[{"publication":"Biochimica et Biophysica Acta - Bioenergetics","language":[{"iso":"eng"}],"volume":1857,"year":"2016","page":"892 - 901","date_created":"2018-12-11T11:52:30Z","intvolume":" 1857","quality_controlled":"1","date_published":"2016-07-01T00:00:00Z","title":"Structure of bacterial respiratory complex I","publisher":"Elsevier","citation":{"ieee":"J. Berrisford, R. Baradaran, and L. A. Sazanov, “Structure of bacterial respiratory complex I,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no. 7. Elsevier, pp. 892–901, 2016.","ama":"Berrisford J, Baradaran R, Sazanov LA. Structure of bacterial respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 2016;1857(7):892-901. doi:10.1016/j.bbabio.2016.01.012","short":"J. Berrisford, R. Baradaran, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1857 (2016) 892–901.","chicago":"Berrisford, John, Rozbeh Baradaran, and Leonid A Sazanov. “Structure of Bacterial Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2016. https://doi.org/10.1016/j.bbabio.2016.01.012.","ista":"Berrisford J, Baradaran R, Sazanov LA. 2016. Structure of bacterial respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(7), 892–901.","apa":"Berrisford, J., Baradaran, R., & Sazanov, L. A. (2016). Structure of bacterial respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2016.01.012","mla":"Berrisford, John, et al. “Structure of Bacterial Respiratory Complex I.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1857, no. 7, Elsevier, 2016, pp. 892–901, doi:10.1016/j.bbabio.2016.01.012."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","author":[{"full_name":"Berrisford, John","first_name":"John","last_name":"Berrisford"},{"first_name":"Rozbeh","full_name":"Baradaran, Rozbeh","last_name":"Baradaran"},{"full_name":"Sazanov, Leonid A","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov"}],"date_updated":"2021-01-12T06:51:21Z","publication_status":"published","acknowledgement":"funded by the Medical Research Council (Grant number MC_U105674180)","oa_version":"None","department":[{"_id":"LeSa"}],"type":"journal_article","month":"07","publist_id":"5654","doi":"10.1016/j.bbabio.2016.01.012","abstract":[{"text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. It is the largest protein assembly of respiratory chains and one of the most elaborate redox membrane proteins known. Bacterial enzyme is about half the size of mitochondrial and thus provides its important "minimal" model. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The L-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. We have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus, the membrane domain from Escherichia coli and recently of the intact, entire complex I from T. thermophilus (536. kDa, 16 subunits, 9 iron-sulphur clusters, 64 transmembrane helices). The 95. Å long electron transfer pathway through the enzyme proceeds from the primary electron acceptor flavin mononucleotide through seven conserved Fe-S clusters to the unusual elongated quinone-binding site at the interface with the membrane domain. Four putative proton translocation channels are found in the membrane domain, all linked by the central flexible axis containing charged residues. The redox energy of electron transfer is coupled to proton translocation by the as yet undefined mechanism proposed to involve long-range conformational changes. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.","lang":"eng"}],"scopus_import":1,"issue":"7","status":"public","_id":"1521"},{"type":"journal_article","oa":1,"author":[{"last_name":"Avvakumov","full_name":"Avvakumov, Serhii","first_name":"Serhii","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Avvakumov, Moscow Mathematical Journal 16 (2016) 1–25.","ama":"Avvakumov S. The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. 2016;16(1):1-25. doi:10.17323/1609-4514-2016-16-1-1-25","chicago":"Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.” Moscow Mathematical Journal. Independent University of Moscow, 2016. https://doi.org/10.17323/1609-4514-2016-16-1-1-25.","ieee":"S. Avvakumov, “The classification of certain linked 3-manifolds in 6-space,” Moscow Mathematical Journal, vol. 16, no. 1. Independent University of Moscow, pp. 1–25, 2016.","ista":"Avvakumov S. 2016. The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. 16(1), 1–25.","apa":"Avvakumov, S. (2016). The classification of certain linked 3-manifolds in 6-space. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2016-16-1-1-25","mla":"Avvakumov, Sergey. “The Classification of Certain Linked 3-Manifolds in 6-Space.” Moscow Mathematical Journal, vol. 16, no. 1, Independent University of Moscow, 2016, pp. 1–25, doi:10.17323/1609-4514-2016-16-1-1-25."},"department":[{"_id":"UlWa"}],"date_updated":"2022-02-25T10:15:57Z","oa_version":"Preprint","_id":"1522","scopus_import":"1","external_id":{"arxiv":["1408.3918"]},"date_created":"2018-12-11T11:52:30Z","volume":16,"article_processing_charge":"No","publication":"Moscow Mathematical Journal","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.3918"}],"year":"2016","quality_controlled":"1","title":"The classification of certain linked 3-manifolds in 6-space","date_published":"2016-01-01T00:00:00Z","month":"01","day":"01","publication_status":"published","acknowledgement":"I thank A. Skopenkov for telling me about the problem and for his useful remarks. I also thank A. Sossinsky,\r\nA. Zhubr, M. Skopenkov, P. Akhmetiev, and an anonymous referee for their feedback. Author was partially\r\nsupported by Dobrushin fellowship, 2013, and by RFBR grant 15-01-06302.","publication_identifier":{"eissn":["1609-4514"]},"status":"public","publist_id":"5652","doi":"10.17323/1609-4514-2016-16-1-1-25","abstract":[{"lang":"eng","text":"We classify smooth Brunnian (i.e., unknotted on both components) embeddings (S2 × S1) ⊔ S3 → ℝ6. Any Brunnian embedding (S2 × S1) ⊔ S3 → ℝ6 is isotopic to an explicitly constructed embedding fk,m,n for some integers k, m, n such that m ≡ n (mod 2). Two embeddings fk,m,n and fk′ ,m′,n′ are isotopic if and only if k = k′, m ≡ m′ (mod 2k) and n ≡ n′ (mod 2k). We use Haefliger’s classification of embeddings S3 ⊔ S3 → ℝ6 in our proof. The relation between the embeddings (S2 × S1) ⊔ S3 → ℝ6 and S3 ⊔ S3 → ℝ6 is not trivial, however. For example, we show that there exist embeddings f: (S2 ×S1) ⊔ S3 → ℝ6 and g, g′ : S3 ⊔ S3 → ℝ6 such that the componentwise embedded connected sum f # g is isotopic to f # g′ but g is not isotopic to g′."}],"issue":"1","article_type":"original","page":"1 - 25","intvolume":" 16","language":[{"iso":"eng"}],"arxiv":1,"publisher":"Independent University of Moscow"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A. Gundert, U. Wagner, Proceedings of the American Mathematical Society 144 (2016) 1815–1828.","ama":"Gundert A, Wagner U. On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. 2016;144(4):1815-1828. doi:10.1090/proc/12824","chicago":"Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial Complexes.” Proceedings of the American Mathematical Society. American Mathematical Society, 2016. https://doi.org/10.1090/proc/12824.","ieee":"A. Gundert and U. Wagner, “On topological minors in random simplicial complexes,” Proceedings of the American Mathematical Society, vol. 144, no. 4. American Mathematical Society, pp. 1815–1828, 2016.","ista":"Gundert A, Wagner U. 2016. On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. 144(4), 1815–1828.","apa":"Gundert, A., & Wagner, U. (2016). On topological minors in random simplicial complexes. Proceedings of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/proc/12824","mla":"Gundert, Anna, and Uli Wagner. “On Topological Minors in Random Simplicial Complexes.” Proceedings of the American Mathematical Society, vol. 144, no. 4, American Mathematical Society, 2016, pp. 1815–28, doi:10.1090/proc/12824."},"oa":1,"author":[{"last_name":"Gundert","full_name":"Gundert, Anna","first_name":"Anna"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","last_name":"Wagner"}],"date_updated":"2021-01-12T06:51:22Z","oa_version":"Preprint","department":[{"_id":"UlWa"}],"type":"journal_article","scopus_import":1,"_id":"1523","publication":"Proceedings of the American Mathematical Society","volume":144,"year":"2016","main_file_link":[{"url":"http://arxiv.org/abs/1404.2106","open_access":"1"}],"date_created":"2018-12-11T11:52:30Z","quality_controlled":"1","title":"On topological minors in random simplicial complexes","date_published":"2016-04-01T00:00:00Z","day":"01","publication_status":"published","acknowledgement":"This research was supported by the Swiss National Science Foundation (SNF Projects 200021-125309 and 200020-138230","month":"04","doi":"10.1090/proc/12824","publist_id":"5650","abstract":[{"lang":"eng","text":"For random graphs, the containment problem considers the probability that a binomial random graph G(n, p) contains a given graph as a substructure. When asking for the graph as a topological minor, i.e., for a copy of a subdivision of the given graph, it is well known that the (sharp) threshold is at p = 1/n. We consider a natural analogue of this question for higher-dimensional random complexes Xk(n, p), first studied by Cohen, Costa, Farber and Kappeler for k = 2. Improving previous results, we show that p = Θ(1/ √n) is the (coarse) threshold for containing a subdivision of any fixed complete 2-complex. For higher dimensions k > 2, we get that p = O(n−1/k) is an upper bound for the threshold probability of containing a subdivision of a fixed k-dimensional complex."