911-7_42."},"date_published":"2017-01-01T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy."}],"status":"public","title":"A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds","intvolume":" 10185","_id":"650","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"01","publication_identifier":{"issn":["03029743"]},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2016/965.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"name":"TAMC: Theory and Applications of Models of Computation","end_date":"2017-04-22","location":"Bern, Switzerland","start_date":"2017-04-20"},"doi":"10.1007/978-3-319-55911-7_42","publist_id":"7119","publication_status":"published","editor":[{"full_name":"Jäger, Gerhard","first_name":"Gerhard","last_name":"Jäger"},{"full_name":"Steila, Silvia","first_name":"Silvia","last_name":"Steila"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"year":"2017","date_created":"2018-12-11T11:47:42Z","date_updated":"2021-01-12T08:07:46Z","volume":10185,"author":[{"last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","full_name":"Skórski, Maciej"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6519","title":"Improved set-based symbolic algorithms for parity games","status":"public","ddc":["004"],"intvolume":" 82","file":[{"relation":"main_file","file_id":"6520","checksum":"7c2c9d09970af79026d7e37d9b632ef8","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-04T12:56:52Z","access_level":"open_access","file_name":"2017_LIPIcs-Chatterjee.pdf","content_type":"application/pdf","file_size":710185,"creator":"kschuh"}],"oa_version":"Published Version","type":"conference","abstract":[{"text":"Graph games with omega-regular winning conditions provide a mathematical framework to analyze a wide range of problems in the analysis of reactive systems and programs (such as the synthesis of reactive systems, program repair, and the verification of branching time properties). Parity conditions are canonical forms to specify omega-regular winning conditions. Graph games with parity conditions are equivalent to mu-calculus model checking, and thus a very important algorithmic problem. Symbolic algorithms are of great significance because they provide scalable algorithms for the analysis of large finite-state systems, as well as algorithms for the analysis of infinite-state systems with finite quotient. A set-based symbolic algorithm uses the basic set operations and the one-step predecessor operators. We consider graph games with n vertices and parity conditions with c priorities (equivalently, a mu-calculus formula with c alternations of least and greatest fixed points). While many explicit algorithms exist for graph games with parity conditions, for set-based symbolic algorithms there are only two algorithms (notice that we use space to refer to the number of sets stored by a symbolic algorithm): (a) the basic algorithm that requires O(n^c) symbolic operations and linear space; and (b) an improved algorithm that requires O(n^{c/2+1}) symbolic operations but also O(n^{c/2+1}) space (i.e., exponential space). In this work we present two set-based symbolic algorithms for parity games: (a) our first algorithm requires O(n^{c/2+1}) symbolic operations and only requires linear space; and (b) developing on our first algorithm, we present an algorithm that requires O(n^{c/3+1}) symbolic operations and only linear space. We also present the first linear space set-based symbolic algorithm for parity games that requires at most a sub-exponential number of symbolic operations. ","lang":"eng"}],"citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Set-Based Symbolic Algorithms for Parity Games,” Vol. 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017. https://doi.org/10.4230/LIPICS.CSL.2017.18.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. Improved Set-Based Symbolic Algorithms for Parity Games. Vol. 82, 18, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017, doi:10.4230/LIPICS.CSL.2017.18.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved set-based symbolic algorithms for parity games (Vol. 82). Presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden: Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik. https://doi.org/10.4230/LIPICS.CSL.2017.18","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Improved set-based symbolic algorithms for parity games,” presented at the CSL: Conference on Computer Science Logic, Stockholm, Sweden, 2017, vol. 82.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2017. Improved set-based symbolic algorithms for parity games. CSL: Conference on Computer Science Logic vol. 82, 18.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Improved set-based symbolic algorithms for parity games. In: Vol 82. Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik; 2017. doi:10.4230/LIPICS.CSL.2017.18"},"date_published":"2017-08-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","year":"2017","publication_status":"published","publisher":"Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik","department":[{"_id":"KrCh"}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Wolfgang","last_name":"Dvorák","full_name":"Dvorák, Wolfgang"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"date_updated":"2023-02-14T10:08:25Z","date_created":"2019-06-04T12:42:43Z","volume":82,"article_number":"18","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"conference":{"location":"Stockholm, Sweden","start_date":"2017-08-20","end_date":"2017-08-24","name":"CSL: Conference on Computer Science Logic"},"doi":"10.4230/LIPICS.CSL.2017.18","language":[{"iso":"eng"}],"month":"08"},{"conference":{"end_date":"2017-12-22","location":"Phuket, Thailand","start_date":"2017-12-09","name":"ISAAC: International Symposium on Algorithms and Computation"},"doi":"10.4230/LIPICS.ISAAC.2017.34","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":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"month":"12","author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"}],"date_updated":"2021-01-12T08:07:51Z","date_created":"2019-06-04T12:11:52Z","volume":92,"year":"2017","publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"article_number":"34","date_published":"2017-12-01T00:00:00Z","citation":{"short":"R. Fulek, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Fulek, Radoslav. Embedding Graphs into Embedded Graphs. Vol. 92, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPICS.ISAAC.2017.34.","chicago":"Fulek, Radoslav. “Embedding Graphs into Embedded Graphs,” Vol. 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPICS.ISAAC.2017.34.","ama":"Fulek R. Embedding graphs into embedded graphs. In: Vol 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPICS.ISAAC.2017.34","apa":"Fulek, R. (2017). Embedding graphs into embedded graphs (Vol. 92). Presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ISAAC.2017.34","ieee":"R. Fulek, “Embedding graphs into embedded graphs,” presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand, 2017, vol. 92.","ista":"Fulek R. 2017. Embedding graphs into embedded graphs. ISAAC: International Symposium on Algorithms and Computation vol. 92, 34."},"day":"01","has_accepted_license":"1","scopus_import":1,"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2017_LIPIcs-Fulek.pdf","file_size":588982,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"6518","checksum":"fc7a643e29621c8bbe49d36b39081f31","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-04T12:20:35Z"}],"_id":"6517","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Embedding graphs into embedded graphs","status":"public","ddc":["510"],"intvolume":" 92","abstract":[{"lang":"eng","text":"A (possibly degenerate) drawing of a graph G in the plane is approximable by an embedding if it can be turned into an embedding by an arbitrarily small perturbation. We show that testing, whether a drawing of a planar graph G in the plane is approximable by an embedding, can be carried out in polynomial time, if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation system (or equivalently the faces) of the embedding of G and the choice of outer face are fixed. In other words, we show that c-planarity with embedded pipes is tractable for graphs with fixed embeddings. To the best of our knowledge an analogous result was previously known essentially only when G is a cycle."}],"type":"conference"},{"abstract":[{"lang":"eng","text":"We present an approach that enables robots to self-organize their sensorimotor behavior from scratch without providing specific information about neither the robot nor its environment. This is achieved by a simple neural control law that increases the consistency between external sensor dynamics and internal neural dynamics of the utterly simple controller. In this way, the embodiment and the agent-environment coupling are the only source of individual development. We show how an anthropomorphic tendon driven arm-shoulder system develops different behaviors depending on that coupling. For instance: Given a bottle half-filled with water, the arm starts to shake it, driven by the physical response of the water. When attaching a brush, the arm can be manipulated into wiping a table, and when connected to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said to discover the affordances of the world. When allowing two (simulated) humanoid robots to interact physically, they engage into a joint behavior development leading to, for instance, spontaneous cooperation. More social effects are observed if the robots can visually perceive each other. Although, as an observer, it is tempting to attribute an apparent intentionality, there is nothing of the kind put in. As a conclusion, we argue that emergent behavior may be much less rooted in explicit intentions, internal motivations, or specific reward systems than is commonly believed."