[{"external_id":{"pmid":["28570059"]},"quality_controlled":"1","doi":"10.1021/acs.chemrev.7b00183","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1520-6890"],"issn":["0009-2665"]},"month":"06","pmid":1,"year":"2017","publisher":"American Chemical Society","publication_status":"published","author":[{"full_name":"Plutschack, Matthew B.","last_name":"Plutschack","first_name":"Matthew B."},{"first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","full_name":"Pieber, Bartholomäus"},{"first_name":"Kerry","last_name":"Gilmore","full_name":"Gilmore, Kerry"},{"first_name":"Peter H.","last_name":"Seeberger","full_name":"Seeberger, Peter H."}],"volume":117,"date_updated":"2023-02-21T10:09:28Z","date_created":"2022-08-24T11:07:46Z","extern":"1","citation":{"chicago":"Plutschack, Matthew B., Bartholomäus Pieber, Kerry Gilmore, and Peter H. Seeberger. “The Hitchhiker’s Guide to Flow Chemistry.” Chemical Reviews. American Chemical Society, 2017. https://doi.org/10.1021/acs.chemrev.7b00183.","mla":"Plutschack, Matthew B., et al. “The Hitchhiker’s Guide to Flow Chemistry.” Chemical Reviews, vol. 117, no. 18, American Chemical Society, 2017, pp. 11796–893, doi:10.1021/acs.chemrev.7b00183.","short":"M.B. Plutschack, B. Pieber, K. Gilmore, P.H. Seeberger, Chemical Reviews 117 (2017) 11796–11893.","ista":"Plutschack MB, Pieber B, Gilmore K, Seeberger PH. 2017. The Hitchhiker’s Guide to flow chemistry. Chemical Reviews. 117(18), 11796–11893.","ieee":"M. B. Plutschack, B. Pieber, K. Gilmore, and P. H. Seeberger, “The Hitchhiker’s Guide to flow chemistry,” Chemical Reviews, vol. 117, no. 18. American Chemical Society, pp. 11796–11893, 2017.","apa":"Plutschack, M. B., Pieber, B., Gilmore, K., & Seeberger, P. H. (2017). The Hitchhiker’s Guide to flow chemistry. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00183","ama":"Plutschack MB, Pieber B, Gilmore K, Seeberger PH. The Hitchhiker’s Guide to flow chemistry. Chemical Reviews. 2017;117(18):11796-11893. doi:10.1021/acs.chemrev.7b00183"},"publication":"Chemical Reviews","page":"11796-11893","article_type":"original","date_published":"2017-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11961","intvolume":" 117","status":"public","title":"The Hitchhiker’s Guide to flow chemistry","oa_version":"None","type":"journal_article","issue":"18","abstract":[{"lang":"eng","text":"Flow chemistry involves the use of channels or tubing to conduct a reaction in a continuous stream rather than in a flask. Flow equipment provides chemists with unique control over reaction parameters enhancing reactivity or in some cases enabling new reactions. This relatively young technology has received a remarkable amount of attention in the past decade with many reports on what can be done in flow. Until recently, however, the question, “Should we do this in flow?” has merely been an afterthought. This review introduces readers to the basic principles and fundamentals of flow chemistry and critically discusses recent flow chemistry accounts."}]},{"author":[{"full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X"},{"first_name":"Kerry","last_name":"Gilmore","full_name":"Gilmore, Kerry"},{"full_name":"Seeberger, Peter H.","first_name":"Peter H.","last_name":"Seeberger"}],"volume":7,"date_created":"2022-08-25T10:47:51Z","date_updated":"2023-02-21T10:10:02Z","year":"2017","publisher":"AKJournals","publication_status":"published","extern":"1","doi":"10.1556/1846.2017.00016","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1556/1846.2017.00016","open_access":"1"}],"oa":1,"quality_controlled":"1","publication_identifier":{"eissn":["2063-0212"],"issn":["2062-249X"]},"month":"09","oa_version":"Published Version","_id":"11976","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 7","status":"public","title":"Integrated flow processing - challenges in continuous multistep synthesis","issue":"3-4","abstract":[{"lang":"eng","text":"The way organic multistep synthesis is performed is changing due to the adoption of flow chemical techniques, which has enabled the development of improved methods to make complex molecules. The modular nature of the technique provides not only access to target molecules via linear flow approaches but also for the targeting of structural cores with single systems. This perspective article summarizes the state of the art of continuous multistep synthesis and discusses the main challenges and opportunities in this area."}],"type":"journal_article","date_published":"2017-09-01T00:00:00Z","citation":{"ama":"Pieber B, Gilmore K, Seeberger PH. Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. 2017;7(3-4):129-136. doi:10.1556/1846.2017.00016","ista":"Pieber B, Gilmore K, Seeberger PH. 2017. Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. 7(3–4), 129–136.","ieee":"B. Pieber, K. Gilmore, and P. H. Seeberger, “Integrated flow processing - challenges in continuous multistep synthesis,” Journal of Flow Chemistry, vol. 7, no. 3–4. AKJournals, pp. 129–136, 2017.","apa":"Pieber, B., Gilmore, K., & Seeberger, P. H. (2017). Integrated flow processing - challenges in continuous multistep synthesis. Journal of Flow Chemistry. AKJournals. https://doi.org/10.1556/1846.2017.00016","mla":"Pieber, Bartholomäus, et al. “Integrated Flow Processing - Challenges in Continuous Multistep Synthesis.” Journal of Flow Chemistry, vol. 7, no. 3–4, AKJournals, 2017, pp. 129–36, doi:10.1556/1846.2017.00016.","short":"B. Pieber, K. Gilmore, P.H. Seeberger, Journal of Flow Chemistry 7 (2017) 129–136.","chicago":"Pieber, Bartholomäus, Kerry Gilmore, and Peter H. Seeberger. “Integrated Flow Processing - Challenges in Continuous Multistep Synthesis.” Journal of Flow Chemistry. AKJournals, 2017. https://doi.org/10.1556/1846.2017.00016."},"publication":"Journal of Flow Chemistry","page":"129-136","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1"},{"date_published":"2017-05-01T00:00:00Z","page":"636-655","publication":"Journal of Statistical Physics","citation":{"mla":"Budanur, Nazmi B., and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics, vol. 167, no. 3–4, Springer, 2017, pp. 636–55, doi:10.1007/s10955-016-1672-z.","short":"N.B. Budanur, P. Cvitanović, Journal of Statistical Physics 167 (2017) 636–655.","chicago":"Budanur, Nazmi B, and Predrag Cvitanović. “Unstable Manifolds of Relative Periodic Orbits in the Symmetry Reduced State Space of the Kuramoto–Sivashinsky System.” Journal of Statistical Physics. Springer, 2017. https://doi.org/10.1007/s10955-016-1672-z.","ama":"Budanur NB, Cvitanović P. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 2017;167(3-4):636-655. doi:10.1007/s10955-016-1672-z","ista":"Budanur NB, Cvitanović P. 2017. Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. 167(3–4), 636–655.","apa":"Budanur, N. B., & Cvitanović, P. (2017). Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-016-1672-z","ieee":"N. B. Budanur and P. Cvitanović, “Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system,” Journal of Statistical Physics, vol. 167, no. 3–4. Springer, pp. 636–655, 2017."},"day":"01","has_accepted_license":"1","scopus_import":1,"file":[{"access_level":"open_access","file_name":"IST-2017-782-v1+1_BudCvi15.pdf","creator":"system","file_size":2820207,"content_type":"application/pdf","file_id":"5319","relation":"main_file","checksum":"3e971d09eb167761aa0888ed415b0056","date_created":"2018-12-12T10:18:01Z","date_updated":"2020-07-14T12:44:39Z"}],"oa_version":"Submitted Version","pubrep_id":"782","title":"Unstable manifolds of relative periodic orbits in the symmetry reduced state space of the Kuramoto–Sivashinsky system","status":"public","ddc":["530"],"intvolume":" 167","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1211","abstract":[{"lang":"eng","text":"Systems such as fluid flows in channels and pipes or the complex Ginzburg–Landau system, defined over periodic domains, exhibit both continuous symmetries, translational and rotational, as well as discrete symmetries under spatial reflections or complex conjugation. The simplest, and very common symmetry of this type is the equivariance of the defining equations under the orthogonal group O(2). We formulate a novel symmetry reduction scheme for such systems by combining the method of slices with invariant polynomial methods, and show how it works by applying it to the Kuramoto–Sivashinsky system in one spatial dimension. As an example, we track a relative periodic orbit through a sequence of bifurcations to the onset of chaos. Within the symmetry-reduced state space we are able to compute and visualize the unstable manifolds of relative periodic orbits, their torus bifurcations, a transition to chaos via torus breakdown, and heteroclinic connections between various relative periodic orbits. It would be very hard to carry through such analysis in the full state space, without a symmetry reduction such as the one we present here."}],"issue":"3-4","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1007/s10955-016-1672-z","quality_controlled":"1","oa":1,"month":"05","date_updated":"2021-01-12T06:49:07Z","date_created":"2018-12-11T11:50:44Z","volume":167,"author":[{"orcid":"0000-0003-0423-5010","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","first_name":"Nazmi B","full_name":"Budanur, Nazmi B"},{"last_name":"Cvitanović","first_name":"Predrag","full_name":"Cvitanović, Predrag"}],"publication_status":"published","department":[{"_id":"BjHo"}],"publisher":"Springer","year":"2017","acknowledgement":"This work was supported by the family of late G. Robinson, Jr. and NSF Grant DMS-1211827. ","file_date_updated":"2020-07-14T12:44:39Z","publist_id":"6136"},{"citation":{"ama":"Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. 2017;13(11):1095-1099. doi:10.1038/nphys4194","ieee":"S. R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, and M. Van Hecke, “Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing,” Nature Physics, vol. 13, no. 11. Nature Publishing Group, pp. 1095–1099, 2017.","apa":"Waitukaitis, S. R., Zuiderwijk, A., Souslov, A., Coulais, C., & Van Hecke, M. (2017). Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/nphys4194","ista":"Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. 2017. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. 13(11), 1095–1099.","short":"S.R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, M. Van Hecke, Nature Physics 13 (2017) 1095–1099.","mla":"Waitukaitis, Scott R., et al. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” Nature Physics, vol. 13, no. 11, Nature Publishing Group, 2017, pp. 1095–99, doi:10.1038/nphys4194.","chicago":"Waitukaitis, Scott R, Antal Zuiderwijk, Anton Souslov, Corentin Coulais, and Martin Van Hecke. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” Nature Physics. Nature Publishing Group, 2017. https://doi.org/10.1038/nphys4194."