[{"date_created":"2018-12-11T11:47:28Z","doi":"10.1007/978-3-319-70500-2_17","date_published":"2017-11-05T00:00:00Z","page":"493 - 526","day":"05","year":"2017","oa":1,"quality_controlled":"1","publisher":"Springer","editor":[{"first_name":"Yael","full_name":"Kalai, Yael","last_name":"Kalai"},{"last_name":"Reyzin","full_name":"Reyzin, Leonid","first_name":"Leonid"}],"title":"Moderately hard functions: Definition, instantiations, and applications","publist_id":"7196","author":[{"first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","full_name":"Alwen, Joel F"},{"first_name":"Björn","last_name":"Tackmann","full_name":"Tackmann, Björn"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations, and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 493–526.","chicago":"Alwen, Joel F, and Björn Tackmann. “Moderately Hard Functions: Definition, Instantiations, and Applications.” edited by Yael Kalai and Leonid Reyzin, 10677:493–526. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_17.","ieee":"J. F. Alwen and B. Tackmann, “Moderately hard functions: Definition, instantiations, and applications,” presented at the TCC: Theory of Cryptography, Baltimore, MD, United States, 2017, vol. 10677, pp. 493–526.","short":"J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 493–526.","apa":"Alwen, J. F., & Tackmann, B. (2017). Moderately hard functions: Definition, instantiations, and applications. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677, pp. 493–526). Presented at the TCC: Theory of Cryptography, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_17","ama":"Alwen JF, Tackmann B. Moderately hard functions: Definition, instantiations, and applications. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:493-526. doi:10.1007/978-3-319-70500-2_17","mla":"Alwen, Joel F., and Björn Tackmann. Moderately Hard Functions: Definition, Instantiations, and Applications. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 493–526, doi:10.1007/978-3-319-70500-2_17."},"volume":10677,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-331970499-9"]},"intvolume":" 10677","month":"11","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/945"}],"scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover."}],"department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T08:06:04Z","status":"public","conference":{"start_date":"2017-11-12","location":"Baltimore, MD, United States","end_date":"2017-11-15","name":"TCC: Theory of Cryptography"},"type":"conference","_id":"609"},{"publisher":"Springer","quality_controlled":"1","oa":1,"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).","date_published":"2017-10-01T00:00:00Z","doi":"10.1007/s11856-017-1607-7","date_created":"2018-12-11T11:47:29Z","page":"841 - 866","day":"01","publication":"Israel Journal of Mathematics","year":"2017","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"title":"On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result","author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","last_name":"Mabillard","full_name":"Mabillard, Isaac"},{"full_name":"Paták, Pavel","last_name":"Paták","first_name":"Pavel"},{"first_name":"Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana"},{"last_name":"Tancer","orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"publist_id":"7194","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866.","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.","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","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","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.","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.","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."},"month":"10","intvolume":" 222","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1610.09063","open_access":"1"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"volume":222,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1511"}]},"issue":"2","ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","_id":"610","department":[{"_id":"UlWa"}],"date_updated":"2023-02-23T10:02:13Z"},{"publication_status":"published","year":"2017","publication_identifier":{"issn":["00368075"]},"publication":"Science","language":[{"iso":"eng"}],"day":"17","page":"925 - 928","date_created":"2018-12-11T11:47:29Z","doi":"10.1126/science.aao3526","date_published":"2017-11-17T00:00:00Z","issue":"6365","volume":358,"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."}],"oa_version":"None","publisher":"American Association for the Advancement of Science","scopus_import":1,"quality_controlled":"1","intvolume":" 358","month":"11","citation":{"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.","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.","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.","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.","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","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","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."},"date_updated":"2021-01-12T08:06:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7193","author":[{"last_name":"Bradley","full_name":"Bradley, Desmond","first_name":"Desmond"},{"full_name":"Xu, Ping","last_name":"Xu","first_name":"Ping"},{"last_name":"Mohorianu","full_name":"Mohorianu, Irina","first_name":"Irina"},{"last_name":"Whibley","full_name":"Whibley, Annabel","first_name":"Annabel"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"},{"first_name":"Hugo","full_name":"Tavares, Hugo","last_name":"Tavares"},{"last_name":"Couchman","full_name":"Couchman, Matthew","first_name":"Matthew"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"first_name":"Rosemary","full_name":"Carpenter, Rosemary","last_name":"Carpenter"},{"first_name":"Miaomiao","last_name":"Li","full_name":"Li, Miaomiao"},{"first_name":"Qun","full_name":"Li, Qun","last_name":"Li"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"last_name":"Dalmay","full_name":"Dalmay, Tamas","first_name":"Tamas"},{"first_name":"Enrico","last_name":"Coen","full_name":"Coen, Enrico"}],"title":"Evolution of flower color pattern through selection on regulatory small RNAs","department":[{"_id":"NiBa"}],"_id":"611","type":"journal_article","status":"public"},{"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:20Z","ddc":["576","579"],"date_updated":"2021-01-12T08:06:15Z","pubrep_id":"911","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"613","ec_funded":1,"issue":"1","volume":8,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5190","checksum":"44bb5d0229926c23a9955d9fe0f9723f","creator":"system","date_updated":"2020-07-14T12:47:20Z","file_size":1951699,"date_created":"2018-12-12T10:16:05Z","file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf"}],"publication_status":"published","publication_identifier":{"issn":["20411723"]},"intvolume":" 8","month":"12","scopus_import":1,"oa_version":"Published Version","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"}],"title":"Shaping bacterial population behavior through computer interfaced control of individual cells","article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Chait","orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller"},{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"}],"publist_id":"7191","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).","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","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","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.","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.","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."},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"article_number":"1535","date_created":"2018-12-11T11:47:30Z","doi":"10.1038/s41467-017-01683-1","date_published":"2017-12-01T00:00:00Z","publication":"Nature Communications","day":"01","year":"2017","has_accepted_license":"1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","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)."},{"_id":"615","type":"journal_article","status":"public","date_updated":"2021-01-12T08:06:22Z","department":[{"_id":"LaEr"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.00650"}],"month":"11","intvolume":" 53","publication_identifier":{"issn":["02460203"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"4","volume":53,"ec_funded":1,"project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"citation":{"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.","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.","short":"L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability and Statistics 53 (2017) 1606–1656.","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","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","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","last_name":"Schnelli"}],"publist_id":"7189","title":"Universality for random matrix flows with time dependent density","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","oa":1,"year":"2017","day":"01","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","page":"1606 - 1656","doi":"10.1214/16-AIHP765","date_published":"2017-11-01T00:00:00Z","date_created":"2018-12-11T11:47:30Z"},{"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.","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Hill Yardin","full_name":"Hill Yardin, Elisa","first_name":"Elisa"},{"full_name":"Mckeown, Sonja","last_name":"Mckeown","first_name":"Sonja"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Grabrucker","full_name":"Grabrucker, Andreas"}],"publist_id":"7177","title":"Extracerebral dysfunction in animal models of autism spectrum disorder","editor":[{"first_name":"Michael","last_name":"Schmeisser","full_name":"Schmeisser, Michael"},{"full_name":"Boekers, Tobias","last_name":"Boekers","first_name":"Tobias"}],"quality_controlled":"1","publisher":"Springer","year":"2017","publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","day":"28","page":"159 - 187","date_created":"2018-12-11T11:47:33Z","doi":"10.1007/978-3-319-52498-6_9","date_published":"2017-05-28T00:00:00Z","series_title":"Advances in Anatomy Embryology and Cell Biology","_id":"623","type":"book_chapter","status":"public","date_updated":"2021-01-12T08:06:46Z","department":[{"_id":"GaNo"}],"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."}],"oa_version":"None","alternative_title":["ADVSANAT"],"scopus_import":1,"intvolume":" 224","month":"05","publication_status":"published","publication_identifier":{"issn":["03015556"],"isbn":["978-3-319-52496-2"]},"language":[{"iso":"eng"}],"volume":224},{"title":"The infinitesimal model: Definition derivation and implications","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}],"publist_id":"7169","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","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.","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.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 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","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"},"project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:47:34Z","doi":"10.1016/j.tpb.2017.06.001","date_published":"2017-12-01T00:00:00Z","page":"50 - 73","publication":"Theoretical Population Biology","day":"01","year":"2017","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Academic Press","file_date_updated":"2020-07-14T12:47:25Z","department":[{"_id":"NiBa"}],"ddc":["576"],"date_updated":"2021-01-12T08:06:50Z","pubrep_id":"908","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"626","ec_funded":1,"volume":118,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf","date_created":"2018-12-12T10:12:45Z","file_size":1133924,"date_updated":"2020-07-14T12:47:25Z","creator":"system","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8","file_id":"4964","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["00405809"]},"intvolume":" 118","month":"12","scopus_import":1,"oa_version":"Published Version","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"}]},{"ddc":["000"],"date_updated":"2022-05-23T08:54:02Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:25Z","series_title":"Theoretical Computer Science and General Issues","_id":"625","status":"public","type":"book_chapter","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"b2402766ec02c79801aac634bd8f9f6c","file_id":"7048","creator":"dernst","date_updated":"2020-07-14T12:47:25Z","file_size":192826,"date_created":"2019-11-19T08:06:50Z","file_name":"2017_ModelsAlgorithms_Chatterjee.pdf"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"isbn":["978-3-319-63120-2"]},"ec_funded":1,"volume":10460,"oa_version":"Submitted Version","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."}],"intvolume":" 10460","month":"07","alternative_title":["LNCS"],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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","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.","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."},"editor":[{"last_name":"Aceto","full_name":"Aceto, Luca","first_name":"Luca"},{"full_name":"Bacci, Giorgio","last_name":"Bacci","first_name":"Giorgio"},{"last_name":"Ingólfsdóttir","full_name":"Ingólfsdóttir, Anna","first_name":"Anna"},{"first_name":"Axel","last_name":"Legay","full_name":"Legay, Axel"},{"first_name":"Radu","last_name":"Mardare","full_name":"Mardare, Radu"}],"title":"The cost of exactness in quantitative reachability","article_processing_charge":"No","publist_id":"7170","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"}],"publication":"Models, Algorithms, Logics and Tools","day":"25","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:47:34Z","doi":"10.1007/978-3-319-63121-9_18","date_published":"2017-07-25T00:00:00Z","page":"367 - 381","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.","oa":1,"publisher":"Springer","quality_controlled":"1"},{"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"09","intvolume":" 2017","scopus_import":1,"file":[{"file_name":"IST-2017-909-v1+1_peerj-3830.pdf","date_created":"2018-12-12T10:11:51Z","creator":"system","file_size":682064,"date_updated":"2020-07-14T12:47:24Z","checksum":"3d79ae6b6eabc90b0eaaed82ff3493b0","file_id":"4908","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["21678359"]},"publication_status":"published","issue":"9","volume":2017,"_id":"624","status":"public","pubrep_id":"909","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["579"],"date_updated":"2021-01-12T08:06:48Z","file_date_updated":"2020-07-14T12:47:24Z","department":[{"_id":"CaGu"}],"acknowledgement":"Austrian Science Fund (FWF): M1697, P22249; Swiss National Science Foundation (SNF): 145706; European Commission;FWF Special Research Program: RNA-REG F43","quality_controlled":"1","publisher":"PeerJ","oa":1,"day":"21","publication":"PeerJ","has_accepted_license":"1","year":"2017","date_published":"2017-09-21T00:00:00Z","doi":"10.7717/peerj.3830","date_created":"2018-12-11T11:47:33Z","article_number":"3830","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"N. Nikolic, Z. Didara, I. Moll, PeerJ 2017 (2017).","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.","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","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","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.","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."},"title":"MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations","publist_id":"7172","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","orcid":"0000-0001-9068-6090","full_name":"Nikolic, Nela","last_name":"Nikolic"},{"first_name":"Zrinka","last_name":"Didara","full_name":"Didara, Zrinka"},{"last_name":"Moll","full_name":"Moll, Isabella","first_name":"Isabella"}]},{"editor":[{"first_name":"Rupak","full_name":"Majumdar, Rupak","last_name":"Majumdar"},{"last_name":"Kunčak","full_name":"Kunčak, Viktor","first_name":"Viktor"}],"title":"Automated recurrence analysis for almost linear expected runtime bounds","publist_id":"7166","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fu","full_name":"Fu, Hongfei","first_name":"Hongfei"},{"first_name":"Aniket","last_name":"Murhekar","full_name":"Murhekar, Aniket"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","short":"K. Chatterjee, H. Fu, A. Murhekar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 118–139.","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","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"},"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:47:35Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-63387-9_6","page":"118 - 139","day":"01","year":"2017","oa":1,"publisher":"Springer","quality_controlled":"1","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T08:06:55Z","status":"public","conference":{"start_date":"2017-07-24","location":"Heidelberg, Germany","end_date":"2017-07-28","name":"CAV: Computer Aided Verification"},"type":"conference","_id":"628","ec_funded":1,"volume":10426,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-331963386-2"]},"intvolume":" 10426","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1705.00314","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}]},{"volume":84,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["978-3-319-53047-5"]},"intvolume":" 84","month":"05","scopus_import":1,"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","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."}],"department":[{"_id":"MaLo"}],"date_updated":"2021-01-12T08:06:57Z","status":"public","type":"book_chapter","series_title":"Sub-Cellular Biochemistry","_id":"629","date_created":"2018-12-11T11:47:35Z","date_published":"2017-05-13T00:00:00Z","doi":"10.1007/978-3-319-53047-5_15","page":"419 - 444","publication":"Prokaryotic Cytoskeletons","day":"13","year":"2017","publisher":"Springer","quality_controlled":"1","title":"Reconstitution of protein dynamics involved in bacterial cell division","external_id":{"pmid":["28500535"]},"publist_id":"7165","author":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"full_name":"Zieske, Katja","last_name":"Zieske","first_name":"Katja"},{"last_name":"Schwille","full_name":"Schwille, Petra","first_name":"Petra"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"M. Loose, K. Zieske, P. Schwille, in:, Prokaryotic Cytoskeletons, Springer, 2017, pp. 419–444.","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.","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","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","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.","ista":"Loose M, Zieske K, Schwille P. 2017.Reconstitution of protein dynamics involved in bacterial cell division. In: Prokaryotic Cytoskeletons. vol. 84, 419–444."}},{"oa":1,"quality_controlled":"1","publisher":"IOS Press","date_created":"2018-12-11T11:47:36Z","doi":"10.3233/978-1-61499-759-7-356","date_published":"2017-01-01T00:00:00Z","page":"356 - 362","day":"01","year":"2017","has_accepted_license":"1","title":"Biosignals standards and FHIR: The way to go","author":[{"last_name":"Sauermann","full_name":"Sauermann, Stefan","first_name":"Stefan"},{"first_name":"Veronika","full_name":"David, Veronika","last_name":"David"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","last_name":"Schlögl"},{"last_name":"Egelkraut","full_name":"Egelkraut, Reinhard","first_name":"Reinhard"},{"first_name":"Matthias","full_name":"Frohner, Matthias","last_name":"Frohner"},{"full_name":"Pohn, Birgit","last_name":"Pohn","first_name":"Birgit"},{"first_name":"Philipp","full_name":"Urbauer, Philipp","last_name":"Urbauer"},{"first_name":"Alexander","full_name":"Mense, Alexander","last_name":"Mense"}],"publist_id":"7164","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","short":"S. Sauermann, V. David, A. Schlögl, R. Egelkraut, M. Frohner, B. Pohn, P. Urbauer, A. Mense, in:, IOS Press, 2017, pp. 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.","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","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","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."},"intvolume":" 236","month":"01","alternative_title":["Studies in Health Technology and Informatics"],"scopus_import":1,"oa_version":"Published Version","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."}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","volume":236,"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-906-v1+1_SHTI236-0356.pdf","date_created":"2018-12-12T10:11:56Z","creator":"system","file_size":443635,"date_updated":"2020-07-14T12:47:27Z","file_id":"4913","checksum":"1254dcc5b04a996d97fad9a726b42727","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"isbn":["978-161499758-0"]},"pubrep_id":"906","status":"public","conference":{"location":"Vienna, Austria","end_date":"2017-05-24","start_date":"2017-05-23","name":"eHealth: Health Informatics Meets eHealth"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"type":"conference","_id":"630","file_date_updated":"2020-07-14T12:47:27Z","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"ddc":["005"],"date_updated":"2021-01-12T08:06:59Z"},{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"publist_id":"7160","author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","last_name":"Nam","full_name":"Nam, Phan"},{"last_name":"Rougerie","full_name":"Rougerie, Nicolas","first_name":"Nicolas"}],"title":"A note on 2D focusing many boson systems","citation":{"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.","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.","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.","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","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","short":"M. Lewin, P. Nam, N. Rougerie, Proceedings of the American Mathematical Society 145 (2017) 2441–2454.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"American Mathematical Society","page":"2441 - 2454","date_created":"2018-12-11T11:47:36Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1090/proc/13468","year":"2017","publication":"Proceedings of the American Mathematical Society","day":"01","type":"journal_article","status":"public","_id":"632","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T08:07:03Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.09045"}],"scopus_import":1,"intvolume":" 145","month":"01","abstract":[{"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. ","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"issue":"6","volume":145,"publication_status":"published","language":[{"iso":"eng"}]},{"citation":{"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","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","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Schroeder","full_name":"Schroeder, Jan","first_name":"Jan"},{"first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293","last_name":"Deliu"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"},{"first_name":"Michael","full_name":"Schmeisser, Michael","last_name":"Schmeisser"}],"publist_id":"7156","editor":[{"full_name":"Schmeisser, Michael","last_name":"Schmeisser","first_name":"Michael"},{"first_name":"Tobias","last_name":"Boekers","full_name":"Boekers, Tobias"}],"title":"Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder","project":[{"name":"Transmembrane Transporters in Health and Disease","grant_number":"F03523","call_identifier":"FWF","_id":"25473368-B435-11E9-9278-68D0E5697425"}],"year":"2017","day":"28","publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","page":"189 - 211","doi":"10.1007/978-3-319-52498-6_10","date_published":"2017-05-28T00:00:00Z","date_created":"2018-12-11T11:47:37Z","quality_controlled":"1","publisher":"Springer","date_updated":"2021-01-12T08:07:08Z","department":[{"_id":"GaNo"}],"_id":"634","series_title":"Advances in Anatomy Embryology and Cell Biology","type":"book_chapter","status":"public","publication_identifier":{"eisbn":["978-3-319-52498-6"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":224,"abstract":[{"lang":"eng","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."}],"oa_version":"None","alternative_title":["ADVSANAT"],"scopus_import":1,"month":"05","intvolume":" 224"},{"citation":{"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.","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.","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.","short":"S. Bak, S. Bogomolov, T.A. Henzinger, A. Kumar, in:, A. Abate, S. Bodo (Eds.), Springer, 2017, 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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bak, Stanley","last_name":"Bak","first_name":"Stanley"},{"first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Kumar","full_name":"Kumar, Aviral","first_name":"Aviral"}],"publist_id":"7159","editor":[{"first_name":"Alessandro","last_name":"Abate","full_name":"Abate, Alessandro"},{"first_name":"Sylvie","last_name":"Bodo","full_name":"Bodo, Sylvie"}],"title":"Challenges and tool implementation of hybrid rapidly exploring random trees","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"}],"year":"2017","day":"01","page":"83 - 89","date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-63501-9_6","date_created":"2018-12-11T11:47:37Z","publisher":"Springer","quality_controlled":"1","date_updated":"2021-01-12T08:07:06Z","department":[{"_id":"ToHe"}],"_id":"633","type":"conference","conference":{"location":"Heidelberg, Germany","end_date":"2017-07-23","start_date":"2017-07-22","name":"NSV: Numerical Software Verification"},"status":"public","publication_identifier":{"isbn":["978-331963500-2"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":10381,"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":"None","scopus_import":1,"alternative_title":["LNCS"],"month":"01","intvolume":" 10381"},{"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/989"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 10212","month":"01","publication_status":"published","publication_identifier":{"isbn":["978-331956616-0"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":10212,"_id":"635","conference":{"start_date":"2017-04-30","end_date":"2017-05-04","location":"Paris, France","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"type":"conference","status":"public","date_updated":"2021-01-12T08:07:10Z","department":[{"_id":"KrPi"}],"oa":1,"quality_controlled":"1","publisher":"Springer","year":"2017","day":"01","page":"33 - 62","date_created":"2018-12-11T11:47:37Z","doi":"10.1007/978-3-319-56617-7_2","date_published":"2017-01-01T00:00:00Z","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"citation":{"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.","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.","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.","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","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","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.","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."