}],"publist_id":"7100","article_number":"7846789","type":"conference","author":[{"last_name":"Der","first_name":"Ralf","full_name":"Der, Ralf"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:47:43Z","date_updated":"2021-01-12T08:07:51Z","oa_version":"None","_id":"652","year":"2017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Dynamical self consistency leads to behavioral development and emergent social interactions in robots","status":"public","publication_status":"published","publisher":"IEEE","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"month":"02","day":"07","publication_identifier":{"isbn":["978-150905069-7"]},"scopus_import":1,"conference":{"name":"ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics ","end_date":"2016-09-22","location":"Cergy-Pontoise, France","start_date":"2016-09-19"},"date_published":"2017-02-07T00:00:00Z","doi":"10.1109/DEVLRN.2016.7846789","language":[{"iso":"eng"}],"citation":{"ieee":"R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral development and emergent social interactions in robots,” presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France, 2017.","apa":"Der, R., & Martius, G. S. (2017). Dynamical self consistency leads to behavioral development and emergent social interactions in robots. Presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France: IEEE. https://doi.org/10.1109/DEVLRN.2016.7846789","ista":"Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , 7846789.","ama":"Der R, Martius GS. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. In: IEEE; 2017. doi:10.1109/DEVLRN.2016.7846789","chicago":"Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots.” IEEE, 2017. https://doi.org/10.1109/DEVLRN.2016.7846789.","short":"R. Der, G.S. Martius, in:, IEEE, 2017.","mla":"Der, Ralf, and Georg S. Martius. Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots. 7846789, IEEE, 2017, doi:10.1109/DEVLRN.2016.7846789."},"quality_controlled":"1"},{"publication_identifier":{"issn":["00280836"]},"day":"11","month":"01","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1038/541161a","date_published":"2017-01-11T00:00:00Z","page":"161 - 162","quality_controlled":"1","citation":{"short":"B. Hof, Nature 541 (2017) 161–162.","mla":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature, vol. 541, no. 7636, Nature Publishing Group, 2017, pp. 161–62, doi:10.1038/541161a.","chicago":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/541161a.","ama":"Hof B. Fluid dynamics: Water flows out of touch. Nature. 2017;541(7636):161-162. doi:10.1038/541161a","ieee":"B. Hof, “Fluid dynamics: Water flows out of touch,” Nature, vol. 541, no. 7636. Nature Publishing Group, pp. 161–162, 2017.","apa":"Hof, B. (2017). Fluid dynamics: Water flows out of touch. Nature. Nature Publishing Group. https://doi.org/10.1038/541161a","ista":"Hof B. 2017. Fluid dynamics: Water flows out of touch. Nature. 541(7636), 161–162."},"publication":"Nature","publist_id":"7116","issue":"7636","abstract":[{"lang":"eng","text":"Superhydrophobic surfaces reduce the frictional drag between water and solid materials, but this effect is often temporary. The realization of sustained drag reduction has applications for water vehicles and pipeline flows.\r\n\r\n"}],"type":"journal_article","volume":541,"oa_version":"None","date_updated":"2021-01-12T08:07:49Z","date_created":"2018-12-11T11:47:43Z","author":[{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"}],"department":[{"_id":"BjHo"}],"intvolume":" 541","publisher":"Nature Publishing Group","status":"public","publication_status":"published","title":"Fluid dynamics: Water flows out of touch","year":"2017","_id":"651","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.1038/ng.3764","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["28092682"]},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"month":"03","publication_identifier":{"issn":["10614036"]},"author":[{"full_name":"Makohon Moore, Alvin","first_name":"Alvin","last_name":"Makohon Moore"},{"full_name":"Zhang, Ming","first_name":"Ming","last_name":"Zhang"},{"full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","first_name":"Johannes","last_name":"Reiter"},{"last_name":"Božić","first_name":"Ivana","full_name":"Božić, Ivana"},{"first_name":"Benjamin","last_name":"Allen","full_name":"Allen, Benjamin"},{"full_name":"Kundu, Deepanjan","first_name":"Deepanjan","last_name":"Kundu","id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Fay","last_name":"Wong","full_name":"Wong, Fay"},{"full_name":"Jiao, Yuchen","last_name":"Jiao","first_name":"Yuchen"},{"full_name":"Kohutek, Zachary","first_name":"Zachary","last_name":"Kohutek"},{"last_name":"Hong","first_name":"Jungeui","full_name":"Hong, Jungeui"},{"full_name":"Attiyeh, Marc","first_name":"Marc","last_name":"Attiyeh"},{"full_name":"Javier, Breanna","last_name":"Javier","first_name":"Breanna"},{"full_name":"Wood, Laura","first_name":"Laura","last_name":"Wood"},{"last_name":"Hruban","first_name":"Ralph","full_name":"Hruban, Ralph"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"},{"last_name":"Papadopoulos","first_name":"Nickolas","full_name":"Papadopoulos, Nickolas"},{"full_name":"Kinzler, Kenneth","last_name":"Kinzler","first_name":"Kenneth"},{"first_name":"Bert","last_name":"Vogelstein","full_name":"Vogelstein, Bert"},{"full_name":"Iacobuzio Donahue, Christine","last_name":"Iacobuzio Donahue","first_name":"Christine"}],"date_updated":"2022-06-10T09:55:08Z","date_created":"2018-12-11T11:47:43Z","volume":49,"acknowledgement":"We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).","year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","file_date_updated":"2020-07-14T12:47:33Z","ec_funded":1,"publist_id":"7092","date_published":"2017-03-01T00:00:00Z","publication":"Nature Genetics","citation":{"short":"A. Makohon Moore, M. Zhang, J. Reiter, I. Božić, B. Allen, D. Kundu, K. Chatterjee, F. Wong, Y. Jiao, Z. Kohutek, J. Hong, M. Attiyeh, B. Javier, L. Wood, R. Hruban, M. Nowak, N. Papadopoulos, K. Kinzler, B. Vogelstein, C. Iacobuzio Donahue, Nature Genetics 49 (2017) 358–366.","mla":"Makohon Moore, Alvin, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics, vol. 49, no. 3, Nature Publishing Group, 2017, pp. 358–66, doi:10.1038/ng.3764.","chicago":"Makohon Moore, Alvin, Ming Zhang, Johannes Reiter, Ivana Božić, Benjamin Allen, Deepanjan Kundu, Krishnendu Chatterjee, et al. “Limited Heterogeneity of Known Driver Gene Mutations among the Metastases of Individual Patients with Pancreatic Cancer.” Nature Genetics. Nature Publishing Group, 2017. https://doi.org/10.1038/ng.3764.","ama":"Makohon Moore A, Zhang M, Reiter J, et al. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 2017;49(3):358-366. doi:10.1038/ng.3764","ieee":"A. Makohon Moore et al., “Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer,” Nature Genetics, vol. 49, no. 3. Nature Publishing Group, pp. 358–366, 2017.","apa":"Makohon Moore, A., Zhang, M., Reiter, J., Božić, I., Allen, B., Kundu, D., … Iacobuzio Donahue, C. (2017). Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng.3764","ista":"Makohon Moore A, Zhang M, Reiter J, Božić I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek Z, Hong J, Attiyeh M, Javier B, Wood L, Hruban R, Nowak M, Papadopoulos N, Kinzler K, Vogelstein B, Iacobuzio Donahue C. 2017. Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nature Genetics. 49(3), 358–366."},"article_type":"original","page":"358 - 366","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","file":[{"file_name":"2017_NatureGenetics_Makohon.pdf","access_level":"open_access","file_size":908099,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"7050","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-11-19T08:13:50Z","checksum":"e442dc3b7420a36ec805e9bb45cc1a2e"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"653","status":"public","ddc":["000"],"title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","intvolume":" 49","abstract":[{"lang":"eng","text":"The extent of heterogeneity among driver gene mutations present in naturally occurring metastases - that is, treatment-naive metastatic disease - is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease."}],"issue":"3","type":"journal_article"},{"author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen"},{"last_name":"Blocki","first_name":"Jeremiah","full_name":"Blocki, Jeremiah"},{"first_name":"Ben","last_name":"Harsha","full_name":"Harsha, Ben"}],"date_created":"2019-06-06T13:21:29Z","date_updated":"2021-01-12T08:07:53Z","oa_version":"Submitted Version","year":"2017","_id":"6527","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Practical graphs for optimal side-channel resistant memory-hard functions","status":"public","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"ACM Press","abstract":[{"text":"A memory-hard function (MHF) ƒn with parameter n can be computed in sequential time and space n. Simultaneously, a high amortized parallel area-time complexity (aAT) is incurred per evaluation. In practice, MHFs are used to limit the rate at which an adversary (using a custom computational device) can evaluate a security sensitive function that still occasionally needs to be evaluated by honest users (using an off-the-shelf general purpose device). The most prevalent examples of such sensitive functions are Key Derivation Functions (KDFs) and password hashing algorithms where rate limits help mitigate off-line dictionary attacks. As the honest users' inputs to these functions are often (low-entropy) passwords special attention is given to a class of side-channel resistant MHFs called iMHFs.