}],"issue":"4","status":"public","language":[{"iso":"eng"}],"page":"1815 - 1828","intvolume":" 144","publisher":"American Mathematical Society"},{"language":[{"iso":"eng"}],"page":"173 - 191","intvolume":" 9271","publisher":"Springer","day":"10","ec_funded":1,"acknowledgement":"This research was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734, and the SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2_148797.","publication_status":"published","month":"01","alternative_title":["LNCS"],"abstract":[{"text":"When designing genetic circuits, the typical primitives used in major existing modelling formalisms are gene interaction graphs, where edges between genes denote either an activation or inhibition relation. However, when designing experiments, it is important to be precise about the low-level mechanistic details as to how each such relation is implemented. The rule-based modelling language Kappa allows to unambiguously specify mechanistic details such as DNA binding sites, dimerisation of transcription factors, or co-operative interactions. Such a detailed description comes with complexity and computationally costly executions. We propose a general method for automatically transforming a rule-based program, by eliminating intermediate species and adjusting the rate constants accordingly. To the best of our knowledge, we show the first automated reduction of rule-based models based on equilibrium approximations.\r\nOur algorithm is an adaptation of an existing algorithm, which was designed for reducing reaction-based programs; our version of the algorithm scans the rule-based Kappa model in search for those interaction patterns known to be amenable to equilibrium approximations (e.g. Michaelis-Menten scheme). Additional checks are then performed in order to verify if the reduction is meaningful in the context of the full model. The reduced model is efficiently obtained by static inspection over the rule-set. The tool is tested on a detailed rule-based model of a λ-phage switch, which lists 92 rules and 13 agents. The reduced model has 11 rules and 5 agents, and provides a dramatic reduction in simulation time of several orders of magnitude.","lang":"eng"}],"publist_id":"5649","doi":"10.1007/978-3-319-26916-0_10","status":"public","volume":9271,"year":"2016","main_file_link":[{"url":"http://arxiv.org/abs/1501.00440","open_access":"1"}],"date_created":"2018-12-11T11:52:31Z","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_published":"2016-01-10T00:00:00Z","title":"Efficient reduction of kappa models by static inspection of the rule-set","conference":{"name":"HSB: Hybrid Systems Biology","end_date":"2015-09-05","location":"Madrid, Spain","start_date":"2015-09-04"},"citation":{"mla":"Beica, Andreea, et al. Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set. Vol. 9271, Springer, 2016, pp. 173–91, doi:10.1007/978-3-319-26916-0_10.","apa":"Beica, A., Guet, C. C., & Petrov, T. (2016). Efficient reduction of kappa models by static inspection of the rule-set (Vol. 9271, pp. 173–191). Presented at the HSB: Hybrid Systems Biology, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-26916-0_10","ista":"Beica A, Guet CC, Petrov T. 2016. Efficient reduction of kappa models by static inspection of the rule-set. HSB: Hybrid Systems Biology, LNCS, vol. 9271, 173–191.","ieee":"A. Beica, C. C. Guet, and T. Petrov, “Efficient reduction of kappa models by static inspection of the rule-set,” presented at the HSB: Hybrid Systems Biology, Madrid, Spain, 2016, vol. 9271, pp. 173–191.","chicago":"Beica, Andreea, Calin C Guet, and Tatjana Petrov. “Efficient Reduction of Kappa Models by Static Inspection of the Rule-Set,” 9271:173–91. Springer, 2016. https://doi.org/10.1007/978-3-319-26916-0_10.","short":"A. Beica, C.C. Guet, T. Petrov, in:, Springer, 2016, pp. 173–191.","ama":"Beica A, Guet CC, Petrov T. Efficient reduction of kappa models by static inspection of the rule-set. In: Vol 9271. Springer; 2016:173-191. doi:10.1007/978-3-319-26916-0_10"},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Andreea","full_name":"Beica, Andreea","last_name":"Beica"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"last_name":"Petrov","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905"}],"oa":1,"date_updated":"2021-01-12T06:51:22Z","oa_version":"Preprint","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"type":"conference","scopus_import":1,"_id":"1524"},{"publist_id":"5647","doi":"10.1007/978-3-662-49122-5_12","abstract":[{"lang":"eng","text":"We present the first study of robustness of systems that are both timed as well as reactive (I/O). We study the behavior of such timed I/O systems in the presence of uncertain inputs and formalize their robustness using the analytic notion of Lipschitz continuity: a timed I/O system is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions over timed words such as the timed version of the Manhattan distance and the Skorokhod distance. We consider two models of timed I/O systems — timed transducers and asynchronous sequential circuits. We show that K-robustness of timed transducers can be decided in polynomial space under certain conditions. For asynchronous sequential circuits, we reduce K-robustness w.r.t. timed Manhattan distances to K-robustness of discrete letter-to-letter transducers and show PSpace-completeness of the problem."}],"status":"public","ec_funded":1,"day":"01","publication_status":"published","acknowledgement":"This research was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","month":"01","alternative_title":["LNCS"],"publisher":"Springer","language":[{"iso":"eng"}],"page":"250 - 267","intvolume":" 9583","scopus_import":1,"_id":"1526","oa":1,"author":[{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop"},{"last_name":"Samanta","full_name":"Samanta, Roopsha","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Springer, 2016, pp. 250–267.","ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of timed I/O systems. In: Vol 9583. Springer; 2016:250-267. doi:10.1007/978-3-662-49122-5_12","chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Timed I/O Systems,” 9583:250–67. Springer, 2016. https://doi.org/10.1007/978-3-662-49122-5_12.","ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of timed I/O systems,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA, 2016, vol. 9583, pp. 250–267.","ista":"Henzinger TA, Otop J, Samanta R. 2016. Lipschitz robustness of timed I/O systems. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 9583, 250–267.","mla":"Henzinger, Thomas A., et al. Lipschitz Robustness of Timed I/O Systems. Vol. 9583, Springer, 2016, pp. 250–67, doi:10.1007/978-3-662-49122-5_12.","apa":"Henzinger, T. A., Otop, J., & Samanta, R. (2016). Lipschitz robustness of timed I/O systems (Vol. 9583, pp. 250–267). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, St. Petersburg, FL, USA: Springer. https://doi.org/10.1007/978-3-662-49122-5_12"},"department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T06:51:23Z","oa_version":"Preprint","type":"conference","quality_controlled":"1","title":"Lipschitz robustness of timed I/O systems","date_published":"2016-01-01T00:00:00Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2016-01-17","location":"St. Petersburg, FL, USA","end_date":"2016-01-19"},"volume":9583,"year":"2016","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1506.01233"}],"date_created":"2018-12-11T11:52:32Z"},{"related_material":{"record":[{"relation":"earlier_version","id":"1820","status":"public"},{"status":"public","relation":"earlier_version","id":"5425"}]},"month":"05","publication_status":"published","acknowledgement":"We thank Blai Bonet for helping us with RTDP-Bel. The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","day":"01","ec_funded":1,"status":"public","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and an integer cost associated with every transition. The optimization objective we study asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost, both double exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst-case running time of our algorithm is double exponential, we also present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples of interest."}],"publist_id":"5642","doi":"10.1016/j.artint.2016.01.007","intvolume":" 234","page":"26 - 48","language":[{"iso":"eng"}],"arxiv":1,"publisher":"Elsevier","type":"journal_article","date_updated":"2023-02-23T12:25:49Z","oa_version":"Preprint","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2016. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 234, 26–48.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., & Kanodia, A. (2016). Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2016.01.007","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence, vol. 234, Elsevier, 2016, pp. 26–48, doi:10.1016/j.artint.2016.01.007.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” Artificial Intelligence, vol. 234. Elsevier, pp. 26–48, 2016.