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Alwen","full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"first_name":"Binchi","last_name":"Chen","full_name":"Chen, Binchi"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Reyzin, Leonid","last_name":"Reyzin","first_name":"Leonid"},{"first_name":"Stefano","last_name":"Tessaro","full_name":"Tessaro, Stefano"}],"publist_id":"7154","title":"Scrypt is maximally memory hard","editor":[{"first_name":"Jean-Sébastien","last_name":"Coron","full_name":"Coron, Jean-Sébastien"},{"first_name":"Jesper","full_name":"Buus Nielsen, Jesper","last_name":"Buus Nielsen"}]},{"project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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.","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.","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.","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","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","short":"A. Bakhirkin, T. Ferrere, O. Maler, D. Ulus, in:, A. Abate, G. Geeraerts (Eds.), Springer, 2017, pp. 189–206.","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."},"editor":[{"first_name":"Alessandro","last_name":"Abate","full_name":"Abate, Alessandro"},{"first_name":"Gilles","full_name":"Geeraerts, Gilles","last_name":"Geeraerts"}],"title":"On the quantitative semantics of regular expressions over real-valued signals","publist_id":"7152","author":[{"first_name":"Alexey","full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin"},{"last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"full_name":"Ulus, Dogan","last_name":"Ulus","first_name":"Dogan"}],"quality_controlled":"1","publisher":"Springer","oa":1,"day":"03","year":"2017","date_published":"2017-08-03T00:00:00Z","doi":"10.1007/978-3-319-65765-3_11","date_created":"2018-12-11T11:47:38Z","page":"189 - 206","_id":"636","status":"public","type":"conference","conference":{"name":"FORMATS: Formal Modelling and Analysis of Timed Systems","start_date":"2017-09-05","location":"Berlin, Germany","end_date":"2017-09-07"},"date_updated":"2021-01-12T08:07:14Z","department":[{"_id":"ToHe"}],"oa_version":"Submitted Version","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"}],"month":"08","intvolume":" 10419","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01552132"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331965764-6"]},"publication_status":"published","volume":10419},{"doi":"10.1007/978-3-319-54292-8","date_published":"2017-01-01T00:00:00Z","volume":10152,"date_created":"2018-12-11T11:47:38Z","day":"01","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-54292-8"]},"year":"2017","publication_status":"published","month":"01","intvolume":" 10152","quality_controlled":"1","publisher":"Springer","oa_version":"None","abstract":[{"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.","lang":"eng"}],"department":[{"_id":"ToHe"}],"editor":[{"orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthieu","full_name":"Martel, Matthieu","last_name":"Martel"},{"full_name":"Prabhakar, Pavithra","last_name":"Prabhakar","first_name":"Pavithra"}],"title":"Numerical Software Verification","publist_id":"7150","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-05-24T07:09:52Z","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.","ista":"Bogomolov S, Martel M, Prabhakar P eds. 2017. Numerical Software Verification, Springer,p.","mla":"Bogomolov, Sergiy, et al., editors. Numerical Software Verification. Vol. 10152, Springer, 2017, doi:10.1007/978-3-319-54292-8.","ieee":"S. Bogomolov, M. Martel, and P. Prabhakar, Eds., Numerical Software Verification, vol. 10152. Springer, 2017.","short":"S. Bogomolov, M. Martel, P. Prabhakar, eds., Numerical Software Verification, Springer, 2017.","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","ama":"Bogomolov S, Martel M, Prabhakar P, eds. Numerical Software Verification. Vol 10152. Springer; 2017. doi:10.1007/978-3-319-54292-8"},"status":"public","type":"conference_editor","conference":{"location":"Toronto, ON, Canada","end_date":"2016-07-18","start_date":"2016-07-17","name":"NSV: Numerical Software Verification"},"series_title":"LNCS","_id":"638"},{"ec_funded":1,"volume":10212,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-331956616-0"]},"intvolume":" 10212","month":"04","main_file_link":[{"url":"https://eprint.iacr.org/2016/875","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Submitted Version","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"}],"department":[{"_id":"KrPi"}],"date_updated":"2021-01-12T08:07:22Z","status":"public","conference":{"location":"Paris, France","end_date":"2017-05-04","start_date":"2017-04-30","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"type":"conference","_id":"640","date_created":"2018-12-11T11:47:39Z","doi":"10.1007/978-3-319-56617-7_1","date_published":"2017-04-01T00:00:00Z","page":"3 - 32","day":"01","year":"2017","oa":1,"publisher":"Springer","quality_controlled":"1","editor":[{"first_name":"Jean-Sébastien","full_name":"Coron, Jean-Sébastien","last_name":"Coron"},{"first_name":"Jesper","last_name":"Buus Nielsen","full_name":"Buus Nielsen, Jesper"}],"title":"Depth-robust graphs and their cumulative memory complexity","publist_id":"7148","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"first_name":"Jeremiah","full_name":"Blocki, Jeremiah","last_name":"Blocki"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 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.","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."},"project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}]},{"oa_version":"None","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."}],"intvolume":" 10302","month":"01","publisher":"Springer","alternative_title":["LNCS"],"scopus_import":1,"quality_controlled":"1","language":[{"iso":"eng"}],"day":"01","year":"2017","publication_status":"published","publication_identifier":{"isbn":["978-331958770-7"]},"date_created":"2018-12-11T11:47:39Z","volume":10302,"date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-58771-4_26","page":"323 - 334","_id":"641","status":"public","conference":{"name":"SSVM: Scale Space and Variational Methods in Computer Vision","start_date":"2017-06-04","end_date":"2017-06-08","location":"Kolding, Denmark"},"type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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","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.","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."},"date_updated":"2021-01-12T08:07:23Z","title":"Graphical model parameter learning by inverse linear programming","department":[{"_id":"VlKo"}],"editor":[{"first_name":"François","last_name":"Lauze","full_name":"Lauze, François"},{"full_name":"Dong, Yiqiu","last_name":"Dong","first_name":"Yiqiu"},{"first_name":"Anders","last_name":"Bjorholm Dahl","full_name":"Bjorholm Dahl, Anders"}],"publist_id":"7147","author":[{"full_name":"Trajkovska, Vera","last_name":"Trajkovska","first_name":"Vera"},{"last_name":"Swoboda","full_name":"Swoboda, Paul","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Åström, Freddie","last_name":"Åström","first_name":"Freddie"},{"last_name":"Petra","full_name":"Petra, Stefanie","first_name":"Stefanie"}]},{"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","oa":1,"month":"08","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."}],"oa_version":"Published Version","page":"28","related_material":{"record":[{"id":"133","status":"public","relation":"later_version"}]},"doi":"10.15479/AT:IST-2018-853-v2-2","date_published":"2017-08-04T00:00:00Z","date_created":"2019-05-13T08:15:55Z","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"year":"2017","publication_status":"published","file":[{"file_name":"main(1).pdf","date_created":"2019-05-13T08:14:44Z","file_size":971347,"date_updated":"2020-07-14T12:47:30Z","creator":"dernst","file_id":"6431","checksum":"b48d42725182d7ca10107a118815f4cf","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"day":"04","language":[{"iso":"eng"}],"type":"technical_report","status":"public","_id":"6426","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"}],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:30Z","title":"Synchronizing the asynchronous","citation":{"mla":"Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria, 2017, doi:10.15479/AT:IST-2018-853-v2-2.","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","ama":"Henzinger TA, Kragl B, Qadeer S. 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.","ieee":"T. A. Henzinger, B. Kragl, and 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.","ista":"Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST Austria, 28p."},"date_updated":"2023-02-21T16:59:21Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":60,"issue":"4","publication_status":"published","publication_identifier":{"issn":["03044920"]},"language":[{"iso":"eng"}],"scopus_import":1,"intvolume":" 60","month":"08","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"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"RySh"}],"date_updated":"2021-01-12T08:07:28Z","ddc":["570"],"article_type":"original","type":"journal_article","status":"public","_id":"643","page":"207 - 214","date_created":"2018-12-11T11:47:40Z","date_published":"2017-08-31T00:00:00Z","doi":"10.4077/CJP.2017.BAF469","year":"2017","publication":"Chinese Journal of Physiology","day":"31","quality_controlled":"1","publisher":"Chinese Physiological Society","article_processing_charge":"No","external_id":{"pmid":["28847140"]},"author":[{"first_name":"Wuping","last_name":"Sun","full_name":"Sun, Wuping"},{"last_name":"Zhai","full_name":"Zhai, Ming-Zhu","id":"34009CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Ming-Zhu"},{"first_name":"Qian","full_name":"Zhou, Qian","last_name":"Zhou"},{"first_name":"Chengrui","full_name":"Qian, Chengrui","last_name":"Qian"},{"last_name":"Jiang","full_name":"Jiang, Changyu","first_name":"Changyu"}],"publist_id":"7142","title":"Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats","citation":{"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","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","short":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology 60 (2017) 207–214.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","type":"journal_article","_id":"642","department":[{"_id":"JaMa"}],"date_updated":"2021-01-12T08:07:26Z","intvolume":" 86","month":"01","main_file_link":[{"url":"https://arxiv.org/abs/1508.05535","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","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."}],"volume":86,"issue":"307","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00255718"]},"title":"Localization errors in solving stochastic partial differential equations in the whole space","publist_id":"7144","author":[{"first_name":"Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","last_name":"Gerencser"},{"last_name":"Gyöngy","full_name":"Gyöngy, István","first_name":"István"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.","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.","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","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","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.","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.","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."},"oa":1,"publisher":"American Mathematical Society","quality_controlled":"1","date_created":"2018-12-11T11:47:40Z","doi":"10.1090/mcom/3201","date_published":"2017-01-01T00:00:00Z","page":"2373 - 2397","publication":"Mathematics of Computation","day":"01","year":"2017"},{"_id":"645","status":"public","conference":{"end_date":"2017-07-28","location":"Heidelberg, Germany","start_date":"2017-07-24","name":"CAV: Computer Aided Verification"},"type":"conference","date_updated":"2021-01-12T08:07:32Z","department":[{"_id":"KrCh"}],"oa_version":"Submitted Version","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"}],"intvolume":" 10426","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1705.02326","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-331963386-2"]},"ec_funded":1,"volume":10426,"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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","short":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 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.","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.","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.","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."},"title":"Value iteration for long run average reward in markov decision processes","editor":[{"full_name":"Majumdar, Rupak","last_name":"Majumdar","first_name":"Rupak"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"author":[{"first_name":"Pranav","full_name":"Ashok, Pranav","last_name":"Ashok"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","full_name":"Daca, Przemyslaw"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias"}],"publist_id":"7135","oa":1,"quality_controlled":"1","publisher":"Springer","day":"13","year":"2017","date_created":"2018-12-11T11:47:41Z","doi":"10.1007/978-3-319-63387-9_10","date_published":"2017-07-13T00:00:00Z","page":"201 - 221"},{"_id":"644","type":"journal_article","status":"public","date_updated":"2023-02-23T10:07:49Z","department":[{"_id":"VlKo"}],"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."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.07327"}],"month":"06","intvolume":" 46","publication_status":"published","language":[{"iso":"eng"}],"issue":"3","related_material":{"record":[{"relation":"other","id":"1637","status":"public"}]},"volume":46,"ec_funded":1,"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"citation":{"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","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","short":"V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017) 1087–1110.","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.","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.","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued CSPs. SIAM Journal on Computing. 46(3), 1087–1110.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Krokhin","full_name":"Krokhin, Andrei","first_name":"Andrei"},{"last_name":"Rolinek","full_name":"Rolinek, Michal","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7138","title":"The complexity of general-valued CSPs","publisher":"SIAM","quality_controlled":"1","oa":1,"year":"2017","day":"29","publication":"SIAM Journal on Computing","page":"1087 - 1110","date_published":"2017-06-29T00:00:00Z","doi":"10.1137/16M1091836","date_created":"2018-12-11T11:47:40Z"},{"volume":10302,"ec_funded":1,"publication_identifier":{"isbn":["978-331958770-7"]},"publication_status":"published","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.03769"}],"month":"06","intvolume":" 10302","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."}],"oa_version":"Submitted Version","department":[{"_id":"VlKo"}],"date_updated":"2021-01-12T08:07:34Z","type":"conference","conference":{"end_date":"2017-06-08","location":"Kolding, Denmark","start_date":"2017-06-04","name":"SSVM: Scale Space and Variational Methods in Computer Vision"},"status":"public","_id":"646","page":"235 - 246","date_published":"2017-06-01T00:00:00Z","doi":"10.1007/978-3-319-58771-4_19","date_created":"2018-12-11T11:47:41Z","year":"2017","day":"01","quality_controlled":"1","publisher":"Springer","oa":1,"author":[{"full_name":"Kuske, Jan","last_name":"Kuske","first_name":"Jan"},{"full_name":"Swoboda, Paul","last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Petra, Stefanie","last_name":"Petra","first_name":"Stefanie"}],"publist_id":"7132","editor":[{"first_name":"François","last_name":"Lauze","full_name":"Lauze, François"},{"last_name":"Dong","full_name":"Dong, Yiqiu","first_name":"Yiqiu"},{"first_name":"Anders","last_name":"Bjorholm Dahl","full_name":"Bjorholm Dahl, Anders"}],"title":"A novel convex relaxation for non binary discrete tomography","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.","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","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","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.","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}]},{"publisher":"Springer","quality_controlled":"1","oa":1,"day":"01","year":"2017","date_published":"2017-04-01T00:00:00Z","doi":"10.1007/978-3-319-55911-7_43","date_created":"2018-12-11T11:47:42Z","page":"600 - 613","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 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.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.","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.","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","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","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."},"editor":[{"first_name":"Gerhard","last_name":"Jäger","full_name":"Jäger, Gerhard"},{"full_name":"Steila, Silvia","last_name":"Steila","first_name":"Silvia"}],"title":"On the complexity of breaking pseudoentropy","publist_id":"7125","author":[{"full_name":"Skórski, Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"}],"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"month":"04","intvolume":" 10185","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"url":"https://eprint.iacr.org/2016/1186.pdf","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331955910-0"]},"publication_status":"published","volume":10185,"_id":"648","status":"public","type":"conference","conference":{"end_date":"2017-04-22","location":"Bern, Switzerland","start_date":"2017-04-20","name":"TAMC: Theory and Applications of Models of Computation"},"date_updated":"2021-01-12T08:07:39Z","department":[{"_id":"KrPi"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 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.","short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174.","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.","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","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","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."},"title":"Entropic Ricci curvature for discrete spaces","editor":[{"full_name":"Najman, Laurent","last_name":"Najman","first_name":"Laurent"},{"last_name":"Romon","full_name":"Romon, Pascal","first_name":"Pascal"}],"author":[{"first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","last_name":"Maas"}],"publist_id":"7123","article_processing_charge":"No","publisher":"Springer","quality_controlled":"1","day":"05","publication":"Modern Approaches to Discrete Curvature","year":"2017","doi":"10.1007/978-3-319-58002-9_5","date_published":"2017-10-05T00:00:00Z","date_created":"2018-12-11T11:47:42Z","page":"159 - 174","series_title":"Lecture Notes in Mathematics","_id":"649","status":"public","type":"book_chapter","date_updated":"2022-05-24T07:01:33Z","department":[{"_id":"JaMa"}],"oa_version":"None","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"}],"month":"10","intvolume":" 2184","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-319-58001-2"],"eissn":["978-3-319-58002-9"]},"publication_status":"published","volume":2184},{"citation":{"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.","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.","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.","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","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","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.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"7119","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"editor":[{"first_name":"Gerhard","full_name":"Jäger, Gerhard","last_name":"Jäger"},{"full_name":"Steila, Silvia","last_name":"Steila","first_name":"Silvia"}],"title":"A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds","year":"2017","day":"01","page":"586 - 599","date_created":"2018-12-11T11:47:42Z","date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-55911-7_42","oa":1,"quality_controlled":"1","publisher":"Springer","date_updated":"2021-01-12T08:07:46Z","department":[{"_id":"KrPi"}],"_id":"650","conference":{"name":"TAMC: Theory and Applications of Models of Computation","start_date":"2017-04-20","location":"Bern, Switzerland","end_date":"2017-04-22"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"issn":["03029743"]},"language":[{"iso":"eng"}],"volume":10185,"abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://eprint.iacr.org/2016/965.pdf","open_access":"1"}],"scopus_import":1,"alternative_title":["LNCS"],"intvolume":" 10185","month":"01"},{"publisher":"Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik","quality_controlled":"1","oa":1,"doi":"10.4230/LIPICS.CSL.2017.18","date_published":"2017-08-01T00:00:00Z","date_created":"2019-06-04T12:42:43Z","has_accepted_license":"1","year":"2017","day":"01","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"article_number":"18","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Wolfgang","full_name":"Dvorák, Wolfgang","last_name":"Dvorák"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika","first_name":"Veronika"}],"article_processing_charge":"No","title":"Improved set-based symbolic algorithms for parity games","citation":{"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.","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.","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","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","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl -Leibniz-Zentrum fuer Informatik, 2017.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"08","intvolume":" 82","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"}],"oa_version":"Published Version","volume":82,"ec_funded":1,"license":"https://creativecommons.org/licenses/by/3.0/","publication_status":"published","file":[{"creator":"kschuh","date_updated":"2020-07-14T12:47:33Z","file_size":710185,"date_created":"2019-06-04T12:56:52Z","file_name":"2017_LIPIcs-Chatterjee.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"7c2c9d09970af79026d7e37d9b632ef8","file_id":"6520"}],"language":[{"iso":"eng"}],"type":"conference","conference":{"start_date":"2017-08-20","location":"Stockholm, Sweden","end_date":"2017-08-24","name":"CSL: Conference on Computer Science Logic"},"tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"status":"public","_id":"6519","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:47:33Z","date_updated":"2023-02-14T10:08:25Z","ddc":["004"]},{"ec_funded":1,"volume":92,"language":[{"iso":"eng"}],"file":[{"file_name":"2017_LIPIcs-Fulek.pdf","date_created":"2019-06-04T12:20:35Z","creator":"kschuh","file_size":588982,"date_updated":"2020-07-14T12:47:33Z","checksum":"fc7a643e29621c8bbe49d36b39081f31","file_id":"6518","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","intvolume":" 92","month":"12","scopus_import":1,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:33Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2021-01-12T08:07:51Z","status":"public","conference":{"location":"Phuket, Thailand","end_date":"2017-12-22","start_date":"2017-12-09","name":"ISAAC: International Symposium on Algorithms and Computation"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","_id":"6517","date_created":"2019-06-04T12:11:52Z","date_published":"2017-12-01T00:00:00Z","doi":"10.4230/LIPICS.ISAAC.2017.34","day":"01","year":"2017","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"Embedding graphs into embedded graphs","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Fulek R. 2017. Embedding graphs into embedded graphs. ISAAC: International Symposium on Algorithms and Computation vol. 92, 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.","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","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","ieee":"R. Fulek, “Embedding graphs into embedded graphs,” presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand, 2017, vol. 92.","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."},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"article_number":"34"},{"_id":"652","article_number":"7846789","type":"conference","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"},"status":"public","citation":{"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","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","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.","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.","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.","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."},"date_updated":"2021-01-12T08:07:51Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"},{"full_name":"Martius, Georg S","last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7100","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"title":"Dynamical self consistency leads to behavioral development and emergent social interactions in robots","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."}],"oa_version":"None","publisher":"IEEE","quality_controlled":"1","scopus_import":1,"month":"02","publication_identifier":{"isbn":["978-150905069-7"]},"publication_status":"published","year":"2017","day":"07","language":[{"iso":"eng"}],"date_published":"2017-02-07T00:00:00Z","doi":"10.1109/DEVLRN.2016.7846789","date_created":"2018-12-11T11:47:43Z"},{"title":"Fluid dynamics: Water flows out of touch","department":[{"_id":"BjHo"}],"publist_id":"7116","author":[{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"B. Hof, Nature 541 (2017) 161–162.","ieee":"B. Hof, “Fluid dynamics: Water flows out of touch,” Nature, vol. 541, no. 7636. Nature Publishing Group, pp. 161–162, 2017.","ama":"Hof B. Fluid dynamics: Water flows out of touch. Nature. 2017;541(7636):161-162. doi:10.1038/541161a","apa":"Hof, B. (2017). Fluid dynamics: Water flows out of touch. Nature. Nature Publishing Group. https://doi.org/10.1038/541161a","chicago":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” Nature. Nature Publishing Group, 2017. https://doi.org/10.1038/541161a.","ista":"Hof B. 2017. Fluid dynamics: Water flows out of touch. Nature. 541(7636), 161–162."