\r\n\r\nEssentially all iMHFs can be viewed as some mode of operation (making n calls to some round function) given by a directed acyclic graph (DAG) with very low indegree. Recently, a combinatorial property of a DAG has been identified (called \"depth-robustness\") which results in good provable security for an iMHF based on that DAG. Depth-robust DAGs have also proven useful in other cryptographic applications. Unfortunately, up till now, all known very depth-robust DAGs are impractically complicated and little is known about their exact (i.e. non-asymptotic) depth-robustness both in theory and in practice.\r\n\r\nIn this work we build and analyze (both formally and empirically) several exceedingly simple and efficient to navigate practical DAGs for use in iMHFs and other applications. For each DAG we:\r\n*Prove that their depth-robustness is asymptotically maximal.\r\n*Prove bounds of at least 3 orders of magnitude better on their exact depth-robustness compared to known bounds for other practical iMHF.\r\n*Implement and empirically evaluate their depth-robustness and aAT against a variety of state-of-the art (and several new) depth-reduction and low aAT attacks. \r\nWe find that, against all attacks, the new DAGs perform significantly better in practice than Argon2i, the most widely deployed iMHF in practice.\r\n\r\nAlong the way we also improve the best known empirical attacks on the aAT of Argon2i by implementing and testing several heuristic versions of a (hitherto purely theoretical) depth-reduction attack. Finally, we demonstrate practicality of our constructions by modifying the Argon2i code base to use one of the new high aAT DAGs. Experimental benchmarks on a standard off-the-shelf CPU show that the new modifications do not adversely affect the impressive throughput of Argon2i (despite seemingly enjoying significantly higher aAT).\r\n","lang":"eng"}],"ec_funded":1,"type":"conference","conference":{"end_date":"2017-11-03","start_date":"2017-10-30","location":"Dallas, TX, USA","name":"CCS: Conference on Computer and Communications Security"},"doi":"10.1145/3133956.3134031","date_published":"2017-10-30T00:00:00Z","language":[{"iso":"eng"}],"publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","citation":{"ista":"Alwen JF, Blocki J, Harsha B. 2017. Practical graphs for optimal side-channel resistant memory-hard functions. Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. CCS: Conference on Computer and Communications Security, 1001–1017.","ieee":"J. F. Alwen, J. Blocki, and B. Harsha, “Practical graphs for optimal side-channel resistant memory-hard functions,” in Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, Dallas, TX, USA, 2017, pp. 1001–1017.","apa":"Alwen, J. F., Blocki, J., & Harsha, B. (2017). Practical graphs for optimal side-channel resistant memory-hard functions. In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security (pp. 1001–1017). Dallas, TX, USA: ACM Press. https://doi.org/10.1145/3133956.3134031","ama":"Alwen JF, Blocki J, Harsha B. Practical graphs for optimal side-channel resistant memory-hard functions. In: Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security. ACM Press; 2017:1001-1017. doi:10.1145/3133956.3134031","chicago":"Alwen, Joel F, Jeremiah Blocki, and Ben Harsha. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” In Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, 1001–17. ACM Press, 2017. https://doi.org/10.1145/3133956.3134031.","mla":"Alwen, Joel F., et al. “Practical Graphs for Optimal Side-Channel Resistant Memory-Hard Functions.” Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–17, doi:10.1145/3133956.3134031.","short":"J.F. Alwen, J. Blocki, B. Harsha, in:, Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security, ACM Press, 2017, pp. 1001–1017."},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/443"}],"oa":1,"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"page":"1001-1017","day":"30","month":"10","publication_identifier":{"isbn":["9781450349468"]},"scopus_import":1},{"project":[{"_id":"B6FC0238-B512-11E9-945C-1524E6697425","grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1242/dev.144915","publication_identifier":{"issn":["09501991"]},"month":"03","publisher":"Company of Biologists","department":[{"_id":"AnKi"}],"publication_status":"published","year":"2017","volume":144,"date_created":"2018-12-11T11:47:44Z","date_updated":"2021-01-12T08:07:54Z","author":[{"full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998"},{"last_name":"Rivron","first_name":"Nicolas","full_name":"Rivron, Nicolas"}],"ec_funded":1,"publist_id":"7089","file_date_updated":"2020-07-14T12:47:33Z","page":"733 - 736","citation":{"short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","mla":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development, vol. 144, no. 5, Company of Biologists, 2017, pp. 733–36, doi:10.1242/dev.144915.","chicago":"Kicheva, Anna, and Nicolas Rivron. “Creating to Understand – Developmental Biology Meets Engineering in Paris.” Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.144915.","ama":"Kicheva A, Rivron N. Creating to understand – developmental biology meets engineering in Paris. Development. 2017;144(5):733-736. doi:10.1242/dev.144915","apa":"Kicheva, A., & Rivron, N. (2017). Creating to understand – developmental biology meets engineering in Paris. Development. Company of Biologists. https://doi.org/10.1242/dev.144915","ieee":"A. Kicheva and N. Rivron, “Creating to understand – developmental biology meets engineering in Paris,” Development, vol. 144, no. 5. Company of Biologists, pp. 733–736, 2017.","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736."},"publication":"Development","date_published":"2017-03-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01","intvolume":" 144","ddc":["571"],"title":"Creating to understand – developmental biology meets engineering in Paris","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"654","file":[{"access_level":"open_access","file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","file_size":228206,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5139","checksum":"eef22a0f42a55b232cb2d1188a2322cb","date_created":"2018-12-12T10:15:20Z","date_updated":"2020-07-14T12:47:33Z"}],"oa_version":"Submitted Version","pubrep_id":"987","type":"journal_article","issue":"5","abstract":[{"text":"In November 2016, developmental biologists, synthetic biologists and engineers gathered in Paris for a meeting called ‘Engineering the embryo’. The participants shared an interest in exploring how synthetic systems can reveal new principles of embryonic development, and how the in vitro manipulation and modeling of development using stem cells can be used to integrate ideas and expertise from physics, developmental biology and tissue engineering. As we review here, the conference pinpointed some of the challenges arising at the intersection of these fields, along with great enthusiasm for finding new approaches and collaborations.","lang":"eng"}]},{"article_number":"8006529","ec_funded":1,"department":[{"_id":"KrPi"}],"publisher":"IEEE","publication_status":"published","year":"2017","date_updated":"2021-01-12T08:07:53Z","date_created":"2019-06-06T12:53:09Z","author":[{"full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","last_name":"Skórski","first_name":"Maciej"}],"publication_identifier":{"isbn":["9781509040964"]},"month":"08","project":[{"call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","external_id":{"arxiv":["1702.01666"]},"main_file_link":[{"url":"https://arxiv.org/abs/1702.01666","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/isit.2017.8006529","conference":{"name":"ISIT: International Symposium on Information Theory","end_date":"2017-06-30","location":"Aachen, Germany","start_date":"2017-06-25"},"type":"conference","abstract":[{"lang":"eng","text":"This paper studies the complexity of estimating Rényi divergences of discrete distributions: p observed from samples and the baseline distribution q known a priori. Extending the results of Acharya et al. (SODA'15) on estimating Rényi entropy, we present improved estimation techniques together with upper and lower bounds on the sample complexity. We show that, contrarily to estimating Rényi entropy where a sublinear (in the alphabet size) number of samples suffices, the sample complexity is heavily dependent on events occurring unlikely in q, and is unbounded in general (no matter what an estimation technique is used). For any divergence of integer order bigger than 1, we provide upper and lower bounds on the number of samples dependent on probabilities of p and q (the lower bounds hold for non-integer orders as well). We conclude that the worst-case sample complexity is polynomial in the alphabet size if and only if the probabilities of q are non-negligible. This gives theoretical insights into heuristics used in the applied literature to handle numerical instability, which occurs for small probabilities of q. Our result shows that they should be handled with care not only because of numerical issues, but also because of a blow up in the sample complexity."}],"title":"On the complexity of estimating Rènyi divergences","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"6526","oa_version":"Preprint","scopus_import":1,"day":"09","citation":{"ista":"Skórski M. 2017. On the complexity of estimating Rènyi divergences. 