},"publication":"Nature Physics","page":"1095 - 1099","date_published":"2017-07-24T00:00:00Z","day":"24","_id":"123","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 13","title":"Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing","status":"public","oa_version":"Preprint","type":"journal_article","issue":"11","abstract":[{"text":"The Leidenfrost effect occurs when an object near a hot surface vaporizes rapidly enough to lift itself up and hover. Although well understood for liquids and stiff sublimable solids, nothing is known about the effect with materials whose stiffness lies between these extremes. Here we introduce a new phenomenon that occurs with vaporizable soft solids - the elastic Leidenfrost effect. By dropping hydrogel spheres onto hot surfaces we find that, rather than hovering, they energetically bounce several times their diameter for minutes at a time. With high-speed video during a single impact, we uncover high-frequency microscopic gap dynamics at the sphere/substrate interface. We show how these otherwise-hidden agitations constitute work cycles that harvest mechanical energy from the vapour and sustain the bouncing. Our findings suggest a new strategy for injecting mechanical energy into a widely used class of soft materials, with potential relevance to fields such as active matter, soft robotics and microfluidics.","lang":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1705.03530","open_access":"1"}],"external_id":{"arxiv":["1705.03530"]},"quality_controlled":"1","doi":"10.1038/nphys4194","language":[{"iso":"eng"}],"month":"07","year":"2017","acknowledgement":"A.S. acknowledges funding from the Delta Institute for Theoretical Physics and the hospitality of the IBS Center for Theoretical Physics of Complex Systems, Daejeon, South Korea. We acknowledge funding from the Netherlands Organisation for Scientific Research through grants VICI No. NWO-680-47-609 (M.v.H. and S.R.W.), VENI No. NWO-680-47-445 (C.C.) and VENI No. NWO-680-47-453 (S.R.W.).","publisher":"Nature Publishing Group","publication_status":"published","author":[{"orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","first_name":"Scott R","full_name":"Waitukaitis, Scott R"},{"last_name":"Zuiderwijk","first_name":"Antal","full_name":"Zuiderwijk, Antal"},{"full_name":"Souslov, Anton","first_name":"Anton","last_name":"Souslov"},{"full_name":"Coulais, Corentin","first_name":"Corentin","last_name":"Coulais"},{"first_name":"Martin","last_name":"Van Hecke","full_name":"Van Hecke, Martin"}],"volume":13,"date_updated":"2021-01-12T06:49:14Z","date_created":"2018-12-11T11:44:45Z","publist_id":"7931","extern":"1"},{"scopus_import":"1","day":"24","article_processing_charge":"No","page":"86-98","publication":"19th International Conference on Integer Programming and Combinatorial Optimization","citation":{"chicago":"Bhattacharya, Sayan, Deeparnab Chakrabarty, and Monika H Henzinger. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” In 19th International Conference on Integer Programming and Combinatorial Optimization, 10328:86–98. Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59250-3_8.","short":"S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, in:, 19th International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2017, pp. 86–98.","mla":"Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” 19th International Conference on Integer Programming and Combinatorial Optimization, vol. 10328, Springer Nature, 2017, pp. 86–98, doi:10.1007/978-3-319-59250-3_8.","apa":"Bhattacharya, S., Chakrabarty, D., & Henzinger, M. H. (2017). Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In 19th International Conference on Integer Programming and Combinatorial Optimization (Vol. 10328, pp. 86–98). Waterloo, ON, Canada: Springer Nature. https://doi.org/10.1007/978-3-319-59250-3_8","ieee":"S. Bhattacharya, D. Chakrabarty, and M. H. Henzinger, “Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time,” in 19th International Conference on Integer Programming and Combinatorial Optimization, Waterloo, ON, Canada, 2017, vol. 10328, pp. 86–98.","ista":"Bhattacharya S, Chakrabarty D, Henzinger MH. 2017. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. 19th International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 10328, 86–98.","ama":"Bhattacharya S, Chakrabarty D, Henzinger MH. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In: 19th International Conference on Integer Programming and Combinatorial Optimization. Vol 10328. Springer Nature; 2017:86-98. doi:10.1007/978-3-319-59250-3_8"},"date_published":"2017-05-24T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"We consider the problems of maintaining approximate maximum matching and minimum vertex cover in a dynamic graph. Starting with the seminal work of Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. Very recently, extending the framework of Baswana, Gupta and Sen [FOCS 2011], Solomon [FOCS 2016] gave a randomized 2-approximation dynamic algorithm for this problem that has amortized update time of O(1) with high probability. We consider the natural open question of derandomizing this result. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya, Henzinger and Italiano [SODA 2015]; it had an approximation ratio of (2+ϵ) and an amortized update time of O(logn/ϵ2). Our result can be generalized to give a fully dynamic O(f3)-approximation algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional matching problems, where every hyperedge has at most f vertices."}],"status":"public","title":"Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time","intvolume":" 10328","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12571","oa_version":"Preprint","month":"05","publication_identifier":{"eisbn":["9783319592503"],"issn":["0302-9743","1611-3349"],"isbn":["9783319592497"]},"quality_controlled":"1","oa":1,"external_id":{"arxiv":["1611.00198"]},"main_file_link":[{"url":"https://arxiv.org/abs/1611.00198","open_access":"1"}],"language":[{"iso":"eng"}],"conference":{"start_date":"2017-06-26","location":"Waterloo, ON, Canada","end_date":"2017-06-28","name":"IPCO: Integer Programming and Combinatorial Optimization"},"doi":"10.1007/978-3-319-59250-3_8","extern":"1","publication_status":"published","publisher":"Springer Nature","year":"2017","date_created":"2023-02-20T07:52:31Z","date_updated":"2023-02-20T07:57:24Z","volume":10328,"author":[{"full_name":"Bhattacharya, Sayan","first_name":"Sayan","last_name":"Bhattacharya"},{"last_name":"Chakrabarty","first_name":"Deeparnab","full_name":"Chakrabarty, Deeparnab"},{"first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"}]},{"ec_funded":1,"publist_id":"6254","file_date_updated":"2019-10-24T10:54:37Z","year":"2017","publisher":"Brown University","department":[{"_id":"UlWa"}],"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1164"},{"status":"public","relation":"earlier_version","id":"1595"}]},"author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pelsmajer, Michael","first_name":"Michael","last_name":"Pelsmajer"},{"first_name":"Marcus","last_name":"Schaefer","full_name":"Schaefer, Marcus"}],"volume":21,"date_created":"2018-12-11T11:50:13Z","date_updated":"2023-02-23T10:05:57Z","month":"01","oa":1,"external_id":{"arxiv":["1608.08662"]},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","doi":"10.7155/jgaa.00408","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","abstract":[{"lang":"eng","text":"A drawing of a graph G is radial if the vertices of G are placed on concentric circles C 1 , . . . , C k with common center c , and edges are drawn radially : every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing-free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Toth."}],"_id":"1113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 21","ddc":["510"],"status":"public","title":"Hanani-Tutte for radial planarity","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":573623,"creator":"dernst","file_name":"2017_JournalGraphAlgorithms_Fulek.pdf","access_level":"open_access","date_created":"2019-10-24T10:54:37Z","date_updated":"2019-10-24T10:54:37Z","success":1,"relation":"main_file","file_id":"6967"}],"scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"ama":"Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 2017;21(1):135-154. doi:10.7155/jgaa.00408","ieee":"R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” Journal of Graph Algorithms and Applications, vol. 21, no. 1. Brown University, pp. 135–154, 2017.","apa":"Fulek, R., Pelsmajer, M., & Schaefer, M. (2017). Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. Brown University. https://doi.org/10.7155/jgaa.00408","ista":"Fulek R, Pelsmajer M, Schaefer M. 2017. Hanani-Tutte for radial planarity. Journal of Graph Algorithms and Applications. 21(1), 135–154.","short":"R. Fulek, M. Pelsmajer, M. Schaefer, Journal of Graph Algorithms and Applications 21 (2017) 135–154.","mla":"Fulek, Radoslav, et al. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications, vol. 21, no. 1, Brown University, 2017, pp. 135–54, doi:10.7155/jgaa.00408.","chicago":"Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity.” Journal of Graph Algorithms and Applications. Brown University, 2017. https://doi.org/10.7155/jgaa.00408."},"publication":"Journal of Graph Algorithms and Applications","page":"135 - 154","article_type":"original","date_published":"2017-01-01T00:00:00Z"},{"day":"19","month":"06","article_processing_charge":"No","publication":"International Mathematics Research Notices","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1609.06097"}],"citation":{"ista":"Browning TD, Kumaraswamy V, Steiner R. 2017. Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices.","ieee":"T. D. Browning, V. Kumaraswamy, and R. Steiner, “Twisted Linnik implies optimal covering exponent for S3,” International Mathematics Research Notices. Oxford University Press, 2017.","apa":"Browning, T. D., Kumaraswamy, V., & Steiner, R. (2017). Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx116","ama":"Browning TD, Kumaraswamy V, Steiner R. Twisted Linnik implies optimal covering exponent for S3. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx116","chicago":"Browning, Timothy D, Vinay Kumaraswamy, and Rapael Steiner. “Twisted Linnik Implies Optimal Covering Exponent for S3.” International Mathematics Research Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx116.","mla":"Browning, Timothy D., et al. “Twisted Linnik Implies Optimal Covering Exponent for S3.” International Mathematics Research Notices, Oxford University Press, 2017, doi:10.1093/imrn/rnx116.","short":"T.D. Browning, V. Kumaraswamy, R. Steiner, International Mathematics Research Notices (2017)."},"oa":1,"external_id":{"arxiv":["1609.06097"]},"quality_controlled":"1","date_published":"2017-06-19T00:00:00Z","doi":"10.1093/imrn/rnx116","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We show that a twisted variant of Linnik’s conjecture on sums of Kloosterman sums leads to an optimal covering exponent for S3."}],"publist_id":"7752","extern":"1","_id":"169","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Twisted Linnik implies optimal covering exponent for S3","status":"public","publication_status":"published","publisher":"Oxford University Press","author":[{"full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","first_name":"Timothy D"},{"full_name":"Kumaraswamy, Vinay","first_name":"Vinay","last_name":"Kumaraswamy"},{"full_name":"Steiner, Rapael","last_name":"Steiner","first_name":"Rapael"}],"date_created":"2018-12-11T11:44:59Z","date_updated":"2021-01-12T06:52:32Z","oa_version":"None"},{"year":"2017","_id":"172","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","publication_status":"published","status":"public","title":"Strong approximation and a conjecture of Harpaz and Wittenberg","author":[{"full_name":"Browning, Timothy D","last_name":"Browning","first_name":"Timothy D","orcid":"0000-0002-8314-0177","id":"35827D50-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Damaris","last_name":"Schindler","full_name":"Schindler, Damaris"}],"oa_version":"None","date_updated":"2021-01-12T06:52:45Z","date_created":"2018-12-11T11:45:00Z","type":"journal_article","publist_id":"7749","abstract":[{"lang":"eng","text":"We study strong approximation for some algebraic varieties over ℚ which are defined using norm forms. This allows us to confirm a special case of a conjecture due to Harpaz and Wittenberg."}],"extern":"1","external_id":{"arxiv":["1509.07744"]},"oa":1,"citation":{"ieee":"T. D. Browning and D. Schindler, “Strong approximation and a conjecture of Harpaz and Wittenberg,” International Mathematics Research Notices. Oxford University Press, 2017.","apa":"Browning, T. D., & Schindler, D. (2017). Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnx252","ista":"Browning TD, Schindler D. 2017. Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices.","ama":"Browning TD, Schindler D. Strong approximation and a conjecture of Harpaz and Wittenberg. International Mathematics Research Notices. 2017. doi:10.1093/imrn/rnx252","chicago":"Browning, Timothy D, and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices. Oxford University Press, 2017. https://doi.org/10.1093/imrn/rnx252.","short":"T.D. Browning, D. Schindler, International Mathematics Research Notices (2017).","mla":"Browning, Timothy D., and Damaris Schindler. “Strong Approximation and a Conjecture of Harpaz and Wittenberg.” International Mathematics Research Notices, Oxford University Press, 2017, doi:10.1093/imrn/rnx252."