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. Artificial Intelligence. 2016;234:26-48. doi:10.1016/j.artint.2016.01.007","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, Artificial Intelligence 234 (2016) 26–48.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” Artificial Intelligence. Elsevier, 2016. https://doi.org/10.1016/j.artint.2016.01.007."},"oa":1,"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"full_name":"Gupta, Raghav","first_name":"Raghav","last_name":"Gupta"},{"first_name":"Ayush","full_name":"Kanodia, Ayush","last_name":"Kanodia"}],"_id":"1529","external_id":{"arxiv":["1411.3880"]},"scopus_import":1,"date_created":"2018-12-11T11:52:33Z","year":"2016","main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"publication":"Artificial Intelligence","article_processing_charge":"No","volume":234,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Optimal cost almost-sure reachability in POMDPs","date_published":"2016-05-01T00:00:00Z","quality_controlled":"1"},{"issue":"11","publist_id":"5626","doi":"10.1016/j.jfa.2015.12.007","abstract":[{"lang":"eng","text":"We provide general conditions for which bosonic quadratic Hamiltonians on Fock spaces can be diagonalized by Bogoliubov transformations. Our results cover the case when quantum systems have infinite degrees of freedom and the associated one-body kinetic and paring operators are unbounded. Our sufficient conditions are optimal in the sense that they become necessary when the relevant one-body operators commute."}],"status":"public","acknowledgement":"We thank Jan Dereziński for several inspiring discussions and useful remarks. We thank the referee for helpful comments. J.P.S. thanks the Erwin Schrödinger Institute for the hospitality during the thematic programme “Quantum many-body systems, random matrices, and disorder”. We gratefully acknowledge the financial supports by the European Union's Seventh Framework Programme under the ERC Advanced Grant ERC-2012-AdG 321029 (J.P.S.) and the REA grant agreement No. 291734 (P.T.N.), as well as the support of the National Science Center (NCN) grant No. 2012/07/N/ST1/03185 and the Austrian Science Fund (FWF) project No. P 27533-N27 (M.N.).","publication_status":"published","day":"01","ec_funded":1,"month":"06","publisher":"Academic Press","language":[{"iso":"eng"}],"intvolume":" 270","page":"4340 - 4368","scopus_import":1,"_id":"1545","oa_version":"Submitted Version","date_updated":"2021-01-12T06:51:30Z","department":[{"_id":"RoSe"}],"citation":{"chicago":"Nam, Phan, Marcin M Napiórkowski, and Jan Solovej. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional Analysis. Academic Press, 2016. https://doi.org/10.1016/j.jfa.2015.12.007.","short":"P. Nam, M.M. Napiórkowski, J. Solovej, Journal of Functional Analysis 270 (2016) 4340–4368.","ama":"Nam P, Napiórkowski MM, Solovej J. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 2016;270(11):4340-4368. doi:10.1016/j.jfa.2015.12.007","ieee":"P. Nam, M. M. Napiórkowski, and J. Solovej, “Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations,” Journal of Functional Analysis, vol. 270, no. 11. Academic Press, pp. 4340–4368, 2016.","mla":"Nam, Phan, et al. “Diagonalization of Bosonic Quadratic Hamiltonians by Bogoliubov Transformations.” Journal of Functional Analysis, vol. 270, no. 11, Academic Press, 2016, pp. 4340–68, doi:10.1016/j.jfa.2015.12.007.","apa":"Nam, P., Napiórkowski, M. M., & Solovej, J. (2016). Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. Academic Press. https://doi.org/10.1016/j.jfa.2015.12.007","ista":"Nam P, Napiórkowski MM, Solovej J. 2016. Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations. Journal of Functional Analysis. 270(11), 4340–4368."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"full_name":"Nam, Phan","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87","last_name":"Nam"},{"id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","last_name":"Napiórkowski"},{"last_name":"Solovej","first_name":"Jan","full_name":"Solovej, Jan"}],"type":"journal_article","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"title":"Diagonalization of bosonic quadratic Hamiltonians by Bogoliubov transformations","date_published":"2016-06-01T00:00:00Z","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1508.07321","open_access":"1"}],"year":"2016","publication":"Journal of Functional Analysis","volume":270,"date_created":"2018-12-11T11:52:38Z"},{"publisher":"Royal Society, The","language":[{"iso":"eng"}],"article_number":"20152452","intvolume":" 283","license":"https://creativecommons.org/licenses/by/4.0/","issue":"1822","doi":"10.1098/rspb.2015.2452","publist_id":"5619","abstract":[{"text":"Antibiotic resistance carries a fitness cost that must be overcome in order for resistance to persist over the long term. Compensatory mutations that recover the functional defects associated with resistance mutations have been argued to play a key role in overcoming the cost of resistance, but compensatory mutations are expected to be rare relative to generally beneficial mutations that increase fitness, irrespective of antibiotic resistance. Given this asymmetry, population genetics theory predicts that populations should adapt by compensatory mutations when the cost of resistance is large, whereas generally beneficial mutations should drive adaptation when the cost of resistance is small. We tested this prediction by determining the genomic mechanisms underpinning adaptation to antibiotic-free conditions in populations of the pathogenic bacterium Pseudomonas aeruginosa that carry costly antibiotic resistance mutations. Whole-genome sequencing revealed that populations founded by high-cost rifampicin-resistant mutants adapted via compensatory mutations in three genes of the RNA polymerase core enzyme, whereas populations founded by low-cost mutants adapted by generally beneficial mutations, predominantly in the quorum-sensing transcriptional regulator gene lasR. Even though the importance of compensatory evolution in maintaining resistance has been widely recognized, our study shows that the roles of general adaptation in maintaining resistance should not be underestimated and highlights the need to understand how selection at other sites in the genome influences the dynamics of resistance alleles in clinical settings.","lang":"eng"}],"status":"public","acknowledgement":"We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics funded by Wellcome\r\nTrust grant reference 090532/Z/09/Z and Medical Research Council Hub grant no. G0900747 91070 for generation of the high-throughput sequencing data. We thank Wook Kim and two anonymous reviewers for their constructive feedback on previous versions of our manuscript.","publication_status":"published","day":"13","month":"01","date_published":"2016-01-13T00:00:00Z","title":"The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2016","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","volume":283,"ddc":["570"],"date_created":"2018-12-11T11:52:40Z","file_date_updated":"2020-07-14T12:45:02Z","scopus_import":1,"_id":"1552","date_updated":"2021-01-12T06:51:33Z","oa_version":"Published Version","department":[{"_id":"ToBo"}],"file":[{"file_size":626804,"content_type":"application/pdf","date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-488-v1+1_20152452.full.pdf","date_created":"2018-12-12T10:11:43Z","file_id":"4899","access_level":"open_access","creator":"system","relation":"main_file","checksum":"78ffe70c1c88af3856d31ca6b7195a27"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Qi, Q., Toll Riera, M., Heilbron, K., Preston, G., & Maclean, R. C. (2016). The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2015.2452","mla":"Qi, Qin, et al. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1822, 20152452, Royal Society, The, 2016, doi:10.1098/rspb.2015.2452.","ista":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. 2016. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. 283(1822), 20152452.","chicago":"Qi, Qin, Macarena Toll Riera, Karl Heilbron, Gail Preston, and R Craig Maclean. “The Genomic Basis of Adaptation to the Fitness Cost of Rifampicin Resistance in Pseudomonas Aeruginosa.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2016. https://doi.org/10.1098/rspb.2015.2452.","ama":"Qi Q, Toll Riera M, Heilbron K, Preston G, Maclean RC. The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa. Proceedings of the Royal Society of London Series B Biological Sciences. 2016;283(1822). doi:10.1098/rspb.2015.2452","short":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, R.C. Maclean, Proceedings of the Royal Society of London Series B Biological Sciences 283 (2016).","ieee":"Q. Qi, M. Toll Riera, K. Heilbron, G. Preston, and R. C. Maclean, “The genomic basis of adaptation to the fitness cost of rifampicin resistance in Pseudomonas aeruginosa,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 283, no. 1822. Royal Society, The, 2016."