2017 IEEE International Symposium on Information Theory (ISIT). ISIT: International Symposium on Information Theory, 8006529.","apa":"Skórski, M. (2017). On the complexity of estimating Rènyi divergences. In 2017 IEEE International Symposium on Information Theory (ISIT). Aachen, Germany: IEEE. https://doi.org/10.1109/isit.2017.8006529","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017.","ama":"Skórski M. On the complexity of estimating Rènyi divergences. In: 2017 IEEE International Symposium on Information Theory (ISIT). IEEE; 2017. doi:10.1109/isit.2017.8006529","chicago":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” In 2017 IEEE International Symposium on Information Theory (ISIT). IEEE, 2017. https://doi.org/10.1109/isit.2017.8006529.","mla":"Skórski, Maciej. “On the Complexity of Estimating Rènyi Divergences.” 2017 IEEE International Symposium on Information Theory (ISIT), 8006529, IEEE, 2017, doi:10.1109/isit.2017.8006529.","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017."},"publication":"2017 IEEE International Symposium on Information Theory (ISIT)","date_published":"2017-08-09T00:00:00Z"},{"date_created":"2018-12-11T11:47:44Z","date_updated":"2021-01-12T08:07:55Z","volume":6,"author":[{"last_name":"Renault","first_name":"Thibaud","full_name":"Renault, Thibaud"},{"last_name":"Abraham","first_name":"Anthony","full_name":"Abraham, Anthony"},{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Paradis","first_name":"Guillaume","full_name":"Paradis, Guillaume"},{"last_name":"Rainville","first_name":"Simon","full_name":"Rainville, Simon"},{"first_name":"Emmanuelle","last_name":"Charpentier","full_name":"Charpentier, Emmanuelle"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"last_name":"Tu","first_name":"Yuhai","full_name":"Tu, Yuhai"},{"full_name":"Namba, Keiichi","first_name":"Keiichi","last_name":"Namba"},{"last_name":"Keener","first_name":"James","full_name":"Keener, James"},{"first_name":"Tohru","last_name":"Minamino","full_name":"Minamino, Tohru"},{"full_name":"Erhardt, Marc","first_name":"Marc","last_name":"Erhardt"}],"publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","year":"2017","file_date_updated":"2020-07-14T12:47:33Z","publist_id":"7082","article_number":"e23136","language":[{"iso":"eng"}],"doi":"10.7554/eLife.23136","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"},"month":"03","publication_identifier":{"issn":["2050084X"]},"oa_version":"Published Version","file":[{"file_id":"4716","relation":"main_file","date_created":"2018-12-12T10:08:53Z","date_updated":"2020-07-14T12:47:33Z","checksum":"39e1c3e82ddac83a30422fa72fa1a383","file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","access_level":"open_access","creator":"system","file_size":5520359,"content_type":"application/pdf"},{"file_id":"4717","relation":"main_file","checksum":"a6d542253028f52e00aa29739ddffe8f","date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:08:54Z","access_level":"open_access","file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf","creator":"system","content_type":"application/pdf","file_size":11242920}],"pubrep_id":"904","title":"Bacterial flagella grow through an injection diffusion mechanism","ddc":["579"],"status":"public","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"655","abstract":[{"lang":"eng","text":"The bacterial flagellum is a self-assembling nanomachine. The external flagellar filament, several times longer than a bacterial cell body, is made of a few tens of thousands subunits of a single protein: flagellin. A fundamental problem concerns the molecular mechanism of how the flagellum grows outside the cell, where no discernible energy source is available. Here, we monitored the dynamic assembly of individual flagella using in situ labelling and real-time immunostaining of elongating flagellar filaments. We report that the rate of flagellum growth, initially ~1,700 amino acids per second, decreases with length and that the previously proposed chain mechanism does not contribute to the filament elongation dynamics. Inhibition of the proton motive force-dependent export apparatus revealed a major contribution of substrate injection in driving filament elongation. The combination of experimental and mathematical evidence demonstrates that a simple, injection-diffusion mechanism controls bacterial flagella growth outside the cell."}],"type":"journal_article","date_published":"2017-03-06T00:00:00Z","publication":"eLife","citation":{"mla":"Renault, Thibaud, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife, vol. 6, e23136, eLife Sciences Publications, 2017, doi:10.7554/eLife.23136.","short":"T. Renault, A. Abraham, T. Bergmiller, G. Paradis, S. Rainville, E. Charpentier, C.C. Guet, Y. Tu, K. Namba, J. Keener, T. Minamino, M. Erhardt, ELife 6 (2017).","chicago":"Renault, Thibaud, Anthony Abraham, Tobias Bergmiller, Guillaume Paradis, Simon Rainville, Emmanuelle Charpentier, Calin C Guet, et al. “Bacterial Flagella Grow through an Injection Diffusion Mechanism.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.23136.","ama":"Renault T, Abraham A, Bergmiller T, et al. Bacterial flagella grow through an injection diffusion mechanism. eLife. 2017;6. doi:10.7554/eLife.23136","ista":"Renault T, Abraham A, Bergmiller T, Paradis G, Rainville S, Charpentier E, Guet CC, Tu Y, Namba K, Keener J, Minamino T, Erhardt M. 2017. Bacterial flagella grow through an injection diffusion mechanism. eLife. 6, e23136.","apa":"Renault, T., Abraham, A., Bergmiller, T., Paradis, G., Rainville, S., Charpentier, E., … Erhardt, M. (2017). Bacterial flagella grow through an injection diffusion mechanism. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.23136","ieee":"T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017."},"day":"06","has_accepted_license":"1","scopus_import":1},{"abstract":[{"lang":"eng","text":"Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator."}],"issue":"12","type":"journal_article","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"657","title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","status":"public","intvolume":" 114","day":"21","scopus_import":1,"date_published":"2017-03-21T00:00:00Z","publication":"PNAS","citation":{"mla":"Möller, Barbara, et al. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS, vol. 114, no. 12, National Academy of Sciences, 2017, pp. E2533–39, doi:10.1073/pnas.1616493114.","short":"B. Möller, C. Ten Hove, D. Xiang, N. Williams, L. López, S. Yoshida, M. Smit, R. Datla, D. Weijers, PNAS 114 (2017) E2533–E2539.","chicago":"Möller, Barbara, Colette Ten Hove, Daoquan Xiang, Nerys Williams, Lorena López, Saiko Yoshida, Margot Smit, Raju Datla, and Dolf Weijers. “Auxin Response Cell Autonomously Controls Ground Tissue Initiation in the Early Arabidopsis Embryo.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1616493114.","ama":"Möller B, Ten Hove C, Xiang D, et al. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 2017;114(12):E2533-E2539. doi:10.1073/pnas.1616493114","ista":"Möller B, Ten Hove C, Xiang D, Williams N, López L, Yoshida S, Smit M, Datla R, Weijers D. 2017. Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. 114(12), E2533–E2539.","apa":"Möller, B., Ten Hove, C., Xiang, D., Williams, N., López, L., Yoshida, S., … Weijers, D. (2017). Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1616493114","ieee":"B. Möller et al., “Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo,” PNAS, vol. 114, no. 12. National Academy of Sciences, pp. E2533–E2539, 2017."},"page":"E2533 - E2539","publist_id":"7076","author":[{"full_name":"Möller, Barbara","first_name":"Barbara","last_name":"Möller"},{"last_name":"Ten Hove","first_name":"Colette","full_name":"Ten Hove, Colette"},{"last_name":"Xiang","first_name":"Daoquan","full_name":"Xiang, Daoquan"},{"first_name":"Nerys","last_name":"Williams","full_name":"Williams, Nerys"},{"full_name":"López, Lorena","last_name":"López","first_name":"Lorena"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","last_name":"Yoshida","first_name":"Saiko","full_name":"Yoshida, Saiko"},{"last_name":"Smit","first_name":"Margot","full_name":"Smit, Margot"},{"first_name":"Raju","last_name":"Datla","full_name":"Datla, Raju"},{"full_name":"Weijers, Dolf","first_name":"Dolf","last_name":"Weijers"}],"date_created":"2018-12-11T11:47:45Z","date_updated":"2021-01-12T08:08:02Z","volume":114,"year":"2017","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","month":"03","publication_identifier":{"issn":["00278424"]},"doi":"10.1073/pnas.1616493114","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["28265057"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/","open_access":"1"}],"quality_controlled":"1"},{"publication":"Science Translational Medicine","citation":{"mla":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine, vol. 9, no. 381, eaam9867, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aam9867.","short":"G. Novarino, Science Translational Medicine 9 (2017).","chicago":"Novarino, Gaia. “Modeling Alzheimer’s Disease in Mice with Human Neurons.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aam9867.","ama":"Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867","ista":"Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 9(381), eaam9867.","apa":"Novarino, G. (2017). Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aam9867","ieee":"G. Novarino, “Modeling Alzheimer’s disease in mice with human neurons,” Science Translational Medicine, vol. 9, no. 381. American Association for the Advancement of Science, 2017."},"quality_controlled":"1","date_published":"2017-03-15T00:00:00Z","doi":"10.1126/scitranslmed.aam9867","language":[{"iso":"eng"}],"scopus_import":1,"month":"03","day":"15","publication_identifier":{"issn":["19466234"]},"_id":"656","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Modeling Alzheimer's disease in mice with human neurons","intvolume":" 9","publisher":"American Association for the Advancement of Science","department":[{"_id":"GaNo"}],"author":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"}],"date_updated":"2021-01-12T08:07:59Z","date_created":"2018-12-11T11:47:45Z","volume":9,"oa_version":"None","article_number":"eaam9867","type":"journal_article","abstract":[{"lang":"eng","text":"Human neurons transplanted into a mouse model for Alzheimer’s disease show human-specific vulnerability to β-amyloid plaques and may help to identify new therapeutic targets."