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.07744"}],"publication":"International Mathematics Research Notices","quality_controlled":"1","doi":"10.1093/imrn/rnx252","date_published":"2017-10-30T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"30","month":"10"},{"day":"03","month":"02","publication":"Nature Communications","citation":{"ista":"Xu Y, Chiu J, Miao L, He H, Alpichshev Z, Kapitulnik A, Biswas R, Wray L. 2017. Disorder enabled band structure engineering of a topological insulator surface. Nature Communications. 8.","ieee":"Y. Xu et al., “Disorder enabled band structure engineering of a topological insulator surface,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Xu, Y., Chiu, J., Miao, L., He, H., Alpichshev, Z., Kapitulnik, A., … Wray, L. (2017). Disorder enabled band structure engineering of a topological insulator surface. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms14081","ama":"Xu Y, Chiu J, Miao L, et al. Disorder enabled band structure engineering of a topological insulator surface. Nature Communications. 2017;8. doi:10.1038/ncomms14081","chicago":"Xu, Yishuai, Janet Chiu, Lin Miao, Haowei He, Zhanybek Alpichshev, Aharon Kapitulnik, Rudro Biswas, and Lewis Wray. “Disorder Enabled Band Structure Engineering of a Topological Insulator Surface.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms14081.","mla":"Xu, Yishuai, et al. “Disorder Enabled Band Structure Engineering of a Topological Insulator Surface.” Nature Communications, vol. 8, Nature Publishing Group, 2017, doi:10.1038/ncomms14081.","short":"Y. Xu, J. Chiu, L. Miao, H. He, Z. Alpichshev, A. Kapitulnik, R. Biswas, L. Wray, Nature Communications 8 (2017)."},"language":[{"iso":"eng"}],"doi":"10.1038/ncomms14081","date_published":"2017-02-03T00:00:00Z","type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"Three-dimensional topological insulators are bulk insulators with Z 2 topological electronic order that gives rise to conducting light-like surface states. These surface electrons are exceptionally resistant to localization by non-magnetic disorder, and have been adopted as the basis for a wide range of proposals to achieve new quasiparticle species and device functionality. Recent studies have yielded a surprise by showing that in spite of resisting localization, topological insulator surface electrons can be reshaped by defects into distinctive resonance states. Here we use numerical simulations and scanning tunnelling microscopy data to show that these resonance states have significance well beyond the localized regime usually associated with impurity bands. At native densities in the model Bi2X3 (X=Bi, Te) compounds, defect resonance states are predicted to generate a new quantum basis for an emergent electron gas that supports diffusive electrical transport. "}],"publist_id":"7438","title":"Disorder enabled band structure engineering of a topological insulator surface","status":"public","publication_status":"published","publisher":"Nature Publishing Group","intvolume":" 8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"391","year":"2017","date_created":"2018-12-11T11:46:12Z","date_updated":"2021-01-12T07:53:08Z","oa_version":"None","volume":8,"author":[{"last_name":"Xu","first_name":"Yishuai","full_name":"Xu, Yishuai"},{"first_name":"Janet","last_name":"Chiu","full_name":"Chiu, Janet"},{"full_name":"Miao, Lin","last_name":"Miao","first_name":"Lin"},{"first_name":"Haowei","last_name":"He","full_name":"He, Haowei"},{"full_name":"Alpichshev, Zhanybek","first_name":"Zhanybek","last_name":"Alpichshev","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7183-5203"},{"full_name":"Kapitulnik, Aharon","last_name":"Kapitulnik","first_name":"Aharon"},{"full_name":"Biswas, Rudro","first_name":"Rudro","last_name":"Biswas"},{"full_name":"Wray, Lewis","first_name":"Lewis","last_name":"Wray"}]},{"_id":"393","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Z.A. gratefully acknowledges discussions with P. A. Lee and A. Kemper. A conversation with J. Zaanen was instrumental in clarifying the physical picture described in this paper. We would also like to thank A. Kogar for thoroughly reading the manuscript and making valuable comments. This work was supported by Army Research Office Grant No. W911NF-15-1-0128 and Gordon and Betty Moore Foundation EPiQS Initiative through Grant No. GBMF4540 (time resolved optical spectroscopy), Skoltech, as part of the Skoltech NGP program (theory) and National Science Foundation Grant No. DMR-1265162 (material growth).\r\n\r\n","publisher":"American Physical Society","intvolume":" 96","title":"Origin of the exciton mass in the frustrated Mott insulator Na2IrO3","publication_status":"published","status":"public","author":[{"full_name":"Alpichshev, Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","first_name":"Zhanybek"},{"full_name":"Sie, Edbert","last_name":"Sie","first_name":"Edbert"},{"full_name":"Mahmood, Fahad","last_name":"Mahmood","first_name":"Fahad"},{"last_name":"Cao","first_name":"Gang","full_name":"Cao, Gang"},{"full_name":"Gedik, Nuh","last_name":"Gedik","first_name":"Nuh"}],"oa_version":"None","volume":96,"date_created":"2018-12-11T11:46:13Z","date_updated":"2021-01-12T07:53:16Z","type":"journal_article","issue":"23","publist_id":"7436","abstract":[{"lang":"eng","text":"We use a three-pulse ultrafast optical spectroscopy to study the relaxation processes in a frustrated Mott insulator Na2IrO3. By being able to independently produce the out-of-equilibrium bound states (excitons) of doublons and holons with the first pulse and suppress the underlying antiferromagnetic order with the second one, we were able to elucidate the relaxation mechanism of quasiparticles in this system. By observing the difference in the exciton dynamics in the magnetically ordered and disordered phases we found that the mass of this quasiparticle is mostly determined by its interaction with the surrounding spins. "}],"extern":"1","main_file_link":[{"open_access":"1","url":"http://dspace.mit.edu/handle/1721.1/114259"}],"citation":{"mla":"Alpichshev, Zhanybek, et al. “Origin of the Exciton Mass in the Frustrated Mott Insulator Na2IrO3.” Physical Review B, vol. 96, no. 23, American Physical Society, 2017, doi:10.1103/PhysRevB.96.235141.","short":"Z. Alpichshev, E. Sie, F. Mahmood, G. Cao, N. Gedik, Physical Review B 96 (2017).","chicago":"Alpichshev, Zhanybek, Edbert Sie, Fahad Mahmood, Gang Cao, and Nuh Gedik. “Origin of the Exciton Mass in the Frustrated Mott Insulator Na2IrO3.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.235141.","ama":"Alpichshev Z, Sie E, Mahmood F, Cao G, Gedik N. Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. 2017;96(23). doi:10.1103/PhysRevB.96.235141","ista":"Alpichshev Z, Sie E, Mahmood F, Cao G, Gedik N. 2017. Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. 96(23).","apa":"Alpichshev, Z., Sie, E., Mahmood, F., Cao, G., & Gedik, N. (2017). Origin of the exciton mass in the frustrated Mott insulator Na2IrO3. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.96.235141","ieee":"Z. Alpichshev, E. Sie, F. Mahmood, G. Cao, and N. Gedik, “Origin of the exciton mass in the frustrated Mott insulator Na2IrO3,” Physical Review B, vol. 96, no. 23. American Physical Society, 2017."},"oa":1,"publication":"Physical Review B","doi":"10.1103/PhysRevB.96.235141","date_published":"2017-12-26T00:00:00Z","language":[{"iso":"eng"}],"day":"26","month":"12"},{"type":"journal_article","issue":"11","publist_id":"7437","abstract":[{"lang":"eng","text":"We used femtosecond optical pump-probe spectroscopy to study the photoinduced change in reflectivity of thin films of the electron-doped cuprate La2-xCexCuO4 (LCCO) with dopings of x=0.08 (underdoped) and x=0.11 (optimally doped). Above Tc, we observe fluence-dependent relaxation rates that begin at a temperature similar to the one where transport measurements first show signatures of antiferromagnetic correlations. Upon suppressing superconductivity with a magnetic field, it is found that the fluence and temperature dependence of relaxation rates are consistent with bimolecular recombination of electrons and holes across a gap (2ΔAF) originating from antiferromagnetic correlations which comprise the pseudogap in electron-doped cuprates. This can be used to learn about coupling between electrons and high-energy (ω>2ΔAF) excitations in these compounds and set limits on the time scales on which antiferromagnetic correlations are static."}],"extern":"1","_id":"392","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Optical pump-probe work was supported by the Gordon and Betty Moore Foundation's EPiQS initiative through Grant No. GBMF4540. Materials growth and characterization was supported by AFOSR FA95501410332 and NSF DMR1410665.","publisher":"American Physical Society","intvolume":" 95","publication_status":"published","status":"public","title":"Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ","author":[{"first_name":"Inna","last_name":"Vishik","full_name":"Vishik, Inna"},{"first_name":"Fahad","last_name":"Mahmood","full_name":"Mahmood, Fahad"},{"last_name":"Alpichshev","first_name":"Zhanybek","orcid":"0000-0002-7183-5203","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Alpichshev, Zhanybek"},{"first_name":"Nuh","last_name":"Gedik","full_name":"Gedik, Nuh"},{"full_name":"Higgins, Joshu","first_name":"Joshu","last_name":"Higgins"},{"full_name":"Greene, Richard","first_name":"Richard","last_name":"Greene"}],"volume":95,"oa_version":"None","date_created":"2018-12-11T11:46:13Z","date_updated":"2021-01-12T07:53:12Z","day":"13","month":"03","citation":{"chicago":"Vishik, Inna, Fahad Mahmood, Zhanybek Alpichshev, Nuh Gedik, Joshu Higgins, and Richard Greene. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.95.115125.","mla":"Vishik, Inna, et al. “Ultrafast Dynamics in the Presence of Antiferromagnetic Correlations in Electron Doped Cuprate La2 XCexCuO4±δ.” Physical Review B, vol. 95, no. 11, American Physical Society, 2017, doi:10.1103/PhysRevB.95.115125.","short":"I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, R. Greene, Physical Review B 95 (2017).","ista":"Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. 2017. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 95(11).","apa":"Vishik, I., Mahmood, F., Alpichshev, Z., Gedik, N., Higgins, J., & Greene, R. (2017). Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.95.115125","ieee":"I. Vishik, F. Mahmood, Z. Alpichshev, N. Gedik, J. Higgins, and R. Greene, “Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ,” Physical Review B, vol. 95, no. 11. American Physical Society, 2017.","ama":"Vishik I, Mahmood F, Alpichshev Z, Gedik N, Higgins J, Greene R. Ultrafast dynamics in the presence of antiferromagnetic correlations in electron doped cuprate La2 xCexCuO4±δ. Physical Review B. 2017;95(11). doi:10.1103/PhysRevB.95.115125"},"main_file_link":[{"url":"http://dspace.mit.edu/handle/1721.1/109835","open_access":"1"}],"oa":1,"publication":"Physical Review B","date_published":"2017-03-13T00:00:00Z","doi":"10.1103/PhysRevB.95.115125","language":[{"iso":"eng"}]},{"has_accepted_license":"1","day":"30","citation":{"ama":"Hardie R, Van Dam E, Cowley M, et al. Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 2017;5(2). doi:10.1186/s40170-017-0164-1","apa":"Hardie, R., Van Dam, E., Cowley, M., Han, T., Balaban, S., Pajic, M., … Saunders, D. (2017). Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. BioMed Central. https://doi.org/10.1186/s40170-017-0164-1","ieee":"R. Hardie et al., “Mitochondrial mutations and metabolic adaptation in pancreatic cancer,” Cancer & Metabolism, vol. 5, no. 2. BioMed Central, 2017.","ista":"Hardie R, Van Dam E, Cowley M, Han T, Balaban S, Pajic M, Pinese M, Iconomou M, Shearer R, Mckenna J, Miller D, Waddell N, Pearson J, Grimmond S, Sazanov LA, Biankin A, Villas Boas S, Hoy A, Turner N, Saunders D. 2017. Mitochondrial mutations and metabolic adaptation in pancreatic cancer. Cancer & Metabolism. 5(2).","short":"R. Hardie, E. Van Dam, M. Cowley, T. Han, S. Balaban, M. Pajic, M. Pinese, M. Iconomou, R. Shearer, J. Mckenna, D. Miller, N. Waddell, J. Pearson, S. Grimmond, L.A. Sazanov, A. Biankin, S. Villas Boas, A. Hoy, N. Turner, D. Saunders, Cancer & Metabolism 5 (2017).","mla":"Hardie, Rae, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic Cancer.” Cancer & Metabolism, vol. 5, no. 2, BioMed Central, 2017, doi:10.1186/s40170-017-0164-1.","chicago":"Hardie, Rae, Ellen Van Dam, Mark Cowley, Ting Han, Seher Balaban, Marina Pajic, Mark Pinese, et al. “Mitochondrial Mutations and Metabolic Adaptation in Pancreatic Cancer.” Cancer & Metabolism. BioMed Central, 2017. https://doi.org/10.1186/s40170-017-0164-1."