},"has_accepted_license":"1","oa":1,"author":[{"last_name":"Qi","id":"3B22D412-F248-11E8-B48F-1D18A9856A87","first_name":"Qin","full_name":"Qi, Qin","orcid":"0000-0002-6148-2416"},{"last_name":"Toll Riera","full_name":"Toll Riera, Macarena","first_name":"Macarena"},{"last_name":"Heilbron","full_name":"Heilbron, Karl","first_name":"Karl"},{"full_name":"Preston, Gail","first_name":"Gail","last_name":"Preston"},{"last_name":"Maclean","full_name":"Maclean, R Craig","first_name":"R Craig"}],"pubrep_id":"488","type":"journal_article"},{"issue":"2","publist_id":"5579","abstract":[{"lang":"eng","text":"A modular approach to constructing cryptographic protocols leads to simple designs but often inefficient instantiations. On the other hand, ad hoc constructions may yield efficient protocols at the cost of losing conceptual simplicity. We suggest a new design paradigm, structure-preserving cryptography, that provides a way to construct modular protocols with reasonable efficiency while retaining conceptual simplicity. A cryptographic scheme over a bilinear group is called structure-preserving if its public inputs and outputs consist of elements from the bilinear groups and their consistency can be verified by evaluating pairing-product equations. As structure-preserving schemes smoothly interoperate with each other, they are useful as building blocks in modular design of cryptographic applications. This paper introduces structure-preserving commitment and signature schemes over bilinear groups with several desirable properties. The commitment schemes include homomorphic, trapdoor and length-reducing commitments to group elements, and the structure-preserving signature schemes are the first ones that yield constant-size signatures on multiple group elements. A structure-preserving signature scheme is called automorphic if the public keys lie in the message space, which cannot be achieved by compressing inputs via a cryptographic hash function, as this would destroy the mathematical structure we are trying to preserve. Automorphic signatures can be used for building certification chains underlying privacy-preserving protocols. Among a vast number of applications of structure-preserving protocols, we present an efficient round-optimal blind-signature scheme and a group signature scheme with an efficient and concurrently secure protocol for enrolling new members."}],"doi":"10.1007/s00145-014-9196-7","scopus_import":1,"status":"public","_id":"1592","publication_status":"published","date_updated":"2021-01-12T06:51:49Z","acknowledgement":"The authors would like to thank the anonymous reviewers of this paper. We also would like to express our appreciation to the program committee and the anonymous reviewers for CRYPTO 2010. The first author thanks Sherman S. M. Chow for his comment on group signatures in Sect. 7.1.","oa_version":"None","department":[{"_id":"KrPi"}],"day":"01","citation":{"ista":"Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. 2016. Structure preserving signatures and commitments to group elements. Journal of Cryptology. 29(2), 363–421.","apa":"Abe, M., Fuchsbauer, G., Groth, J., Haralambiev, K., & Ohkubo, M. (2016). Structure preserving signatures and commitments to group elements. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-014-9196-7","mla":"Abe, Masayuki, et al. “Structure Preserving Signatures and Commitments to Group Elements.” Journal of Cryptology, vol. 29, no. 2, Springer, 2016, pp. 363–421, doi:10.1007/s00145-014-9196-7.","ieee":"M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, and M. Ohkubo, “Structure preserving signatures and commitments to group elements,” Journal of Cryptology, vol. 29, no. 2. Springer, pp. 363–421, 2016.","ama":"Abe M, Fuchsbauer G, Groth J, Haralambiev K, Ohkubo M. Structure preserving signatures and commitments to group elements. Journal of Cryptology. 2016;29(2):363-421. doi:10.1007/s00145-014-9196-7","short":"M. Abe, G. Fuchsbauer, J. Groth, K. Haralambiev, M. Ohkubo, Journal of Cryptology 29 (2016) 363–421.","chicago":"Abe, Masayuki, Georg Fuchsbauer, Jens Groth, Kristiyan Haralambiev, and Miyako Ohkubo. “Structure Preserving Signatures and Commitments to Group Elements.” Journal of Cryptology. Springer, 2016. https://doi.org/10.1007/s00145-014-9196-7."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Masayuki","full_name":"Abe, Masayuki","last_name":"Abe"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg","first_name":"Georg","last_name":"Fuchsbauer"},{"full_name":"Groth, Jens","first_name":"Jens","last_name":"Groth"},{"last_name":"Haralambiev","full_name":"Haralambiev, Kristiyan","first_name":"Kristiyan"},{"last_name":"Ohkubo","first_name":"Miyako","full_name":"Ohkubo, Miyako"}],"type":"journal_article","month":"04","date_published":"2016-04-01T00:00:00Z","title":"Structure preserving signatures and commitments to group elements","quality_controlled":"1","publisher":"Springer","year":"2016","publication":"Journal of Cryptology","volume":29,"language":[{"iso":"eng"}],"intvolume":" 29","date_created":"2018-12-11T11:52:54Z","page":"363 - 421"},{"day":"01","ec_funded":1,"acknowledgement":"This work was supported by the Boehringer Ingelheim Fonds, the European Research Council (ERC StG 281556), and a START Award of the Austrian Science Foundation (FWF). We thank Robert Hauschild, Anne Reversat, and Jack Merrin for valuable input and the Imaging Facility of IST Austria for excellent support.","publication_status":"published","month":"01","abstract":[{"lang":"eng","text":"Chemokines are the main guidance cues directing leukocyte migration. Opposed to early assumptions, chemokines do not necessarily act as soluble cues but are often immobilized within tissues, e.g., dendritic cell migration toward lymphatic vessels is guided by a haptotactic gradient of the chemokine CCL21. Controlled assay systems to quantitatively study haptotaxis in vitro are still missing. In this chapter, we describe an in vitro haptotaxis assay optimized for the unique properties of dendritic cells. The chemokine CCL21 is immobilized in a bioactive state, using laser-assisted protein adsorption by photobleaching. The cells follow this immobilized CCL21 gradient in a haptotaxis chamber, which provides three dimensionally confined migration conditions."}],"doi":"10.1016/bs.mie.2015.11.004","publist_id":"5573","acknowledged_ssus":[{"_id":"Bio"}],"status":"public","pmid":1,"language":[{"iso":"eng"}],"article_type":"original","page":"567 - 581","intvolume":" 570","publisher":"Elsevier","citation":{"ista":"Schwarz J, Sixt MK. 2016. Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. 570, 567–581.","mla":"Schwarz, Jan, and Michael K. Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” Methods in Enzymology, vol. 570, Elsevier, 2016, pp. 567–81, doi:10.1016/bs.mie.2015.11.004.","apa":"Schwarz, J., & Sixt, M. K. (2016). Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. Elsevier. https://doi.org/10.1016/bs.mie.2015.11.004","ama":"Schwarz J, Sixt MK. Quantitative analysis of dendritic cell haptotaxis. Methods in Enzymology. 2016;570:567-581. doi:10.1016/bs.mie.2015.11.004","short":"J. Schwarz, M.K. Sixt, Methods in Enzymology 570 (2016) 567–581.","chicago":"Schwarz, Jan, and Michael K Sixt. “Quantitative Analysis of Dendritic Cell Haptotaxis.” Methods in Enzymology. Elsevier, 2016. https://doi.org/10.1016/bs.mie.2015.11.004.","ieee":"J. Schwarz and M. K. Sixt, “Quantitative analysis of dendritic cell haptotaxis,” Methods in Enzymology, vol. 570. Elsevier, pp. 567–581, 2016."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan","last_name":"Schwarz"},{"last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"}],"oa_version":"None","date_updated":"2021-01-12T06:51:51Z","department":[{"_id":"MiSi"}],"type":"journal_article","scopus_import":1,"external_id":{"pmid":["26921962"]},"_id":"1597","publication":"Methods in Enzymology","article_processing_charge":"No","volume":570,"year":"2016","date_created":"2018-12-11T11:52:56Z","quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","grant_number":"Y 564-B12"}],"title":"Quantitative analysis of dendritic cell haptotaxis","date_published":"2016-01-01T00:00:00Z"},{"pmid":1,"status":"public","issue":"6269","acknowledged_ssus":[{"_id":"SSU"}],"doi":"10.1126/science.aad0512","publist_id":"5570","abstract":[{"lang":"eng","text":"The addition of polysialic acid to N- and/or O-linked glycans, referred to as polysialylation, is a rare posttranslational modification that is mainly known to control the developmental plasticity of the nervous system. Here we show that CCR7, the central chemokine receptor controlling immune cell trafficking to secondary lymphatic organs, carries polysialic acid. This modification is essential for the recognition of the CCR7 ligand CCL21. As a consequence, dendritic cell trafficking is abrogated in polysialyltransferase-deficient mice, manifesting as disturbed lymph node homeostasis and unresponsiveness to inflammatory stimuli. Structure-function analysis of chemokine-receptor interactions reveals that CCL21 adopts an autoinhibited conformation, which is released upon interaction with polysialic acid. Thus, we describe a glycosylation-mediated immune cell trafficking disorder and its mechanistic basis.