},"date_updated":"2021-01-12T08:07:49Z","status":"public","type":"journal_article","_id":"651","date_created":"2018-12-11T11:47:43Z","volume":541,"doi":"10.1038/541161a","issue":"7636","date_published":"2017-01-11T00:00:00Z","page":"161 - 162","publication":"Nature","language":[{"iso":"eng"}],"day":"11","year":"2017","publication_status":"published","publication_identifier":{"issn":["00280836"]},"intvolume":" 541","month":"01","scopus_import":1,"quality_controlled":"1","publisher":"Nature Publishing Group","oa_version":"None","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"}]},{"project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"}],"title":"Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer","external_id":{"pmid":["28092682"]},"article_processing_charge":"No","publist_id":"7092","author":[{"full_name":"Makohon Moore, Alvin","last_name":"Makohon Moore","first_name":"Alvin"},{"first_name":"Ming","last_name":"Zhang","full_name":"Zhang, Ming"},{"last_name":"Reiter","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ivana","last_name":"Božić","full_name":"Božić, Ivana"},{"first_name":"Benjamin","last_name":"Allen","full_name":"Allen, Benjamin"},{"id":"1d4c0f4f-e8a3-11ec-a351-e36772758c45","first_name":"Deepanjan","full_name":"Kundu, Deepanjan","last_name":"Kundu"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Fay","full_name":"Wong, Fay","last_name":"Wong"},{"first_name":"Yuchen","full_name":"Jiao, Yuchen","last_name":"Jiao"},{"full_name":"Kohutek, Zachary","last_name":"Kohutek","first_name":"Zachary"},{"first_name":"Jungeui","full_name":"Hong, Jungeui","last_name":"Hong"},{"first_name":"Marc","full_name":"Attiyeh, Marc","last_name":"Attiyeh"},{"last_name":"Javier","full_name":"Javier, Breanna","first_name":"Breanna"},{"last_name":"Wood","full_name":"Wood, Laura","first_name":"Laura"},{"first_name":"Ralph","last_name":"Hruban","full_name":"Hruban, Ralph"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"},{"last_name":"Papadopoulos","full_name":"Papadopoulos, Nickolas","first_name":"Nickolas"},{"first_name":"Kenneth","full_name":"Kinzler, Kenneth","last_name":"Kinzler"},{"first_name":"Bert","last_name":"Vogelstein","full_name":"Vogelstein, Bert"},{"full_name":"Iacobuzio Donahue, Christine","last_name":"Iacobuzio Donahue","first_name":"Christine"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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.","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","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","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."},"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","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.).","date_created":"2018-12-11T11:47:43Z","doi":"10.1038/ng.3764","date_published":"2017-03-01T00:00:00Z","page":"358 - 366","publication":"Nature Genetics","day":"01","year":"2017","has_accepted_license":"1","status":"public","type":"journal_article","article_type":"original","_id":"653","file_date_updated":"2020-07-14T12:47:33Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2022-06-10T09:55:08Z","intvolume":" 49","month":"03","scopus_import":"1","oa_version":"Submitted Version","pmid":1,"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."}],"ec_funded":1,"issue":"3","volume":49,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"e442dc3b7420a36ec805e9bb45cc1a2e","file_id":"7050","file_size":908099,"date_updated":"2020-07-14T12:47:33Z","creator":"dernst","file_name":"2017_NatureGenetics_Makohon.pdf","date_created":"2019-11-19T08:13:50Z"}],"publication_status":"published","publication_identifier":{"issn":["10614036"]}},{"conference":{"start_date":"2017-10-30","location":"Dallas, TX, USA","end_date":"2017-11-03","name":"CCS: Conference on Computer and Communications Security"},"type":"conference","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}],"status":"public","_id":"6527","author":[{"full_name":"Alwen, Joel F","last_name":"Alwen","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F"},{"first_name":"Jeremiah","last_name":"Blocki","full_name":"Blocki, Jeremiah"},{"first_name":"Ben","full_name":"Harsha, Ben","last_name":"Harsha"}],"title":"Practical graphs for optimal side-channel resistant memory-hard functions","department":[{"_id":"KrPi"}],"citation":{"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","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","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.","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.","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.","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.","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."},"date_updated":"2021-01-12T08:07:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2017/443","open_access":"1"}],"quality_controlled":"1","scopus_import":1,"publisher":"ACM Press","month":"10","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"}],"oa_version":"Submitted Version","page":"1001-1017","ec_funded":1,"date_created":"2019-06-06T13:21:29Z","doi":"10.1145/3133956.3134031","date_published":"2017-10-30T00:00:00Z","publication_status":"published","year":"2017","publication_identifier":{"isbn":["9781450349468"]},"language":[{"iso":"eng"}],"publication":"Proceedings of the 2017 ACM SIGSAC Conference on Computer and Communications Security","day":"30"},{"ddc":["571"],"date_updated":"2021-01-12T08:07:54Z","department":[{"_id":"AnKi"}],"file_date_updated":"2020-07-14T12:47:33Z","_id":"654","pubrep_id":"987","status":"public","type":"journal_article","language":[{"iso":"eng"}],"file":[{"checksum":"eef22a0f42a55b232cb2d1188a2322cb","file_id":"5139","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:15:20Z","file_name":"IST-2018-987-v1+1_2017_KichevaRivron__Creating_to.pdf","date_updated":"2020-07-14T12:47:33Z","file_size":228206,"creator":"system"}],"publication_status":"published","publication_identifier":{"issn":["09501991"]},"ec_funded":1,"volume":144,"issue":"5","oa_version":"Submitted Version","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"}],"intvolume":" 144","month":"03","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"A. Kicheva, N. Rivron, Development 144 (2017) 733–736.","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.","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","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.","ista":"Kicheva A, Rivron N. 2017. Creating to understand – developmental biology meets engineering in Paris. Development. 144(5), 733–736."},"title":"Creating to understand – developmental biology meets engineering in Paris","author":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva"},{"last_name":"Rivron","full_name":"Rivron, Nicolas","first_name":"Nicolas"}],"publist_id":"7089","project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"publication":"Development","day":"01","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:47:44Z","date_published":"2017-03-01T00:00:00Z","doi":"10.1242/dev.144915","page":"733 - 736","oa":1,"publisher":"Company of Biologists","quality_controlled":"1"},{"_id":"6526","status":"public","type":"conference","conference":{"location":"Aachen, Germany","end_date":"2017-06-30","start_date":"2017-06-25","name":"ISIT: International Symposium on Information Theory"},"date_updated":"2021-01-12T08:07:53Z","department":[{"_id":"KrPi"}],"oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"month":"08","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.01666"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781509040964"]},"publication_status":"published","ec_funded":1,"article_number":"8006529","project":[{"grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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","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","short":"M. Skórski, in:, 2017 IEEE International Symposium on Information Theory (ISIT), IEEE, 2017.","ieee":"M. Skórski, “On the complexity of estimating Rènyi divergences,” in 2017 IEEE International Symposium on Information Theory (ISIT), Aachen, Germany, 2017.","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.","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.","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."},"title":"On the complexity of estimating Rènyi divergences","author":[{"full_name":"Skórski, Maciej","last_name":"Skórski","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"}],"external_id":{"arxiv":["1702.01666"]},"publisher":"IEEE","quality_controlled":"1","oa":1,"day":"09","publication":"2017 IEEE International Symposium on Information Theory (ISIT)","year":"2017","date_published":"2017-08-09T00:00:00Z","doi":"10.1109/isit.2017.8006529","date_created":"2019-06-06T12:53:09Z"},{"article_number":"e23136","citation":{"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.","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.","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).","ieee":"T. Renault et al., “Bacterial flagella grow through an injection diffusion mechanism,” eLife, vol. 6. eLife Sciences Publications, 2017.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7082","author":[{"first_name":"Thibaud","last_name":"Renault","full_name":"Renault, Thibaud"},{"full_name":"Abraham, Anthony","last_name":"Abraham","first_name":"Anthony"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"last_name":"Paradis","full_name":"Paradis, Guillaume","first_name":"Guillaume"},{"first_name":"Simon","last_name":"Rainville","full_name":"Rainville, Simon"},{"first_name":"Emmanuelle","last_name":"Charpentier","full_name":"Charpentier, Emmanuelle"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"first_name":"Yuhai","full_name":"Tu, Yuhai","last_name":"Tu"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"first_name":"James","last_name":"Keener","full_name":"Keener, James"},{"last_name":"Minamino","full_name":"Minamino, Tohru","first_name":"Tohru"},{"full_name":"Erhardt, Marc","last_name":"Erhardt","first_name":"Marc"}],"title":"Bacterial flagella grow through an injection diffusion mechanism","oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","year":"2017","has_accepted_license":"1","publication":"eLife","day":"06","date_created":"2018-12-11T11:47:44Z","doi":"10.7554/eLife.23136","date_published":"2017-03-06T00:00:00Z","_id":"655","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"904","status":"public","date_updated":"2021-01-12T08:07:55Z","ddc":["579"],"department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:47:33Z","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."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 6","month":"03","publication_status":"published","publication_identifier":{"issn":["2050084X"]},"language":[{"iso":"eng"}],"file":[{"file_name":"IST-2017-904-v1+1_elife-23136-v2.pdf","date_created":"2018-12-12T10:08:53Z","file_size":5520359,"date_updated":"2020-07-14T12:47:33Z","creator":"system","file_id":"4716","checksum":"39e1c3e82ddac83a30422fa72fa1a383","content_type":"application/pdf","relation":"main_file","access_level":"open_access"},{"creator":"system","date_updated":"2020-07-14T12:47:33Z","file_size":11242920,"date_created":"2018-12-12T10:08:54Z","file_name":"IST-2017-904-v1+2_elife-23136-figures-v2.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4717","checksum":"a6d542253028f52e00aa29739ddffe8f"}],"volume":6},{"publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"page":"E2533 - E2539","doi":"10.1073/pnas.1616493114","date_published":"2017-03-21T00:00:00Z","date_created":"2018-12-11T11:47:45Z","year":"2017","day":"21","publication":"PNAS","author":[{"first_name":"Barbara","last_name":"Möller","full_name":"Möller, Barbara"},{"full_name":"Ten Hove, Colette","last_name":"Ten Hove","first_name":"Colette"},{"full_name":"Xiang, Daoquan","last_name":"Xiang","first_name":"Daoquan"},{"first_name":"Nerys","last_name":"Williams","full_name":"Williams, Nerys"},{"last_name":"López","full_name":"López, Lorena","first_name":"Lorena"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"full_name":"Smit, Margot","last_name":"Smit","first_name":"Margot"},{"first_name":"Raju","full_name":"Datla, Raju","last_name":"Datla"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"}],"publist_id":"7076","external_id":{"pmid":["28265057"]},"title":"Auxin response cell autonomously controls ground tissue initiation in the early arabidopsis embryo","citation":{"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.","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.","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.","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","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373392/"}],"month":"03","intvolume":" 114","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"volume":114,"issue":"12","publication_identifier":{"issn":["00278424"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"657","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T08:08:02Z"},{"publication_identifier":{"issn":["19466234"]},"year":"2017","publication_status":"published","day":"15","publication":"Science Translational Medicine","language":[{"iso":"eng"}],"issue":"381","volume":9,"doi":"10.1126/scitranslmed.aam9867","date_published":"2017-03-15T00:00:00Z","date_created":"2018-12-11T11:47:45Z","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."}],"oa_version":"None","scopus_import":1,"publisher":"American Association for the Advancement of Science","quality_controlled":"1","month":"03","intvolume":" 9","date_updated":"2021-01-12T08:07:59Z","citation":{"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.","ista":"Novarino G. 2017. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 9(381), eaam9867.","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.","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.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ama":"Novarino G. Modeling Alzheimer’s disease in mice with human neurons. Science Translational Medicine. 2017;9(381). doi:10.1126/scitranslmed.aam9867","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"},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7079","title":"Modeling Alzheimer's disease in mice with human neurons","department":[{"_id":"GaNo"}],"_id":"656","article_number":"eaam9867","type":"journal_article","status":"public"},{"article_number":"00008","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 2017;11(MAR). doi:10.3389/fnbot.2017.00008","short":"R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017).","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.","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.","ista":"Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008."},"title":"Self organized behavior generation for musculoskeletal robots","article_processing_charge":"Yes","publist_id":"7078","author":[{"last_name":"Der","full_name":"Der, Ralf","first_name":"Ralf"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"}],"oa":1,"publisher":"Frontiers Research Foundation","quality_controlled":"1","publication":"Frontiers in Neurorobotics","day":"16","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:47:45Z","date_published":"2017-03-16T00:00:00Z","doi":"10.3389/fnbot.2017.00008","_id":"658","pubrep_id":"903","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["006"],"date_updated":"2021-01-12T08:08:04Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:33Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 11","month":"03","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"creator":"system","file_size":8439566,"date_updated":"2020-07-14T12:47:33Z","file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","date_created":"2018-12-12T10:18:49Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b1bc43f96d1df3313c03032c2a46388d","file_id":"5371"}],"publication_status":"published","publication_identifier":{"issn":["16625218"]},"ec_funded":1,"volume":11,"issue":"MAR"},{"volume":8,"publication_status":"published","publication_identifier":{"issn":["20411723"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"dae30190291c3630e8102d8714a8d23e","file_id":"5072","file_size":9523746,"date_updated":"2020-07-14T12:47:34Z","creator":"system","file_name":"IST-2017-902-v1+1_Kage_et_al-2017-Nature_Communications.pdf","date_created":"2018-12-12T10:14:21Z"}],"scopus_import":1,"intvolume":" 8","month":"03","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."}],"oa_version":"Published Version","department":[{"_id":"MiSi"}],"file_date_updated":"2020-07-14T12:47:34Z","date_updated":"2021-01-12T08:08:06Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"902","status":"public","_id":"659","date_created":"2018-12-11T11:47:46Z","date_published":"2017-03-22T00:00:00Z","doi":"10.1038/ncomms14832","year":"2017","has_accepted_license":"1","publication":"Nature Communications","day":"22","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","article_processing_charge":"No","publist_id":"7075","author":[{"last_name":"Kage","full_name":"Kage, Frieda","first_name":"Frieda"},{"full_name":"Winterhoff, Moritz","last_name":"Winterhoff","first_name":"Moritz"},{"last_name":"Dimchev","full_name":"Dimchev, Vanessa","first_name":"Vanessa"},{"id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan","last_name":"Müller","full_name":"Müller, Jan"},{"last_name":"Thalheim","full_name":"Thalheim, Tobias","first_name":"Tobias"},{"last_name":"Freise","full_name":"Freise, Anika","first_name":"Anika"},{"last_name":"Brühmann","full_name":"Brühmann, Stefan","first_name":"Stefan"},{"full_name":"Kollasser, Jana","last_name":"Kollasser","first_name":"Jana"},{"full_name":"Block, Jennifer","last_name":"Block","first_name":"Jennifer"},{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A"},{"first_name":"Matthias","last_name":"Geyer","full_name":"Geyer, Matthias"},{"first_name":"Hams","full_name":"Schnittler, Hams","last_name":"Schnittler"},{"first_name":"Cord","full_name":"Brakebusch, Cord","last_name":"Brakebusch"},{"first_name":"Theresia","full_name":"Stradal, Theresia","last_name":"Stradal"},{"last_name":"Carlier","full_name":"Carlier, Marie","first_name":"Marie"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"first_name":"Josef","last_name":"Käs","full_name":"Käs, Josef"},{"full_name":"Faix, Jan","last_name":"Faix","first_name":"Jan"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"}],"title":"FMNL formins boost lamellipodial force generation","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.","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","ama":"Kage F, Winterhoff M, Dimchev V, et al. FMNL formins boost lamellipodial force generation. Nature Communications. 2017;8. doi:10.1038/ncomms14832","ieee":"F. Kage et al., “FMNL formins boost lamellipodial force generation,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"14832"},{"author":[{"full_name":"Rickman, Jamie","last_name":"Rickman","first_name":"Jamie"},{"id":"459064DC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian F","full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","last_name":"Düllberg"},{"first_name":"Nicholas","last_name":"Cade","full_name":"Cade, Nicholas"},{"first_name":"Lewis","last_name":"Griffin","full_name":"Griffin, Lewis"},{"full_name":"Surrey, Thomas","last_name":"Surrey","first_name":"Thomas"}],"publist_id":"7073","external_id":{"pmid":["28280102"]},"title":"Steady state EB cap size fluctuations are determined by stochastic microtubule growth and maturation","citation":{"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.","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.","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","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.","short":"J. Rickman, C.F. Düllberg, N. Cade, L. Griffin, T. Surrey, PNAS 114 (2017) 3427–3432.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"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.).","page":"3427 - 3432","date_published":"2017-03-28T00:00:00Z","doi":"10.1073/pnas.1620274114","date_created":"2018-12-11T11:47:46Z","year":"2017","day":"28","publication":"PNAS","type":"journal_article","status":"public","_id":"660","department":[{"_id":"MaLo"}],"date_updated":"2021-01-12T08:08:09Z","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5380103/","open_access":"1"}],"month":"03","intvolume":" 114","abstract":[{"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.","lang":"eng"}],"oa_version":"Submitted Version","pmid":1,"issue":"13","volume":114,"publication_identifier":{"issn":["00278424"]},"publication_status":"published","language":[{"iso":"eng"}]},{"department":[{"_id":"BjHo"}],"date_updated":"2021-01-12T08:08:15Z","status":"public","type":"journal_article","_id":"662","issue":"4","volume":29,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["10706631"]},"intvolume":" 29","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1703.01714","open_access":"1"}],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"title":"Hydrodynamic turbulence in quasi Keplerian rotating flows","publist_id":"7072","author":[{"full_name":"Shi, Liang","last_name":"Shi","first_name":"Liang"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"},{"first_name":"Markus","last_name":"Rampp","full_name":"Rampp, Markus"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Shi L, Hof B, Rampp M, Avila M. 2017. Hydrodynamic turbulence in quasi Keplerian rotating flows. Physics of Fluids. 29(4), 044107.","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.","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","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","short":"L. Shi, B. Hof, M. Rampp, M. Avila, Physics of Fluids 29 (2017).","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.","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."},"project":[{"_id":"2511D90C-B435-11E9-9278-68D0E5697425","name":"Astrophysical instability of currents and turbulences","grant_number":"SFB 963 TP A8"}],"article_number":"044107","date_created":"2018-12-11T11:47:47Z","doi":"10.1063/1.4981525","date_published":"2017-04-01T00:00:00Z","publication":"Physics of Fluids","day":"01","year":"2017","oa":1,"publisher":"American Institute of Physics","quality_controlled":"1"},{"page":"163 - 172","doi":"10.1145/3049797.3049814","date_published":"2017-04-01T00:00:00Z","date_created":"2018-12-11T11:47:47Z","has_accepted_license":"1","year":"2017","day":"01","publication":"Proceedings of the 20th International Conference on Hybrid Systems","publisher":"ACM","quality_controlled":"1","oa":1,"author":[{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui","last_name":"Kong"},{"last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","first_name":"Sergiy"},{"first_name":"Christian","full_name":"Schilling, Christian","last_name":"Schilling"},{"full_name":"Jiang, Yu","last_name":"Jiang","first_name":"Yu"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"publist_id":"7067","title":"Safety verification of nonlinear hybrid systems based on invariant clusters","citation":{"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.","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.","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","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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["978-145034590-3"]},"publication_status":"published","file":[{"creator":"system","date_updated":"2020-07-14T12:47:34Z","file_size":1650530,"date_created":"2018-12-12T10:11:20Z","file_name":"IST-2017-817-v1+1_p163-kong.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4873","checksum":"b7667434cbf5b5f0ade3bea1dbe5bf63"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"04","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. "}],"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T08:08:17Z","ddc":["000"],"type":"conference","conference":{"start_date":"2017-04-18","end_date":"2017-04-20","location":"Pittsburgh, PA, United States","name":"HSCC: Hybrid Systems Computation and Control "},"status":"public","pubrep_id":"817","_id":"663"},{"type":"journal_article","status":"public","_id":"667","article_number":"2786","author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"publist_id":"7060","title":"The antisocial side of antibiotics","department":[{"_id":"GaNo"}],"citation":{"ista":"Novarino G. 2017. The antisocial side of antibiotics. Science Translational Medicine. 9(387), 2786.","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.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “The antisocial side of antibiotics,” Science Translational Medicine, vol. 9, no. 387. American Association for the Advancement of Science, 2017.","ama":"Novarino G. The antisocial side of antibiotics. Science Translational Medicine. 2017;9(387). doi:10.1126/scitranslmed.aan2786","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."},"date_updated":"2021-01-12T08:08:30Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","intvolume":" 9","month":"04","abstract":[{"text":"Perinatal exposure to penicillin may result in longlasting gut and behavioral changes.","lang":"eng"}],"oa_version":"None","date_created":"2018-12-11T11:47:48Z","date_published":"2017-04-26T00:00:00Z","doi":"10.1126/scitranslmed.aan2786","issue":"387","volume":9,"publication_status":"published","year":"2017","publication_identifier":{"issn":["19466234"]},"publication":"Science Translational Medicine","language":[{"iso":"eng"}],"day":"26"},{"quality_controlled":"1","publisher":"American Society for Biochemistry and Molecular Biology","oa":1,"has_accepted_license":"1","year":"2017","day":"28","publication":"Journal of Biological Chemistry","page":"7258 - 7273","doi":"10.1074/jbc.M116.766923","date_published":"2017-04-28T00:00:00Z","date_created":"2018-12-11T11:47:49Z","citation":{"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","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","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.","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.","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7059","author":[{"first_name":"Markus","last_name":"Horsthemke","full_name":"Horsthemke, Markus"},{"full_name":"Bachg, Anne","last_name":"Bachg","first_name":"Anne"},{"first_name":"Katharina","full_name":"Groll, Katharina","last_name":"Groll"},{"full_name":"Moyzio, Sven","last_name":"Moyzio","first_name":"Sven"},{"first_name":"Barbara","last_name":"Müther","full_name":"Müther, Barbara"},{"full_name":"Hemkemeyer, Sandra","last_name":"Hemkemeyer","first_name":"Sandra"},{"last_name":"Wedlich Söldner","full_name":"Wedlich Söldner, Roland","first_name":"Roland"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"},{"first_name":"Sebastian","last_name":"Tacke","full_name":"Tacke, Sebastian"},{"full_name":"Bähler, Martin","last_name":"Bähler","first_name":"Martin"},{"full_name":"Hanley, Peter","last_name":"Hanley","first_name":"Peter"}],"title":"Multiple roles of filopodial dynamics in particle capture and phagocytosis and phenotypes of Cdc42 and Myo10 deletion","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_version":"Published Version","scopus_import":1,"month":"04","intvolume":" 292","publication_identifier":{"issn":["00219258"]},"publication_status":"published","file":[{"date_created":"2019-10-24T15:25:42Z","file_name":"2017_JBC_Horsthemke.