},"publication":"Cancer & Metabolism","date_published":"2017-01-30T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"text":"Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited.","lang":"eng"}],"intvolume":" 5","status":"public","title":"Mitochondrial mutations and metabolic adaptation in pancreatic cancer","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"443","oa_version":"Published Version","file":[{"file_name":"2017_Cancer_Hardie.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1609174,"file_id":"5868","relation":"main_file","date_updated":"2020-07-14T12:46:29Z","date_created":"2019-01-22T08:17:56Z","checksum":"337a65786875f64a1fe9fc0ac24767dc"}],"month":"01","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1186/s40170-017-0164-1","extern":"1","license":"https://creativecommons.org/licenses/by/4.0/","publist_id":"7380","file_date_updated":"2020-07-14T12:46:29Z","publisher":"BioMed Central","publication_status":"published","year":"2017","volume":5,"date_created":"2018-12-11T11:46:30Z","date_updated":"2021-01-12T07:56:55Z","author":[{"full_name":"Hardie, Rae","last_name":"Hardie","first_name":"Rae"},{"full_name":"Van Dam, Ellen","first_name":"Ellen","last_name":"Van Dam"},{"full_name":"Cowley, Mark","first_name":"Mark","last_name":"Cowley"},{"full_name":"Han, Ting","first_name":"Ting","last_name":"Han"},{"full_name":"Balaban, Seher","first_name":"Seher","last_name":"Balaban"},{"full_name":"Pajic, Marina","last_name":"Pajic","first_name":"Marina"},{"last_name":"Pinese","first_name":"Mark","full_name":"Pinese, Mark"},{"last_name":"Iconomou","first_name":"Mary","full_name":"Iconomou, Mary"},{"full_name":"Shearer, Robert","last_name":"Shearer","first_name":"Robert"},{"first_name":"Jessie","last_name":"Mckenna","full_name":"Mckenna, Jessie"},{"full_name":"Miller, David","last_name":"Miller","first_name":"David"},{"full_name":"Waddell, Nicola","last_name":"Waddell","first_name":"Nicola"},{"full_name":"Pearson, John","first_name":"John","last_name":"Pearson"},{"last_name":"Grimmond","first_name":"Sean","full_name":"Grimmond, Sean"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A"},{"full_name":"Biankin, Andrew","last_name":"Biankin","first_name":"Andrew"},{"full_name":"Villas Boas, Silas","first_name":"Silas","last_name":"Villas Boas"},{"full_name":"Hoy, Andrew","last_name":"Hoy","first_name":"Andrew"},{"first_name":"Nigel","last_name":"Turner","full_name":"Turner, Nigel"},{"first_name":"Darren","last_name":"Saunders","full_name":"Saunders, Darren"}]},{"publication_identifier":{"isbn":["978-1-78262-865-1"]},"day":"29","month":"11","series_title":"Mechanisms of Primary Energy Transduction in Biology ","doi":"10.1039/9781788010405-00025","date_published":"2017-11-29T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Sazanov LA. Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Wikström M, ed. Mechanisms of Primary Energy Transduction in Biology . Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry; 2017:25-59. doi:10.1039/9781788010405-00025","apa":"Sazanov, L. A. (2017). Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In M. Wikström (Ed.), Mechanisms of primary energy transduction in biology (pp. 25–59). Royal Society of Chemistry. https://doi.org/10.1039/9781788010405-00025","ieee":"L. A. Sazanov, “Structure of respiratory complex I: ‘Minimal’ bacterial and ‘de luxe’ mammalian versions,” in Mechanisms of primary energy transduction in biology , M. Wikström, Ed. Royal Society of Chemistry, 2017, pp. 25–59.","ista":"Sazanov LA. 2017.Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions. In: Mechanisms of primary energy transduction in biology . , 25–59.","short":"L.A. Sazanov, in:, M. Wikström (Ed.), Mechanisms of Primary Energy Transduction in Biology , Royal Society of Chemistry, 2017, pp. 25–59.","mla":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, Royal Society of Chemistry, 2017, pp. 25–59, doi:10.1039/9781788010405-00025.","chicago":"Sazanov, Leonid A. “Structure of Respiratory Complex I: ‘Minimal’ Bacterial and ‘de Luxe’ Mammalian Versions.” In Mechanisms of Primary Energy Transduction in Biology , edited by Mårten Wikström, 25–59. Mechanisms of Primary Energy Transduction in Biology . Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781788010405-00025."},"publication":"Mechanisms of primary energy transduction in biology ","page":"25 - 59","quality_controlled":"1","publist_id":"7379","abstract":[{"text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy generation, contributing to the proton motive force used to produce ATP. It couples the transfer of two electrons between NADH and quinone to translocation of four protons across the membrane. It is the largest protein assembly of bacterial and mitochondrial respiratory chains, composed, in mammals, of up to 45 subunits with a total molecular weight of ∼1 MDa. Bacterial enzyme is about half the size, providing the important “minimal” model of complex I. The l-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. Previously, we have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus and of the membrane domain from Escherichia coli, followed by the atomic structure of intact, entire complex I from T. thermophilus. Recently, we have solved by cryo-EM a first complete atomic structure of mammalian (ovine) mitochondrial complex I. Core subunits are well conserved from the bacterial version, whilst supernumerary subunits form an interlinked, stabilizing shell around the core. Subunits containing additional cofactors, including Zn ion, NADPH and phosphopantetheine, probably have regulatory roles. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The structure of mammalian enzyme provides many insights into complex I mechanism, assembly, maturation and dysfunction, allowing detailed molecular analysis of disease-causing mutations.","lang":"eng"}],"type":"book_chapter","author":[{"full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","date_updated":"2021-01-12T07:56:59Z","date_created":"2018-12-11T11:46:30Z","year":"2017","_id":"444","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Royal Society of Chemistry","department":[{"_id":"LeSa"}],"editor":[{"full_name":"Wikström, Mårten","last_name":"Wikström","first_name":"Mårten"}],"status":"public","publication_status":"published","title":"Structure of respiratory complex I: “Minimal” bacterial and “de luxe” mammalian versions"},{"publication":"Physical Review B - Condensed Matter and Materials Physics","main_file_link":[{"url":"https://arxiv.org/abs/1701.07772","open_access":"1"}],"oa":1,"citation":{"ista":"Serbyn M, Abanin D. 2017. Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. 96(1).","ieee":"M. Serbyn and D. Abanin, “Loschmidt echo in many body localized phases,” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 1. American Physical Society, 2017.","apa":"Serbyn, M., & Abanin, D. (2017). Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.96.014202","ama":"Serbyn M, Abanin D. Loschmidt echo in many body localized phases. Physical Review B - Condensed Matter and Materials Physics. 2017;96(1). doi:10.1103/PhysRevB.96.014202","chicago":"Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized Phases.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevB.96.014202.","mla":"Serbyn, Maksym, and Dimitry Abanin. “Loschmidt Echo in Many Body Localized Phases.” Physical Review B - Condensed Matter and Materials Physics, vol. 96, no. 1, American Physical Society, 2017, doi:10.1103/PhysRevB.96.014202.","short":"M. Serbyn, D. Abanin, Physical Review B - Condensed Matter and Materials Physics 96 (2017)."},"quality_controlled":0,"date_published":"2017-07-12T00:00:00Z","doi":"10.1103/PhysRevB.96.014202","month":"07","day":"12","_id":"445","acknowledgement":"This research was supported in part by the National\nScience Foundation under Grant No. NSF PHY11-25915.\nM.S. was supported by Gordon and Betty Moore Foundation’s\nEPiQS Initiative through Grant No. GBMF4307. D.A. also\nacknowledges support by Swiss National Science Foundation.","year":"2017","status":"public","title":"Loschmidt echo in many body localized phases","publication_status":"published","intvolume":" 96","publisher":"American Physical Society","author":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","first_name":"Maksym","full_name":"Maksym Serbyn"},{"first_name":"Dimitry","last_name":"Abanin","full_name":"Abanin, Dimitry A"}],"date_updated":"2021-01-12T07:57:03Z","date_created":"2018-12-11T11:46:31Z","volume":96,"type":"journal_article","abstract":[{"text":"The Loschmidt echo, defined as the overlap between quantum wave function evolved with different Hamiltonians, quantifies the sensitivity of quantum dynamics to perturbations and is often used as a probe of quantum chaos. In this work we consider the behavior of the Loschmidt echo in the many-body localized phase, which is characterized by emergent local integrals of motion and provides a generic example of nonergodic dynamics. We demonstrate that the fluctuations of the Loschmidt echo decay as a power law in time in the many-body localized phase, in contrast to the exponential decay in few-body ergodic systems. We consider the spin-echo generalization of the Loschmidt echo and argue that the corresponding correlation function saturates to a finite value in localized systems. Slow, power-law decay of fluctuations of such spin-echo-type overlap is related to the operator spreading and is present only in the many-body localized phase, but not in a noninteracting Anderson insulator. While most of the previously considered probes of dephasing dynamics could be understood by approximating physical spin operators with local integrals of motion, the Loschmidt echo and its generalizations crucially depend on the full expansion of the physical operators via local integrals of motion operators, as well as operators which flip local integrals of motion. Hence these probes allow one to get insights into the relation between physical operators and local integrals of motion and access the operator spreading in the many-body localized phase.","lang":"eng"}],"publist_id":"7378","issue":"1","extern":1},{"language":[{"iso":"eng"}],"doi":"10.1145/3068766","date_published":"2017-08-01T00:00:00Z","page":"92 - 99","citation":{"ama":"Bächer M, Bickel B, Whiting E, Sorkine Hornung O. Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. 2017;60(8):92-99. doi:10.1145/3068766","apa":"Bächer, M., Bickel, B., Whiting, E., & Sorkine Hornung, O. (2017). Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. ACM. https://doi.org/10.1145/3068766","ieee":"M. Bächer, B. Bickel, E. Whiting, and O. Sorkine Hornung, “Spin it: Optimizing moment of inertia for spinnable objects,” Communications of the ACM, vol. 60, no. 8. ACM, pp. 92–99, 2017.","ista":"Bächer M, Bickel B, Whiting E, Sorkine Hornung O. 2017. Spin it: Optimizing moment of inertia for spinnable objects. Communications of the ACM. 60(8), 92–99.","short":"M. Bächer, B. Bickel, E. Whiting, O. Sorkine Hornung, Communications of the ACM 60 (2017) 92–99.","mla":"Bächer, Moritz, et al. “Spin It: Optimizing Moment of Inertia for Spinnable Objects.” Communications of the ACM, vol. 60, no. 8, ACM, 2017, pp. 92–99, doi:10.1145/3068766.","chicago":"Bächer, Moritz, Bernd Bickel, Emily Whiting, and Olga Sorkine Hornung. “Spin It: Optimizing Moment of Inertia for Spinnable Objects.” Communications of the ACM. ACM, 2017. https://doi.org/10.1145/3068766."