\r\n"}],"month":"01","publication_status":"published","acknowledgement":"We thank S. Schüchner and E. Ogris for kindly providing the antibody to GFP, M. Helmbrecht and A. Huber for providing Nrp2−/− mice, the IST Scientific Support Facilities for excellent services, and J. Renkawitz and K. Vaahtomeri for critically reading the manuscript. ","day":"08","ec_funded":1,"publisher":"American Association for the Advancement of Science","intvolume":" 351","article_type":"original","page":"186 - 190","language":[{"iso":"eng"}],"_id":"1599","external_id":{"pmid":["26657283"]},"scopus_import":1,"type":"journal_article","oa_version":"Submitted Version","date_updated":"2021-01-12T06:51:52Z","department":[{"_id":"MiSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kiermaier, Eva, Christine Moussion, Christopher Veldkamp, Rita Gerardy Schahn, Ingrid de Vries, Larry Williams, Gary Chaffee, et al. “Polysialylation Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aad0512.","short":"E. Kiermaier, C. Moussion, C. Veldkamp, R. Gerardy Schahn, I. de Vries, L. Williams, G. Chaffee, A. Phillips, F. Freiberger, R. Imre, D. Taleski, R. Payne, A. Braun, R. Förster, K. Mechtler, M. Mühlenhoff, B. Volkman, M.K. Sixt, Science 351 (2016) 186–190.","ama":"Kiermaier E, Moussion C, Veldkamp C, et al. Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. 2016;351(6269):186-190. doi:10.1126/science.aad0512","ieee":"E. Kiermaier et al., “Polysialylation controls dendritic cell trafficking by regulating chemokine recognition,” Science, vol. 351, no. 6269. American Association for the Advancement of Science, pp. 186–190, 2016.","apa":"Kiermaier, E., Moussion, C., Veldkamp, C., Gerardy Schahn, R., de Vries, I., Williams, L., … Sixt, M. K. (2016). Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aad0512","mla":"Kiermaier, Eva, et al. “Polysialylation Controls Dendritic Cell Trafficking by Regulating Chemokine Recognition.” Science, vol. 351, no. 6269, American Association for the Advancement of Science, 2016, pp. 186–90, doi:10.1126/science.aad0512.","ista":"Kiermaier E, Moussion C, Veldkamp C, Gerardy Schahn R, de Vries I, Williams L, Chaffee G, Phillips A, Freiberger F, Imre R, Taleski D, Payne R, Braun A, Förster R, Mechtler K, Mühlenhoff M, Volkman B, Sixt MK. 2016. Polysialylation controls dendritic cell trafficking by regulating chemokine recognition. Science. 351(6269), 186–190."},"oa":1,"author":[{"orcid":"0000-0001-6165-5738","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","full_name":"Kiermaier, Eva","first_name":"Eva","last_name":"Kiermaier"},{"last_name":"Moussion","first_name":"Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87","full_name":"Moussion, Christine"},{"full_name":"Veldkamp, Christopher","first_name":"Christopher","last_name":"Veldkamp"},{"last_name":"Gerardy Schahn","full_name":"Gerardy Schahn, Rita","first_name":"Rita"},{"last_name":"De Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","full_name":"De Vries, Ingrid"},{"first_name":"Larry","full_name":"Williams, Larry","last_name":"Williams"},{"full_name":"Chaffee, Gary","first_name":"Gary","last_name":"Chaffee"},{"first_name":"Andrew","full_name":"Phillips, Andrew","last_name":"Phillips"},{"last_name":"Freiberger","full_name":"Freiberger, Friedrich","first_name":"Friedrich"},{"full_name":"Imre, Richard","first_name":"Richard","last_name":"Imre"},{"last_name":"Taleski","first_name":"Deni","full_name":"Taleski, Deni"},{"last_name":"Payne","first_name":"Richard","full_name":"Payne, Richard"},{"first_name":"Asolina","full_name":"Braun, Asolina","last_name":"Braun"},{"full_name":"Förster, Reinhold","first_name":"Reinhold","last_name":"Förster"},{"first_name":"Karl","full_name":"Mechtler, Karl","last_name":"Mechtler"},{"first_name":"Martina","full_name":"Mühlenhoff, Martina","last_name":"Mühlenhoff"},{"full_name":"Volkman, Brian","first_name":"Brian","last_name":"Volkman"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"}],"project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"grant_number":"289720","name":"Stromal Cell-immune Cell Interactions in Health and Disease","_id":"25A76F58-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"Y 564-B12","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425"}],"date_published":"2016-01-08T00:00:00Z","title":"Polysialylation controls dendritic cell trafficking by regulating chemokine recognition","quality_controlled":"1","date_created":"2018-12-11T11:52:57Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583642/","open_access":"1"}],"year":"2016","publication":"Science","volume":351,"article_processing_charge":"No"},{"day":"01","ec_funded":1,"publication_status":"published","month":"07","abstract":[{"lang":"eng","text":"We show that the Anderson model has a transition from localization to delocalization at exactly 2 dimensional growth rate on antitrees with normalized edge weights which are certain discrete graphs. The kinetic part has a one-dimensional structure allowing a description through transfer matrices which involve some Schur complement. For such operators we introduce the notion of having one propagating channel and extend theorems from the theory of one-dimensional Jacobi operators that relate the behavior of transfer matrices with the spectrum. These theorems are then applied to the considered model. In essence, in a certain energy region the kinetic part averages the random potentials along shells and the transfer matrices behave similar as for a one-dimensional operator with random potential of decaying variance. At d dimensional growth for d>2 this effective decay is strong enough to obtain absolutely continuous spectrum, whereas for some uniform d dimensional growth with d<2 one has pure point spectrum in this energy region. At exactly uniform 2 dimensional growth also some singular continuous spectrum appears, at least at small disorder. As a corollary we also obtain a change from singular spectrum (d≤2) to absolutely continuous spectrum (d≥3) for random operators of the type rΔdr+λ on ℤd, where r is an orthogonal radial projection, Δd the discrete adjacency operator (Laplacian) on ℤd and λ a random potential. "}],"publist_id":"5558","doi":"10.1007/s00023-015-0456-3","issue":"7","status":"public","language":[{"iso":"eng"}],"page":"1631 - 1675","intvolume":" 17","publisher":"Birkhäuser","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"C. Sadel, “Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel,” Annales Henri Poincare, vol. 17, no. 7. Birkhäuser, pp. 1631–1675, 2016.","chicago":"Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales Henri Poincare. Birkhäuser, 2016. https://doi.org/10.1007/s00023-015-0456-3.","ama":"Sadel C. Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. 2016;17(7):1631-1675. doi:10.1007/s00023-015-0456-3","short":"C. Sadel, Annales Henri Poincare 17 (2016) 1631–1675.","mla":"Sadel, Christian. “Anderson Transition at 2 Dimensional Growth Rate on Antitrees and Spectral Theory for Operators with One Propagating Channel.” Annales Henri Poincare, vol. 17, no. 7, Birkhäuser, 2016, pp. 1631–75, doi:10.1007/s00023-015-0456-3.","apa":"Sadel, C. (2016). Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-015-0456-3","ista":"Sadel C. 2016. Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel. Annales Henri Poincare. 17(7), 1631–1675."},"oa":1,"author":[{"orcid":"0000-0001-8255-3968","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","full_name":"Sadel, Christian","first_name":"Christian","last_name":"Sadel"}],"date_updated":"2021-01-12T06:51:58Z","oa_version":"Preprint","department":[{"_id":"LaEr"}],"type":"journal_article","scopus_import":1,"_id":"1608","publication":"Annales Henri Poincare","volume":17,"main_file_link":[{"url":"http://arxiv.org/abs/1501.04287","open_access":"1"}],"year":"2016","date_created":"2018-12-11T11:53:00Z","quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_published":"2016-07-01T00:00:00Z","title":"Anderson transition at 2 dimensional growth rate on antitrees and spectral theory for operators with one propagating channel"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"apa":"Kazda, A. (2016). CSP for binary conservative relational structures. Algebra Universalis. Springer. https://doi.org/10.1007/s00012-015-0358-8","mla":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra Universalis, vol. 75, no. 1, Springer, 2016, pp. 75–84, doi:10.1007/s00012-015-0358-8.","ista":"Kazda A. 2016. CSP for binary conservative relational structures. Algebra Universalis. 75(1), 75–84.","ieee":"A. Kazda, “CSP for binary conservative relational structures,” Algebra Universalis, vol. 75, no. 1. Springer, pp. 75–84, 2016.","chicago":"Kazda, Alexandr. “CSP for Binary Conservative Relational Structures.” Algebra Universalis. Springer, 2016. https://doi.org/10.1007/s00012-015-0358-8.","ama":"Kazda A. CSP for binary conservative relational structures. Algebra Universalis. 2016;75(1):75-84. doi:10.1007/s00012-015-0358-8","short":"A. Kazda, Algebra Universalis 75 (2016) 75–84."},"oa":1,"author":[{"last_name":"Kazda","first_name":"Alexandr","full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa_version":"Preprint","date_updated":"2021-01-12T06:52:00Z","department":[{"_id":"VlKo"}],"type":"journal_article","month":"02","abstract":[{"lang":"eng","text":"We prove that whenever A is a 3-conservative relational structure with only binary and unary relations,then the algebra of polymorphisms of A either has no Taylor operation (i.e.,CSP(A)is NP-complete),or it generates an SD(∧) variety (i.e.,CSP(A)has bounded width)."