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:37Z","file_size":5647880,"checksum":"d488162874326a4bb056065fa549dc4a","file_id":"6971","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":292,"issue":"17","_id":"668","article_type":"original","type":"journal_article","status":"public","date_updated":"2021-01-12T08:08:34Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"MiSi"}]},{"external_id":{"pmid":["28356503"]},"article_processing_charge":"No","publist_id":"7058","author":[{"full_name":"Synek, Lukáš","last_name":"Synek","first_name":"Lukáš"},{"first_name":"Nemanja","last_name":"Vukašinović","full_name":"Vukašinović, Nemanja"},{"first_name":"Ivan","last_name":"Kulich","full_name":"Kulich, Ivan"},{"first_name":"Michal","full_name":"Hála, Michal","last_name":"Hála"},{"full_name":"Aldorfová, Klára","last_name":"Aldorfová","first_name":"Klára"},{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Žárský, Viktor","last_name":"Žárský","first_name":"Viktor"}],"title":"EXO70C2 is a key regulatory factor for optimal tip growth of pollen","citation":{"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.","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.","short":"L. Synek, N. Vukašinović, I. Kulich, M. Hála, K. Aldorfová, M. Fendrych, V. Žárský, Plant Physiology 174 (2017) 223–240.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"American Society of Plant Biologists","page":"223 - 240","date_created":"2018-12-11T11:47:49Z","doi":"10.1104/pp.16.01282","date_published":"2017-05-01T00:00:00Z","year":"2017","has_accepted_license":"1","publication":"Plant Physiology","day":"01","type":"journal_article","article_type":"original","status":"public","_id":"669","file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"JiFr"}],"date_updated":"2021-01-12T08:08:35Z","ddc":["580"],"scopus_import":1,"intvolume":" 174","month":"05","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. "}],"pmid":1,"oa_version":"Submitted Version","issue":"1","volume":174,"publication_status":"published","publication_identifier":{"issn":["00320889"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-18T16:16:18Z","file_name":"2017_PlantPhysio_Synek.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:37Z","file_size":2176903,"file_id":"7041","checksum":"97155acc6aa5f0d0a78e0589a932fe02","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}]},{"department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T08:08:37Z","status":"public","type":"journal_article","_id":"671","volume":114,"issue":"18","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"publication_status":"published","month":"05","intvolume":" 114","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5422766/","open_access":"1"}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"title":"Memory-n strategies of direct reciprocity","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"first_name":"Vaquero","full_name":"Martinez, Vaquero","last_name":"Martinez"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"publist_id":"7053","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["28420786"]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Hilbe C, Martinez V, Chatterjee K, Nowak M. 2017. Memory-n strategies of direct reciprocity. PNAS. 114(18), 4715–4720.","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.","short":"C. Hilbe, V. Martinez, K. Chatterjee, M. Nowak, PNAS 114 (2017) 4715–4720.","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.","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","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."},"project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"}],"doi":"10.1073/pnas.1621239114","date_published":"2017-05-02T00:00:00Z","date_created":"2018-12-11T11:47:50Z","page":"4715 - 4720","day":"02","publication":"PNAS","year":"2017","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1},{"ddc":["000"],"date_updated":"2021-01-12T08:08:37Z","department":[{"_id":"ChWo"}],"_id":"670","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["01677055"]},"publication_status":"published","issue":"2","volume":36,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"05","intvolume":" 36","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01647113/file/eg_2017_schreck_paper_tearing.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"C. Schreck, D. Rohmer, S. Hahmann, Computer Graphics Forum 36 (2017) 95–106.","ieee":"C. Schreck, D. Rohmer, and S. Hahmann, “Interactive paper tearing,” Computer Graphics Forum, vol. 36, no. 2. Wiley, pp. 95–106, 2017.","ama":"Schreck C, Rohmer D, Hahmann S. Interactive paper tearing. Computer Graphics Forum. 2017;36(2):95-106. doi:10.1111/cgf.13110","apa":"Schreck, C., Rohmer, D., & Hahmann, S. (2017). Interactive paper tearing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13110","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.","ista":"Schreck C, Rohmer D, Hahmann S. 2017. Interactive paper tearing. Computer Graphics Forum. 36(2), 95–106.","chicago":"Schreck, Camille, Damien Rohmer, and Stefanie Hahmann. “Interactive Paper Tearing.” Computer Graphics Forum. Wiley, 2017. https://doi.org/10.1111/cgf.13110."},"title":"Interactive paper tearing","publist_id":"7056","author":[{"full_name":"Schreck, Camille","last_name":"Schreck","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","first_name":"Camille"},{"first_name":"Damien","last_name":"Rohmer","full_name":"Rohmer, Damien"},{"first_name":"Stefanie","last_name":"Hahmann","full_name":"Hahmann, Stefanie"}],"article_processing_charge":"No","project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"day":"01","publication":"Computer Graphics Forum","year":"2017","doi":"10.1111/cgf.13110","date_published":"2017-05-01T00:00:00Z","date_created":"2018-12-11T11:47:49Z","page":"95 - 106","publisher":"Wiley","quality_controlled":"1","oa":1},{"year":"2017","has_accepted_license":"1","publication":"Cell Reports","day":"02","page":"902 - 909","date_created":"2018-12-11T11:47:50Z","date_published":"2017-05-02T00:00:00Z","doi":"10.1016/j.celrep.2017.04.027","oa":1,"quality_controlled":"1","publisher":"Cell Press","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.","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","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","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.","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","publist_id":"7052","author":[{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari","orcid":"0000-0001-7829-3518"},{"id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","first_name":"Markus","full_name":"Brown, Markus","last_name":"Brown"},{"last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid","last_name":"De Vries"},{"last_name":"Leithner","full_name":"Leithner, Alexander F","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","id":"3C23B994-F248-11E8-B48F-1D18A9856A87","full_name":"Mehling, Matthias","orcid":"0000-0001-8599-1226","last_name":"Mehling"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"title":"Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556","call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12"}],"publication_status":"published","publication_identifier":{"issn":["22111247"]},"language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:47:38Z","file_size":2248814,"date_created":"2018-12-12T10:14:54Z","file_name":"IST-2017-900-v1+1_1-s2.0-S2211124717305211-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"8fdddaab1f1d76a6ec9ca94dcb6b07a2","file_id":"5109"}],"ec_funded":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","issue":"5","volume":19,"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"}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 19","month":"05","date_updated":"2023-02-23T12:50:09Z","ddc":["570"],"department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"file_date_updated":"2020-07-14T12:47:38Z","_id":"672","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","pubrep_id":"900","status":"public"},{"month":"05","intvolume":" 27","scopus_import":1,"oa_version":"None","abstract":[{"text":"Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo.","lang":"eng"}],"volume":27,"issue":"9","ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09609822"]},"publication_status":"published","status":"public","type":"journal_article","_id":"674","department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"date_updated":"2023-02-23T12:50:44Z","quality_controlled":"1","publisher":"Cell Press","date_published":"2017-05-09T00:00:00Z","doi":"10.1016/j.cub.2017.04.004","date_created":"2018-12-11T11:47:51Z","page":"1314 - 1325","day":"09","publication":"Current Biology","year":"2017","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)"}],"title":"Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6","author":[{"full_name":"Schwarz, Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"first_name":"Veronika","id":"3FD04378-F248-11E8-B48F-1D18A9856A87","full_name":"Bierbaum, Veronika","last_name":"Bierbaum"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"full_name":"Brown, Markus","last_name":"Brown","first_name":"Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"De Vries, Ingrid","last_name":"De Vries","first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Leithner, Alexander F","last_name":"Leithner","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Reversat","orcid":"0000-0003-0666-8928","full_name":"Reversat, Anne","id":"35B76592-F248-11E8-B48F-1D18A9856A87","first_name":"Anne"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tarrant, Teresa","last_name":"Tarrant","first_name":"Teresa"},{"first_name":"Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7050","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Schwarz et al., “Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6,” Current Biology, vol. 27, no. 9. Cell Press, pp. 1314–1325, 2017.","short":"J. Schwarz, V. Bierbaum, K. Vaahtomeri, R. Hauschild, M. Brown, I. de Vries, A.F. Leithner, A. Reversat, J. Merrin, T. Tarrant, M.T. Bollenbach, M.K. Sixt, Current Biology 27 (2017) 1314–1325.","apa":"Schwarz, J., Bierbaum, V., Vaahtomeri, K., Hauschild, R., Brown, M., de Vries, I., … Sixt, M. K. (2017). Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.04.004","ama":"Schwarz J, Bierbaum V, Vaahtomeri K, et al. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 2017;27(9):1314-1325. doi:10.1016/j.cub.2017.04.004","mla":"Schwarz, Jan, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology, vol. 27, no. 9, Cell Press, 2017, pp. 1314–25, doi:10.1016/j.cub.2017.04.004.","ista":"Schwarz J, Bierbaum V, Vaahtomeri K, Hauschild R, Brown M, de Vries I, Leithner AF, Reversat A, Merrin J, Tarrant T, Bollenbach MT, Sixt MK. 2017. Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6. Current Biology. 27(9), 1314–1325.","chicago":"Schwarz, Jan, Veronika Bierbaum, Kari Vaahtomeri, Robert Hauschild, Markus Brown, Ingrid de Vries, Alexander F Leithner, et al. “Dendritic Cells Interpret Haptotactic Chemokine Gradients in a Manner Governed by Signal to Noise Ratio and Dependent on GRK6.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.04.004."}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Lademann C, Renkawitz J, Pfander B, Jentsch S. 2017. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 19(7), 1294–1303.","chicago":"Lademann, Claudio, Jörg Renkawitz, Boris Pfander, and Stefan Jentsch. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports. Cell Press, 2017. https://doi.org/10.1016/j.celrep.2017.04.051.","apa":"Lademann, C., Renkawitz, J., Pfander, B., & Jentsch, S. (2017). The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2017.04.051","ama":"Lademann C, Renkawitz J, Pfander B, Jentsch S. The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination. Cell Reports. 2017;19(7):1294-1303. doi:10.1016/j.celrep.2017.04.051","short":"C. Lademann, J. Renkawitz, B. Pfander, S. Jentsch, Cell Reports 19 (2017) 1294–1303.","ieee":"C. Lademann, J. Renkawitz, B. Pfander, and S. Jentsch, “The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination,” Cell Reports, vol. 19, no. 7. Cell Press, pp. 1294–1303, 2017.","mla":"Lademann, Claudio, et al. “The INO80 Complex Removes H2A.Z to Promote Presynaptic Filament Formation during Homologous Recombination.” Cell Reports, vol. 19, no. 7, Cell Press, 2017, pp. 1294–303, doi:10.1016/j.celrep.2017.04.051."},"title":"The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination","publist_id":"7046","author":[{"first_name":"Claudio","last_name":"Lademann","full_name":"Lademann, Claudio"},{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","first_name":"Jörg"},{"first_name":"Boris","full_name":"Pfander, Boris","last_name":"Pfander"},{"full_name":"Jentsch, Stefan","last_name":"Jentsch","first_name":"Stefan"}],"publication":"Cell Reports","day":"16","year":"2017","has_accepted_license":"1","date_created":"2018-12-11T11:47:52Z","doi":"10.1016/j.celrep.2017.04.051","date_published":"2017-05-16T00:00:00Z","page":"1294 - 1303","oa":1,"publisher":"Cell Press","quality_controlled":"1","ddc":["570"],"date_updated":"2021-01-12T08:08:57Z","file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"MiSi"}],"_id":"677","pubrep_id":"899","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:47:40Z","file_size":3005610,"date_created":"2018-12-12T10:15:48Z","file_name":"IST-2017-899-v1+1_1-s2.0-S2211124717305454-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"efc7287d9c6354983cb151880e9ad72a","file_id":"5171"}],"publication_status":"published","publication_identifier":{"issn":["22111247"]},"issue":"7","volume":19,"oa_version":"Published Version","abstract":[{"text":"The INO80 complex (INO80-C) is an evolutionarily conserved nucleosome remodeler that acts in transcription, replication, and genome stability. It is required for resistance against genotoxic agents and is involved in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the causes of the HR defect in INO80-C mutant cells are controversial. Here, we unite previous findings using a system to study HR with high spatial resolution in budding yeast. We find that INO80-C has at least two distinct functions during HR—DNA end resection and presynaptic filament formation. Importantly, the second function is linked to the histone variant H2A.Z. In the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-C-deficient mutants, suggesting that presynaptic filament formation is the crucial INO80-C function during HR.","lang":"eng"}],"intvolume":" 19","month":"05","scopus_import":1},{"month":"05","intvolume":" 19","scopus_import":1,"quality_controlled":"1","publisher":"Nature Publishing Group","oa_version":"None","abstract":[{"lang":"eng","text":"The seminal observation that mechanical signals can elicit changes in biochemical signalling within cells, a process commonly termed mechanosensation and mechanotransduction, has revolutionized our understanding of the role of cell mechanics in various fundamental biological processes, such as cell motility, adhesion, proliferation and differentiation. In this Review, we will discuss how the interplay and feedback between mechanical and biochemical signals control tissue morphogenesis and cell fate specification in embryonic development."}],"doi":"10.1038/ncb3524","volume":19,"date_published":"2017-05-31T00:00:00Z","issue":"6","date_created":"2018-12-11T11:47:53Z","page":"581 - 588","day":"31","language":[{"iso":"eng"}],"publication":"Nature Cell Biology","publication_identifier":{"issn":["14657392"]},"publication_status":"published","year":"2017","status":"public","project":[{"name":"The generation and function of anisotropic tissue tension in zebrafish epiboly (EMBO Fellowship)","grant_number":"ALTF534-2016","_id":"25236028-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","_id":"678","department":[{"_id":"CaHe"}],"title":"Multiscale force sensing in development","author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta","last_name":"Petridou","orcid":"0000-0002-8451-1195","full_name":"Petridou, Nicoletta"},{"full_name":"Spiro, Zoltan P","last_name":"Spiro","first_name":"Zoltan P","id":"426AD026-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"publist_id":"7040","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:08:59Z","citation":{"chicago":"Petridou, Nicoletta, Zoltan P Spiro, and Carl-Philipp J Heisenberg. “Multiscale Force Sensing in Development.” Nature Cell Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/ncb3524.","ista":"Petridou N, Spiro ZP, Heisenberg C-PJ. 2017. Multiscale force sensing in development. Nature Cell Biology. 19(6), 581–588.","mla":"Petridou, Nicoletta, et al. “Multiscale Force Sensing in Development.” Nature Cell Biology, vol. 19, no. 6, Nature Publishing Group, 2017, pp. 581–88, doi:10.1038/ncb3524.","short":"N. Petridou, Z.P. Spiro, C.-P.J. Heisenberg, Nature Cell Biology 19 (2017) 581–588.","ieee":"N. Petridou, Z. P. Spiro, and C.-P. J. Heisenberg, “Multiscale force sensing in development,” Nature Cell Biology, vol. 19, no. 6. Nature Publishing Group, pp. 581–588, 2017.","apa":"Petridou, N., Spiro, Z. P., & Heisenberg, C.-P. J. (2017). Multiscale force sensing in development. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3524","ama":"Petridou N, Spiro ZP, Heisenberg C-PJ. Multiscale force sensing in development. Nature Cell Biology. 2017;19(6):581-588. doi:10.1038/ncb3524"}},{"citation":{"ista":"Chatterjee K, Doyen L, Filiot E, Raskin J. 2017. Doomsday equilibria for omega-regular games. Information and Computation. 254, 296–315.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean Raskin. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation. Elsevier, 2017. https://doi.org/10.1016/j.ic.2016.10.012.","short":"K. Chatterjee, L. Doyen, E. Filiot, J. Raskin, Information and Computation 254 (2017) 296–315.","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J. Raskin, “Doomsday equilibria for omega-regular games,” Information and Computation, vol. 254. Elsevier, pp. 296–315, 2017.","apa":"Chatterjee, K., Doyen, L., Filiot, E., & Raskin, J. (2017). Doomsday equilibria for omega-regular games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.012","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J. Doomsday equilibria for omega-regular games. Information and Computation. 2017;254:296-315. doi:10.1016/j.ic.2016.10.012","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” Information and Computation, vol. 254, Elsevier, 2017, pp. 296–315, doi:10.1016/j.ic.2016.10.012."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7036","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"first_name":"Emmanuel","last_name":"Filiot","full_name":"Filiot, Emmanuel"},{"last_name":"Raskin","full_name":"Raskin, Jean","first_name":"Jean"}],"external_id":{"arxiv":["1311.3238"]},"article_processing_charge":"No","title":"Doomsday equilibria for omega-regular games","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"year":"2017","day":"01","publication":"Information and Computation","page":"296 - 315","date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.ic.2016.10.012","date_created":"2018-12-11T11:47:53Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"date_updated":"2023-02-21T16:06:02Z","department":[{"_id":"KrCh"}],"_id":"681","type":"journal_article","article_type":"original","status":"public","publication_identifier":{"issn":["08905401"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":254,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10885"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information. In this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile where all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players' objective, then the objective of every player is violated. We present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games. We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games."}],"oa_version":"Submitted Version","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1311.3238"}],"month":"06","intvolume":" 254"},{"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"status":"public","conference":{"start_date":"2017-04-24","end_date":"2017-04-26","location":"Toulon, France","name":"ICLR: International Conference on Learning Representations"},"type":"conference","_id":"6841","title":"Extrapolation and learning equations","department":[{"_id":"ChLa"}],"external_id":{"arxiv":["1610.02995"]},"author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:09:17Z","citation":{"chicago":"Martius, Georg S, and Christoph Lampert. “Extrapolation and Learning Equations.” In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations, 2017.","ista":"Martius GS, Lampert C. 2017. Extrapolation and learning equations. 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. ICLR: International Conference on Learning Representations.","mla":"Martius, Georg S., and Christoph Lampert. “Extrapolation and Learning Equations.” 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","ieee":"G. S. Martius and C. Lampert, “Extrapolation and learning equations,” in 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, Toulon, France, 2017.","short":"G.S. Martius, C. Lampert, in:, 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings, International Conference on Learning Representations, 2017.","ama":"Martius GS, Lampert C. Extrapolation and learning equations. In: 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. International Conference on Learning Representations; 2017.","apa":"Martius, G. S., & Lampert, C. (2017). Extrapolation and learning equations. In 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings. Toulon, France: International Conference on Learning Representations."},"month":"02","main_file_link":[{"url":"https://arxiv.org/abs/1610.02995","open_access":"1"}],"oa":1,"publisher":"International Conference on Learning Representations","scopus_import":1,"quality_controlled":"1","oa_version":"Preprint","abstract":[{"text":"In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified.","lang":"eng"}],"ec_funded":1,"date_created":"2019-09-01T22:01:00Z","date_published":"2017-02-21T00:00:00Z","language":[{"iso":"eng"}],"publication":"5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings","day":"21","publication_status":"published","year":"2017"},{"page":"420 - 452","date_created":"2018-12-11T11:47:54Z","doi":"10.1017/jsl.2016.71","date_published":"2017-06-01T00:00:00Z","year":"2017","publication":"Journal of Symbolic Logic","day":"01","oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","article_processing_charge":"No","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Nir","last_name":"Piterman","full_name":"Piterman, Nir"}],"publist_id":"7026","title":"Obligation blackwell games and p-automata","citation":{"chicago":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic. Cambridge University Press, 2017. https://doi.org/10.1017/jsl.2016.71.","ista":"Chatterjee K, Piterman N. 2017. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 82(2), 420–452.","mla":"Chatterjee, Krishnendu, and Nir Piterman. “Obligation Blackwell Games and P-Automata.” Journal of Symbolic Logic, vol. 82, no. 2, Cambridge University Press, 2017, pp. 420–52, doi:10.1017/jsl.2016.71.","apa":"Chatterjee, K., & Piterman, N. (2017). Obligation blackwell games and p-automata. Journal of Symbolic Logic. Cambridge University Press. https://doi.org/10.1017/jsl.2016.71","ama":"Chatterjee K, Piterman N. Obligation blackwell games and p-automata. Journal of Symbolic Logic. 2017;82(2):420-452. doi:10.1017/jsl.2016.71","short":"K. Chatterjee, N. Piterman, Journal of Symbolic Logic 82 (2017) 420–452.","ieee":"K. Chatterjee and N. Piterman, “Obligation blackwell games and p-automata,” Journal of Symbolic Logic, vol. 82, no. 2. Cambridge University Press, pp. 420–452, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","volume":82,"publication_status":"published","publication_identifier":{"eissn":["1943-5886"],"issn":["0022-4812"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1206.5174","open_access":"1"}],"scopus_import":"1","intvolume":" 82","month":"06","abstract":[{"lang":"eng","text":"We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic."}],"oa_version":"Submitted Version","department":[{"_id":"KrCh"}],"date_updated":"2021-04-16T12:10:53Z","type":"journal_article","status":"public","_id":"684"},{"quality_controlled":"1","publisher":"Elsevier","oa":1,"date_published":"2017-06-01T00:00:00Z","doi":"10.1016/j.mod.2017.03.005","date_created":"2018-12-11T11:47:55Z","page":"26 - 31","day":"01","publication":"Mechanisms of Development","has_accepted_license":"1","year":"2017","project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020"}],"title":"The physics of development 100 years after D'Arcy Thompson's “on growth and form”","author":[{"first_name":"James","last_name":"Briscoe","full_name":"Briscoe, James"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna"}],"publist_id":"7025","external_id":{"pmid":["28366718"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Briscoe J, Kicheva A. 2017. The physics of development 100 years after D’Arcy Thompson’s “on growth and form”. Mechanisms of Development. 145, 26–31.","chicago":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.005.","ama":"Briscoe J, Kicheva A. The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. 2017;145:26-31. doi:10.1016/j.mod.2017.03.005","apa":"Briscoe, J., & Kicheva, A. (2017). The physics of development 100 years after D’Arcy Thompson’s “on growth and form.” Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.005","short":"J. Briscoe, A. Kicheva, Mechanisms of Development 145 (2017) 26–31.","ieee":"J. Briscoe and A. Kicheva, “The physics of development 100 years after D’Arcy Thompson’s ‘on growth and form,’” Mechanisms of Development, vol. 145. Elsevier, pp. 26–31, 2017.","mla":"Briscoe, James, and Anna Kicheva. “The Physics of Development 100 Years after D’Arcy Thompson’s ‘on Growth and Form.’” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 26–31, doi:10.1016/j.mod.2017.03.005."},"month":"06","intvolume":" 145","scopus_import":1,"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube."}],"volume":145,"ec_funded":1,"file":[{"date_updated":"2020-07-14T12:47:42Z","file_size":652313,"creator":"dernst","date_created":"2019-04-17T07:58:48Z","file_name":"2017_Briscoe_Kicheva_and_DArcy_accepted_version.