}],"publist_id":"7079","issue":"381"},{"year":"2017","publisher":"Frontiers Research Foundation","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publication_status":"published","author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"volume":11,"date_created":"2018-12-11T11:47:45Z","date_updated":"2021-01-12T08:08:04Z","article_number":"00008","ec_funded":1,"publist_id":"7078","file_date_updated":"2020-07-14T12:47:33Z","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":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.3389/fnbot.2017.00008","language":[{"iso":"eng"}],"publication_identifier":{"issn":["16625218"]},"month":"03","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","_id":"658","intvolume":" 11","status":"public","title":"Self organized behavior generation for musculoskeletal robots","ddc":["006"],"pubrep_id":"903","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5371","date_updated":"2020-07-14T12:47:33Z","date_created":"2018-12-12T10:18:49Z","checksum":"b1bc43f96d1df3313c03032c2a46388d","file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","access_level":"open_access","content_type":"application/pdf","file_size":8439566,"creator":"system"}],"type":"journal_article","issue":"MAR","abstract":[{"text":"With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors "waiting" to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics.","lang":"eng"}],"citation":{"chicago":"Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics. Frontiers Research Foundation, 2017. https://doi.org/10.3389/fnbot.2017.00008.","mla":"Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” Frontiers in Neurorobotics, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:10.3389/fnbot.2017.00008.","short":"R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).","ista":"Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.","apa":"Der, R., & Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. Frontiers Research Foundation. https://doi.org/10.3389/fnbot.2017.00008","ieee":"R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” Frontiers in Neurorobotics, vol. 11, no. MAR. Frontiers Research Foundation, 2017.","ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008"},"publication":"Frontiers in Neurorobotics","date_published":"2017-03-16T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"Yes","day":"16"},{"month":"03","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms14832","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"},"file_date_updated":"2020-07-14T12:47:34Z","publist_id":"7075","article_number":"14832","date_updated":"2021-01-12T08:08:06Z","date_created":"2018-12-11T11:47:46Z","volume":8,"author":[{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"full_name":"Winterhoff, Moritz","first_name":"Moritz","last_name":"Winterhoff"},{"full_name":"Dimchev, Vanessa","first_name":"Vanessa","last_name":"Dimchev"},{"full_name":"Müller, Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","last_name":"Müller"},{"full_name":"Thalheim, Tobias","first_name":"Tobias","last_name":"Thalheim"},{"full_name":"Freise, Anika","last_name":"Freise","first_name":"Anika"},{"full_name":"Brühmann, Stefan","first_name":"Stefan","last_name":"Brühmann"},{"last_name":"Kollasser","first_name":"Jana","full_name":"Kollasser, Jana"},{"full_name":"Block, Jennifer","first_name":"Jennifer","last_name":"Block"},{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A"},{"full_name":"Geyer, Matthias","last_name":"Geyer","first_name":"Matthias"},{"full_name":"Schnittler, Hams","first_name":"Hams","last_name":"Schnittler"},{"full_name":"Brakebusch, Cord","last_name":"Brakebusch","first_name":"Cord"},{"last_name":"Stradal","first_name":"Theresia","full_name":"Stradal, Theresia"},{"last_name":"Carlier","first_name":"Marie","full_name":"Carlier, Marie"},{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Käs, Josef","last_name":"Käs","first_name":"Josef"},{"full_name":"Faix, Jan","first_name":"Jan","last_name":"Faix"},{"full_name":"Rottner, Klemens","first_name":"Klemens","last_name":"Rottner"}],"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"}],"year":"2017","day":"22","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"date_published":"2017-03-22T00:00:00Z","publication":"Nature Communications","citation":{"mla":"Kage, Frieda, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications, vol. 8, 14832, Nature Publishing Group, 2017, doi:10.1038/ncomms14832.","short":"F. Kage, M. Winterhoff, V. Dimchev, J. Müller, T. Thalheim, A. Freise, S. Brühmann, J. Kollasser, J. Block, G.A. Dimchev, M. Geyer, H. Schnittler, C. Brakebusch, T. Stradal, M. Carlier, M.K. Sixt, J. Käs, J. Faix, K. Rottner, Nature Communications 8 (2017).","chicago":"Kage, Frieda, Moritz Winterhoff, Vanessa Dimchev, Jan Müller, Tobias Thalheim, Anika Freise, Stefan Brühmann, et al. “FMNL Formins Boost Lamellipodial Force Generation.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14832.","ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832","ista":"Kage F, Winterhoff M, Dimchev V, Müller J, Thalheim T, Freise A, Brühmann S, Kollasser J, Block J, Dimchev GA, Geyer M, Schnittler H, Brakebusch C, Stradal T, Carlier M, Sixt MK, Käs J, Faix J, Rottner K. 2017. FMNL formins boost lamellipodial force generation. Nature Communications. 8, 14832.","ieee":"F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Kage, F., Winterhoff, M., Dimchev, V., Müller, J., Thalheim, T., Freise, A., … Rottner, K. (2017). FMNL formins boost lamellipodial force generation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14832"},"abstract":[{"lang":"eng","text":"Migration frequently involves Rac-mediated protrusion of lamellipodia, formed by Arp2/3 complex-dependent branching thought to be crucial for force generation and stability of these networks. The formins FMNL2 and FMNL3 are Cdc42 effectors targeting to the lamellipodium tip and shown here to nucleate and elongate actin filaments with complementary activities in vitro. In migrating B16-F1 melanoma cells, both formins contribute to the velocity of lamellipodium protrusion. Loss of FMNL2/3 function in melanoma cells and fibroblasts reduces lamellipodial width, actin filament density and -bundling, without changing patterns of Arp2/3 complex incorporation. Strikingly, in melanoma cells, FMNL2/3 gene inactivation almost completely abolishes protrusion forces exerted by lamellipodia and modifies their ultrastructural organization. Consistently, CRISPR/Cas-mediated depletion of FMNL2/3 in fibroblasts reduces both migration and capability of cells to move against viscous media. Together, we conclude that force generation in lamellipodia strongly depends on FMNL formin activity, operating in addition to Arp2/3 complex-dependent filament branching."}],"type":"journal_article","file":[{"file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","access_level":"open_access","content_type":"application/pdf","file_size":9523746,"creator":"system","relation":"main_file","file_id":"5072","date_created":"2018-12-12T10:14:21Z","date_updated":"2020-07-14T12:47:34Z","checksum":"dae30190291c3630e8102d8714a8d23e"}],"oa_version":"Published Version","pubrep_id":"902","title":"FMNL formins boost lamellipodial force generation","status":"public","ddc":["570"],"intvolume":" 8","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"659"},{"intvolume":" 114","title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","status":"public","_id":"660","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"13","abstract":[{"lang":"eng","text":"Growing microtubules are protected from depolymerization by the presence of a GTP or GDP/Pi cap. End-binding proteins of the EB1 family bind to the stabilizing cap, allowing monitoring of its size in real time. The cap size has been shown to correlate with instantaneous microtubule stability. Here we have quantitatively characterized the properties of cap size fluctuations during steadystate growth and have developed a theory predicting their timescale and amplitude from the kinetics of microtubule growth and cap maturation. In contrast to growth speed fluctuations, cap size fluctuations show a characteristic timescale, which is defined by the lifetime of the cap sites. Growth fluctuations affect the amplitude of cap size fluctuations; however, cap size does not affect growth speed, indicating that microtubules are far from instability during most of their time of growth. Our theory provides the basis for a quantitative understanding of microtubule stability fluctuations during steady-state growth."}],"page":"3427 - 3432","citation":{"chicago":"Rickman, Jamie, Christian F Düllberg, Nicholas Cade, Lewis Griffin, and Thomas Surrey. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1620274114.","mla":"Rickman, Jamie, et al. “Steady State EB Cap Size Fluctuations Are Determined by Stochastic Microtubule Growth and Maturation.” PNAS, vol. 114, no. 13, National Academy of Sciences, 2017, pp. 3427–32, doi:10.1073/pnas.1620274114.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","ista":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. 2017. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 114(13), 3427–3432.","apa":"Rickman, J., Düllberg, C. F., Cade, N., Griffin, L., & Surrey, T. (2017). Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1620274114","ieee":"J. Rickman, C. F. Düllberg, N. Cade, L. Griffin, and T. Surrey, “Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation,” PNAS, vol. 114, no. 13. National Academy of Sciences, pp. 3427–3432, 2017.","ama":"Rickman J, Düllberg CF, Cade N, Griffin L, Surrey T. Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation. PNAS. 2017;114(13):3427-3432. doi:10.1073/pnas.1620274114"},"publication":"PNAS","date_published":"2017-03-28T00:00:00Z","scopus_import":1,"day":"28","department":[{"_id":"MaLo"}],"publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2017","acknowledgement":"We thank Philippe Cluzel for helpful discussions and Gunnar Pruessner for data analysis advice. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK Grant FC001163, Medical Research Council Grant FC001163, and Wellcome Trust Grant FC001163. This work was also supported by European Research Council Advanced Grant Project 323042 (to C.D. and T.S.).","volume":114,"date_created":"2018-12-11T11:47:46Z","date_updated":"2021-01-12T08:08:09Z","author":[{"first_name":"Jamie","last_name":"Rickman","full_name":"Rickman, Jamie"},{"first_name":"Christian F","last_name":"Düllberg","id":"459064DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6335-9748","full_name":"Düllberg, Christian F"},{"full_name":"Cade, Nicholas","last_name":"Cade","first_name":"Nicholas"},{"full_name":"Griffin, Lewis","first_name":"Lewis","last_name":"Griffin"},{"full_name":"Surrey, Thomas","last_name":"Surrey","first_name":"Thomas"}],"publist_id":"7073","quality_controlled":"1","external_id":{"pmid":["28280102"]},"oa":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1620274114","publication_identifier":{"issn":["00278424"]},"month":"03"},{"scopus_import":1,"day":"01","publication":"Physics of Fluids","citation":{"ama":"Shi L, Hof B, Rampp M, Avila M. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 2017;29(4). doi:10.1063/1.4981525","ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","ieee":"L. Shi, B. Hof, M. Rampp, and M. Avila, “Hydrodynamic turbulence in quasi Keplerian rotating flows,” Physics of Fluids, vol. 29, no. 4. American Institute of Physics, 2017.","apa":"Shi, L., Hof, B., Rampp, M., & Avila, M. (2017). Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4981525","mla":"Shi, Liang, et al. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids, vol. 29, no. 4, 044107, American Institute of Physics, 2017, doi:10.1063/1.4981525.","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).","chicago":"Shi, Liang, Björn Hof, Markus Rampp, and Marc Avila. “Hydrodynamic Turbulence in Quasi Keplerian Rotating Flows.” Physics of Fluids. American Institute of Physics, 2017. https://doi.org/10.1063/1.4981525."},"date_published":"2017-04-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to (105). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays."}],"issue":"4","title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","status":"public","intvolume":" 29","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"662","oa_version":"Submitted Version","month":"04","publication_identifier":{"issn":["10706631"]},"quality_controlled":"1","project":[{"_id":"2511D90C-B435-11E9-9278-68D0E5697425","grant_number":"SFB 963 TP A8","name":"Astrophysical instability of currents and turbulences"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.01714"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1063/1.4981525","article_number":"044107","publist_id":"7072","publication_status":"published","publisher":"American Institute of Physics","department":[{"_id":"BjHo"}],"year":"2017","date_created":"2018-12-11T11:47:47Z","date_updated":"2021-01-12T08:08:15Z","volume":29,"author":[{"last_name":"Shi","first_name":"Liang","full_name":"Shi, Liang"},{"orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn"},{"full_name":"Rampp, Markus","last_name":"Rampp","first_name":"Markus"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"}]},{"publist_id":"7067","file_date_updated":"2020-07-14T12:47:34Z","author":[{"full_name":"Kong, Hui","first_name":"Hui","last_name":"Kong","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941"},{"orcid":"0000-0002-0686-0365","first_name":"Sergiy","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"},{"full_name":"Jiang, Yu","first_name":"Yu","last_name":"Jiang"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"}],"date_updated":"2021-01-12T08:08:17Z","date_created":"2018-12-11T11:47:47Z","year":"2017","department":[{"_id":"ToHe"}],"publisher":"ACM","publication_status":"published","publication_identifier":{"isbn":["978-145034590-3"]},"month":"04","doi":"10.1145/3049797.3049814","conference":{"name":"HSCC: Hybrid Systems Computation and Control ","location":"Pittsburgh, PA, United States","start_date":"2017-04-18","end_date":"2017-04-20"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","abstract":[{"lang":"eng","text":"In this paper, we propose an approach to automatically compute invariant clusters for nonlinear semialgebraic hybrid systems. An invariant cluster for an ordinary differential equation (ODE) is a multivariate polynomial invariant g(u→, x→) = 0, parametric in u→, which can yield an infinite number of concrete invariants by assigning different values to u→ so that every trajectory of the system can be overapproximated precisely by the intersection of a group of concrete invariants. For semialgebraic systems, which involve ODEs with multivariate polynomial right-hand sides, given a template multivariate polynomial g(u→, x→), an invariant cluster can be obtained by first computing the remainder of the Lie derivative of g(u→, x→) divided by g(u→, x→) and then solving the system of polynomial equations obtained from the coefficients of the remainder. Based on invariant clusters and sum-of-squares (SOS) programming, we present a new method for the safety verification of hybrid systems. Experiments on nonlinear benchmark systems from biology and control theory show that our approach is efficient. "}],"type":"conference","pubrep_id":"817","file":[{"file_name":"IST-2017-817-v1+1_p163-kong.pdf","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":1650530,"file_id":"4873","relation":"main_file","date_created":"2018-12-12T10:11:20Z","date_updated":"2020-07-14T12:47:34Z","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63"}],"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"663","title":"Safety verification of nonlinear hybrid systems based on invariant clusters","status":"public","ddc":["000"],"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2017-04-01T00:00:00Z","citation":{"chicago":"Kong, Hui, Sergiy Bogomolov, Christian Schilling, Yu Jiang, and Thomas A Henzinger. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” In Proceedings of the 20th International Conference on Hybrid Systems, 163–72. ACM, 2017. https://doi.org/10.1145/3049797.3049814.","mla":"Kong, Hui, et al. “Safety Verification of Nonlinear Hybrid Systems Based on Invariant Clusters.” Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–72, doi:10.1145/3049797.3049814.","short":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, T.A. Henzinger, in:, Proceedings of the 20th International Conference on Hybrid Systems, ACM, 2017, pp. 163–172.","ista":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. 2017. Safety verification of nonlinear hybrid systems based on invariant clusters. Proceedings of the 20th International Conference on Hybrid Systems. HSCC: Hybrid Systems Computation and Control , 163–172.","apa":"Kong, H., Bogomolov, S., Schilling, C., Jiang, Y., & Henzinger, T. A. (2017). Safety verification of nonlinear hybrid systems based on invariant clusters. In Proceedings of the 20th International Conference on Hybrid Systems (pp. 163–172). Pittsburgh, PA, United States: ACM. https://doi.org/10.1145/3049797.3049814","ieee":"H. Kong, S. Bogomolov, C. Schilling, Y. Jiang, and T. A. Henzinger, “Safety verification of nonlinear hybrid systems based on invariant clusters,” in Proceedings of the 20th International Conference on Hybrid Systems, Pittsburgh, PA, United States, 2017, pp. 163–172.","ama":"Kong H, Bogomolov S, Schilling C, Jiang Y, Henzinger TA. Safety verification of nonlinear hybrid systems based on invariant clusters. In: Proceedings of the 20th International Conference on Hybrid Systems. ACM; 2017:163-172. doi:10.1145/3049797.3049814"},"publication":"Proceedings of the 20th International Conference on Hybrid Systems","page":"163 - 172"},{"day":"26","month":"04","publication_identifier":{"issn":["19466234"]},"scopus_import":1,"doi":"10.1126/scitranslmed.aan2786","date_published":"2017-04-26T00:00:00Z","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","citation":{"ama":"Novarino G. The antisocial side of antibiotics. Science Translational Medicine. 2017;9(387). doi:10.1126/scitranslmed.aan2786","ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786.","ieee":"G. Novarino, “The antisocial side of antibiotics,” Science Translational Medicine, vol. 9, no. 387. American Association for the Advancement of Science, 2017.","apa":"Novarino, G. (2017). The antisocial side of antibiotics. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan2786","mla":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine, vol. 9, no. 387, 2786, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan2786.","short":"G. Novarino, Science Translational Medicine 9 (2017).","chicago":"Novarino, Gaia. “The Antisocial Side of Antibiotics.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan2786."