}],"doi":"10.1007/s00012-015-0358-8","publist_id":"5554","scopus_import":1,"issue":"1","status":"public","_id":"1612","publication":"Algebra Universalis","volume":75,"language":[{"iso":"eng"}],"year":"2016","main_file_link":[{"url":"http://arxiv.org/abs/1112.1099","open_access":"1"}],"page":"75 - 84","intvolume":" 75","date_created":"2018-12-11T11:53:01Z","quality_controlled":"1","date_published":"2016-02-01T00:00:00Z","title":"CSP for binary conservative relational structures","publisher":"Springer"},{"title":"Modeling Alzheimer's disease with human induced pluripotent stem (iPS) cells","date_published":"2016-06-01T00:00:00Z","quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"year":"2016","volume":73,"publication":"Molecular and Cellular Neuroscience","date_created":"2018-12-11T11:53:02Z","ddc":["616"],"file_date_updated":"2020-07-14T12:45:07Z","_id":"1613","file":[{"date_created":"2018-12-12T10:12:50Z","file_id":"4970","access_level":"open_access","file_size":632915,"date_updated":"2020-07-14T12:45:07Z","content_type":"application/pdf","file_name":"IST-2018-979-v1+1_Mungenast_2015_acceptedManuscript.pdf","creator":"system","relation":"main_file","checksum":"620254114e04d5d6e7f37d15e4b8ace4"}],"date_updated":"2021-01-12T06:52:00Z","oa_version":"Submitted Version","oa":1,"author":[{"last_name":"Mungenast","first_name":"Alison","full_name":"Mungenast, Alison"},{"last_name":"Siegert","first_name":"Sandra","full_name":"Siegert, Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877"},{"first_name":"Li","full_name":"Tsai, Li","last_name":"Tsai"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","citation":{"mla":"Mungenast, Alison, et al. “Modeling Alzheimer’s Disease with Human Induced Pluripotent Stem (IPS) Cells.” Molecular and Cellular Neuroscience, vol. 73, Academic Press, 2016, pp. 13–31, doi:doi:10.1016/j.mcn.2015.11.010.","apa":"Mungenast, A., Siegert, S., & Tsai, L. (2016). Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells. Molecular and Cellular Neuroscience. Academic Press. https://doi.org/doi:10.1016/j.mcn.2015.11.010","ista":"Mungenast A, Siegert S, Tsai L. 2016. Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells. Molecular and Cellular Neuroscience. 73, 13–31.","chicago":"Mungenast, Alison, Sandra Siegert, and Li Tsai. “Modeling Alzheimer’s Disease with Human Induced Pluripotent Stem (IPS) Cells.” Molecular and Cellular Neuroscience. Academic Press, 2016. https://doi.org/doi:10.1016/j.mcn.2015.11.010.","short":"A. Mungenast, S. Siegert, L. Tsai, Molecular and Cellular Neuroscience 73 (2016) 13–31.","ama":"Mungenast A, Siegert S, Tsai L. Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells. Molecular and Cellular Neuroscience. 2016;73:13-31. doi:doi:10.1016/j.mcn.2015.11.010","ieee":"A. Mungenast, S. Siegert, and L. Tsai, “Modeling Alzheimer’s disease with human induced pluripotent stem (iPS) cells,” Molecular and Cellular Neuroscience, vol. 73. Academic Press, pp. 13–31, 2016."},"pubrep_id":"979","type":"journal_article","publisher":"Academic Press","language":[{"iso":"eng"}],"intvolume":" 73","page":"13 - 31","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","doi":"doi:10.1016/j.mcn.2015.11.010","abstract":[{"lang":"eng","text":"In the last decade, induced pluripotent stem (iPS) cells have revolutionized the utility of human in vitro models of neurological disease. The iPS-derived and differentiated cells allow researchers to study the impact of a distinct cell type in health and disease as well as performing therapeutic drug screens on a human genetic background. In particular, clinical trials for Alzheimer's disease (AD) have been often failing. Two of the potential reasons are first, the species gap involved in proceeding from initial discoveries in rodent models to human studies, and second, an unsatisfying patient stratification, meaning subgrouping patients based on the disease severity due to the lack of phenotypic and genetic markers. iPS cells overcome this obstacles and will improve our understanding of disease subtypes in AD. They allow researchers conducting in depth characterization of neural cells from both familial and sporadic AD patients as well as preclinical screens on human cells.\r\n\r\nIn this review, we briefly outline the status quo of iPS cell research in neurological diseases along with the general advantages and pitfalls of these models. We summarize how genome-editing techniques such as CRISPR/Cas will allow researchers to reduce the problem of genomic variability inherent to human studies, followed by recent iPS cell studies relevant to AD. We then focus on current techniques for the differentiation of iPS cells into neural cell types that are relevant to AD research. Finally, we discuss how the generation of three-dimensional cell culture systems will be important for understanding AD phenotypes in a complex cellular milieu, and how both two- and three-dimensional iPS cell models can provide platforms for drug discovery and translational studies into the treatment of AD."}],"publist_id":"5553","status":"public","acknowledgement":"This work was supported by NIH grant R01-AG047661 to LHT. The art in Fig. 1 was created by Julian Wong.","publication_status":"published","extern":"1","day":"01","month":"06"},{"publisher":"eLife Sciences Publications","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"quality_controlled":0,"title":"Reconstruction of genetically identified neurons imaged by serial-section electron microscopy","date_published":"2016-07-07T00:00:00Z","intvolume":" 5","date_created":"2018-12-11T11:51:16Z","publication":"eLife","volume":5,"year":"2016","status":"public","_id":"1306","publist_id":"5965","doi":"10.7554/eLife.15015","abstract":[{"text":"Resolving patterns of synaptic connectivity in neural circuits currently requires serial section electron microscopy. However, complete circuit reconstruction is prohibitively slow and may not be necessary for many purposes such as comparing neuronal structure and connectivity among multiple animals. Here, we present an alternative strategy, targeted reconstruction of specific neuronal types. We used viral vectors to deliver peroxidase derivatives, which catalyze production of an electron-dense tracer, to genetically identify neurons, and developed a protocol that enhances the electron-density of the labeled cells while retaining the quality of the ultrastructure. The high contrast of the marked neurons enabled two innovations that speed data acquisition: targeted high-resolution reimaging of regions selected from rapidly-acquired lower resolution reconstruction, and an unsupervised segmentation algorithm. This pipeline reduces imaging and reconstruction times by two orders of magnitude, facilitating directed inquiry of circuit motifs.","lang":"eng"}],"issue":"2016JULY","type":"journal_article","month":"07","day":"07","citation":{"chicago":"Jösch, Maximilian A, David Mankus, Masahito Yamagata, Ali Shahbazi, Richard Schalek, Adi Suissa Peleg, Markus Meister, Jeff Lichtman, Walter Scheirer, and Joshua Sanes. “Reconstruction of Genetically Identified Neurons Imaged by Serial-Section Electron Microscopy.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.15015.","short":"M.A. Jösch, D. Mankus, M. Yamagata, A. Shahbazi, R. Schalek, A. Suissa Peleg, M. Meister, J. Lichtman, W. Scheirer, J. Sanes, ELife 5 (2016).","ama":"Jösch MA, Mankus D, Yamagata M, et al. Reconstruction of genetically identified neurons imaged by serial-section electron microscopy. eLife. 2016;5(2016JULY). doi:10.7554/eLife.15015","ieee":"M. A. Jösch et al., “Reconstruction of genetically identified neurons imaged by serial-section electron microscopy,” eLife, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.","apa":"Jösch, M. A., Mankus, D., Yamagata, M., Shahbazi, A., Schalek, R., Suissa Peleg, A., … Sanes, J. (2016). Reconstruction of genetically identified neurons imaged by serial-section electron microscopy. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.15015","mla":"Jösch, Maximilian A., et al. “Reconstruction of Genetically Identified Neurons Imaged by Serial-Section Electron Microscopy.” ELife, vol. 5, no. 2016JULY, eLife Sciences Publications, 2016, doi:10.7554/eLife.15015.","ista":"Jösch MA, Mankus D, Yamagata M, Shahbazi A, Schalek R, Suissa Peleg A, Meister M, Lichtman J, Scheirer W, Sanes J. 2016. Reconstruction of genetically identified neurons imaged by serial-section electron microscopy. eLife. 5(2016JULY)."