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6335","checksum":"727043d2e4199fbef6b3704e6d1ac105"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["09254773"]},"publication_status":"published","status":"public","pubrep_id":"985","type":"journal_article","_id":"685","department":[{"_id":"AnKi"}],"file_date_updated":"2020-07-14T12:47:42Z","ddc":["571"],"date_updated":"2021-01-12T08:09:20Z"},{"_id":"688","type":"conference","conference":{"name":"Symposium on Computational Geometry, SoCG","start_date":"2017-07-04","location":"Brisbane, Australia","end_date":"2017-07-07"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"895","date_updated":"2021-01-12T08:09:26Z","ddc":["514","516"],"department":[{"_id":"HeEd"},{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:42Z","abstract":[{"lang":"eng","text":"We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. "}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"month":"06","intvolume":" 77","publication_identifier":{"issn":["18688969"]},"publication_status":"published","file":[{"file_size":990546,"date_updated":"2020-07-14T12:47:42Z","creator":"system","file_name":"IST-2017-895-v1+1_LIPIcs-SoCG-2017-39.pdf","date_created":"2018-12-12T10:11:03Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"067ab0cb3f962bae6c3af6bf0094e0f3","file_id":"4856"}],"language":[{"iso":"eng"}],"volume":77,"citation":{"ista":"Edelsbrunner H, Wagner H. 2017. Topological data analysis with Bregman divergences. Symposium on Computational Geometry, SoCG, LIPIcs, vol. 77, 391–3916.","chicago":"Edelsbrunner, Herbert, and Hubert Wagner. “Topological Data Analysis with Bregman Divergences,” 77:391–3916. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.SoCG.2017.39.","ama":"Edelsbrunner H, Wagner H. Topological data analysis with Bregman divergences. In: Vol 77. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017:391-3916. doi:10.4230/LIPIcs.SoCG.2017.39","apa":"Edelsbrunner, H., & Wagner, H. (2017). Topological data analysis with Bregman divergences (Vol. 77, pp. 391–3916). Presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2017.39","short":"H. Edelsbrunner, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916.","ieee":"H. Edelsbrunner and H. Wagner, “Topological data analysis with Bregman divergences,” presented at the Symposium on Computational Geometry, SoCG, Brisbane, Australia, 2017, vol. 77, pp. 391–3916.","mla":"Edelsbrunner, Herbert, and Hubert Wagner. Topological Data Analysis with Bregman Divergences. Vol. 77, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, pp. 391–3916, doi:10.4230/LIPIcs.SoCG.2017.39."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Hubert"}],"publist_id":"7021","title":"Topological data analysis with Bregman divergences","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2017","day":"01","page":"391-3916","doi":"10.4230/LIPIcs.SoCG.2017.39","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:47:56Z"},{"date_updated":"2021-01-12T08:09:24Z","department":[{"_id":"TaHa"}],"_id":"687","type":"journal_article","status":"public","publication_identifier":{"issn":["00335606"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":68,"issue":"2","ec_funded":1,"abstract":[{"lang":"eng","text":"Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs."}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1311.7172","open_access":"1"}],"month":"06","intvolume":" 68","citation":{"ista":"Davison B. 2017. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 68(2), 635–703.","chicago":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics. Oxford University Press, 2017. https://doi.org/10.1093/qmath/haw053.","ama":"Davison B. The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. 2017;68(2):635-703. doi:10.1093/qmath/haw053","apa":"Davison, B. (2017). The critical CoHA of a quiver with potential. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haw053","short":"B. Davison, Quarterly Journal of Mathematics 68 (2017) 635–703.","ieee":"B. Davison, “The critical CoHA of a quiver with potential,” Quarterly Journal of Mathematics, vol. 68, no. 2. Oxford University Press, pp. 635–703, 2017.","mla":"Davison, Ben. “The Critical CoHA of a Quiver with Potential.” Quarterly Journal of Mathematics, vol. 68, no. 2, Oxford University Press, 2017, pp. 635–703, doi:10.1093/qmath/haw053."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Davison","orcid":"0000-0002-8944-4390","full_name":"Davison, Ben","first_name":"Ben","id":"4634AB1E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7022","title":"The critical CoHA of a quiver with potential","project":[{"name":"Arithmetic and physics of Higgs moduli spaces","grant_number":"320593","_id":"25E549F4-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"year":"2017","day":"01","publication":"Quarterly Journal of Mathematics","page":"635 - 703","date_published":"2017-06-01T00:00:00Z","doi":"10.1093/qmath/haw053","date_created":"2018-12-11T11:47:55Z","quality_controlled":"1","publisher":"Oxford University Press","oa":1},{"day":"01","publication":"Mechanisms of Development","language":[{"iso":"eng"}],"publication_identifier":{"issn":["09254773"]},"year":"2017","publication_status":"published","volume":145,"doi":"10.1016/j.mod.2017.03.006","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:47:55Z","page":"32 - 37","oa_version":"None","abstract":[{"lang":"eng","text":"Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology."}],"month":"06","intvolume":" 145","quality_controlled":"1","scopus_import":1,"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:09:23Z","citation":{"ama":"Heisenberg C-PJ. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 2017;145:32-37. doi:10.1016/j.mod.2017.03.006","apa":"Heisenberg, C.-P. J. (2017). D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2017.03.006","short":"C.-P.J. Heisenberg, Mechanisms of Development 145 (2017) 32–37.","ieee":"C.-P. J. Heisenberg, “D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization,” Mechanisms of Development, vol. 145. Elsevier, pp. 32–37, 2017.","mla":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development, vol. 145, Elsevier, 2017, pp. 32–37, doi:10.1016/j.mod.2017.03.006.","ista":"Heisenberg C-PJ. 2017. D’Arcy Thompson’s ‘on growth and form’: From soap bubbles to tissue self organization. Mechanisms of Development. 145, 32–37.","chicago":"Heisenberg, Carl-Philipp J. “D’Arcy Thompson’s ‘on Growth and Form’: From Soap Bubbles to Tissue Self Organization.” Mechanisms of Development. Elsevier, 2017. https://doi.org/10.1016/j.mod.2017.03.006."},"department":[{"_id":"CaHe"}],"title":"D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization","author":[{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"publist_id":"7024","_id":"686","status":"public","type":"journal_article"},{"volume":9,"date_published":"2017-06-07T00:00:00Z","issue":"393","doi":"10.1126/scitranslmed.aan8196","date_created":"2018-12-11T11:47:56Z","publication_identifier":{"issn":["19466234"]},"publication_status":"published","year":"2017","day":"07","publication":"Science Translational Medicine","language":[{"iso":"eng"}],"scopus_import":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","month":"06","intvolume":" 9","abstract":[{"lang":"eng","text":"Rett syndrome modeling in monkey mirrors the human disorder."}],"oa_version":"None","publist_id":"7019","author":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"title":"Rett syndrome modeling goes simian","department":[{"_id":"GaNo"}],"date_updated":"2021-01-12T08:09:29Z","citation":{"chicago":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aan8196.","ista":"Novarino G. 2017. Rett syndrome modeling goes simian. Science Translational Medicine. 9(393), eaan8196.","mla":"Novarino, Gaia. “Rett Syndrome Modeling Goes Simian.” Science Translational Medicine, vol. 9, no. 393, eaan8196, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aan8196.","apa":"Novarino, G. (2017). Rett syndrome modeling goes simian. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aan8196","ama":"Novarino G. Rett syndrome modeling goes simian. Science Translational Medicine. 2017;9(393). doi:10.1126/scitranslmed.aan8196","short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “Rett syndrome modeling goes simian,” Science Translational Medicine, vol. 9, no. 393. American Association for the Advancement of Science, 2017."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"689","article_number":"eaan8196"},{"title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","publist_id":"7013","author":[{"first_name":"Takafumi","last_name":"Miki","full_name":"Miki, Takafumi"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter"},{"first_name":"Gerardo","full_name":"Malagon, Gerardo","last_name":"Malagon"},{"full_name":"Gomez, Laura","last_name":"Gomez","first_name":"Laura"},{"first_name":"Katsuhiko","full_name":"Tabuchi, Katsuhiko","last_name":"Tabuchi"},{"first_name":"Masahiko","last_name":"Watanabe","full_name":"Watanabe, Masahiko"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Alain","last_name":"Marty","full_name":"Marty, Alain"}],"external_id":{"pmid":["28607047"]},"article_processing_charge":"Yes (in subscription journal)","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"T. Miki et al., “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” PNAS, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1704470114","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 2017;114(26):E5246-E5255. doi:10.1073/pnas.1704470114","mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:10.1073/pnas.1704470114.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1704470114."},"date_published":"2017-06-27T00:00:00Z","doi":"10.1073/pnas.1704470114","date_created":"2018-12-11T11:47:57Z","page":"E5246 - E5255","day":"27","publication":"PNAS","has_accepted_license":"1","year":"2017","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:44Z","ddc":["570"],"date_updated":"2023-02-23T12:54:57Z","status":"public","type":"journal_article","_id":"693","issue":"26","volume":114,"file":[{"file_name":"2017_PNAS_Miki.pdf","date_created":"2020-01-03T13:27:29Z","file_size":2721544,"date_updated":"2020-07-14T12:47:44Z","creator":"kschuh","checksum":"2ab75d554f3df4a34d20fa8040589b7e","file_id":"7223","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"publication_status":"published","month":"06","intvolume":" 114","scopus_import":1,"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. "}]},{"year":"2017","has_accepted_license":"1","publication":"Journal of Cell Science","day":"01","page":"2172 - 2184","date_created":"2018-12-11T11:47:58Z","date_published":"2017-07-01T00:00:00Z","doi":"10.1242/jcs.200899","oa":1,"quality_controlled":"1","publisher":"Company of Biologists","citation":{"mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:10.1242/jcs.200899.","ieee":"A. Veß et al., “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” Journal of Cell Science, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 2017;130(13):2172-2184. doi:10.1242/jcs.200899","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., & Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.200899","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” Journal of Cell Science. Company of Biologists, 2017. https://doi.org/10.1242/jcs.200899.","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28515231"]},"publist_id":"7008","author":[{"first_name":"Astrid","full_name":"Veß, Astrid","last_name":"Veß"},{"first_name":"Ulrich","last_name":"Blache","full_name":"Blache, Ulrich"},{"full_name":"Leitner, Laura","last_name":"Leitner","first_name":"Laura"},{"full_name":"Kurz, Angela","last_name":"Kurz","first_name":"Angela"},{"full_name":"Ehrenpfordt, Anja","last_name":"Ehrenpfordt","first_name":"Anja"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Guido","last_name":"Posern","full_name":"Posern, Guido"}],"title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","publication_status":"published","publication_identifier":{"issn":["00219533"]},"language":[{"iso":"eng"}],"file":[{"file_id":"6966","checksum":"42c81a0a4fc3128883b391c3af3f74bc","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2017_CellScience_Vess.pdf","date_created":"2019-10-24T09:43:56Z","file_size":10847596,"date_updated":"2020-07-14T12:47:45Z","creator":"dernst"}],"issue":"13","volume":130,"abstract":[{"text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":1,"intvolume":" 130","month":"07","date_updated":"2021-01-12T08:09:41Z","ddc":["570"],"file_date_updated":"2020-07-14T12:47:45Z","department":[{"_id":"MiSi"}],"_id":"694","type":"journal_article","article_type":"original","status":"public"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.ICALP.2017.39","apa":"Pietrzak, K. Z., & Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ICALP.2017.39","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. Non Uniform Attacks against Pseudoentropy. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.ICALP.2017.39.","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.ICALP.2017.39."},"title":"Non uniform attacks against pseudoentropy","author":[{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"last_name":"Skórski","full_name":"Skórski, Maciej","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"publist_id":"7003","article_number":"39","project":[{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"day":"01","has_accepted_license":"1","year":"2017","date_published":"2017-07-01T00:00:00Z","doi":"10.4230/LIPIcs.ICALP.2017.39","date_created":"2018-12-11T11:47:59Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"ddc":["005"],"date_updated":"2021-01-12T08:11:15Z","department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:47:46Z","_id":"697","status":"public","pubrep_id":"893","type":"conference","conference":{"start_date":"2017-07-10","location":"Warsaw, Poland","end_date":"2017-07-14","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"e95618a001692f1af2d68f5fde43bc1f","file_id":"4701","creator":"system","file_size":601004,"date_updated":"2020-07-14T12:47:46Z","file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","date_created":"2018-12-12T10:08:40Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["18688969"]},"publication_status":"published","volume":80,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. "}],"month":"07","intvolume":" 80","scopus_import":1,"alternative_title":["LIPIcs"]},{"status":"public","pubrep_id":"892","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"_id":"698","file_date_updated":"2020-07-14T12:47:46Z","department":[{"_id":"CaUh"}],"ddc":["519"],"date_updated":"2021-01-12T08:11:17Z","month":"07","intvolume":" 28","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"volume":28,"issue":"14","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4844","checksum":"de01dac9e30970cfa6ae902480a4e04d","creator":"system","date_updated":"2020-07-14T12:47:46Z","file_size":1086097,"date_created":"2018-12-12T10:10:53Z","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["10591524"]},"publication_status":"published","project":[{"name":"Gaussian Graphical Models: Theory and Applications","grant_number":"Y 903-N35","call_identifier":"FWF","_id":"2530CA10-B435-11E9-9278-68D0E5697425"}],"title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","publist_id":"7001","author":[{"first_name":"Yejun","full_name":"Wang, Yejun","last_name":"Wang"},{"first_name":"Mallika","full_name":"Nagarajan, Mallika","last_name":"Nagarajan"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216"},{"first_name":"Gv","last_name":"Shivashankar","full_name":"Shivashankar, Gv"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825","ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” Molecular Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017.","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825.","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell. American Society for Cell Biology, 2017. https://doi.org/10.1091/mbc.E16-12-0825."},"publisher":"American Society for Cell Biology","quality_controlled":"1","oa":1,"date_published":"2017-07-07T00:00:00Z","doi":"10.1091/mbc.E16-12-0825","date_created":"2018-12-11T11:47:59Z","page":"1997 - 2009","day":"07","publication":"Molecular Biology of the Cell","has_accepted_license":"1","year":"2017"},{"month":"07","intvolume":" 114","scopus_import":1,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502615/","open_access":"1"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. "}],"volume":114,"issue":"27","language":[{"iso":"eng"}],"publication_identifier":{"issn":["00278424"]},"publication_status":"published","status":"public","type":"journal_article","_id":"699","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T08:11:21Z","publisher":"National Academy of Sciences","quality_controlled":"1","oa":1,"date_published":"2017-07-03T00:00:00Z","doi":"10.1073/pnas.1702020114","date_created":"2018-12-11T11:48:00Z","page":"E5396 - E5405","day":"03","publication":"PNAS","year":"2017","title":"The red queen and king in finite populations","publist_id":"7002","author":[{"full_name":"Veller, Carl","last_name":"Veller","first_name":"Carl"},{"first_name":"Laura","last_name":"Hayward","full_name":"Hayward, Laura"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian"}],"external_id":{"pmid":["28630336"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Veller, Carl, Laura Hayward, Martin Nowak, and Christian Hilbe. “The Red Queen and King in Finite Populations.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1702020114.","ista":"Veller C, Hayward L, Nowak M, Hilbe C. 2017. The red queen and king in finite populations. PNAS. 114(27), E5396–E5405.","mla":"Veller, Carl, et al. “The Red Queen and King in Finite Populations.” PNAS, vol. 114, no. 27, National Academy of Sciences, 2017, pp. E5396–405, doi:10.1073/pnas.1702020114.","ama":"Veller C, Hayward L, Nowak M, Hilbe C. The red queen and king in finite populations. PNAS. 2017;114(27):E5396-E5405. doi:10.1073/pnas.1702020114","apa":"Veller, C., Hayward, L., Nowak, M., & Hilbe, C. (2017). The red queen and king in finite populations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1702020114","ieee":"C. Veller, L. Hayward, M. Nowak, and C. Hilbe, “The red queen and king in finite populations,” PNAS, vol. 114, no. 27. National Academy of Sciences, pp. E5396–E5405, 2017.","short":"C. Veller, L. Hayward, M. Nowak, C. Hilbe, PNAS 114 (2017) E5396–E5405."}},{"date_updated":"2023-02-23T12:56:35Z","department":[{"_id":"JoFi"}],"_id":"700","type":"journal_article","status":"public","publication_identifier":{"issn":["24700045"]},"publication_status":"published","language":[{"iso":"eng"}],"issue":"1","volume":96,"ec_funded":1,"abstract":[{"text":"Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/pdf/1612.07061.pdf"}],"month":"07","intvolume":" 96","citation":{"chicago":"Barzanjeh, Shabir, Vahid Salari, Jack Tuszynski, Michal Cifra, and Christoph Simon. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.96.012404.","ista":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. 2017. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 96(1), 012404.","mla":"Barzanjeh, Shabir, et al. “Optomechanical Proposal for Monitoring Microtubule Mechanical Vibrations.” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1, 012404, American Institute of Physics, 2017, doi:10.1103/PhysRevE.96.012404.","short":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, C. Simon, Physical Review E Statistical Nonlinear and Soft Matter Physics 96 (2017).","ieee":"S. Barzanjeh, V. Salari, J. Tuszynski, M. Cifra, and C. Simon, “Optomechanical proposal for monitoring microtubule mechanical vibrations,” Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 96, no. 1. American Institute of Physics, 2017.","apa":"Barzanjeh, S., Salari, V., Tuszynski, J., Cifra, M., & Simon, C. (2017). Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.96.012404","ama":"Barzanjeh S, Salari V, Tuszynski J, Cifra M, Simon C. Optomechanical proposal for monitoring microtubule mechanical vibrations. Physical Review E Statistical Nonlinear and Soft Matter Physics . 2017;96(1). doi:10.1103/PhysRevE.96.012404"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6997","author":[{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"first_name":"Vahid","last_name":"Salari","full_name":"Salari, Vahid"},{"last_name":"Tuszynski","full_name":"Tuszynski, Jack","first_name":"Jack"},{"full_name":"Cifra, Michal","last_name":"Cifra","first_name":"Michal"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"title":"Optomechanical proposal for monitoring microtubule mechanical vibrations","article_number":"012404","project":[{"_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics"}],"year":"2017","day":"12","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","doi":"10.1103/PhysRevE.96.012404","date_published":"2017-07-12T00:00:00Z","date_created":"2018-12-11T11:48:00Z","quality_controlled":"1","publisher":"American Institute of Physics","oa":1},{"date_updated":"2021-01-12T08:11:28Z","ddc":["500"],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:47:47Z","_id":"701","type":"journal_article","status":"public","pubrep_id":"984","publication_identifier":{"issn":["10778926"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"a431e573e31df13bc0f66de3061006ec","file_id":"5077","creator":"system","file_size":544042,"date_updated":"2020-07-14T12:47:47Z","file_name":"IST-2018-984-v1+1_Patakova_on_the_nonexistence_of_k-reptile_simplices_in_R_3_and_R_4_2017.pdf","date_created":"2018-12-12T10:14:25Z"}],"language":[{"iso":"eng"}],"issue":"3","volume":24,"abstract":[{"text":"A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2.","lang":"eng"}],"oa_version":"Submitted Version","month":"07","intvolume":" 24","citation":{"apa":"Kynčl, J., & Patakova, Z. (2017). On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. International Press.","ama":"Kynčl J, Patakova Z. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 2017;24(3):1-44.","ieee":"J. Kynčl and Z. Patakova, “On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4,” The Electronic Journal of Combinatorics, vol. 24, no. 3. International Press, pp. 1–44, 2017.","short":"J. Kynčl, Z. Patakova, The Electronic Journal of Combinatorics 24 (2017) 1–44.","mla":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics, vol. 24, no. 3, International Press, 2017, pp. 1–44.","ista":"Kynčl J, Patakova Z. 2017. On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4. The Electronic Journal of Combinatorics. 24(3), 1–44.","chicago":"Kynčl, Jan, and Zuzana Patakova. “On the Nonexistence of k Reptile Simplices in ℝ^3 and ℝ^4.” The Electronic Journal of Combinatorics. International Press, 2017."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"},{"first_name":"Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova"}],"publist_id":"6996","title":"On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4","has_accepted_license":"1","year":"2017","day":"14","publication":"The Electronic Journal of Combinatorics","page":"1-44","date_published":"2017-07-14T00:00:00Z","date_created":"2018-12-11T11:48:00Z","publisher":"International Press","quality_controlled":"1","oa":1},{"publication_identifier":{"issn":["19466234"]},"year":"2017","publication_status":"published","day":"19","publication":"Science Translational Medicine","language":[{"iso":"eng"}],"page":"eaao0972","volume":9,"issue":"399","date_published":"2017-07-19T00:00:00Z","doi":"10.1126/scitranslmed.aao0972","date_created":"2018-12-11T11:48:01Z","abstract":[{"text":"Leading autism-associated mutation in mouse partially mimics human disorder.\r\n\r\n","lang":"eng"}],"oa_version":"None","publisher":"American Association for the Advancement of Science","quality_controlled":"1","scopus_import":1,"month":"07","intvolume":" 9","citation":{"ista":"Novarino G. 2017. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 9(399), eaao0972.","chicago":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao0972.","apa":"Novarino, G. (2017). The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao0972","ama":"Novarino G. The riddle of CHD8 haploinsufficiency in autism spectrum disorder. Science Translational Medicine. 2017;9(399):eaao0972. doi:10.1126/scitranslmed.aao0972","ieee":"G. Novarino, “The riddle of CHD8 haploinsufficiency in autism spectrum disorder,” Science Translational Medicine, vol. 9, no. 399. American Association for the Advancement of Science, p. eaao0972, 2017.","short":"G. Novarino, Science Translational Medicine 9 (2017) eaao0972.","mla":"Novarino, Gaia. “The Riddle of CHD8 Haploinsufficiency in Autism Spectrum Disorder.” Science Translational Medicine, vol. 9, no. 399, American Association for the Advancement of Science, 2017, p. eaao0972, doi:10.1126/scitranslmed.aao0972."},"date_updated":"2021-01-12T08:11:31Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"publist_id":"6993","department":[{"_id":"GaNo"}],"title":"The riddle of CHD8 haploinsufficiency in autism spectrum disorder","_id":"702","type":"journal_article","status":"public"},{"department":[{"_id":"PeJo"}],"title":"Roles of afadin in functional differentiations of hippocampal mossy fiber synapse","author":[{"first_name":"Xiaoqi","id":"3395256A-F248-11E8-B48F-1D18A9856A87","full_name":"Geng, Xiaoqi","last_name":"Geng"},{"last_name":"Maruo","full_name":"Maruo, Tomohiko","first_name":"Tomohiko"},{"full_name":"Mandai, Kenji","last_name":"Mandai","first_name":"Kenji"},{"first_name":"Irwan","last_name":"Supriyanto","full_name":"Supriyanto, Irwan"},{"last_name":"Miyata","full_name":"Miyata, Muneaki","first_name":"Muneaki"},{"first_name":"Shotaro","full_name":"Sakakibara, Shotaro","last_name":"Sakakibara"},{"first_name":"Akira","last_name":"Mizoguchi","full_name":"Mizoguchi, Akira"},{"full_name":"Takai, Yoshimi","last_name":"Takai","first_name":"Yoshimi"},{"last_name":"Mori","full_name":"Mori, Masahiro","first_name":"Masahiro"}],"publist_id":"6987","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Geng, Xiaoqi, et al. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells, vol. 22, no. 8, Wiley-Blackwell, 2017, pp. 715–22, doi:10.1111/gtc.12508.","ama":"Geng X, Maruo T, Mandai K, et al. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 2017;22(8):715-722. doi:10.1111/gtc.12508","apa":"Geng, X., Maruo, T., Mandai, K., Supriyanto, I., Miyata, M., Sakakibara, S., … Mori, M. (2017). Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. Wiley-Blackwell. https://doi.org/10.1111/gtc.12508","short":"X. Geng, T. Maruo, K. Mandai, I. Supriyanto, M. Miyata, S. Sakakibara, A. Mizoguchi, Y. Takai, M. Mori, Genes to Cells 22 (2017) 715–722.","ieee":"X. Geng et al., “Roles of afadin in functional differentiations of hippocampal mossy fiber synapse,” Genes to Cells, vol. 22, no. 8. Wiley-Blackwell, pp. 715–722, 2017.","chicago":"Geng, Xiaoqi, Tomohiko Maruo, Kenji Mandai, Irwan Supriyanto, Muneaki Miyata, Shotaro Sakakibara, Akira Mizoguchi, Yoshimi Takai, and Masahiro Mori. “Roles of Afadin in Functional Differentiations of Hippocampal Mossy Fiber Synapse.” Genes to Cells. Wiley-Blackwell, 2017. https://doi.org/10.1111/gtc.12508.","ista":"Geng X, Maruo T, Mandai K, Supriyanto I, Miyata M, Sakakibara S, Mizoguchi A, Takai Y, Mori M. 2017. Roles of afadin in functional differentiations of hippocampal mossy fiber synapse. Genes to Cells. 22(8), 715–722."},"date_updated":"2021-01-12T08:11:37Z","status":"public","type":"journal_article","_id":"706","doi":"10.1111/gtc.12508","volume":22,"date_published":"2017-08-01T00:00:00Z","issue":"8","date_created":"2018-12-11T11:48:02Z","page":"715 - 722","day":"01","language":[{"iso":"eng"}],"publication":"Genes to Cells","publication_identifier":{"issn":["13569597"]},"year":"2017","publication_status":"published","month":"08","intvolume":" 22","scopus_import":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","oa_version":"None","abstract":[{"text":"A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse.","lang":"eng"}]},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00246093"]},"publication_status":"published","volume":49,"issue":"4","ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"We answer a question of M. Gromov on the waist of the unit ball.","lang":"eng"}],"month":"08","intvolume":" 49","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.06279"}],"date_updated":"2021-01-12T08:11:41Z","department":[{"_id":"HeEd"}],"_id":"707","status":"public","type":"journal_article","day":"01","publication":"Bulletin of the London Mathematical Society","year":"2017","doi":"10.1112/blms.12062","date_published":"2017-08-01T00:00:00Z","date_created":"2018-12-11T11:48:02Z","page":"690 - 693","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Akopyan A, Karasev R. 2017. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 49(4), 690–693.","chicago":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society. Wiley-Blackwell, 2017. https://doi.org/10.1112/blms.12062.","short":"A. Akopyan, R. Karasev, Bulletin of the London Mathematical Society 49 (2017) 690–693.","ieee":"A. Akopyan and R. Karasev, “A tight estimate for the waist of the ball ,” Bulletin of the London Mathematical Society, vol. 49, no. 4. Wiley-Blackwell, pp. 690–693, 2017.","apa":"Akopyan, A., & Karasev, R. (2017). A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. Wiley-Blackwell. https://doi.org/10.1112/blms.12062","ama":"Akopyan A, Karasev R. A tight estimate for the waist of the ball . Bulletin of the London Mathematical Society. 2017;49(4):690-693. doi:10.1112/blms.12062","mla":"Akopyan, Arseniy, and Roman Karasev. “A Tight Estimate for the Waist of the Ball .” Bulletin of the London Mathematical Society, vol. 49, no. 4, Wiley-Blackwell, 2017, pp. 690–93, doi:10.1112/blms.12062."},"title":"A tight estimate for the waist of the ball ","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"},{"last_name":"Karasev","full_name":"Karasev, Roman","first_name":"Roman"}],"publist_id":"6982","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}]},{"date_updated":"2021-01-12T08:11:45Z","ddc":["576","610"],"file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"SaSi"}],"_id":"708","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"889","publication_identifier":{"issn":["15449173"]},"publication_status":"published","file":[{"file_id":"5156","checksum":"0c974f430682dc832ea7b27ab5a93124","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-889-v1+1_journal.pbio.2001993.pdf","date_created":"2018-12-12T10:15:35Z","file_size":18155365,"date_updated":"2020-07-14T12:47:49Z","creator":"system"}],"language":[{"iso":"eng"}],"issue":"8","volume":15,"abstract":[{"text":"In the developing and adult brain, oligodendrocyte precursor cells (OPCs) are influenced by neuronal activity: they are involved in synaptic signaling with neurons, and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing. An important question that has been unanswered is whether OPCs can discriminate different patterns of neuronal activity and respond to them in a distinct way. Here, we demonstrate in brain slices that the pattern of neuronal activity determines the functional changes triggered at synapses between axons and OPCs. Furthermore, we show that stimulation of the corpus callosum at different frequencies in vivo affects proliferation and differentiation of OPCs in a dissimilar way. Our findings suggest that neurons do not influence OPCs in “all-or-none” fashion but use their firing pattern to tune the response and behavior of these nonneuronal cells.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"month":"08","intvolume":" 15","citation":{"mla":"Nagy, Balint, et al. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology, vol. 15, no. 8, e2001993, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001993.","ieee":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, and M. Kukley, “Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum,” PLoS Biology, vol. 15, no. 8. Public Library of Science, 2017.","short":"B. Nagy, A. Hovhannisyan, R. Barzan, T. Chen, M. Kukley, PLoS Biology 15 (2017).","ama":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 2017;15(8). doi:10.1371/journal.pbio.2001993","apa":"Nagy, B., Hovhannisyan, A., Barzan, R., Chen, T., & Kukley, M. (2017). Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001993","chicago":"Nagy, Balint, Anahit Hovhannisyan, Ruxandra Barzan, Ting Chen, and Maria Kukley. “Different Patterns of Neuronal Activity Trigger Distinct Responses of Oligodendrocyte Precursor Cells in the Corpus Callosum.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001993.","ista":"Nagy B, Hovhannisyan A, Barzan R, Chen T, Kukley M. 2017. Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum. PLoS Biology. 15(8), e2001993."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"30F830CE-02D1-11E9-9BAA-DAF4881429F2","first_name":"Balint","last_name":"Nagy","orcid":"0000-0002-4002-4686","full_name":"Nagy, Balint"},{"last_name":"Hovhannisyan","full_name":"Hovhannisyan, Anahit","first_name":"Anahit"},{"full_name":"Barzan, Ruxandra","last_name":"Barzan","first_name":"Ruxandra"},{"last_name":"Chen","full_name":"Chen, Ting","first_name":"Ting"},{"full_name":"Kukley, Maria","last_name":"Kukley","first_name":"Maria"}],"publist_id":"6983","title":"Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum","article_number":"e2001993","has_accepted_license":"1","year":"2017","day":"22","publication":"PLoS Biology","doi":"10.1371/journal.pbio.2001993","date_published":"2017-08-22T00:00:00Z","date_created":"2018-12-11T11:48:03Z","publisher":"Public Library of Science","quality_controlled":"1","oa":1},{"day":"01","publication":"Cell Biology International","language":[{"iso":"eng"}],"publication_identifier":{"issn":["10656995"]},"publication_status":"published","year":"2017","issue":"8","date_published":"2017-08-01T00:00:00Z","volume":41,"doi":"10.1002/cbin.10783","date_created":"2018-12-11T11:48:04Z","page":"908 - 913","oa_version":"None","abstract":[{"lang":"eng","text":"Adipose tissues play key roles in energy homeostasis. Brown adipocytes and beige adipocytes in white adipose tissue (WAT) share the similar characters of thermogenesis, both of them could be potential targets for obesity management. Several thermo-sensitive transient receptor potential channels (thermoTRPs) are shown to be involved in adipocyte biology. However, the expression pattern of thermoTRPs in adipose tissues from obese mice is still unknown. The mRNA expression of thermoTRPs in subcutaneous WAT (sWAT) and interscapular brown adipose tissue (iBAT) from lean and obese mice were measured using reverse transcriptase-quantitative PCRs (RT-qPCR). The results demonstrated that all 10 thermoTRPs are expressed in both iBAT and sWAT, and without significant difference in the mRNA expression level of thermoTRPs between these two tissues. Moreover, Trpv1 and Trpv3 mRNA expression levels in both iBAT and sWAT were significantly decreased in high fat diet (HFD)-induced obese mice and db/db (leptin receptor deficient) mice. Trpm2 mRNA expression level was significantly decreased only in sWAT from HFD-induced obese mice and db/db mice. On the other hand, Trpv2 and Trpv4 mRNA expression levels in iBAT and sWAT were significantly increased in HFD-induced obese mice and db/db mice. Taken together, we conclude that all 10 thermoTRPs are expressed in iBAT and sWAT. And several thermoTRPs differentially expressed in adipose tissues from HFD-induced obese mice and db/db mice, suggesting a potential involvement in anti-obesity regulations."}],"month":"08","intvolume":" 41","scopus_import":1,"publisher":"Wiley-Blackwell","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:47Z","citation":{"ista":"Sun W, Li C, Zhang Y, Jiang C, Zhai M-Z, Zhou Q, Xiao L, Deng Q. 2017. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 41(8), 908–913.","chicago":"Sun, Wuping, Chen Li, Yonghong Zhang, Changyu Jiang, Ming-Zhu Zhai, Qian Zhou, Lizu Xiao, and Qiwen Deng. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International. Wiley-Blackwell, 2017. https://doi.org/10.1002/cbin.10783.","apa":"Sun, W., Li, C., Zhang, Y., Jiang, C., Zhai, M.-Z., Zhou, Q., … Deng, Q. (2017). Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. Wiley-Blackwell. https://doi.org/10.1002/cbin.10783","ama":"Sun W, Li C, Zhang Y, et al. Gene expression changes of thermo sensitive transient receptor potential channels in obese mice. Cell Biology International. 2017;41(8):908-913. doi:10.1002/cbin.10783","short":"W. Sun, C. Li, Y. Zhang, C. Jiang, M.-Z. Zhai, Q. Zhou, L. Xiao, Q. Deng, Cell Biology International 41 (2017) 908–913.","ieee":"W. Sun et al., “Gene expression changes of thermo sensitive transient receptor potential channels in obese mice,” Cell Biology International, vol. 41, no. 8. Wiley-Blackwell, pp. 908–913, 2017.","mla":"Sun, Wuping, et al. “Gene Expression Changes of Thermo Sensitive Transient Receptor Potential Channels in Obese Mice.” Cell Biology International, vol. 41, no. 8, Wiley-Blackwell, 2017, pp. 908–13, doi:10.1002/cbin.10783."},"title":"Gene expression changes of thermo sensitive transient receptor potential channels in obese mice","department":[{"_id":"RySh"}],"author":[{"first_name":"Wuping","last_name":"Sun","full_name":"Sun, Wuping"},{"last_name":"Li","full_name":"Li, Chen","first_name":"Chen"},{"last_name":"Zhang","full_name":"Zhang, Yonghong","first_name":"Yonghong"},{"full_name":"Jiang, Changyu","last_name":"Jiang","first_name":"Changyu"},{"last_name":"Zhai","full_name":"Zhai, Ming-Zhu","id":"34009CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Ming-Zhu"},{"first_name":"Qian","last_name":"Zhou","full_name":"Zhou, Qian"},{"first_name":"Lizu","full_name":"Xiao, Lizu","last_name":"Xiao"},{"first_name":"Qiwen","full_name":"Deng, Qiwen","last_name":"Deng"}],"publist_id":"6981","_id":"709","status":"public","type":"journal_article"},{"publication_status":"published","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"file_id":"4991","checksum":"89225c7dcec2c93838458c9102858985","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2017-888-v1+1_LIPIcs-APPROX-RANDOM-2017-20.pdf","date_created":"2018-12-12T10:13:10Z","file_size":604813,"date_updated":"2020-07-14T12:47:49Z","creator":"system"}],"ec_funded":1,"volume":81,"abstract":[{"lang":"eng","text":"We revisit the problem of estimating entropy of discrete distributions from independent samples, studied recently by Acharya, Orlitsky, Suresh and Tyagi (SODA 2015), improving their upper and lower bounds on the necessary sample size n. For estimating Renyi entropy of order alpha, up to constant accuracy and error probability, we show the following * Upper bounds n = O(1) 2^{(1-1/alpha)H_alpha} for integer alpha>1, as the worst case over distributions with Renyi entropy equal to H_alpha. * Lower bounds n = Omega(1) K^{1-1/alpha} for any real alpha>1, with the constant being an inverse polynomial of the accuracy, as the worst case over all distributions on K elements. Our upper bounds essentially replace the alphabet size by a factor exponential in the entropy, which offers improvements especially in low or medium entropy regimes (interesting for example in anomaly detection). As for the lower bounds, our proof explicitly shows how the complexity depends on both alphabet and accuracy, partially solving the open problem posted in previous works. The argument for upper bounds derives a clean identity for the variance of falling-power sum of a multinomial distribution. Our approach for lower bounds utilizes convex optimization to find a distribution with possibly worse estimation performance, and may be of independent interest as a tool to work with Le Cam’s two point method. "}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 81","month":"08","date_updated":"2021-01-12T08:11:50Z","ddc":["005","600"],"file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"KrPi"}],"_id":"710","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX","start_date":"2017-08-18","end_date":"2017-08-18","location":"Berkeley, USA"},"type":"conference","pubrep_id":"888","status":"public","year":"2017","has_accepted_license":"1","day":"01","date_created":"2018-12-11T11:48:04Z","date_published":"2017-08-01T00:00:00Z","doi":"10.4230/LIPIcs.APPROX-RANDOM.2017.20","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"mla":"Obremski, Maciej, and Maciej Skórski. Renyi Entropy Estimation Revisited. Vol. 81, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20.","ieee":"M. Obremski and M. Skórski, “Renyi entropy estimation revisited,” presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA, 2017, vol. 81.","short":"M. Obremski, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Obremski, M., & Skórski, M. (2017). Renyi entropy estimation revisited (Vol. 81). Presented at the 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, Berkeley, USA: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20","ama":"Obremski M, Skórski M. Renyi entropy estimation revisited. In: Vol 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.APPROX-RANDOM.2017.20","chicago":"Obremski, Maciej, and Maciej Skórski. “Renyi Entropy Estimation Revisited,” Vol. 81. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.APPROX-RANDOM.2017.20.","ista":"Obremski M, Skórski M. 2017. Renyi entropy estimation revisited. 20th International Workshop on Approximation Algorithms for Combinatorial Optimization Problems, APPROX, LIPIcs, vol. 81, 20."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Maciej","last_name":"Obremski","full_name":"Obremski, Maciej"},{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","full_name":"Skórski, Maciej","last_name":"Skórski"}],"publist_id":"6979","title":"Renyi entropy estimation revisited","article_number":"20","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks","grant_number":"682815"}]},{"volume":6,"language":[{"iso":"eng"}],"file":[{"file_size":6399510,"date_updated":"2020-07-14T12:47:50Z","creator":"system","file_name":"IST-2017-885-v1+1_elife-25125-figures-v2.pdf","date_created":"2018-12-12T10:13:36Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5020","checksum":"1ace3462e64a971b9ead896091829549"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6241dc31eeb87b03facadec3a53a6827","file_id":"5021","date_updated":"2020-07-14T12:47:50Z","file_size":4264398,"creator":"system","date_created":"2018-12-12T10:13:36Z","file_name":"IST-2017-885-v1+2_elife-25125-v2.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2050084X"]},"intvolume":" 6","month":"08","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta.","lang":"eng"}],"department":[{"_id":"GaNo"},{"_id":"SiHi"}],"file_date_updated":"2020-07-14T12:47:50Z","ddc":["576"],"date_updated":"2021-01-12T08:11:57Z","pubrep_id":"885","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"713","date_created":"2018-12-11T11:48:05Z","date_published":"2017-08-14T00:00:00Z","doi":"10.7554/eLife.25125","publication":"eLife","day":"14","year":"2017","has_accepted_license":"1","oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","title":"Mapping the mouse Allelome reveals tissue specific regulation of allelic expression","author":[{"first_name":"Daniel","last_name":"Andergassen","full_name":"Andergassen, Daniel"},{"first_name":"Christoph","id":"4C66542E-F248-11E8-B48F-1D18A9856A87","full_name":"Dotter, Christoph","last_name":"Dotter"},{"first_name":"Dyniel","last_name":"Wenzel","full_name":"Wenzel, Dyniel"},{"first_name":"Verena","last_name":"Sigl","full_name":"Sigl, Verena"},{"last_name":"Bammer","full_name":"Bammer, Philipp","first_name":"Philipp"},{"last_name":"Muckenhuber","full_name":"Muckenhuber, Markus","first_name":"Markus"},{"last_name":"Mayer","full_name":"Mayer, Daniela","first_name":"Daniela"},{"first_name":"Tomasz","last_name":"Kulinski","full_name":"Kulinski, Tomasz"},{"first_name":"Hans","last_name":"Theussl","full_name":"Theussl, Hans"},{"first_name":"Josef","full_name":"Penninger, Josef","last_name":"Penninger"},{"last_name":"Bock","full_name":"Bock, Christoph","first_name":"Christoph"},{"full_name":"Barlow, Denise","last_name":"Barlow","first_name":"Denise"},{"full_name":"Pauler, Florian","last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Quanah","full_name":"Hudson, Quanah","last_name":"Hudson"}],"publist_id":"6971","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Andergassen D, Dotter C, Wenzel D, Sigl V, Bammer P, Muckenhuber M, Mayer D, Kulinski T, Theussl H, Penninger J, Bock C, Barlow D, Pauler F, Hudson Q. 2017. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 6, e25125.","chicago":"Andergassen, Daniel, Christoph Dotter, Dyniel Wenzel, Verena Sigl, Philipp Bammer, Markus Muckenhuber, Daniela Mayer, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25125.","ama":"Andergassen D, Dotter C, Wenzel D, et al. Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. eLife. 2017;6. doi:10.7554/eLife.25125","apa":"Andergassen, D., Dotter, C., Wenzel, D., Sigl, V., Bammer, P., Muckenhuber, M., … Hudson, Q. (2017). Mapping the mouse Allelome reveals tissue specific regulation of allelic expression. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25125","ieee":"D. Andergassen et al., “Mapping the mouse Allelome reveals tissue specific regulation of allelic expression,” eLife, vol. 6. eLife Sciences Publications, 2017.","short":"D. Andergassen, C. Dotter, D. Wenzel, V. Sigl, P. Bammer, M. Muckenhuber, D. Mayer, T. Kulinski, H. Theussl, J. Penninger, C. Bock, D. Barlow, F. Pauler, Q. Hudson, ELife 6 (2017).","mla":"Andergassen, Daniel, et al. “Mapping the Mouse Allelome Reveals Tissue Specific Regulation of Allelic Expression.” ELife, vol. 6, e25125, eLife Sciences Publications, 2017, doi:10.7554/eLife.25125."},"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"}],"article_number":"e25125"},{"volume":85,"publication_status":"published","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:49Z","file_size":570294,"creator":"system","date_created":"2018-12-12T10:08:02Z","file_name":"IST-2017-886-v1+1_LIPIcs-CONCUR-2017-5.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4661","checksum":"d2bda4783821a6358333fe27f11f4737"}],"alternative_title":["LIPIcs"],"scopus_import":1,"intvolume":" 85","month":"08","abstract":[{"lang":"eng","text":"Nested weighted automata (NWA) present a robust and convenient automata-theoretic formalism for quantitative specifications. Previous works have considered NWA that processed input words only in the forward direction. It is natural to allow the automata to process input words backwards as well, for example, to measure the maximal or average time between a response and the preceding request. We therefore introduce and study bidirectional NWA that can process input words in both directions. First, we show that bidirectional NWA can express interesting quantitative properties that are not expressible by forward-only NWA. Second, for the fundamental decision problems of emptiness and universality, we establish decidability and complexity results for the new framework which match the best-known results for the special case of forward-only NWA. Thus, for NWA, the increased expressiveness of bidirectionality is achieved at no additional computational complexity. This is in stark contrast to the unweighted case, where bidirectional finite automata are no more expressive but exponentially more succinct than their forward-only counterparts."}],"oa_version":"Published Version","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:49Z","date_updated":"2021-01-12T08:11:53Z","ddc":["004","005"],"conference":{"start_date":"2017-09-05","location":"Berlin, Germany","end_date":"2017-09-08","name":"28th International Conference on Concurrency Theory, CONCUR"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference","pubrep_id":"886","status":"public","_id":"711","date_created":"2018-12-11T11:48:04Z","date_published":"2017-08-01T00:00:00Z","doi":"10.4230/LIPIcs.CONCUR.2017.5","year":"2017","has_accepted_license":"1","day":"01","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop"}],"publist_id":"6976","title":"Bidirectional nested weighted automata","citation":{"ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Bidirectional nested weighted automata,” presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany, 2017, vol. 85.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Bidirectional nested weighted automata (Vol. 85). Presented at the 28th International Conference on Concurrency Theory, CONCUR, Berlin, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5","ama":"Chatterjee K, Henzinger TA, Otop J. Bidirectional nested weighted automata. In: Vol 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.5","mla":"Chatterjee, Krishnendu, et al. Bidirectional Nested Weighted Automata. Vol. 85, 5, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.5.","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Bidirectional nested weighted automata. 28th International Conference on Concurrency Theory, CONCUR, LIPIcs, vol. 85, 5.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Bidirectional Nested Weighted Automata,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.CONCUR.2017.5."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"5"},{"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We establish a weak–strong uniqueness principle for solutions to entropy-dissipating reaction–diffusion equations: As long as a strong solution to the reaction–diffusion equation exists, any weak solution and even any renormalized solution must coincide with this strong solution. Our assumptions on the reaction rates are just the entropy condition and local Lipschitz continuity; in particular, we do not impose any growth restrictions on the reaction rates. Therefore, our result applies to any single reversible reaction with mass-action kinetics as well as to systems of reversible reactions with mass-action kinetics satisfying the detailed balance condition. Renormalized solutions are known to exist globally in time for reaction–diffusion equations with entropy-dissipating reaction rates; in contrast, the global-in-time existence of weak solutions is in general still an open problem–even for smooth data–, thereby motivating the study of renormalized solutions. The key ingredient of our result is a careful adjustment of the usual relative entropy functional, whose evolution cannot be controlled properly for weak solutions or renormalized solutions."}],"intvolume":" 159","month":"08","main_file_link":[{"url":"https://arxiv.org/abs/1703.00730","open_access":"1"}],"oa":1,"scopus_import":1,"publisher":"Elsevier","quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Nonlinear Analysis: Theory, Methods and Applications","day":"01","year":"2017","publication_status":"published","publication_identifier":{"issn":["0362546X"]},"date_created":"2018-12-11T11:48:05Z","volume":159,"date_published":"2017-08-01T00:00:00Z","doi":"10.1016/j.na.2017.03.001","page":"181 - 207","_id":"712","status":"public","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:11:55Z","citation":{"ista":"Fischer JL. 2017. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 159, 181–207.","chicago":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications. Elsevier, 2017. https://doi.org/10.1016/j.na.2017.03.001.","apa":"Fischer, J. L. (2017). Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. Elsevier. https://doi.org/10.1016/j.na.2017.03.001","ama":"Fischer JL. Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations. Nonlinear Analysis: Theory, Methods and Applications. 2017;159:181-207. doi:10.1016/j.na.2017.03.001","ieee":"J. L. Fischer, “Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations,” Nonlinear Analysis: Theory, Methods and Applications, vol. 159. Elsevier, pp. 181–207, 2017.","short":"J.L. Fischer, Nonlinear Analysis: Theory, Methods and Applications 159 (2017) 181–207.","mla":"Fischer, Julian L. “Weak–Strong Uniqueness of Solutions to Entropy Dissipating Reaction–Diffusion Equations.” Nonlinear Analysis: Theory, Methods and Applications, vol. 159, Elsevier, 2017, pp. 181–207, doi:10.1016/j.na.2017.03.001."},"department":[{"_id":"JuFi"}],"title":"Weak–strong uniqueness of solutions to entropy dissipating reaction–diffusion equations","publist_id":"6975","author":[{"last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L"}]},{"_id":"714","status":"public","type":"journal_article","article_type":"original","date_updated":"2021-01-12T08:12:00Z","department":[{"_id":"GaNo"}],"pmid":1,"oa_version":"Submitted Version","abstract":[{"text":"Background HIV-1 infection and drug abuse are frequently co-morbid and their association greatly increases the severity of HIV-1-induced neuropathology. While nucleus accumbens (NAcc) function is severely perturbed by drugs of abuse, little is known about how HIV-1 infection affects NAcc. Methods We used calcium and voltage imaging to investigate the effect of HIV-1 trans-activator of transcription (Tat) on rat NAcc. Based on previous neuronal studies, we hypothesized that Tat modulates intracellular Ca2+ homeostasis of NAcc neurons. Results We provide evidence that Tat triggers a Ca2+ signaling cascade in NAcc medium spiny neurons (MSN) expressing D1-like dopamine receptors leading to neuronal depolarization. Firstly, Tat induced inositol 1,4,5-trisphsophate (IP3) receptor-mediated Ca2+ release from endoplasmic reticulum, followed by Ca2+ and Na+ influx via transient receptor potential canonical channels. The influx of cations depolarizes the membrane promoting additional Ca2+ entry through voltage-gated P/Q-type Ca2+ channels and opening of tetrodotoxin-sensitive Na+ channels. By activating this mechanism, Tat elicits a feed-forward depolarization increasing the excitability of D1-phosphatidylinositol-linked NAcc MSN. We previously found that cocaine targets NAcc neurons directly (independent of the inhibition of dopamine transporter) only when IP3-generating mechanisms are concomitantly initiated. When tested here, cocaine produced a dose-dependent potentiation of the effect of Tat on cytosolic Ca2+. Conclusion We describe for the first time a HIV-1 Tat-triggered Ca2+ signaling in MSN of NAcc involving TRPC and depolarization and a potentiation of the effect of Tat by cocaine, which may be relevant for the reward axis in cocaine-abusing HIV-1-positive patients.","lang":"eng"}],"intvolume":" 178","month":"09","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5797705","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["03768716"]},"volume":178,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Brailoiu G, Deliu E, Barr J, Console Bram L, Ciuciu A, Abood M, Unterwald E, Brǎiloiu E. 2017. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 178, 7–14.","chicago":"Brailoiu, Gabriela, Elena Deliu, Jeffrey Barr, Linda Console Bram, Alexandra Ciuciu, Mary Abood, Ellen Unterwald, and Eugen Brǎiloiu. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence. Elsevier, 2017. https://doi.org/10.1016/j.drugalcdep.2017.04.015.","ieee":"G. Brailoiu et al., “HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens,” Drug and Alcohol Dependence, vol. 178. Elsevier, pp. 7–14, 2017.","short":"G. Brailoiu, E. Deliu, J. Barr, L. Console Bram, A. Ciuciu, M. Abood, E. Unterwald, E. Brǎiloiu, Drug and Alcohol Dependence 178 (2017) 7–14.","apa":"Brailoiu, G., Deliu, E., Barr, J., Console Bram, L., Ciuciu, A., Abood, M., … Brǎiloiu, E. (2017). HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. Elsevier. https://doi.org/10.1016/j.drugalcdep.2017.04.015","ama":"Brailoiu G, Deliu E, Barr J, et al. HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens. Drug and Alcohol Dependence. 2017;178:7-14. doi:10.1016/j.drugalcdep.2017.04.015","mla":"Brailoiu, Gabriela, et al. “HIV Tat Excites D1 Receptor-like Expressing Neurons from Rat Nucleus Accumbens.” Drug and Alcohol Dependence, vol. 178, Elsevier, 2017, pp. 7–14, doi:10.1016/j.drugalcdep.2017.04.015."},"title":"HIV Tat excites D1 receptor-like expressing neurons from rat nucleus accumbens","external_id":{"pmid":["28623807"]},"article_processing_charge":"No","publist_id":"6967","author":[{"first_name":"Gabriela","last_name":"Brailoiu","full_name":"Brailoiu, Gabriela"},{"full_name":"Deliu, Elena","orcid":"0000-0002-7370-5293","last_name":"Deliu","first_name":"Elena","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barr","full_name":"Barr, Jeffrey","first_name":"Jeffrey"},{"last_name":"Console Bram","full_name":"Console Bram, Linda","first_name":"Linda"},{"first_name":"Alexandra","full_name":"Ciuciu, Alexandra","last_name":"Ciuciu"},{"first_name":"Mary","last_name":"Abood","full_name":"Abood, Mary"},{"first_name":"Ellen","last_name":"Unterwald","full_name":"Unterwald, Ellen"},{"first_name":"Eugen","last_name":"Brǎiloiu","full_name":"Brǎiloiu, Eugen"}],"acknowledgement":"This work was supported by the National Institutes of Health grants DA035926 (to MEA), and P30DA013429 (to EMU).","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Drug and Alcohol Dependence","day":"01","year":"2017","date_created":"2018-12-11T11:48:05Z","date_published":"2017-09-01T00:00:00Z","doi":"10.1016/j.drugalcdep.2017.04.015","page":"7 - 14"},{"author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"publist_id":"6968","title":"More excitation for Rett syndrome","department":[{"_id":"GaNo"}],"date_updated":"2021-01-12T08:12:04Z","citation":{"mla":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine, vol. 9, no. 405, aao4218, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aao4218.","short":"G. Novarino, Science Translational Medicine 9 (2017).","ieee":"G. Novarino, “More excitation for Rett syndrome,” Science Translational Medicine, vol. 9, no. 405. American Association for the Advancement of Science, 2017.","ama":"Novarino G. More excitation for Rett syndrome. Science Translational Medicine. 2017;9(405). doi:10.1126/scitranslmed.aao4218","apa":"Novarino, G. (2017). More excitation for Rett syndrome. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.aao4218","chicago":"Novarino, Gaia. “More Excitation for Rett Syndrome.” Science Translational Medicine. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/scitranslmed.aao4218.","ista":"Novarino G. 2017. More excitation for Rett syndrome. Science Translational Medicine. 9(405), aao4218."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"715","article_number":"aao4218","date_created":"2018-12-11T11:48:06Z","doi":"10.1126/scitranslmed.aao4218","volume":9,"issue":"405","date_published":"2017-08-30T00:00:00Z","year":"2017","publication_status":"published","publication_identifier":{"issn":["19466234"]},"language":[{"iso":"eng"}],"publication":"Science Translational Medicine","day":"30","publisher":"American Association for the Advancement of Science","quality_controlled":"1","scopus_import":1,"intvolume":" 9","month":"08","abstract":[{"lang":"eng","text":"D-cycloserine ameliorates breathing abnormalities and survival rate in a mouse model of Rett syndrome."}],"oa_version":"None"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["00045411"]},"publication_status":"published","volume":64,"issue":"5","ec_funded":1,"oa_version":"Preprint","abstract":[{"text":"Two-player games on graphs are central in many problems in formal verification and program analysis, such as synthesis and verification of open systems. In this work, we consider solving recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion.While pushdown games have been studied before with qualitative objectives-such as reachability and ?-regular objectives- in this work, we study for the first time such games with the most well-studied quantitative objective, the mean-payoff objective. In pushdown games, two types of strategies are relevant: (1) global strategies, which depend on the entire global history; and (2) modular strategies, which have only local memory and thus do not depend on the context of invocation but rather only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two-player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP-hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity by showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games and memoryless modular strategies are sufficient in two-player pushdown games. Finally, we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded.","lang":"eng"}],"month":"09","intvolume":" 64","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1201.2829","open_access":"1"}],"date_updated":"2021-01-12T08:12:08Z","department":[{"_id":"KrCh"}],"_id":"716","status":"public","article_type":"original","type":"journal_article","day":"01","publication":"Journal of the ACM","year":"2017","date_published":"2017-09-01T00:00:00Z","doi":"10.1145/3121408","date_created":"2018-12-11T11:48:06Z","page":"34","quality_controlled":"1","publisher":"ACM","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Velner Y. 2017. The complexity of mean-payoff pushdown games. Journal of the ACM. 64(5), 34.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM. ACM, 2017. https://doi.org/10.1145/3121408.","ieee":"K. Chatterjee and Y. Velner, “The complexity of mean-payoff pushdown games,” Journal of the ACM, vol. 64, no. 5. ACM, p. 34, 2017.","short":"K. Chatterjee, Y. Velner, Journal of the ACM 64 (2017) 34.","apa":"Chatterjee, K., & Velner, Y. (2017). The complexity of mean-payoff pushdown games. Journal of the ACM. ACM. https://doi.org/10.1145/3121408","ama":"Chatterjee K, Velner Y. The complexity of mean-payoff pushdown games. Journal of the ACM. 2017;64(5):34. doi:10.1145/3121408","mla":"Chatterjee, Krishnendu, and Yaron Velner. “The Complexity of Mean-Payoff Pushdown Games.” Journal of the ACM, vol. 64, no. 5, ACM, 2017, p. 34, doi:10.1145/3121408."},"title":"The complexity of mean-payoff pushdown games","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"publist_id":"6964","external_id":{"arxiv":["1201.2829"]},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"abstract":[{"lang":"eng","text":"We consider finite-state and recursive game graphs with multidimensional mean-payoff objectives. In recursive games two types of strategies are relevant: global strategies and modular strategies. Our contributions are: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of weights are fixed; whereas for arbitrary dimensions the problem is coNP-complete. (2) We show that one-player recursive games with multidimensional mean-payoff objectives can be solved in polynomial time. Both above algorithms are based on hyperplane separation technique. (3) For recursive games we show that under modular strategies the multidimensional problem is undecidable. We show that if the number of modules, exits, and the maximal absolute value of the weights are fixed, then one-dimensional recursive mean-payoff games under modular strategies can be solved in polynomial time, whereas for unbounded number of exits or modules the problem is NP-hard."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1210.3141"}],"month":"09","intvolume":" 88","publication_status":"published","language":[{"iso":"eng"}],"volume":88,"related_material":{"record":[{"relation":"earlier_version","id":"2329","status":"public"}]},"ec_funded":1,"_id":"717","type":"journal_article","status":"public","date_updated":"2023-02-23T10:38:15Z","department":[{"_id":"KrCh"}],"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23, FWF NFN Grant No. S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the RICH Model Toolkit (ICT COST Action IC0901), and was carried out in partial fulfillment of the requirements for the Ph.D. degree of the second author.","publisher":"Academic Press","quality_controlled":"1","oa":1,"year":"2017","day":"01","publication":"Journal of Computer and System Sciences","page":"236 - 259","date_published":"2017-09-01T00:00:00Z","doi":"10.1016/j.jcss.2017.04.005","date_created":"2018-12-11T11:48:07Z","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Chatterjee K, Velner Y. 2017. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 88, 236–259.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences. Academic Press, 2017. https://doi.org/10.1016/j.jcss.2017.04.005.","apa":"Chatterjee, K., & Velner, Y. (2017). Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. Academic Press. https://doi.org/10.1016/j.jcss.2017.04.005","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. Journal of Computer and System Sciences. 2017;88:236-259. doi:10.1016/j.jcss.2017.04.005","short":"K. Chatterjee, Y. Velner, Journal of Computer and System Sciences 88 (2017) 236–259.","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” Journal of Computer and System Sciences, vol. 88. Academic Press, pp. 236–259, 2017.","mla":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Journal of Computer and System Sciences, vol. 88, Academic Press, 2017, pp. 236–59, doi:10.1016/j.jcss.2017.04.005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6963","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"title":"Hyperplane separation technique for multidimensional mean-payoff games"},{"year":"2017","publication_status":"published","publication_identifier":{"issn":["00015903"]},"publication":"Acta Informatica","language":[{"iso":"eng"}],"day":"01","page":"543 - 544","date_created":"2018-12-11T11:48:07Z","doi":"10.1007/s00236-017-0299-0","issue":"6","date_published":"2017-09-01T00:00:00Z","volume":54,"abstract":[{"lang":"eng","text":"The ubiquity of computation in modern machines and devices imposes a need to assert the correctness of their behavior. Especially in the case of safety-critical systems, their designers need to take measures that enforce their safe operation. Formal methods has emerged as a research field that addresses this challenge: by rigorously proving that all system executions adhere to their specifications, the correctness of an implementation under concern can be assured. To achieve this goal, a plethora of techniques are nowadays available, all of which are optimized for different system types and application domains."}],"oa_version":"None","quality_controlled":"1","publisher":"Springer","scopus_import":1,"intvolume":" 54","month":"09","citation":{"chicago":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-017-0299-0.","ista":"Chatterjee K, Ehlers R. 2017. Special issue: Synthesis and SYNT 2014. Acta Informatica. 54(6), 543–544.","mla":"Chatterjee, Krishnendu, and Rüdiger Ehlers. “Special Issue: Synthesis and SYNT 2014.” Acta Informatica, vol. 54, no. 6, Springer, 2017, pp. 543–44, doi:10.1007/s00236-017-0299-0.","ama":"Chatterjee K, Ehlers R. Special issue: Synthesis and SYNT 2014. Acta Informatica. 2017;54(6):543-544. doi:10.1007/s00236-017-0299-0","apa":"Chatterjee, K., & Ehlers, R. (2017). Special issue: Synthesis and SYNT 2014. Acta Informatica. Springer. https://doi.org/10.1007/s00236-017-0299-0","ieee":"K. Chatterjee and R. Ehlers, “Special issue: Synthesis and SYNT 2014,” Acta Informatica, vol. 54, no. 6. Springer, pp. 543–544, 2017.","short":"K. Chatterjee, R. Ehlers, Acta Informatica 54 (2017) 543–544."},"date_updated":"2021-01-12T08:12:18Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"6961","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Rüdiger","full_name":"Ehlers, Rüdiger","last_name":"Ehlers"}],"title":"Special issue: Synthesis and SYNT 2014","department":[{"_id":"KrCh"}],"_id":"719","type":"journal_article","status":"public"},{"date_created":"2018-12-11T11:48:08Z","doi":"10.1371/journal.pcbi.1005763","date_published":"2017-09-19T00:00:00Z","publication":"PLoS Computational Biology","day":"19","year":"2017","has_accepted_license":"1","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","title":"Probabilistic models for neural populations that naturally capture global coupling and criticality","article_processing_charge":"Yes","publist_id":"6960","author":[{"id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik","full_name":"Humplik, Jan"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 2017;13(9). doi:10.1371/journal.pcbi.1005763","apa":"Humplik, J., & Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005763","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” PLoS Computational Biology, vol. 13, no. 9. Public Library of Science, 2017.","chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005763.","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763."},"project":[{"grant_number":"RGP0065/2012","name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26"}],"article_number":"e1005763","volume":13,"issue":"9","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"81107096c19771c36ddbe6f0282a3acb","file_id":"5352","file_size":14167050,"date_updated":"2020-07-14T12:47:53Z","creator":"system","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","date_created":"2018-12-12T10:18:30Z"}],"publication_status":"published","publication_identifier":{"issn":["1553734X"]},"intvolume":" 13","month":"09","scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality.","lang":"eng"}],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:53Z","ddc":["530","571"],"date_updated":"2021-01-12T08:12:21Z","pubrep_id":"884","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"720"},{"_id":"721","status":"public","type":"journal_article","date_updated":"2021-01-12T08:12:24Z","department":[{"_id":"LaEr"}],"oa_version":"Submitted Version","abstract":[{"text":"Let S be a positivity-preserving symmetric linear operator acting on bounded functions. The nonlinear equation -1/m=z+Sm with a parameter z in the complex upper half-plane ℍ has a unique solution m with values in ℍ. We show that the z-dependence of this solution can be represented as the Stieltjes transforms of a family of probability measures v on ℝ. Under suitable conditions on S, we show that v has a real analytic density apart from finitely many algebraic singularities of degree at most 3. Our motivation comes from large random matrices. The solution m determines the density of eigenvalues of two prominent matrix ensembles: (i) matrices with centered independent entries whose variances are given by S and (ii) matrices with correlated entries with a translation-invariant correlation structure. Our analysis shows that the limiting eigenvalue density has only square root singularities or cubic root cusps; no other singularities occur.","lang":"eng"}],"intvolume":" 70","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1512.03703","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00103640"]},"ec_funded":1,"volume":70,"issue":"9","project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Ajanki, O. H., Krüger, T. H., & Erdös, L. (2017). Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21639","ama":"Ajanki OH, Krüger TH, Erdös L. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 2017;70(9):1672-1705. doi:10.1002/cpa.21639","short":"O.H. Ajanki, T.H. Krüger, L. Erdös, Communications on Pure and Applied Mathematics 70 (2017) 1672–1705.","ieee":"O. H. Ajanki, T. H. Krüger, and L. Erdös, “Singularities of solutions to quadratic vector equations on the complex upper half plane,” Communications on Pure and Applied Mathematics, vol. 70, no. 9. Wiley-Blackwell, pp. 1672–1705, 2017.","mla":"Ajanki, Oskari H., et al. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics, vol. 70, no. 9, Wiley-Blackwell, 2017, pp. 1672–705, doi:10.1002/cpa.21639.","ista":"Ajanki OH, Krüger TH, Erdös L. 2017. Singularities of solutions to quadratic vector equations on the complex upper half plane. Communications on Pure and Applied Mathematics. 70(9), 1672–1705.","chicago":"Ajanki, Oskari H, Torben H Krüger, and László Erdös. “Singularities of Solutions to Quadratic Vector Equations on the Complex Upper Half Plane.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2017. https://doi.org/10.1002/cpa.21639."},"title":"Singularities of solutions to quadratic vector equations on the complex upper half plane","author":[{"last_name":"Ajanki","full_name":"Ajanki, Oskari H","first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös"}],"publist_id":"6959","oa":1,"quality_controlled":"1","publisher":"Wiley-Blackwell","publication":"Communications on Pure and Applied Mathematics","day":"01","year":"2017","date_created":"2018-12-11T11:48:08Z","doi":"10.1002/cpa.21639","date_published":"2017-09-01T00:00:00Z","page":"1672 - 1705"},{"_id":"722","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","pubrep_id":"982","date_updated":"2021-01-12T08:12:29Z","ddc":["581"],"department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:54Z","abstract":[{"lang":"eng","text":"Plants are sessile organisms rooted in one place. The soil resources that plants require are often distributed in a highly heterogeneous pattern. To aid foraging, plants have evolved roots whose growth and development are highly responsive to soil signals. As a result, 3D root architecture is shaped by myriad environmental signals to ensure resource capture is optimised and unfavourable environments are avoided. The first signals sensed by newly germinating seeds — gravity and light — direct root growth into the soil to aid seedling establishment. Heterogeneous soil resources, such as water, nitrogen and phosphate, also act as signals that shape 3D root growth to optimise uptake. Root architecture is also modified through biotic interactions that include soil fungi and neighbouring plants. This developmental plasticity results in a ‘custom-made’ 3D root system that is best adapted to forage for resources in each soil environment that a plant colonises."}],"pmid":1,"oa_version":"Submitted Version","scopus_import":1,"month":"09","intvolume":" 27","publication_identifier":{"issn":["09609822"]},"publication_status":"published","file":[{"checksum":"e45588b21097b408da6276a3e5eedb2e","file_id":"6332","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-04-17T07:46:40Z","file_name":"2017_CurrentBiology_Morris.pdf","date_updated":"2020-07-14T12:47:54Z","file_size":1576593,"creator":"dernst"}],"language":[{"iso":"eng"}],"volume":27,"issue":"17","ec_funded":1,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"citation":{"ista":"Morris E, Griffiths M, Golebiowska A, Mairhofer S, Burr Hersey J, Goh T, von Wangenheim D, Atkinson B, Sturrock C, Lynch J, Vissenberg K, Ritz K, Wells D, Mooney S, Bennett M. 2017. Shaping 3D root system architecture. Current Biology. 27(17), R919–R930.","chicago":"Morris, Emily, Marcus Griffiths, Agata Golebiowska, Stefan Mairhofer, Jasmine Burr Hersey, Tatsuaki Goh, Daniel von Wangenheim, et al. “Shaping 3D Root System Architecture.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.06.043.","apa":"Morris, E., Griffiths, M., Golebiowska, A., Mairhofer, S., Burr Hersey, J., Goh, T., … Bennett, M. (2017). Shaping 3D root system architecture. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.06.043","ama":"Morris E, Griffiths M, Golebiowska A, et al. Shaping 3D root system architecture. Current Biology. 2017;27(17):R919-R930. doi:10.1016/j.cub.2017.06.043","ieee":"E. Morris et al., “Shaping 3D root system architecture,” Current Biology, vol. 27, no. 17. Cell Press, pp. R919–R930, 2017.","short":"E. Morris, M. Griffiths, A. Golebiowska, S. Mairhofer, J. Burr Hersey, T. Goh, D. von Wangenheim, B. Atkinson, C. Sturrock, J. Lynch, K. Vissenberg, K. Ritz, D. Wells, S. Mooney, M. Bennett, Current Biology 27 (2017) R919–R930.","mla":"Morris, Emily, et al. “Shaping 3D Root System Architecture.” Current Biology, vol. 27, no. 17, Cell Press, 2017, pp. R919–30, doi:10.1016/j.cub.2017.06.043."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6956","author":[{"first_name":"Emily","full_name":"Morris, Emily","last_name":"Morris"},{"last_name":"Griffiths","full_name":"Griffiths, Marcus","first_name":"Marcus"},{"first_name":"Agata","full_name":"Golebiowska, Agata","last_name":"Golebiowska"},{"first_name":"Stefan","last_name":"Mairhofer","full_name":"Mairhofer, Stefan"},{"last_name":"Burr Hersey","full_name":"Burr Hersey, Jasmine","first_name":"Jasmine"},{"full_name":"Goh, Tatsuaki","last_name":"Goh","first_name":"Tatsuaki"},{"last_name":"Von Wangenheim","full_name":"Von Wangenheim, Daniel","orcid":"0000-0002-6862-1247","id":"49E91952-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"full_name":"Atkinson, Brian","last_name":"Atkinson","first_name":"Brian"},{"full_name":"Sturrock, Craig","last_name":"Sturrock","first_name":"Craig"},{"full_name":"Lynch, Jonathan","last_name":"Lynch","first_name":"Jonathan"},{"first_name":"Kris","last_name":"Vissenberg","full_name":"Vissenberg, Kris"},{"full_name":"Ritz, Karl","last_name":"Ritz","first_name":"Karl"},{"last_name":"Wells","full_name":"Wells, Darren","first_name":"Darren"},{"last_name":"Mooney","full_name":"Mooney, Sacha","first_name":"Sacha"},{"full_name":"Bennett, Malcolm","last_name":"Bennett","first_name":"Malcolm"}],"external_id":{"pmid":["28898665"]},"title":"Shaping 3D root system architecture","quality_controlled":"1","publisher":"Cell Press","oa":1,"has_accepted_license":"1","year":"2017","day":"11","publication":"Current Biology","page":"R919 - R930","doi":"10.1016/j.cub.2017.06.043","date_published":"2017-09-11T00:00:00Z","date_created":"2018-12-11T11:48:08Z"},{"abstract":[{"text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/","open_access":"1"}],"scopus_import":1,"intvolume":" 114","month":"09","publication_status":"published","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"volume":114,"issue":"38","_id":"725","type":"journal_article","status":"public","date_updated":"2021-01-12T08:12:36Z","department":[{"_id":"GaTk"}],"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","year":"2017","publication":"PNAS","day":"19","page":"10149 - 10154","date_created":"2018-12-11T11:48:10Z","doi":"10.1073/pnas.1703817114","date_published":"2017-09-19T00:00:00Z","citation":{"short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” PNAS, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","apa":"Harpaz, R., Tkačik, G., & Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1703817114","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 2017;114(38):10149-10154. doi:10.1073/pnas.1703817114","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.","ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1703817114."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["28874581"]},"publist_id":"6953","author":[{"first_name":"Roy","last_name":"Harpaz","full_name":"Harpaz, Roy"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"}],"title":"Discrete modes of social information processing predict individual behavior of fish in a group"},{"date_updated":"2021-01-12T08:12:35Z","department":[{"_id":"MaSe"}],"_id":"724","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"issn":["24699950"]},"language":[{"iso":"eng"}],"volume":96,"issue":"10","abstract":[{"lang":"eng","text":"We investigate the stationary and dynamical behavior of an Anderson localized chain coupled to a single central bound state. Although this coupling partially dilutes the Anderson localized peaks towards nearly resonant sites, the most weight of the original peaks remains unchanged. This leads to multifractal wave functions with a frozen spectrum of fractal dimensions, which is characteristic for localized phases in models with power-law hopping. Using a perturbative approach we identify two different dynamical regimes. At weak couplings to the central site, the transport of particles and information is logarithmic in time, a feature usually attributed to many-body localization. We connect such transport to the persistence of the Poisson statistics of level spacings in parts of the spectrum. In contrast, at stronger couplings the level repulsion is established in the entire spectrum, the problem can be mapped to the Fano resonance, and the transport is ballistic."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1701.02744","open_access":"1"}],"scopus_import":1,"intvolume":" 96","month":"09","citation":{"chicago":"Hetterich, Daniel, Maksym Serbyn, Fernando Domínguez, Frank Pollmann, and Björn Trauzettel. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.104203.","ista":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. 2017. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 96(10), 104203.","mla":"Hetterich, Daniel, et al. “Noninteracting Central Site Model Localization and Logarithmic Entanglement Growth.” Physical Review B, vol. 96, no. 10, 104203, American Physical Society, 2017, doi:10.1103/PhysRevB.96.104203.","ama":"Hetterich D, Serbyn M, Domínguez F, Pollmann F, Trauzettel B. Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. 2017;96(10). doi:10.1103/PhysRevB.96.104203","apa":"Hetterich, D., Serbyn, M., Domínguez, F., Pollmann, F., & Trauzettel, B. (2017). Noninteracting central site model localization and logarithmic entanglement growth. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.104203","ieee":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, and B. Trauzettel, “Noninteracting central site model localization and logarithmic entanglement growth,” Physical Review B, vol. 96, no. 10. American Physical Society, 2017.","short":"D. Hetterich, M. Serbyn, F. Domínguez, F. Pollmann, B. Trauzettel, Physical Review B 96 (2017)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Hetterich, Daniel","last_name":"Hetterich","first_name":"Daniel"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"Fernando","full_name":"Domínguez, Fernando","last_name":"Domínguez"},{"first_name":"Frank","last_name":"Pollmann","full_name":"Pollmann, Frank"},{"first_name":"Björn","full_name":"Trauzettel, Björn","last_name":"Trauzettel"}],"publist_id":"6955","title":"Noninteracting central site model localization and logarithmic entanglement growth","article_number":"104203","year":"2017","publication":"Physical Review B","day":"13","date_created":"2018-12-11T11:48:09Z","date_published":"2017-09-13T00:00:00Z","doi":"10.1103/PhysRevB.96.104203","acknowledgement":"We would like to thank Dmitry Abanin, Christophe De\r\nBeule, Joel Moore, Romain Vasseur, and Norman Yao for\r\nmany stimulating discussions. Financial support has been\r\nprovided by the Deutsche Forschungsgemeinschaft (DFG)\r\nvia Grant No. TR950/8-1, SFB 1170 “ToCoTronics” and the\r\nENB Graduate School on Topological Insulators. M.S. was\r\nsupported by Gordon and Betty Moore Foundation’s EPiQS\r\nInitiative through Grant No. GBMF4307. F.P. acknowledges\r\nsupport from the DFG Research Unit FOR 1807 through Grant\r\nNo. PO 1370/2-1.","oa":1,"quality_controlled":"1","publisher":"American Physical Society"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:12:57Z","citation":{"mla":"Novarino, Gaia. “The Science of Love in ASD and ADHD.” Science Translational Medicine, vol. 9, no. 411, eaap8168, American Association for the Advancement of Science, 2017, doi:10.1126/scitranslmed.aap8168.","ieee":"G. Novarino, “The science of love in ASD and ADHD,” Science Translational Medicine, vol. 9, no. 411. American Association for the Advancement of Science, 2017.","short":"G. 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Science Translational Medicine. 9(411), eaap8168."},"title":"The science of love in ASD and ADHD","department":[{"_id":"GaNo"}],"author":[{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia"}],"publist_id":"6938","article_number":"eaap8168","_id":"731","status":"public","type":"journal_article","day":"11","language":[{"iso":"eng"}],"publication":"Science Translational Medicine","publication_identifier":{"issn":["19466234"]},"publication_status":"published","year":"2017","issue":"411","doi":"10.1126/scitranslmed.aap8168","date_published":"2017-10-11T00:00:00Z","volume":9,"date_created":"2018-12-11T11:48:12Z","oa_version":"None","abstract":[{"lang":"eng","text":"Genetic variations in the oxytocin receptor gene affect patients with ASD and ADHD differently."}],"month":"10","intvolume":" 9","quality_controlled":"1","publisher":"American Association for the Advancement of Science","scopus_import":1},{"_id":"7360","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"status":"public","date_updated":"2021-01-12T08:13:14Z","ddc":["570"],"department":[{"_id":"MaLo"}],"file_date_updated":"2020-07-14T12:47:56Z","abstract":[{"lang":"eng","text":"Inflammation, which is a highly regulated host response against danger signals, may be harmful if it is excessive and deregulated. Ideally, anti-inflammatory therapy should autonomously commence as soon as possible after the onset of inflammation, should be controllable by a physician, and should not systemically block beneficial immune response in the long term. We describe a genetically encoded anti-inflammatory mammalian cell device based on a modular engineered genetic circuit comprising a sensor, an amplifier, a “thresholder” to restrict activation of a positive-feedback loop, a combination of advanced clinically used biopharmaceutical proteins, and orthogonal regulatory elements that linked modules into the functional device. This genetic circuit was autonomously activated by inflammatory signals, including endogenous cecal ligation and puncture (CLP)-induced inflammation in mice and serum from a systemic juvenile idiopathic arthritis (sIJA) patient, and could be reset externally by a chemical signal. The microencapsulated anti-inflammatory device significantly reduced the pathology in dextran sodium sulfate (DSS)-induced acute murine colitis, demonstrating a synthetic immunological approach for autonomous anti-inflammatory therapy."}],"oa_version":"Published Version","pmid":1,"month":"01","intvolume":" 25","publication_identifier":{"issn":["1525-0016"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"ea8b1b28606dd1edab7379ba4fa3641f","file_id":"7561","creator":"dernst","file_size":3404806,"date_updated":"2020-07-14T12:47:56Z","file_name":"2017_MolecularTherapy_Smole.pdf","date_created":"2020-03-03T10:55:13Z"}],"language":[{"iso":"eng"}],"volume":25,"issue":"1","citation":{"chicago":"Smole, Anže, Duško Lainšček, Urban Bezeljak, Simon Horvat, and Roman Jerala. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy. Elsevier, 2017. https://doi.org/10.1016/j.ymthe.2016.10.005.","ista":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. 2017. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 25(1), 102–119.","mla":"Smole, Anže, et al. “A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation.” Molecular Therapy, vol. 25, no. 1, Elsevier, 2017, pp. 102–19, doi:10.1016/j.ymthe.2016.10.005.","apa":"Smole, A., Lainšček, D., Bezeljak, U., Horvat, S., & Jerala, R. (2017). A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. Elsevier. https://doi.org/10.1016/j.ymthe.2016.10.005","ama":"Smole A, Lainšček D, Bezeljak U, Horvat S, Jerala R. A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation. Molecular Therapy. 2017;25(1):102-119. doi:10.1016/j.ymthe.2016.10.005","short":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, R. Jerala, Molecular Therapy 25 (2017) 102–119.","ieee":"A. Smole, D. Lainšček, U. Bezeljak, S. Horvat, and R. Jerala, “A synthetic mammalian therapeutic gene circuit for sensing and suppressing inflammation,” Molecular Therapy, vol. 25, no. 1. 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However, such volunteer efforts must be well coordinated and monitored, in order to offer an effective relief to the professionals. In this paper we extend earlier work on optimally assigning volunteers to selected landmark locations. In particular, we emphasize the aspect that obtaining good assignments requires not only advanced computational tools, but also a realistic measure of distance between volunteers and landmarks. Specifically, we propose the use of the Open Street Map (OSM) driving distance instead of he previously used flight distance. We find the OSM driving distance to be better aligned with the interests of volunteers and first responders. Furthermore, we show that relying on the flying distance leads to a substantial underestimation of the number of required volunteers, causing negative side effects in case of an actual crisis situation.","lang":"eng"}],"title":"Optimal geospatial volunteer allocation needs realistic distances","department":[{"_id":"ChLa"}],"author":[{"last_name":"Pielorz","full_name":"Pielorz, Jasmin","first_name":"Jasmin","id":"49BC895A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","last_name":"Prandtstetter","full_name":"Prandtstetter, Matthias"},{"first_name":"Markus","full_name":"Straub, Markus","last_name":"Straub"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"publist_id":"6906","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:13:55Z","citation":{"mla":"Pielorz, Jasmin, et al. “Optimal Geospatial Volunteer Allocation Needs Realistic Distances.” 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–63, doi:10.1109/BigData.2017.8258375.","ieee":"J. Pielorz, M. Prandtstetter, M. Straub, and C. Lampert, “Optimal geospatial volunteer allocation needs realistic distances,” in 2017 IEEE International Conference on Big Data, Boston, MA, United States, 2017, pp. 3760–3763.","short":"J. Pielorz, M. Prandtstetter, M. Straub, C. Lampert, in:, 2017 IEEE International Conference on Big Data, IEEE, 2017, pp. 3760–3763.","apa":"Pielorz, J., Prandtstetter, M., Straub, M., & Lampert, C. (2017). Optimal geospatial volunteer allocation needs realistic distances. In 2017 IEEE International Conference on Big Data (pp. 3760–3763). Boston, MA, United States: IEEE. https://doi.org/10.1109/BigData.2017.8258375","ama":"Pielorz J, Prandtstetter M, Straub M, Lampert C. Optimal geospatial volunteer allocation needs realistic distances. In: 2017 IEEE International Conference on Big Data. 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Big Data, 3760–3763."},"status":"public","type":"conference","conference":{"name":"Big Data","end_date":"2017-12-14","location":"Boston, MA, United States","start_date":"2017-12-11"},"_id":"750"},{"year":"2017","has_accepted_license":"1","publication":"Electronic Journal of Combinatorics","day":"28","date_created":"2018-12-11T11:48:32Z","date_published":"2017-07-28T00:00:00Z","doi":"10.37236/6663","oa":1,"publisher":"International Press","quality_controlled":"1","citation":{"ista":"Fulek R, Kynčl J, Pálvölgyi D. 2017. Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 24(3), P3.18.","chicago":"Fulek, Radoslav, Jan Kynčl, and Dömötör Pálvölgyi. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics. International Press, 2017. https://doi.org/10.37236/6663.","apa":"Fulek, R., Kynčl, J., & Pálvölgyi, D. (2017). Unified Hanani Tutte theorem. Electronic Journal of Combinatorics. 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International Press, 2017.","mla":"Fulek, Radoslav, et al. “Unified Hanani Tutte Theorem.” Electronic Journal of Combinatorics, vol. 24, no. 3, P3.18, International Press, 2017, doi:10.37236/6663."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"},{"full_name":"Pálvölgyi, Dömötör","last_name":"Pálvölgyi","first_name":"Dömötör"}],"publist_id":"6859","title":"Unified Hanani Tutte theorem","article_number":"P3.18","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"issn":["10778926"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-01-18T14:04:08Z","file_name":"2017_ElectrCombi_Fulek.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:06Z","file_size":236944,"checksum":"ef320cff0f062051e858f929be6a3581","file_id":"5853","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"ec_funded":1,"volume":24,"issue":"3","abstract":[{"lang":"eng","text":"We introduce a common generalization of the strong Hanani–Tutte theorem and the weak Hanani–Tutte theorem: if a graph G has a drawing D in the plane where every pair of independent edges crosses an even number of times, then G has a planar drawing preserving the rotation of each vertex whose incident edges cross each other evenly in D. The theorem is implicit in the proof of the strong Hanani–Tutte theorem by Pelsmajer, Schaefer and Štefankovič. We give a new, somewhat simpler proof."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 24","month":"07","date_updated":"2022-03-18T12:58:53Z","ddc":["000"],"file_date_updated":"2020-07-14T12:48:06Z","department":[{"_id":"UlWa"}],"_id":"795","article_type":"original","type":"journal_article","status":"public"},{"publication_status":"published","year":"2017","language":[{"iso":"eng"}],"publication":"Physik in unserer Zeit","day":"01","page":"111 - 113","date_created":"2018-12-11T11:48:33Z","issue":"3","date_published":"2017-05-01T00:00:00Z","volume":48,"doi":"10.1002/piuz.201770305","abstract":[{"lang":"ger","text":"Phasenübergänge helfen beim Verständnis von Vielteilchensystemen in der Festkörperphysik und Fluiddynamik bis hin zur Teilchenphysik. Unserer internationalen Kollaboration ist es gelungen, einen neuartigen Phasenübergang in einem Quantensystem zu beobachten [1]. In einem Mikrowellenresonator konnte erstmals die spontane Zustandsänderung von undurchsichtig zu transparent nachgewiesen werden."}],"oa_version":"None","quality_controlled":"1","publisher":"Wiley","intvolume":" 48","month":"05","citation":{"chicago":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit. Wiley, 2017. https://doi.org/10.1002/piuz.201770305.","ista":"Fink JM. 2017. Photonenblockade aufgelöst. Physik in unserer Zeit. 48(3), 111–113.","mla":"Fink, Johannes M. “Photonenblockade Aufgelöst.” Physik in Unserer Zeit, vol. 48, no. 3, Wiley, 2017, pp. 111–13, doi:10.1002/piuz.201770305.","ama":"Fink JM. Photonenblockade aufgelöst. Physik in unserer Zeit. 2017;48(3):111-113. doi:10.1002/piuz.201770305","apa":"Fink, J. M. (2017). Photonenblockade aufgelöst. Physik in Unserer Zeit. 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Villányi, “Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB, pp. 274–280, 2017.","short":"M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare 70 (2017) 274–280.","ama":"Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898","apa":"Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898","mla":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.","ista":"Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.","chicago":"Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1898."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"VÖB","oa":1,"page":"274 - 280","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1898","date_created":"2018-12-11T11:48:36Z","has_accepted_license":"1","popular_science":"1","year":"2017","day":"01","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"807","file_date_updated":"2020-07-14T12:48:09Z","department":[{"_id":"E-Lib"}],"date_updated":"2021-01-12T08:16:45Z","ddc":["020"],"scopus_import":1,"month":"08","intvolume":" 70","abstract":[{"text":"On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries and the publisher Springer took its effect: this deal covers accessing the licensed content on the one hand, and publishing open access on the other hand. More than 1000 papers by Austrian authors were published open access at Springer in the first year alone. The working group "Springer Compact Evaluierung" made the data for these articles available via the platform OpenAPC and would like to use this opportunity to give a short account of what this publishing agreement actually entails and the working group intends to do.","lang":"eng"}],"oa_version":"Published Version","issue":"2","volume":70,"publication_identifier":{"issn":["10222588"]},"publication_status":"published","file":[{"checksum":"558c18bcf5580d87dd371ec626d52075","file_id":"5851","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2017_VOEB_Andrae.pdf","date_created":"2019-01-18T13:39:26Z","creator":"dernst","file_size":125065,"date_updated":"2020-07-14T12:48:09Z"}],"language":[{"iso":"eng"}]},{"title":"Metadata for research data in practice","publist_id":"6823","author":[{"first_name":"Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara","last_name":"Petritsch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Petritsch B. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2017;70(2):200-207. doi:10.31263/voebm.v70i2.1678","apa":"Petritsch, B. (2017). Metadata for research data in practice. Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1678","short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 70 (2017) 200–207.","ieee":"B. Petritsch, “Metadata for research data in practice,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:10.31263/voebm.v70i2.1678.","ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 70(2), 200–207.","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2017. https://doi.org/10.31263/voebm.v70i2.1678."},"date_created":"2018-12-11T11:48:42Z","date_published":"2017-08-01T00:00:00Z","doi":"10.31263/voebm.v70i2.1678","page":"200 - 207","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","day":"01","year":"2017","has_accepted_license":"1","oa":1,"publisher":"VÖB","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:48:11Z","ddc":["020"],"date_updated":"2021-01-12T08:17:44Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","_id":"825","issue":"2","volume":70,"language":[{"iso":"eng"}],"file":[{"date_created":"2019-01-18T13:32:17Z","file_name":"2017_VOEB_Petritsch.pdf","date_updated":"2020-07-14T12:48:11Z","file_size":7843975,"creator":"dernst","file_id":"5850","checksum":"7c4544d07efa2c2add8612b489abb4e2","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["10222588"]},"intvolume":" 70","month":"08","scopus_import":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep."}]},{"oa":1,"quality_controlled":"1","publisher":"eLife Sciences Publications","date_created":"2021-06-02T14:28:58Z","date_published":"2017-11-15T00:00:00Z","doi":"10.7554/elife.30674","publication":"eLife","day":"15","year":"2017","has_accepted_license":"1","article_number":"e30674","title":"DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes","article_processing_charge":"No","external_id":{"pmid":["29140247"]},"author":[{"first_name":"David B","last_name":"Lyons","full_name":"Lyons, David B"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/elife.30674.","ista":"Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 6, e30674.","mla":"Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications, 2017, doi:10.7554/elife.30674.","short":"D.B. Lyons, D. Zilberman, ELife 6 (2017).","ieee":"D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications, 2017.","ama":"Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674","apa":"Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674"},"intvolume":" 6","month":"11","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation."}],"volume":6,"language":[{"iso":"eng"}],"file":[{"date_updated":"2021-06-02T14:33:36Z","file_size":1603102,"creator":"cziletti","date_created":"2021-06-02T14:33:36Z","file_name":"2017_eLife_Lyons.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"9446","checksum":"4cfcdd67511ae4aed3d993550e46e146","success":1}],"publication_status":"published","publication_identifier":{"eissn":["2050-084X"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"9445","file_date_updated":"2021-06-02T14:33:36Z","department":[{"_id":"DaZi"}],"ddc":["570"],"extern":"1","date_updated":"2021-12-14T07:54:36Z"},{"year":"2017","publication":"Synthetic Protein Switches","day":"15","page":"71 - 87","date_created":"2018-12-11T11:49:24Z","doi":"10.1007/978-1-4939-6940-1_5","date_published":"2017-03-15T00:00:00Z","publisher":"Springer","quality_controlled":"1","citation":{"apa":"Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C., Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer. https://doi.org/10.1007/978-1-4939-6940-1_5","ama":"Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5","ieee":"B. Clifton et al., “Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors,” in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.","short":"B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L. Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp. 71–87.","mla":"Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.","ista":"Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein Switches. Methods in Molecular Biology, vol. 1596, 71–87.","chicago":"Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde, Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"6451","author":[{"last_name":"Clifton","full_name":"Clifton, Ben","first_name":"Ben"},{"last_name":"Whitfield","full_name":"Whitfield, Jason","first_name":"Jason"},{"full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada"},{"last_name":"Herde","full_name":"Herde, Michel","first_name":"Michel"},{"full_name":"Henneberger, Christian","last_name":"Henneberger","first_name":"Christian"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jackson","full_name":"Jackson, Colin","first_name":"Colin"}],"title":"Ancestral protein reconstruction and circular permutation for improving the stability and dynamic range of FRET sensors","editor":[{"first_name":"Viktor","last_name":"Stein","full_name":"Stein, Viktor"}],"project":[{"name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"issn":["10643745"]},"language":[{"iso":"eng"}],"volume":1596,"abstract":[{"text":"Small molecule biosensors based on Forster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.","lang":"eng"}],"oa_version":"None","alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"intvolume":" 1596","month":"03","date_updated":"2021-01-12T08:22:13Z","department":[{"_id":"HaJa"}],"series_title":"Synthetic Protein Switches","_id":"957","type":"book_chapter","status":"public"},{"publist_id":"6438","author":[{"first_name":"Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy","orcid":"0000-0001-5588-8287","last_name":"Avni"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"title":"Timed network games with clocks","citation":{"mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark, 2017, vol. 83.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"37","doi":"10.4230/LIPIcs.MFCS.2017.37","date_published":"2017-06-01T00:00:00Z","date_created":"2018-12-11T11:49:26Z","has_accepted_license":"1","year":"2017","day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:48:18Z","department":[{"_id":"ToHe"}],"date_updated":"2023-02-23T12:35:50Z","ddc":["004"],"type":"conference","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Aalborg, Denmark","end_date":"2017-08-25","start_date":"2017-08-21","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"status":"public","pubrep_id":"829","_id":"963","volume":83,"related_material":{"record":[{"relation":"later_version","id":"6005","status":"public"}]},"publication_identifier":{"issn":["18688969"]},"publication_status":"published","file":[{"file_id":"5059","checksum":"f55eaf7f3c36ea07801112acfedd17d5","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf","date_created":"2018-12-12T10:14:10Z","creator":"system","file_size":369730,"date_updated":"2020-07-14T12:48:18Z"}],"language":[{"iso":"eng"}],"alternative_title":["LIPIcs"],"scopus_import":1,"month":"06","intvolume":" 83","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ","lang":"eng"}],"oa_version":"Published Version"},{"month":"10","main_file_link":[{"url":"https://doi.org/10.5061/dryad.1f1rc","open_access":"1"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina."}],"date_created":"2021-07-23T11:34:34Z","doi":"10.5061/dryad.1f1rc","date_published":"2017-10-18T00:00:00Z","related_material":{"record":[{"status":"public","id":"1197","relation":"used_in_publication"}]},"day":"18","year":"2017","status":"public","type":"research_data_reference","_id":"9709","department":[{"_id":"GaTk"}],"title":"Data from: Error-robust modes of the retinal population code","article_processing_charge":"No","author":[{"last_name":"Prentice","full_name":"Prentice, Jason","first_name":"Jason"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"last_name":"Ioffe","full_name":"Ioffe, Mark","first_name":"Mark"},{"full_name":"Loback, Adrianna","last_name":"Loback","first_name":"Adrianna"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.","mla":"Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017."},"date_updated":"2023-02-21T16:34:41Z"},{"quality_controlled":"1","publisher":"Public Library of Science","oa":1,"day":"18","publication":"PLoS Genetics","has_accepted_license":"1","year":"2017","doi":"10.1371/journal.pgen.1007122","date_published":"2017-12-18T00:00:00Z","date_created":"2018-12-11T11:47:04Z","article_number":"e1007122","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers M, Ackermann M. 2017. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 13(12), e1007122.","chicago":"Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller, Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics. Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.","apa":"Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann, S., … Ackermann, M. (2017). Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122","ama":"Nikolic N, Schreiber F, Dal Co A, et al. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations. PLoS Genetics. 2017;13(12). doi:10.1371/journal.pgen.1007122","ieee":"N. Nikolic et al., “Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations,” PLoS Genetics, vol. 13, no. 12. Public Library of Science, 2017.","short":"N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann, M. Kuypers, M. Ackermann, PLoS Genetics 13 (2017).","mla":"Nikolic, Nela, et al. “Cell-to-Cell Variation and Specialization in Sugar Metabolism in Clonal Bacterial Populations.” PLoS Genetics, vol. 13, no. 12, e1007122, Public Library of Science, 2017, doi:10.1371/journal.pgen.1007122."},"title":"Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","full_name":"Nikolic, Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic"},{"full_name":"Schreiber, Frank","last_name":"Schreiber","first_name":"Frank"},{"first_name":"Alma","last_name":"Dal Co","full_name":"Dal Co, Alma"},{"full_name":"Kiviet, Daniel","last_name":"Kiviet","first_name":"Daniel"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346"},{"first_name":"Sten","last_name":"Littmann","full_name":"Littmann, Sten"},{"last_name":"Kuypers","full_name":"Kuypers, Marcel","first_name":"Marcel"},{"first_name":"Martin","last_name":"Ackermann","full_name":"Ackermann, Martin"}],"publist_id":"7275","oa_version":"Published Version","abstract":[{"lang":"eng","text":"While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed."}],"month":"12","intvolume":" 13","scopus_import":1,"file":[{"file_size":1308475,"date_updated":"2020-07-14T12:46:46Z","creator":"system","file_name":"IST-2018-959-v1+1_2017_Nikolic_Cell-to-cell.pdf","date_created":"2018-12-12T10:14:35Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"22426d9382f21554bad5fa5967afcfd0","file_id":"5088"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15537390"]},"publication_status":"published","volume":13,"issue":"12","related_material":{"record":[{"relation":"research_data","id":"9844","status":"public"},{"relation":"research_data","id":"9845","status":"public"},{"status":"public","id":"9846","relation":"research_data"}]},"ec_funded":1,"_id":"541","status":"public","pubrep_id":"959","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["576","579"],"date_updated":"2023-02-23T14:10:34Z","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:46:46Z"}]