},"quality_controlled":"1","abstract":[{"text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes.","lang":"eng"}],"issue":"387","publist_id":"7060","article_number":"2786","type":"journal_article","author":[{"full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"}],"date_created":"2018-12-11T11:47:48Z","date_updated":"2021-01-12T08:08:30Z","volume":9,"oa_version":"None","_id":"667","year":"2017","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"The antisocial side of antibiotics","status":"public","intvolume":" 9","department":[{"_id":"GaNo"}],"publisher":"American Association for the Advancement of Science"},{"citation":{"chicago":"Horsthemke, Markus, Anne Bachg, Katharina Groll, Sven Moyzio, Barbara Müther, Sandra Hemkemeyer, Roland Wedlich Söldner, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology, 2017. https://doi.org/10.1074/jbc.M116.766923.","mla":"Horsthemke, Markus, et al. “Multiple Roles of Filopodial Dynamics in Particle Capture and Phagocytosis and Phenotypes of Cdc42 and Myo10 Deletion.” Journal of Biological Chemistry, vol. 292, no. 17, American Society for Biochemistry and Molecular Biology, 2017, pp. 7258–73, doi:10.1074/jbc.M116.766923.","short":"M. Horsthemke, A. Bachg, K. Groll, S. Moyzio, B. Müther, S. Hemkemeyer, R. Wedlich Söldner, M.K. Sixt, S. Tacke, M. Bähler, P. Hanley, Journal of Biological Chemistry 292 (2017) 7258–7273.","ista":"Horsthemke M, Bachg A, Groll K, Moyzio S, Müther B, Hemkemeyer S, Wedlich Söldner R, Sixt MK, Tacke S, Bähler M, Hanley P. 2017. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 292(17), 7258–7273.","ieee":"M. Horsthemke et al., “Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion,” Journal of Biological Chemistry, vol. 292, no. 17. American Society for Biochemistry and Molecular Biology, pp. 7258–7273, 2017.","apa":"Horsthemke, M., Bachg, A., Groll, K., Moyzio, S., Müther, B., Hemkemeyer, S., … Hanley, P. (2017). Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M116.766923","ama":"Horsthemke M, Bachg A, Groll K, et al. Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion. Journal of Biological Chemistry. 2017;292(17):7258-7273. doi:10.1074/jbc.M116.766923"},"publication":"Journal of Biological Chemistry","page":"7258 - 7273","article_type":"original","date_published":"2017-04-28T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"668","intvolume":" 292","title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","ddc":["570"],"status":"public","file":[{"access_level":"open_access","file_name":"2017_JBC_Horsthemke.pdf","creator":"dernst","content_type":"application/pdf","file_size":5647880,"file_id":"6971","relation":"main_file","checksum":"d488162874326a4bb056065fa549dc4a","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-10-24T15:25:42Z"}],"oa_version":"Published Version","type":"journal_article","issue":"17","abstract":[{"text":"Macrophage filopodia, finger-like membrane protrusions, were first implicated in phagocytosis more than 100 years ago, but little is still known about the involvement of these actin-dependent structures in particle clearance. Using spinning disk confocal microscopy to image filopodial dynamics in mouse resident Lifeact-EGFP macrophages, we show that filopodia, or filopodia-like structures, support pathogen clearance by multiple means. Filopodia supported the phagocytic uptake of bacterial (Escherichia coli) particles by (i) capturing along the filopodial shaft and surfing toward the cell body, the most common mode of capture; (ii) capturing via the tip followed by retraction; (iii) combinations of surfing and retraction; or (iv) sweeping actions. In addition, filopodia supported the uptake of zymosan (Saccharomyces cerevisiae) particles by (i) providing fixation, (ii) capturing at the tip and filopodia-guided actin anterograde flow with phagocytic cup formation, and (iii) the rapid growth of new protrusions. To explore the role of filopodia-inducing Cdc42, we generated myeloid-restricted Cdc42 knock-out mice. Cdc42-deficient macrophages exhibited rapid phagocytic cup kinetics, but reduced particle clearance, which could be explained by the marked rounded-up morphology of these cells. Macrophages lacking Myo10, thought to act downstream of Cdc42, had normal morphology, motility, and phagocytic cup formation, but displayed markedly reduced filopodia formation. In conclusion, live-cell imaging revealed multiple mechanisms involving macrophage filopodia in particle capture and engulfment. Cdc42 is not critical for filopodia or phagocytic cup formation, but plays a key role in driving macrophage lamellipodial spreading.","lang":"eng"}],"oa":1,"quality_controlled":"1","doi":"10.1074/jbc.M116.766923","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00219258"]},"month":"04","year":"2017","department":[{"_id":"MiSi"}],"publisher":"American Society for Biochemistry and Molecular Biology","publication_status":"published","author":[{"first_name":"Markus","last_name":"Horsthemke","full_name":"Horsthemke, Markus"},{"last_name":"Bachg","first_name":"Anne","full_name":"Bachg, Anne"},{"last_name":"Groll","first_name":"Katharina","full_name":"Groll, Katharina"},{"last_name":"Moyzio","first_name":"Sven","full_name":"Moyzio, Sven"},{"first_name":"Barbara","last_name":"Müther","full_name":"Müther, Barbara"},{"full_name":"Hemkemeyer, Sandra","first_name":"Sandra","last_name":"Hemkemeyer"},{"full_name":"Wedlich Söldner, Roland","first_name":"Roland","last_name":"Wedlich Söldner"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Tacke, Sebastian","first_name":"Sebastian","last_name":"Tacke"},{"full_name":"Bähler, Martin","last_name":"Bähler","first_name":"Martin"},{"full_name":"Hanley, Peter","first_name":"Peter","last_name":"Hanley"}],"volume":292,"date_updated":"2021-01-12T08:08:34Z","date_created":"2018-12-11T11:47:49Z","publist_id":"7059","file_date_updated":"2020-07-14T12:47:37Z"},{"abstract":[{"lang":"eng","text":"The exocyst, a eukaryotic tethering complex, coregulates targeted exocytosis as an effector of small GTPases in polarized cell growth. In land plants, several exocyst subunits are encoded by double or triple paralogs, culminating in tens of EXO70 paralogs. Out of 23 Arabidopsis thaliana EXO70 isoforms, we analyzed seven isoforms expressed in pollen. Genetic and microscopic analyses of single mutants in EXO70A2, EXO70C1, EXO70C2, EXO70F1, EXO70H3, EXO70H5, and EXO70H6 genes revealed that only a loss-of-function EXO70C2 allele resulted in a significant male-specific transmission defect (segregation 40%:51%:9%) due to aberrant pollen tube growth. Mutant pollen tubes grown in vitro exhibited an enhanced growth rate and a decreased thickness of the tip cell wall, causing tip bursts. However, exo70C2 pollen tubes could frequently recover and restart their speedy elongation, resulting in a repetitive stop-and-go growth dynamics. A pollenspecific depletion of the closest paralog, EXO70C1, using artificial microRNA in the exo70C2 mutant background, resulted in a complete pollen-specific transmission defect, suggesting redundant functions of EXO70C1 and EXO70C2. Both EXO70C1 and EXO70C2, GFP tagged and expressed under the control of their native promoters, localized in the cytoplasm of pollen grains, pollen tubes, and also root trichoblast cells. The expression of EXO70C2-GFP complemented the aberrant growth of exo70C2 pollen tubes. The absent EXO70C2 interactions with core exocyst subunits in the yeast two-hybrid assay, cytoplasmic localization, and genetic effect suggest an unconventional EXO70 function possibly as a regulator of exocytosis outside the exocyst complex. In conclusion, EXO70C2 is a novel factor contributing to the regulation of optimal tip growth of Arabidopsis pollen tubes. "}],"issue":"1","type":"journal_article","file":[{"date_updated":"2020-07-14T12:47:37Z","date_created":"2019-11-18T16:16:18Z","checksum":"97155acc6aa5f0d0a78e0589a932fe02","relation":"main_file","file_id":"7041","content_type":"application/pdf","file_size":2176903,"creator":"dernst","file_name":"2017_PlantPhysio_Synek.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","_id":"669","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","status":"public","ddc":["580"],"intvolume":" 174","day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":1,"date_published":"2017-05-01T00:00:00Z","publication":"Plant Physiology","citation":{"ama":"Synek L, Vukašinović N, Kulich I, et al. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 2017;174(1):223-240. doi:10.1104/pp.16.01282","apa":"Synek, L., Vukašinović, N., Kulich, I., Hála, M., Aldorfová, K., Fendrych, M., & Žárský, V. (2017). EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.16.01282","ieee":"L. Synek et al., “EXO70C2 is a key regulatory factor for optimal tip growth of pollen,” Plant Physiology, vol. 174, no. 1. American Society of Plant Biologists, pp. 223–240, 2017.","ista":"Synek L, Vukašinović N, Kulich I, Hála M, Aldorfová K, Fendrych M, Žárský V. 2017. EXO70C2 is a key regulatory factor for optimal tip growth of pollen. Plant Physiology. 174(1), 223–240.","short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240.","mla":"Synek, Lukáš, et al. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology, vol. 174, no. 1, American Society of Plant Biologists, 2017, pp. 223–40, doi:10.1104/pp.16.01282.","chicago":"Synek, Lukáš, Nemanja Vukašinović, Ivan Kulich, Michal Hála, Klára Aldorfová, Matyas Fendrych, and Viktor Žárský. “EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.” Plant Physiology. American Society of Plant Biologists, 2017. https://doi.org/10.1104/pp.16.01282."