},"extern":1,"author":[{"orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Maximilian Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch"},{"last_name":"Mankus","first_name":"David","full_name":"Mankus, David"},{"last_name":"Yamagata","full_name":"Yamagata, Masahito","first_name":"Masahito"},{"first_name":"Ali","full_name":"Shahbazi, Ali","last_name":"Shahbazi"},{"full_name":"Schalek, Richard L","first_name":"Richard","last_name":"Schalek"},{"last_name":"Suissa Peleg","full_name":"Suissa-Peleg, Adi","first_name":"Adi"},{"last_name":"Meister","full_name":"Meister, Markus","first_name":"Markus"},{"first_name":"Jeff","full_name":"Lichtman, Jeff W","last_name":"Lichtman"},{"first_name":"Walter","full_name":"Scheirer, Walter J","last_name":"Scheirer"},{"last_name":"Sanes","full_name":"Sanes, Joshua R","first_name":"Joshua"}],"date_updated":"2021-01-12T06:49:46Z","acknowledgement":"This work was supported by NIH grant NS76467 to MM, JL and JRS, an HHMI Collaborative Innovation Award to JRS, an IARPA contract #D16PC00002 to WJS and by The International Human Frontier Science Program Organization fellowship to MJ.","publication_status":"published"},{"volume":54,"publication":"SIAM Journal on Numerical Analysis","year":"2016","page":"2359 - 2378","date_created":"2018-12-11T11:51:19Z","intvolume":" 54","quality_controlled":0,"title":"Analysis of a modified second-order mixed hybrid BDM1 finite element method for transport problems in divergence form","date_published":"2016-01-01T00:00:00Z","publisher":"Society for Industrial and Applied Mathematics ","extern":1,"author":[{"last_name":"Brunner","first_name":"Fabian","full_name":"Brunner, Fabian"},{"last_name":"Fischer","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Julian Fischer","first_name":"Julian L"},{"last_name":"Knabner","full_name":"Knabner, Peter","first_name":"Peter"}],"citation":{"ista":"Brunner F, Fischer JL, Knabner P. 2016. Analysis of a modified second-order mixed hybrid BDM1 finite element method for transport problems in divergence form. SIAM Journal on Numerical Analysis. 54(4), 2359–2378.","apa":"Brunner, F., Fischer, J. L., & Knabner, P. (2016). Analysis of a modified second-order mixed hybrid BDM1 finite element method for transport problems in divergence form. SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/15M1035379","mla":"Brunner, Fabian, et al. “Analysis of a Modified Second-Order Mixed Hybrid BDM1 Finite Element Method for Transport Problems in Divergence Form.” SIAM Journal on Numerical Analysis, vol. 54, no. 4, Society for Industrial and Applied Mathematics , 2016, pp. 2359–78, doi:10.1137/15M1035379.","ama":"Brunner F, Fischer JL, Knabner P. Analysis of a modified second-order mixed hybrid BDM1 finite element method for transport problems in divergence form. SIAM Journal on Numerical Analysis. 2016;54(4):2359-2378. doi:10.1137/15M1035379","short":"F. Brunner, J.L. Fischer, P. Knabner, SIAM Journal on Numerical Analysis 54 (2016) 2359–2378.","chicago":"Brunner, Fabian, Julian L Fischer, and Peter Knabner. “Analysis of a Modified Second-Order Mixed Hybrid BDM1 Finite Element Method for Transport Problems in Divergence Form.” SIAM Journal on Numerical Analysis. Society for Industrial and Applied Mathematics , 2016. https://doi.org/10.1137/15M1035379.","ieee":"F. Brunner, J. L. Fischer, and P. Knabner, “Analysis of a modified second-order mixed hybrid BDM1 finite element method for transport problems in divergence form,” SIAM Journal on Numerical Analysis, vol. 54, no. 4. Society for Industrial and Applied Mathematics , pp. 2359–2378, 2016."},"day":"01","publication_status":"published","date_updated":"2021-01-12T06:49:49Z","month":"01","type":"journal_article","doi":"10.1137/15M1035379","publist_id":"5954","abstract":[{"text":"We prove optimal second order convergence of a modified lowest-order Brezzi-Douglas-Marini (BDM1) mixed finite element scheme for advection-diffusion problems in divergence form. If advection is present, it is known that the total flux is approximated only with first-order accuracy by the classical BDM1 mixed method, which is suboptimal since the same order of convergence is obtained if the computationally less expensive Raviart-Thomas (RT0) element is used. The modification that was first proposed by Brunner et al. [Adv. Water Res., 35 (2012),pp. 163-171] is based on the hybrid problem formulation and consists in using the Lagrange multipliers for the discretization of the advective term instead of the cellwise constant approximation of the scalar unknown.","lang":"eng"}],"issue":"4","_id":"1315","status":"public"},{"extern":1,"author":[{"orcid":"0000-0002-0479-558X","full_name":"Julian Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer"}],"citation":{"ista":"Fischer JL. 2016. Behaviour of free boundaries in thin-film flow: The regime of strong slippage and the regime of very weak slippage. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 33(5), 1301–1327.","apa":"Fischer, J. L. (2016). Behaviour of free boundaries in thin-film flow: The regime of strong slippage and the regime of very weak slippage. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2015.05.001","mla":"Fischer, Julian L. “Behaviour of Free Boundaries in Thin-Film Flow: The Regime of Strong Slippage and the Regime of Very Weak Slippage.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 33, no. 5, Elsevier, 2016, pp. 1301–27, doi:10.1016/j.anihpc.2015.05.001.","ama":"Fischer JL. Behaviour of free boundaries in thin-film flow: The regime of strong slippage and the regime of very weak slippage. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2016;33(5):1301-1327. doi:10.1016/j.anihpc.2015.05.001","short":"J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 33 (2016) 1301–1327.","chicago":"Fischer, Julian L. “Behaviour of Free Boundaries in Thin-Film Flow: The Regime of Strong Slippage and the Regime of Very Weak Slippage.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2016. https://doi.org/10.1016/j.anihpc.2015.05.001.","ieee":"J. L. Fischer, “Behaviour of free boundaries in thin-film flow: The regime of strong slippage and the regime of very weak slippage,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 33, no. 5. Elsevier, pp. 1301–1327, 2016."},"day":"01","acknowledgement":"This research was partly supported by the Lithuanian–Swiss cooperation program under the project agreement No. CH-SMM-01/0.","date_updated":"2021-01-12T06:49:50Z","publication_status":"published","month":"09","type":"journal_article","abstract":[{"text":"We analyze the behaviour of free boundaries in thin-film flow in the regime of strong slippage n∈[1,2) and in the regime of very weak slippage n∈,3) qualitatively and quantitatively. In the regime of strong slippage, we construct initial data which are bounded from above by the steady state but for which nevertheless instantaneous forward motion of the free boundary occurs. This shows that the initial behaviour of the free boundary is not determined just by the growth of the initial data at the free boundary. Note that this is a new phenomenon for degenerate parabolic equations which is specific for higher-order equations. Furthermore, this result resolves a controversy in the literature over optimality of sufficient conditions for the occurrence of a waiting time phenomenon. In contrast, in the regime of very weak slippage we derive lower bounds on free boundary propagation which are optimal in the sense that they coincide up to a constant factor with the known upper bounds. In particular, in this regime the growth of the initial data at the free boundary fully determines the initial behaviour of the interface.","lang":"eng"}],"publist_id":"5952","doi":"10.1016/j.anihpc.2015.05.001","issue":"5","_id":"1317","status":"public","volume":33,"publication":"Annales de l'Institut Henri Poincare (C) Non Linear Analysis","year":"2016","page":"1301 - 1327","date_created":"2018-12-11T11:51:20Z","intvolume":" 33","quality_controlled":0,"date_published":"2016-09-01T00:00:00Z","title":"Behaviour of free boundaries in thin-film flow: The regime of strong slippage and the regime of very weak slippage","publisher":"Elsevier"},{"_id":"1318","status":"public","issue":"7","doi":"10.1080/03605302.2016.1179318","publist_id":"5953","abstract":[{"lang":"eng","text":"We develop a large-scale regularity theory of higher order for divergence-form elliptic equations with heterogeneous coefficient fields a in the context of stochastic homogenization. The large-scale regularity of a-harmonic functions is encoded by Liouville principles: The space of a-harmonic functions that grow at most like a polynomial of degree k has the same dimension as in the constant-coefficient case. This result can be seen as the qualitative side of a large-scale Ck,α-regularity theory, which in the present work is developed in the form of a corresponding Ck,α-“excess decay” estimate: For a given a-harmonic function u on a ball BR, its energy distance on some ball Br to the above space of a-harmonic functions that grow at most like a polynomial of degree k has the natural decay in the radius r above some minimal radius r0. Though motivated by stochastic homogenization, the contribution of this paper is of purely deterministic nature: We work under the assumption that for the given realization a of the coefficient field, the couple (φ, σ) of scalar and vector potentials of the harmonic coordinates, where φ is the usual corrector, grows sublinearly in a mildly quantified way. We then construct “kth-order correctors” and thereby the space of a-harmonic functions that grow at most like a polynomial of degree k, establish the above excess decay, and then the corresponding Liouville principle."