},"publication":"Communications of the ACM","article_processing_charge":"No","day":"01","month":"08","scopus_import":"1","volume":60,"oa_version":"None","date_updated":"2022-03-18T12:55:28Z","date_created":"2018-12-11T11:46:33Z","author":[{"first_name":"Moritz","last_name":"Bächer","full_name":"Bächer, Moritz"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd"},{"full_name":"Whiting, Emily","first_name":"Emily","last_name":"Whiting"},{"last_name":"Sorkine Hornung","first_name":"Olga","full_name":"Sorkine Hornung, Olga"}],"publisher":"ACM","intvolume":" 60","status":"public","publication_status":"published","title":"Spin it: Optimizing moment of inertia for spinnable objects","_id":"452","acknowledgement":"This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting was supported by the ETH Zurich/Marie Curie COFUND Postdoctoral Fellowship. \r\nFirst and foremost, we would like to thank our editor Steve Marschner for his invaluable feedback. We were fortunate to get further help from Maurizio Nitti for model design, Romain Prévost for Make-It-Stand comparisons, Alexander Sorkine-Hornung, Kaan Yücer, and Changil Kim for video and photo assistance, Ronnie Gänsli for metal casting, Alec Jacobson for the posed Elephant and Armadillo models, and Romain Prévost and Amit Bermano for print preparation. Model sources include: Woven Ring: generated by “Sculpture Generator 1” by Carlo H. Séquin, UC Berkeley; Elephant: De Espona model library, courtesy of Robert Sumner; T-Rex: TurboSquid; Armadillo: Stanford Computer Graphics Laboratory; and Utah Teapot: Martin Newell, University of Utah. ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","extern":"1","publist_id":"7370","issue":"8","abstract":[{"text":"Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. Yet, due to the exceeding difficulty of creating stably spinning objects of asymmetric shape in a manual trial-and-error process, there has been little departure from rotationally symmetric designs. With modern 3D printing technologies, however, we can manufacture shapes of almost unbounded complexity at the press of a button, shifting this design complexity toward computation. In this article, we describe an algorithm to generate designs for spinning objects by optimizing their mass distribution: as input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the interior mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. To create voids inside the model, we represent its volume with an adaptive multiresolution voxelization and optimize the discrete voxel fill values using a continuous, nonlinear formulation. We further optimize for rotational stability by maximizing the dominant principal moment. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance.","lang":"eng"}],"type":"journal_article"},{"file_date_updated":"2020-07-14T12:46:31Z","publist_id":"7369","publication_status":"published","department":[{"_id":"MaLo"}],"publisher":"Biophysical Society","year":"2017","acknowledgement":"The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ","date_created":"2018-12-11T11:46:33Z","date_updated":"2021-01-12T07:59:28Z","volume":113,"author":[{"first_name":"Todd","last_name":"Fallesen","full_name":"Fallesen, Todd"},{"full_name":"Roostalu, Johanna","last_name":"Roostalu","first_name":"Johanna"},{"full_name":"Düllberg, Christian F","last_name":"Düllberg","first_name":"Christian F","orcid":"0000-0001-6335-9748","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pruessner, Gunnar","last_name":"Pruessner","first_name":"Gunnar"},{"full_name":"Surrey, Thomas","last_name":"Surrey","first_name":"Thomas"}],"month":"11","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2017.09.006","type":"journal_article","abstract":[{"text":"Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.","lang":"eng"}],"issue":"9","title":"Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement","status":"public","ddc":["570"],"intvolume":" 113","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"453","oa_version":"Published Version","file":[{"checksum":"99a2474088e20ac74b1882c4fbbb45b1","date_updated":"2020-07-14T12:46:31Z","date_created":"2018-12-12T10:14:03Z","file_id":"5052","relation":"main_file","creator":"system","file_size":977192,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf"}],"pubrep_id":"965","day":"07","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"2055 - 2067","publication":"Biophysical Journal","citation":{"chicago":"Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal. Biophysical Society, 2017. https://doi.org/10.1016/j.bpj.2017.09.006.","short":"T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067.","mla":"Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” Biophysical Journal, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:10.1016/j.bpj.2017.09.006.","ieee":"T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” Biophysical Journal, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017.","apa":"Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., & Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.09.006","ista":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067.","ama":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 2017;113(9):2055-2067. doi:10.1016/j.bpj.2017.09.006"},"date_published":"2017-11-07T00:00:00Z"},{"pubrep_id":"956","file":[{"creator":"system","file_size":582940,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-956-v1+1_2017_Chatterjee_Improved_algorithms.pdf","checksum":"12d469ae69b80361333d7dead965cf5d","date_created":"2018-12-12T10:13:27Z","date_updated":"2020-07-14T12:46:32Z","file_id":"5010","relation":"main_file"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"464","status":"public","ddc":["004"],"title":"Improved algorithms for parity and Streett objectives","intvolume":" 13","abstract":[{"text":"The computation of the winning set for parity objectives and for Streett objectives in graphs as well as in game graphs are central problems in computer-aided verification, with application to the verification of closed systems with strong fairness conditions, the verification of open systems, checking interface compatibility, well-formedness of specifications, and the synthesis of reactive systems. We show how to compute the winning set on n vertices for (1) parity-3 (aka one-pair Streett) objectives in game graphs in time O(n5/2) and for (2) k-pair Streett objectives in graphs in time O(n2+nklogn). For both problems this gives faster algorithms for dense graphs and represents the first improvement in asymptotic running time in 15 years.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2017-09-26T00:00:00Z","publication":"Logical Methods in Computer Science","citation":{"mla":"Chatterjee, Krishnendu, et al. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science, vol. 13, no. 3, 26, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:26)2017.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, Logical Methods in Computer Science 13 (2017).","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Veronika Loitzenbauer. “Improved Algorithms for Parity and Streett Objectives.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:26)2017.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:26)2017","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V. 2017. Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. 13(3), 26.","apa":"Chatterjee, K., Henzinger, M. H., & Loitzenbauer, V. (2017). Improved algorithms for parity and Streett objectives. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:26)2017","ieee":"K. Chatterjee, M. H. Henzinger, and V. Loitzenbauer, “Improved algorithms for parity and Streett objectives,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017."},"day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","first_name":"Veronika","last_name":"Loitzenbauer"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"1661"}]},"date_updated":"2023-02-23T10:08:55Z","date_created":"2018-12-11T11:46:37Z","volume":13,"year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","file_date_updated":"2020-07-14T12:46:32Z","publist_id":"7357","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","article_number":"26","doi":"10.23638/LMCS-13(3:26)2017","language":[{"iso":"eng"}],"external_id":{"arxiv":["1410.0833"]},"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FWF","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","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"month":"09","publication_identifier":{"issn":["1860-5974"]}},{"scopus_import":1,"day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication":"ACM Transactions on Graphics","citation":{"chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics. ACM, 2017. https://doi.org/10.1145/3072959.3073678.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” ACM Transactions on Graphics, vol. 36, no. 4, 103, ACM, 2017, doi:10.1145/3072959.3073678.","apa":"Jeschke, S., & Wojtan, C. (2017). Water wave packets. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3072959.3073678","ieee":"S. Jeschke and C. Wojtan, “Water wave packets,” ACM Transactions on Graphics, vol. 36, no. 4. ACM, 2017.","ista":"Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103.","ama":"Jeschke S, Wojtan C. Water wave packets. ACM Transactions on Graphics. 2017;36(4). doi:10.1145/3072959.3073678"},"article_type":"original","date_published":"2017-07-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios."}],"issue":"4","_id":"470","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Water wave packets","status":"public","ddc":["006"],"intvolume":" 36","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"wavepackets_final.pdf","creator":"wojtan","content_type":"application/pdf","file_size":13131683,"file_id":"7359","relation":"main_file","checksum":"82a3b2bfeee4ddef16ecc21675d1a48a","date_created":"2020-01-24T09:32:35Z","date_updated":"2020-07-14T12:46:34Z"}],"month":"07","publication_identifier":{"issn":["07300301"]},"oa":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176"}],"doi":"10.1145/3072959.3073678","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"article_number":"103","file_date_updated":"2020-07-14T12:46:34Z","publist_id":"7350","ec_funded":1,"year":"2017","publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","last_name":"Jeschke","full_name":"Jeschke, Stefan"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J"}],"date_created":"2018-12-11T11:46:39Z","date_updated":"2023-02-23T12:20:26Z","volume":36},{"scopus_import":1,"day":"01","citation":{"ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 2017;18(2). doi:10.1145/3060139","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Faster statistical model checking for unbounded temporal properties,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2. ACM, 2017.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2017). Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3060139","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2017. Faster statistical model checking for unbounded temporal properties. ACM Transactions on Computational Logic (TOCL). 18(2), 12.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, ACM Transactions on Computational Logic (TOCL) 18 (2017).","mla":"Daca, Przemyslaw, et al. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 2, 12, ACM, 2017, doi:10.1145/3060139.","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Faster Statistical Model Checking for Unbounded Temporal Properties.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3060139."},"publication":"ACM Transactions on Computational Logic (TOCL)","date_published":"2017-05-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We present a new algorithm for the statistical model checking of Markov chains with respect to unbounded temporal properties, including full linear temporal logic. The main idea is that we monitor each simulation run on the fly, in order to detect quickly if a bottom strongly connected component is entered with high probability, in which case the simulation run can be terminated early. As a result, our simulation runs are often much shorter than required by termination bounds that are computed a priori for a desired level of confidence on a large state space. In comparison to previous algorithms for statistical model checking our method is not only faster in many cases but also requires less information about the system, namely, only the minimum transition probability that occurs in the Markov chain. In addition, our method can be generalised to unbounded quantitative properties such as mean-payoff bounds. "}],"_id":"471","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 18","title":"Faster statistical model checking for unbounded temporal properties","status":"public","oa_version":"Submitted Version","publication_identifier":{"issn":["15293785"]},"month":"05","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.05739"}],"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"},{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","doi":"10.1145/3060139","language":[{"iso":"eng"}],"article_number":"12","publist_id":"7349","ec_funded":1,"year":"2017","publisher":"ACM","department":[{"_id":"ToHe"}],"publication_status":"published","related_material":{"record":[{"id":"1234","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","last_name":"Daca"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Petrov","first_name":"Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"}],"volume":18,"date_updated":"2023-02-21T16:48:11Z","date_created":"2018-12-11T11:46:39Z"},{"page":"6043 - 6052","quality_controlled":"1","citation":{"ista":"Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. 