},"article_type":"original","page":"223 - 240","file_date_updated":"2020-07-14T12:47:37Z","publist_id":"7058","author":[{"last_name":"Synek","first_name":"Lukáš","full_name":"Synek, Lukáš"},{"first_name":"Nemanja","last_name":"Vukašinović","full_name":"Vukašinović, Nemanja"},{"full_name":"Kulich, Ivan","last_name":"Kulich","first_name":"Ivan"},{"full_name":"Hála, Michal","first_name":"Michal","last_name":"Hála"},{"last_name":"Aldorfová","first_name":"Klára","full_name":"Aldorfová, Klára"},{"full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","orcid":"0000-0002-9767-8699","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Viktor","last_name":"Žárský","full_name":"Žárský, Viktor"}],"date_updated":"2021-01-12T08:08:35Z","date_created":"2018-12-11T11:47:49Z","volume":174,"year":"2017","pmid":1,"publication_status":"published","publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"month":"05","publication_identifier":{"issn":["00320889"]},"doi":"10.1104/pp.16.01282","language":[{"iso":"eng"}],"external_id":{"pmid":["28356503"]},"oa":1,"quality_controlled":"1"},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1621239114","quality_controlled":"1","project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/"}],"external_id":{"pmid":["28420786"]},"oa":1,"month":"05","publication_identifier":{"issn":["00278424"]},"date_created":"2018-12-11T11:47:50Z","date_updated":"2021-01-12T08:08:37Z","volume":114,"author":[{"full_name":"Hilbe, Christian","first_name":"Christian","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X"},{"first_name":"Vaquero","last_name":"Martinez","full_name":"Martinez, Vaquero"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"National Academy of Sciences","year":"2017","pmid":1,"ec_funded":1,"publist_id":"7053","date_published":"2017-05-02T00:00:00Z","page":"4715 - 4720","publication":"PNAS","citation":{"ama":"Hilbe C, Martinez V, Chatterjee K, Nowak M. Memory-n strategies of direct reciprocity. PNAS. 2017;114(18):4715-4720. doi:10.1073/pnas.1621239114","apa":"Hilbe, C., Martinez, V., Chatterjee, K., & Nowak, M. (2017). Memory-n strategies of direct reciprocity. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1621239114","ieee":"C. Hilbe, V. Martinez, K. Chatterjee, and M. Nowak, “Memory-n strategies of direct reciprocity,” PNAS, vol. 114, no. 18. National Academy of Sciences, pp. 4715–4720, 2017.","ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720.","short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","mla":"Hilbe, Christian, et al. “Memory-n Strategies of Direct Reciprocity.” PNAS, vol. 114, no. 18, National Academy of Sciences, 2017, pp. 4715–20, doi:10.1073/pnas.1621239114.","chicago":"Hilbe, Christian, Vaquero Martinez, Krishnendu Chatterjee, and Martin Nowak. “Memory-n Strategies of Direct Reciprocity.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1621239114."},"day":"02","article_processing_charge":"Yes (in subscription journal)","scopus_import":1,"oa_version":"Published Version","title":"Memory-n strategies of direct reciprocity","status":"public","intvolume":" 114","_id":"671","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Humans routinely use conditionally cooperative strategies when interacting in repeated social dilemmas. They are more likely to cooperate if others cooperated before, and are ready to retaliate if others defected. To capture the emergence of reciprocity, most previous models consider subjects who can only choose from a restricted set of representative strategies, or who react to the outcome of the very last round only. As players memorize more rounds, the dimension of the strategy space increases exponentially. This increasing computational complexity renders simulations for individuals with higher cognitive abilities infeasible, especially if multiplayer interactions are taken into account. Here, we take an axiomatic approach instead. We propose several properties that a robust cooperative strategy for a repeated multiplayer dilemma should have. These properties naturally lead to a unique class of cooperative strategies, which contains the classical Win-Stay Lose-Shift rule as a special case. A comprehensive numerical analysis for the prisoner's dilemma and for the public goods game suggests that strategies of this class readily evolve across various memory-n spaces. Our results reveal that successful strategies depend not only on how cooperative others were in the past but also on the respective context of cooperation.","lang":"eng"}],"issue":"18","type":"journal_article"},{"publication_identifier":{"issn":["01677055"]},"month":"05","doi":"10.1111/cgf.13110","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf","open_access":"1"}],"oa":1,"project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"quality_controlled":"1","publist_id":"7056","author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","first_name":"Camille","full_name":"Schreck, Camille"},{"last_name":"Rohmer","first_name":"Damien","full_name":"Rohmer, Damien"},{"last_name":"Hahmann","first_name":"Stefanie","full_name":"Hahmann, Stefanie"}],"volume":36,"date_updated":"2021-01-12T08:08:37Z","date_created":"2018-12-11T11:47:49Z","year":"2017","department":[{"_id":"ChWo"}],"publisher":"Wiley","publication_status":"published","article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2017-05-01T00:00:00Z","citation":{"chicago":"Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” Computer Graphics Forum. Wiley, 2017. https://doi.org/10.1111/cgf.13110.","short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106.","mla":"Schreck, Camille, et al. “Interactive Paper Tearing.” Computer Graphics Forum, vol. 36, no. 2, Wiley, 2017, pp. 95–106, doi:10.1111/cgf.13110.","ieee":"C. Schreck, D. Rohmer, and S. Hahmann, “Interactive paper tearing,” Computer Graphics Forum, vol. 36, no. 2. Wiley, pp. 95–106, 2017.","apa":"Schreck, C., Rohmer, D., & Hahmann, S. (2017). Interactive paper tearing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13110","ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106.","ama":"Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. Computer Graphics Forum. 2017;36(2):95-106. doi:10.1111/cgf.13110"},"publication":"Computer Graphics Forum","page":"95 - 106","article_type":"original","issue":"2","abstract":[{"lang":"eng","text":"We propose an efficient method to model paper tearing in the context of interactive modeling. The method uses geometrical information to automatically detect potential starting points of tears. We further introduce a new hybrid geometrical and physical-based method to compute the trajectory of tears while procedurally synthesizing high resolution details of the tearing path using a texture based approach. The results obtained are compared with real paper and with previous studies on the expected geometric paths of paper that tears."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"670","intvolume":" 36","title":"Interactive paper tearing","status":"public","ddc":["000"]},{"publisher":"Cell Press","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_status":"published","year":"2017","volume":19,"date_created":"2018-12-11T11:47:50Z","date_updated":"2023-02-23T12:50:09Z","author":[{"full_name":"Vaahtomeri, Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7829-3518","first_name":"Kari","last_name":"Vaahtomeri"},{"full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Markus"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leithner, Alexander F","first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","last_name":"Mehling","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8599-1226","full_name":"Mehling, Matthias"},{"orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","ec_funded":1,"publist_id":"7052","file_date_updated":"2020-07-14T12:47:38Z","project":[{"grant_number":"281556","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2017.04.027","publication_identifier":{"issn":["22111247"]},"month":"05","intvolume":" 19","ddc":["570"],"status":"public","title":"Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"672","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:14:54Z","date_updated":"2020-07-14T12:47:38Z","checksum":"8fdddaab1f1d76a6ec9ca94dcb6b07a2","file_id":"5109","relation":"main_file","creator":"system","file_size":2248814,"content_type":"application/pdf","file_name":"IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf","access_level":"open_access"}],"pubrep_id":"900","type":"journal_article","issue":"5","abstract":[{"text":"Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration.","lang":"eng"}],"page":"902 - 909","citation":{"mla":"Vaahtomeri, Kari, et al. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports, vol. 19, no. 5, Cell Press, 2017, pp. 902–09, doi:10.1016/j.celrep.2017.04.027.","short":"K. Vaahtomeri, M. Brown, R. Hauschild, I. de Vries, A.F. Leithner, M. Mehling, W. Kaufmann, M.K. Sixt, Cell Reports 19 (2017) 902–909.","chicago":"Vaahtomeri, Kari, Markus Brown, Robert Hauschild, Ingrid de Vries, Alexander F Leithner, Matthias Mehling, Walter Kaufmann, and Michael K Sixt. “Locally Triggered Release of the Chemokine CCL21 Promotes Dendritic Cell Transmigration across Lymphatic Endothelia.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.027.","ama":"Vaahtomeri K, Brown M, Hauschild R, et al. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 2017;19(5):902-909. doi:10.1016/j.celrep.2017.04.027","ista":"Vaahtomeri K, Brown M, Hauschild R, de Vries I, Leithner AF, Mehling M, Kaufmann W, Sixt MK. 2017. Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. 19(5), 902–909.","apa":"Vaahtomeri, K., Brown, M., Hauschild, R., de Vries, I., Leithner, A. F., Mehling, M., … Sixt, M. K. (2017). Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.027","ieee":"K. Vaahtomeri et al., “Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia,” Cell Reports, vol. 19, no. 5. Cell Press, pp. 902–909, 2017."},"publication":"Cell Reports","date_published":"2017-05-02T00:00:00Z","scopus_import":1,"article_processing_charge":"Yes","has_accepted_license":"1","day":"02"}]