}],"month":"07","type":"journal_article","publication_status":"published","date_updated":"2021-01-12T06:49:50Z","extern":1,"author":[{"last_name":"Fischer","orcid":"0000-0002-0479-558X","first_name":"Julian L","full_name":"Julian Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Otto, Felix","first_name":"Felix","last_name":"Otto"}],"oa":1,"citation":{"ista":"Fischer JL, Otto F. 2016. A higher-order large scale regularity theory for random elliptic operators. Communications in Partial Differential Equations. 41(7), 1108–1148.","apa":"Fischer, J. L., & Otto, F. (2016). A higher-order large scale regularity theory for random elliptic operators. Communications in Partial Differential Equations. Taylor & Francis. https://doi.org/10.1080/03605302.2016.1179318","mla":"Fischer, Julian L., and Felix Otto. “A Higher-Order Large Scale Regularity Theory for Random Elliptic Operators.” Communications in Partial Differential Equations, vol. 41, no. 7, Taylor & Francis, 2016, pp. 1108–48, doi:10.1080/03605302.2016.1179318.","short":"J.L. Fischer, F. Otto, Communications in Partial Differential Equations 41 (2016) 1108–1148.","ama":"Fischer JL, Otto F. A higher-order large scale regularity theory for random elliptic operators. Communications in Partial Differential Equations. 2016;41(7):1108-1148. doi:10.1080/03605302.2016.1179318","chicago":"Fischer, Julian L, and Felix Otto. “A Higher-Order Large Scale Regularity Theory for Random Elliptic Operators.” Communications in Partial Differential Equations. Taylor & Francis, 2016. https://doi.org/10.1080/03605302.2016.1179318.","ieee":"J. L. Fischer and F. Otto, “A higher-order large scale regularity theory for random elliptic operators,” Communications in Partial Differential Equations, vol. 41, no. 7. Taylor & Francis, pp. 1108–1148, 2016."},"day":"02","publisher":"Taylor & Francis","title":"A higher-order large scale regularity theory for random elliptic operators","date_published":"2016-07-02T00:00:00Z","quality_controlled":0,"date_created":"2018-12-11T11:51:20Z","intvolume":" 41","page":"1108 - 1148","year":"2016","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1503.07578"}],"volume":41,"publication":"Communications in Partial Differential Equations"},{"conference":{"location":"San Jose, California, USA","start_date":"2016-05-07","end_date":"2016-05-12","name":"CHI: Conference on Human Factors in Computing Systems"},"publisher":"ACM","date_published":"2016-05-07T00:00:00Z","title":"DefSense: computational design of customized deformable input devices","quality_controlled":"1","date_created":"2018-12-11T11:51:21Z","page":"3806 - 3816","year":"2016","language":[{"iso":"eng"}],"status":"public","_id":"1319","doi":"10.1145/2858036.2858354","abstract":[{"lang":"eng","text":"We present a novel optimization-based algorithm for the design and fabrication of customized, deformable input devices, capable of continuously sensing their deformation. We propose to embed piezoresistive sensing elements into flexible 3D printed objects. These sensing elements are then utilized to recover rich and natural user interactions at runtime. Designing such objects is a challenging and hard problem if attempted manually for all but the simplest geometries and deformations. Our method simultaneously optimizes the internal routing of the sensing elements and computes a mapping from low-level sensor readings to user-specified outputs in order to minimize reconstruction error. We demonstrate the power and flexibility of the approach by designing and fabricating a set of flexible input devices. Our results indicate that the optimization-based design greatly outperforms manual routings in terms of reconstruction accuracy and thus interaction fidelity."}],"publist_id":"5951","scopus_import":1,"type":"conference","month":"05","publication_status":"published","acknowledgement":"We thank Damian Karrer, Rocco Ghielmini and Jemin\r\nHwangbo for their help in our initial explorations. We would\r\nlike to thank Christian Schumacher for creating the video and\r\nC\r\n ́\r\necile Edwards-Rietmann for providing the voiceover. Mau-\r\nrizio Nitti helped us in designing our 3D characters. We thank\r\nChiara Daraio for insightful discussions on material proper-\r\nties and 3D printing. We also thank the CHI reviewers for\r\ntheir feedback and guidance. Fabrizio Pece was supported by\r\nan ETH/Marie Curie fellowship (FEL-3314-1).","oa_version":"None","date_updated":"2021-01-12T06:49:51Z","department":[{"_id":"BeBi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"07","citation":{"ieee":"M. Bächer et al., “DefSense: computational design of customized deformable input devices,” presented at the CHI: Conference on Human Factors in Computing Systems, San Jose, California, USA, 2016, pp. 3806–3816.","chicago":"Bächer, Moritz, Benjamin Hepp, Fabrizio Pece, Paul Kry, Bernd Bickel, Bernhard Thomaszewski, and Otmar Hilliges. “DefSense: Computational Design of Customized Deformable Input Devices,” 3806–16. ACM, 2016. https://doi.org/10.1145/2858036.2858354.","short":"M. Bächer, B. Hepp, F. Pece, P. Kry, B. Bickel, B. Thomaszewski, O. Hilliges, in:, ACM, 2016, pp. 3806–3816.","ama":"Bächer M, Hepp B, Pece F, et al. DefSense: computational design of customized deformable input devices. In: ACM; 2016:3806-3816. doi:10.1145/2858036.2858354","apa":"Bächer, M., Hepp, B., Pece, F., Kry, P., Bickel, B., Thomaszewski, B., & Hilliges, O. (2016). DefSense: computational design of customized deformable input devices (pp. 3806–3816). Presented at the CHI: Conference on Human Factors in Computing Systems, San Jose, California, USA: ACM. https://doi.org/10.1145/2858036.2858354","mla":"Bächer, Moritz, et al. DefSense: Computational Design of Customized Deformable Input Devices. ACM, 2016, pp. 3806–16, doi:10.1145/2858036.2858354.","ista":"Bächer M, Hepp B, Pece F, Kry P, Bickel B, Thomaszewski B, Hilliges O. 2016. DefSense: computational design of customized deformable input devices. CHI: Conference on Human Factors in Computing Systems, 3806–3816."},"author":[{"full_name":"Bächer, Moritz","first_name":"Moritz","last_name":"Bächer"},{"full_name":"Hepp, Benjamin","first_name":"Benjamin","last_name":"Hepp"},{"last_name":"Pece","first_name":"Fabrizio","full_name":"Pece, Fabrizio"},{"full_name":"Kry, Paul","first_name":"Paul","last_name":"Kry"},{"last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"last_name":"Thomaszewski","full_name":"Thomaszewski, Bernhard","first_name":"Bernhard"},{"last_name":"Hilliges","first_name":"Otmar","full_name":"Hilliges, Otmar"}]},{"month":"07","publication_status":"published","acknowledgement":"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 n° [291734]. Work supported in part by grants AFOSR FA9550-14-1-0060 and NIH 1R01GM100473.","day":"28","ec_funded":1,"status":"public","publist_id":"5950","doi":"10.1109/ACC.2016.7526722","abstract":[{"lang":"eng","text":"In recent years, several biomolecular systems have been shown to be scale-invariant (SI), i.e. to show the same output dynamics when exposed to geometrically scaled input signals (u → pu, p > 0) after pre-adaptation to accordingly scaled constant inputs. In this article, we show that SI systems-as well as systems invariant with respect to other input transformations-can realize nonlinear differential operators: when excited by inputs obeying functional forms characteristic for a given class of invariant systems, the systems' outputs converge to constant values directly quantifying the speed of the input."}],"article_number":"7526722","language":[{"iso":"eng"}],"publisher":"IEEE","pubrep_id":"810","type":"conference","date_updated":"2021-01-12T06:49:51Z","oa_version":"Preprint","file":[{"file_size":539166,"date_updated":"2020-07-14T12:44:43Z","content_type":"application/pdf","file_name":"IST-2017-810-v1+1_root.pdf","date_created":"2018-12-12T10:16:17Z","file_id":"5203","access_level":"local","creator":"system","relation":"main_file","checksum":"7219432b43defc62a0d45f48d4ce6a19"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"citation":{"apa":"Lang, M., & Sontag, E. (2016). Scale-invariant systems realize nonlinear differential operators (Vol. 2016–July). Presented at the ACC: American Control Conference, Boston, MA, USA: IEEE. https://doi.org/10.1109/ACC.2016.7526722","mla":"Lang, Moritz, and Eduardo Sontag. Scale-Invariant Systems Realize Nonlinear Differential Operators. Vol. 2016–July, 7526722, IEEE, 2016, doi:10.1109/ACC.2016.7526722.","ista":"Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722.","chicago":"Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722.","short":"M. Lang, E. Sontag, in:, IEEE, 2016.","ama":"Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722","ieee":"M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July."},"has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Moritz","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang"},{"last_name":"Sontag","full_name":"Sontag, Eduardo","first_name":"Eduardo"}],"_id":"1320","file_date_updated":"2020-07-14T12:44:43Z","scopus_import":1,"ddc":["003","621"],"date_created":"2018-12-11T11:51:21Z","year":"2016","volume":"2016-July","conference":{"end_date":"2016-07-08","location":"Boston, MA, USA","start_date":"2016-07-06","name":"ACC: American Control Conference"},"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"title":"Scale-invariant systems realize nonlinear differential operators","date_published":"2016-07-28T00:00:00Z","quality_controlled":"1"}]