2017. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. 37(25), 6043–6052.","apa":"Eguchi, K., Taoufiq, Z., Thorn Seshold, O., Trauner, D., Hasegawa, M., & Takahashi, T. (2017). Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. Wiley-Blackwell. https://doi.org/10.1523/JNEUROSCI.0179-17.2017","ieee":"K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, and T. Takahashi, “Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held,” European Journal of Neuroscience, vol. 37, no. 25. Wiley-Blackwell, pp. 6043–6052, 2017.","ama":"Eguchi K, Taoufiq Z, Thorn Seshold O, Trauner D, Hasegawa M, Takahashi T. Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held. European Journal of Neuroscience. 2017;37(25):6043-6052. doi:10.1523/JNEUROSCI.0179-17.2017","chicago":"Eguchi, Kohgaku, Zachari Taoufiq, Oliver Thorn Seshold, Dirk Trauner, Masato Hasegawa, and Tomoyuki Takahashi. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.” European Journal of Neuroscience. Wiley-Blackwell, 2017. https://doi.org/10.1523/JNEUROSCI.0179-17.2017.","mla":"Eguchi, Kohgaku, et al. “Wild-Type Monomeric α-Synuclein Can Impair Vesicle Endocytosis and Synaptic Fidelity via Tubulin Polymerization at the Calyx of Held.” European Journal of Neuroscience, vol. 37, no. 25, Wiley-Blackwell, 2017, pp. 6043–52, doi:10.1523/JNEUROSCI.0179-17.2017.","short":"K. Eguchi, Z. Taoufiq, O. Thorn Seshold, D. Trauner, M. Hasegawa, T. Takahashi, European Journal of Neuroscience 37 (2017) 6043–6052."},"publication":"European Journal of Neuroscience","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.0179-17.2017","date_published":"2017-06-21T00:00:00Z","publication_identifier":{"issn":["02706474"]},"day":"21","month":"06","intvolume":" 37","publisher":"Wiley-Blackwell","status":"public","publication_status":"published","title":"Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held","_id":"472","year":"2017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":37,"oa_version":"None","date_created":"2018-12-11T11:46:40Z","date_updated":"2021-01-12T08:00:51Z","author":[{"full_name":"Eguchi, Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6170-2546","first_name":"Kohgaku","last_name":"Eguchi"},{"last_name":"Taoufiq","first_name":"Zachari","full_name":"Taoufiq, Zachari"},{"last_name":"Thorn Seshold","first_name":"Oliver","full_name":"Thorn Seshold, Oliver"},{"full_name":"Trauner, Dirk","last_name":"Trauner","first_name":"Dirk"},{"full_name":"Hasegawa, Masato","first_name":"Masato","last_name":"Hasegawa"},{"full_name":"Takahashi, Tomoyuki","last_name":"Takahashi","first_name":"Tomoyuki"}],"type":"journal_article","extern":"1","issue":"25","publist_id":"7348","abstract":[{"text":"α-Synuclein is a presynaptic protein the function of which has yet to be identified, but its neuronal content increases in patients of synucleinopa-thies including Parkinson’s disease. Chronic overexpression of α-synuclein reportedly expresses various phenotypes of synaptic dysfunction, but the primary target of its toxicity has not been determined. To investigate this, we acutely loaded human recombinant α-synuclein or its pathological mutants in their monomeric forms into the calyces of Held presynaptic terminals in slices from auditorily mature and immature rats of either sex. Membrane capacitance measurements revealed significant and specific inhibitory effects of WT monomeric α-synuclein on vesicle endocytosis throughout development. However, the α-synuclein A53T mutant affected vesicle endocytosis only at immature calyces, where as the A30P mutant had no effect throughout. The endocytic impairment by WTα-synuclein was rescued by intraterminal coloading of the microtubule (MT) polymerization blocker nocodazole. Furthermore, it was reversibly rescued by presynaptically loaded photostatin-1, a pho-toswitcheable inhibitor of MT polymerization, inalight-wavelength-dependent manner. Incontrast, endocyticinhibition by the A53T mutant at immature calyces was not rescued by nocodazole. Functionally, presynaptically loaded WT α-synuclein had no effect on basal synaptic transmission evoked at a low frequency, but significantly attenuated exocytosis and impaired the fidelity of neurotransmission during prolonged high-frequency stimulation. We conclude that monomeric WTα-synuclein primarily inhibits vesicle endocytosis via MT overassembly, thereby impairing high-frequency neurotransmission.","lang":"eng"}]},{"oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":769296,"access_level":"open_access","file_name":"IST-2018-949-v1+1_2016_huber_PLanar_matchings.pdf","checksum":"f79e8558bfe4b368dfefeb8eec2e3a5e","date_created":"2018-12-12T10:09:34Z","date_updated":"2020-07-14T12:46:35Z","file_id":"4758","relation":"main_file"}],"pubrep_id":"949","title":"Planar matchings for weighted straight skeletons","status":"public","ddc":["004","514","516"],"intvolume":" 26","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"481","abstract":[{"text":"We introduce planar matchings on directed pseudo-line arrangements, which yield a planar set of pseudo-line segments such that only matching-partners are adjacent. By translating the planar matching problem into a corresponding stable roommates problem we show that such matchings always exist. Using our new framework, we establish, for the first time, a complete, rigorous definition of weighted straight skeletons, which are based on a so-called wavefront propagation process. We present a generalized and unified approach to treat structural changes in the wavefront that focuses on the restoration of weak planarity by finding planar matchings.","lang":"eng"}],"issue":"3-4","type":"journal_article","date_published":"2017-04-13T00:00:00Z","page":"211 - 229","publication":"International Journal of Computational Geometry and Applications","citation":{"ama":"Biedl T, Huber S, Palfrader P. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 2017;26(3-4):211-229. doi:10.1142/S0218195916600050","apa":"Biedl, T., Huber, S., & Palfrader, P. (2017). Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195916600050","ieee":"T. Biedl, S. Huber, and P. Palfrader, “Planar matchings for weighted straight skeletons,” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4. World Scientific Publishing, pp. 211–229, 2017.","ista":"Biedl T, Huber S, Palfrader P. 2017. Planar matchings for weighted straight skeletons. International Journal of Computational Geometry and Applications. 26(3–4), 211–229.","short":"T. Biedl, S. Huber, P. Palfrader, International Journal of Computational Geometry and Applications 26 (2017) 211–229.","mla":"Biedl, Therese, et al. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications, vol. 26, no. 3–4, World Scientific Publishing, 2017, pp. 211–29, doi:10.1142/S0218195916600050.","chicago":"Biedl, Therese, Stefan Huber, and Peter Palfrader. “Planar Matchings for Weighted Straight Skeletons.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2017. https://doi.org/10.1142/S0218195916600050."},"day":"13","has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T11:46:43Z","date_updated":"2023-02-21T16:06:22Z","volume":26,"author":[{"full_name":"Biedl, Therese","first_name":"Therese","last_name":"Biedl"},{"first_name":"Stefan","last_name":"Huber","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan"},{"last_name":"Palfrader","first_name":"Peter","full_name":"Palfrader, Peter"}],"related_material":{"record":[{"id":"10892","relation":"earlier_version","status":"public"}]},"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"World Scientific Publishing","acknowledgement":"Supported by NSERC and the Ross and Muriel Cheriton Fellowship. Research supported by Austrian Science Fund (FWF): P25816-N15.","year":"2017","file_date_updated":"2020-07-14T12:46:35Z","publist_id":"7338","language":[{"iso":"eng"}],"doi":"10.1142/S0218195916600050","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"04"},{"issue":"3","abstract":[{"lang":"eng","text":"We consider the dynamics of a large quantum system of N identical bosons in 3D interacting via a two-body potential of the form N3β-1w(Nβ(x - y)). For fixed 0 = β < 1/3 and large N, we obtain a norm approximation to the many-body evolution in the Nparticle Hilbert space. The leading order behaviour of the dynamics is determined by Hartree theory while the second order is given by Bogoliubov theory."}],"type":"journal_article","oa_version":"Submitted Version","_id":"484","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 21","status":"public","title":"Bogoliubov correction to the mean-field dynamics of interacting bosons","day":"01","scopus_import":1,"date_published":"2017-01-01T00:00:00Z","citation":{"chicago":"Nam, Phan, and Marcin M Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a4.","mla":"Nam, Phan, and Marcin M. Napiórkowski. “Bogoliubov Correction to the Mean-Field Dynamics of Interacting Bosons.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 683–738, doi:10.4310/ATMP.2017.v21.n3.a4.","short":"P. Nam, M.M. Napiórkowski, Advances in Theoretical and Mathematical Physics 21 (2017) 683–738.","ista":"Nam P, Napiórkowski MM. 2017. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 21(3), 683–738.","ieee":"P. Nam and M. M. Napiórkowski, “Bogoliubov correction to the mean-field dynamics of interacting bosons,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 683–738, 2017.","apa":"Nam, P., & Napiórkowski, M. M. (2017). Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a4","ama":"Nam P, Napiórkowski MM. Bogoliubov correction to the mean-field dynamics of interacting bosons. Advances in Theoretical and Mathematical Physics. 2017;21(3):683-738. doi:10.4310/ATMP.2017.v21.n3.a4"},"publication":"Advances in Theoretical and Mathematical Physics","page":"683 - 738","ec_funded":1,"publist_id":"7336","author":[{"full_name":"Nam, Phan","first_name":"Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","last_name":"Napiórkowski","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"}],"volume":21,"date_created":"2018-12-11T11:46:43Z","date_updated":"2021-01-12T08:00:58Z","year":"2017","department":[{"_id":"RoSe"}],"publisher":"International Press","publication_status":"published","publication_identifier":{"issn":["10950761"]},"month":"01","doi":"10.4310/ATMP.2017.v21.n3.a4","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1509.04631","open_access":"1"}],"oa":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1"},{"date_published":"2017-08-25T00:00:00Z","page":"739 - 800","publication":"Advances in Theoretical and Mathematical Physics","citation":{"chicago":"Bourgade, Paul, László Erdös, Horng Yau, and Jun Yin. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics. International Press, 2017. https://doi.org/10.4310/ATMP.2017.v21.n3.a5.","mla":"Bourgade, Paul, et al. “Universality for a Class of Random Band Matrices.” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3, International Press, 2017, pp. 739–800, doi:10.4310/ATMP.2017.v21.n3.a5.","short":"P. Bourgade, L. Erdös, H. Yau, J. Yin, Advances in Theoretical and Mathematical Physics 21 (2017) 739–800.","ista":"Bourgade P, Erdös L, Yau H, Yin J. 2017. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 21(3), 739–800.","apa":"Bourgade, P., Erdös, L., Yau, H., & Yin, J. (2017). Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. International Press. https://doi.org/10.4310/ATMP.2017.v21.n3.a5","ieee":"P. Bourgade, L. Erdös, H. Yau, and J. Yin, “Universality for a class of random band matrices,” Advances in Theoretical and Mathematical Physics, vol. 21, no. 3. International Press, pp. 739–800, 2017.","ama":"Bourgade P, Erdös L, Yau H, Yin J. Universality for a class of random band matrices. Advances in Theoretical and Mathematical Physics. 2017;21(3):739-800. doi:10.4310/ATMP.2017.v21.n3.a5"},"day":"25","scopus_import":1,"oa_version":"Submitted Version","status":"public","title":"Universality for a class of random band matrices","intvolume":" 21","_id":"483","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We prove the universality for the eigenvalue gap statistics in the bulk of the spectrum for band matrices, in the regime where the band width is comparable with the dimension of the matrix, W ~ N. All previous results concerning universality of non-Gaussian random matrices are for mean-field models. By relying on a new mean-field reduction technique, we deduce universality from quantum unique ergodicity for band matrices.","lang":"eng"}],"issue":"3","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.4310/ATMP.2017.v21.n3.a5","quality_controlled":"1","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1602.02312","open_access":"1"}],"month":"08","publication_identifier":{"issn":["10950761"]},"date_created":"2018-12-11T11:46:43Z","date_updated":"2021-01-12T08:00:57Z","volume":21,"author":[{"last_name":"Bourgade","first_name":"Paul","full_name":"Bourgade, Paul"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"full_name":"Yau, Horng","last_name":"Yau","first_name":"Horng"},{"full_name":"Yin, Jun","last_name":"Yin","first_name":"Jun"}],"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"International Press","year":"2017","ec_funded":1,"publist_id":"7337"},{"scopus_import":1,"publication_identifier":{"isbn":["978-145035422-6"]},"day":"28","month":"11","page":"2 - 14","quality_controlled":"1","citation":{"ama":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. Towards unlicensed cellular networks in TV white spaces. In: Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies. ACM; 2017:2-14. doi:10.1145/3143361.3143367","ista":"Baig G, Radunovic B, Alistarh D-A, Balkwill M, Karagiannis T, Qiu L. 2017. Towards unlicensed cellular networks in TV white spaces. Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies. CoNEXT: Conference on emerging Networking EXperiments and Technologies, 2–14.","ieee":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, and L. Qiu, “Towards unlicensed cellular networks in TV white spaces,” in Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies, Incheon, South Korea, 2017, pp. 2–14.","apa":"Baig, G., Radunovic, B., Alistarh, D.-A., Balkwill, M., Karagiannis, T., & Qiu, L. (2017). Towards unlicensed cellular networks in TV white spaces. In Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies (pp. 2–14). Incheon, South Korea: ACM. https://doi.org/10.1145/3143361.3143367","mla":"Baig, Ghufran, et al. “Towards Unlicensed Cellular Networks in TV White Spaces.” Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14, doi:10.1145/3143361.3143367.","short":"G. Baig, B. Radunovic, D.-A. Alistarh, M. Balkwill, T. Karagiannis, L. Qiu, in:, Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, ACM, 2017, pp. 2–14.","chicago":"Baig, Ghufran, Bozidar Radunovic, Dan-Adrian Alistarh, Matthew Balkwill, Thomas Karagiannis, and Lili Qiu. “Towards Unlicensed Cellular Networks in TV White Spaces.” In Proceedings of the 2017 13th International Conference on Emerging Networking EXperiments and Technologies, 2–14. ACM, 2017. https://doi.org/10.1145/3143361.3143367."},"publication":"Proceedings of the 2017 13th International Conference on emerging Networking EXperiments and Technologies","language":[{"iso":"eng"}],"doi":"10.1145/3143361.3143367","date_published":"2017-11-28T00:00:00Z","conference":{"location":"Incheon, South Korea","start_date":"2017-12-12","end_date":"2017-12-15","name":"CoNEXT: Conference on emerging Networking EXperiments and Technologies"},"type":"conference","publist_id":"7333","abstract":[{"text":"In this paper we study network architecture for unlicensed cellular networking for outdoor coverage in TV white spaces. The main technology proposed for TV white spaces is 802.11af, a Wi-Fi variant adapted for TV frequencies. However, 802.11af is originally designed for improved indoor propagation. We show that long links, typical for outdoor use, exacerbate known Wi-Fi issues, such as hidden and exposed terminal, and significantly reduce its efficiency. Instead, we propose CellFi, an alternative architecture based on LTE. LTE is designed for long-range coverage and throughput efficiency, but it is also designed to operate in tightly controlled and centrally managed networks. CellFi overcomes these problems by designing an LTE-compatible spectrum database component, mandatory for TV white space networking, and introducing an interference management component for distributed coordination. CellFi interference management is compatible with existing LTE mechanisms, requires no explicit communication between base stations, and is more efficient than CSMA for long links. We evaluate our design through extensive real world evaluation on of-the-shelf LTE equipment and simulations. We show that, compared to 802.11af, it increases coverage by 40% and reduces median flow completion times by 2.3x.","lang":"eng"}],"publisher":"ACM","department":[{"_id":"DaAl"}],"publication_status":"published","title":"Towards unlicensed cellular networks in TV white spaces","status":"public","year":"2017","_id":"487","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","date_updated":"2023-02-23T12:21:11Z","date_created":"2018-12-11T11:46:45Z","author":[{"full_name":"Baig, Ghufran","first_name":"Ghufran","last_name":"Baig"},{"full_name":"Radunovic, Bozidar","first_name":"Bozidar","last_name":"Radunovic"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"},{"first_name":"Matthew","last_name":"Balkwill","full_name":"Balkwill, Matthew"},{"last_name":"Karagiannis","first_name":"Thomas","full_name":"Karagiannis, Thomas"},{"full_name":"Qiu, Lili","first_name":"Lili","last_name":"Qiu"}]},{"type":"journal_article","abstract":[{"text":"Orientation in space is represented in specialized brain circuits. Persistent head direction signals are transmitted from anterior thalamus to the presubiculum, but the identity of the presubicular target neurons, their connectivity and function in local microcircuits are unknown. Here, we examine how thalamic afferents recruit presubicular principal neurons and Martinotti interneurons, and the ensuing synaptic interactions between these cells. Pyramidal neuron activation of Martinotti cells in superficial layers is strongly facilitating such that high-frequency head directional stimulation efficiently unmutes synaptic excitation. Martinotti-cell feedback plays a dual role: precisely timed spikes may not inhibit the firing of in-tune head direction cells, while exerting lateral inhibition. Autonomous attractor dynamics emerge from a modelled network implementing wiring motifs and timing sensitive synaptic interactions in the pyramidal - Martinotti-cell feedback loop. This inhibitory microcircuit is therefore tuned to refine and maintain head direction information in the presubiculum.","lang":"eng"}],"intvolume":" 8","status":"public","ddc":["571"],"title":"Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum","_id":"514","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"5083","relation":"main_file","checksum":"76d8a2b72a58e56adb410ec37dfa7eee","date_created":"2018-12-12T10:14:31Z","date_updated":"2020-07-14T12:46:36Z","access_level":"open_access","file_name":"IST-2018-937-v1+1_2017_Stella_Activity_dependent.pdf","creator":"system","file_size":2948357,"content_type":"application/pdf"}],"pubrep_id":"937","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"apa":"Simonnet, J., Nassar, M., Stella, F., Cohen, I., Mathon, B., Boccara, C. N., … Fricker, D. (2017). Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms16032","ieee":"J. Simonnet et al., “Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","ista":"Simonnet J, Nassar M, Stella F, Cohen I, Mathon B, Boccara CN, Miles R, Fricker D. 2017. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 8, 16032.","ama":"Simonnet J, Nassar M, Stella F, et al. Activity dependent feedback inhibition may maintain head direction signals in mouse presubiculum. Nature Communications. 2017;8. doi:10.1038/ncomms16032","chicago":"Simonnet, Jean, Mérie Nassar, Federico Stella, Ivan Cohen, Bertrand Mathon, Charlotte N. Boccara, Richard Miles, and Desdemona Fricker. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms16032.","short":"J. Simonnet, M. Nassar, F. Stella, I. Cohen, B. Mathon, C.N. Boccara, R. Miles, D. Fricker, Nature Communications 8 (2017).","mla":"Simonnet, Jean, et al. “Activity Dependent Feedback Inhibition May Maintain Head Direction Signals in Mouse Presubiculum.” Nature Communications, vol. 8, 16032, Nature Publishing Group, 2017, doi:10.1038/ncomms16032."},"publication":"Nature Communications","date_published":"2017-07-01T00:00:00Z","article_number":"16032","publist_id":"7305","file_date_updated":"2020-07-14T12:46:36Z","publisher":"Nature Publishing Group","department":[{"_id":"JoCs"}],"publication_status":"published","year":"2017","volume":8,"date_updated":"2021-01-12T08:01:16Z","date_created":"2018-12-11T11:46:54Z","author":[{"first_name":"Jean","last_name":"Simonnet","full_name":"Simonnet, Jean"},{"full_name":"Nassar, Mérie","last_name":"Nassar","first_name":"Mérie"},{"full_name":"Stella, Federico","orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","last_name":"Stella","first_name":"Federico"},{"first_name":"Ivan","last_name":"Cohen","full_name":"Cohen, Ivan"},{"first_name":"Bertrand","last_name":"Mathon","full_name":"Mathon, Bertrand"},{"full_name":"Boccara, Charlotte","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7237-5109","first_name":"Charlotte","last_name":"Boccara"},{"first_name":"Richard","last_name":"Miles","full_name":"Miles, Richard"},{"last_name":"Fricker","first_name":"Desdemona","full_name":"Fricker, Desdemona"}],"publication_identifier":{"issn":["20411723"]},"month":"07","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/ncomms16032"},{"publist_id":"7304","ec_funded":1,"file_date_updated":"2020-07-14T12:46:36Z","volume":24,"date_updated":"2021-01-12T08:01:17Z","date_created":"2018-12-11T11:46:54Z","author":[{"full_name":"Letts, James A","orcid":"0000-0002-9864-3586","id":"322DA418-F248-11E8-B48F-1D18A9856A87","last_name":"Letts","first_name":"James A"},{"full_name":"Sazanov, Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","first_name":"Leonid A","last_name":"Sazanov"}],"publisher":"Nature Publishing Group","department":[{"_id":"LeSa"}],"publication_status":"published","year":"2017","publication_identifier":{"issn":["15459993"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1038/nsmb.3460","project":[{"_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"quality_controlled":"1","oa":1,"issue":"10","abstract":[{"text":"The oxidative phosphorylation electron transport chain (OXPHOS-ETC) of the inner mitochondrial membrane is composed of five large protein complexes, named CI-CV. These complexes convert energy from the food we eat into ATP, a small molecule used to power a multitude of essential reactions throughout the cell. OXPHOS-ETC complexes are organized into supercomplexes (SCs) of defined stoichiometry: CI forms a supercomplex with CIII2 and CIV (SC I+III2+IV, known as the respirasome), as well as with CIII2 alone (SC I+III2). CIII2 forms a supercomplex with CIV (SC III2+IV) and CV forms dimers (CV2). Recent cryo-EM studies have revealed the structures of SC I+III2+IV and SC I+III2. Furthermore, recent work has shed light on the assembly and function of the SCs. Here we review and compare these recent studies and discuss how they have advanced our understanding of mitochondrial electron transport.","lang":"eng"}],"type":"journal_article","file":[{"file_name":"29893_2_merged_1501257589_red.pdf","access_level":"open_access","file_size":4118385,"content_type":"application/pdf","creator":"lsazanov","relation":"main_file","file_id":"6993","date_updated":"2020-07-14T12:46:36Z","date_created":"2019-11-07T12:51:07Z","checksum":"9bc7e8c41b43636dd7566289e511f096"}],"oa_version":"Submitted Version","intvolume":" 24","status":"public","ddc":["572"],"title":"Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain","_id":"515","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","day":"05","scopus_import":1,"date_published":"2017-10-05T00:00:00Z","page":"800 - 808","article_type":"original","citation":{"chicago":"Letts, James A, and Leonid A Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3460.","mla":"Letts, James A., and Leonid A. Sazanov. “Clarifying the Supercomplex: The Higher-Order Organization of the Mitochondrial Electron Transport Chain.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 800–08, doi:10.1038/nsmb.3460.","short":"J.A. Letts, L.A. Sazanov, Nature Structural and Molecular Biology 24 (2017) 800–808.","ista":"Letts JA, Sazanov LA. 2017. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 24(10), 800–808.","apa":"Letts, J. A., & Sazanov, L. A. (2017). Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3460","ieee":"J. A. Letts and L. A. Sazanov, “Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 800–808, 2017.","ama":"Letts JA, Sazanov LA. Clarifying the supercomplex: The higher-order organization of the mitochondrial electron transport chain. Nature Structural and Molecular Biology. 2017;24(10):800-808. doi:10.1038/nsmb.3460"},"publication":"Nature Structural and Molecular Biology"},{"volume":2,"oa_version":"Preprint","date_updated":"2021-01-12T08:01:16Z","date_created":"2018-12-11T11:46:54Z","author":[{"first_name":"Lukasz","last_name":"Klotz","id":"2C9AF1C2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1740-7635","full_name":"Klotz, Lukasz"},{"last_name":"Lemoult","first_name":"Grégoire M","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","full_name":"Lemoult, Grégoire M"},{"first_name":"Idalia","last_name":"Frontczak","full_name":"Frontczak, Idalia"},{"full_name":"Tuckerman, Laurette","last_name":"Tuckerman","first_name":"Laurette"},{"full_name":"Wesfreid, José","first_name":"José","last_name":"Wesfreid"}],"department":[{"_id":"BjHo"}],"intvolume":" 2","publisher":"American Physical Society","status":"public","publication_status":"published","title":"Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence","_id":"513","year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","publist_id":"7306","abstract":[{"lang":"eng","text":"We present an experimental setup that creates a shear flow with zero mean advection velocity achieved by counterbalancing the nonzero streamwise pressure gradient by moving boundaries, which generates plane Couette-Poiseuille flow. We obtain experimental results in the transitional regime for this flow. Using flow visualization, we characterize the subcritical transition to turbulence in Couette-Poiseuille flow and show the existence of turbulent spots generated by a permanent perturbation. Due to the zero mean advection velocity of the base profile, these turbulent structures are nearly stationary. We distinguish two regions of the turbulent spot: the active turbulent core, which is characterized by waviness of the streaks similar to traveling waves, and the surrounding region, which includes in addition the weak undisturbed streaks and oblique waves at the laminar-turbulent interface. We also study the dependence of the size of these two regions on Reynolds number. Finally, we show that the traveling waves move in the downstream (Poiseuille) direction."}],"type":"journal_article","article_number":"043904","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevFluids.2.043904","date_published":"2017-04-01T00:00:00Z","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1704.02619","open_access":"1"}],"citation":{"short":"L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical Review Fluids 2 (2017).","mla":"Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids, vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.","chicago":"Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman, and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids. American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.","ama":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904","ieee":"L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence,” Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.","apa":"Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J. (2017). Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904","ista":"Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical transition to turbulence. Physical Review Fluids. 2(4), 043904."},"publication":"Physical Review Fluids","month":"04","day":"01","scopus_import":1},{"title":"Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803","status":"public","intvolume":" 6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"520","oa_version":"None","type":"journal_article","abstract":[{"text":"Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic manipulations alone. Here, by modulating the concentration of allosteric effectors, we focus on increasing product formation without further burdening the cells with increased expression of enzymes. Resorting to a novel 96-well microplate cultivation system for cyanobacteria, and using lactate-producing strains of Synechocystis PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of lactate productivity. Furthermore, we observed that as carbon is increasingly deviated during growth toward product formation, there is an increased fixation rate in the population of spontaneous mutants harboring an impaired production pathway. This is a challenge in the development of green cell factories, which may be countered by the incorporation in biotechnological processes of strategies such as the one pioneered here.","lang":"eng"}],"issue":"3","article_type":"letter_note","page":"395 - 401","publication":"ACS Synthetic Biology","citation":{"mla":"Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235.","short":"W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf, F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.","chicago":"Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann, Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235.","ama":"Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235","ista":"Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. 6(3), 395–401.","apa":"Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf, K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235","ieee":"W. Du et al., “Nonhierarchical flux regulation exposes the fitness burden associated with lactate production in Synechocystis sp. PCC6803,” ACS Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401, 2017."},"date_published":"2017-03-17T00:00:00Z","scopus_import":1,"day":"17","publication_status":"published","department":[{"_id":"ToBo"}],"publisher":"American Chemical Society","year":"2017","pmid":1,"date_updated":"2021-01-12T08:01:21Z","date_created":"2018-12-11T11:46:56Z","volume":6,"author":[{"last_name":"Du","first_name":"Wei","full_name":"Du, Wei"},{"orcid":"0000-0001-8619-2223","id":"4677C796-F248-11E8-B48F-1D18A9856A87","last_name":"Angermayr","first_name":"Andreas","full_name":"Angermayr, Andreas"},{"first_name":"Joeri","last_name":"Jongbloets","full_name":"Jongbloets, Joeri"},{"full_name":"Molenaar, Douwe","last_name":"Molenaar","first_name":"Douwe"},{"full_name":"Bachmann, Herwig","last_name":"Bachmann","first_name":"Herwig"},{"full_name":"Hellingwerf, Klaas","first_name":"Klaas","last_name":"Hellingwerf"},{"full_name":"Branco Dos Santos, Filipe","first_name":"Filipe","last_name":"Branco Dos Santos"}],"publist_id":"7298","quality_controlled":"1","external_id":{"pmid":["27936615"]},"language":[{"iso":"eng"}],"doi":"10.1021/acssynbio.6b00235","month":"03","publication_identifier":{"issn":["21615063"]}},{"language":[{"iso":"eng"}],"date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.topol.2016.10.005","page":"45 - 57","quality_controlled":"1","citation":{"chicago":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005.","short":"K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.","mla":"Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.” Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.","apa":"Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising. Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005","ieee":"K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.","ista":"Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology and its Applications. 215, 45–57.","ama":"Austin K, Virk Z. Higson compactification and dimension raising. Topology and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1608.03954v1"}],"oa":1,"publication":"Topology and its Applications","publication_identifier":{"issn":["01668641"]},"day":"01","month":"01","volume":215,"oa_version":"Submitted Version","date_created":"2018-12-11T11:46:56Z","date_updated":"2021-01-12T08:01:21Z","author":[{"first_name":"Kyle","last_name":"Austin","full_name":"Austin, Kyle"},{"id":"2E36B656-F248-11E8-B48F-1D18A9856A87","first_name":"Ziga","last_name":"Virk","full_name":"Virk, Ziga"}],"publisher":"Elsevier","department":[{"_id":"HeEd"}],"intvolume":" 215","title":"Higson compactification and dimension raising","status":"public","publication_status":"published","year":"2017","_id":"521","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7299","abstract":[{"text":"Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful in showing that the classical dimension raising theorems hold in large scale; that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely n-to-1 maps, which include the natural quotient maps via a finite group action, and prove that they preserve the asymptotic dimension.","lang":"eng"}],"type":"journal_article"},{"status":"public","publication_status":"published","title":"Plant biology: Building barriers… in roots","intvolume":" 27","publisher":"Cell Press","_id":"525","acknowledgement":"Biotechnology and Biological Sciences Research Council:\tBBSRC BB/M001806/1 and BB/H020314/1\t","year":"2017","date_updated":"2021-01-12T08:01:23Z","date_created":"2018-12-11T11:46:58Z","file":[{"file_name":"IST-2018-983-v1+1_Plant_biology_Building_barriers__in_roots.pdf","access_level":"open_access","file_size":2840413,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5330","date_updated":"2020-07-14T12:46:38Z","date_created":"2018-12-12T10:18:11Z","checksum":"81fd4475c5a2a2c6f4313beeab215ed9"}],"volume":27,"author":[{"id":"49E91952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6862-1247","first_name":"Daniel","last_name":"Von Wangenheim","full_name":"Daniel von Wangenheim"},{"last_name":"Goh","first_name":"Tatsuaki","full_name":"Goh, Tatsuaki"},{"full_name":"Dietrich, Daniela","first_name":"Daniela","last_name":"Dietrich"},{"full_name":"Bennett, Malcolm J","last_name":"Bennett","first_name":"Malcolm"}],"pubrep_id":"983","type":"journal_article","extern":1,"file_date_updated":"2020-07-14T12:46:38Z","abstract":[{"text":"The Casparian strip is an important barrier regulating water and nutrient uptake into root tissues. New research reveals two peptide signals and their co-receptors play critical roles patterning and maintaining barrier integrity. ","lang":"eng"}],"issue":"5","publist_id":"7294","quality_controlled":0,"page":"R172 - R174","publication":"Current Biology","citation":{"short":"D. von Wangenheim, T. Goh, D. Dietrich, M. Bennett, Current Biology 27 (2017) R172–R174.","mla":"von Wangenheim, Daniel, et al. “Plant Biology: Building Barriers… in Roots.” Current Biology, vol. 27, no. 5, Cell Press, 2017, pp. R172–74, doi:10.1016/j.cub.2017.01.060.","chicago":"Wangenheim, Daniel von, Tatsuaki Goh, Daniela Dietrich, and Malcolm Bennett. “Plant Biology: Building Barriers… in Roots.” Current Biology. Cell Press, 2017. https://doi.org/10.1016/j.cub.2017.01.060.","ama":"von Wangenheim D, Goh T, Dietrich D, Bennett M. Plant biology: Building barriers… in roots. Current Biology. 2017;27(5):R172-R174. doi:10.1016/j.cub.2017.01.060","ieee":"D. von Wangenheim, T. Goh, D. Dietrich, and M. Bennett, “Plant biology: Building barriers… in roots,” Current Biology, vol. 27, no. 5. Cell Press, pp. R172–R174, 2017.","apa":"von Wangenheim, D., Goh, T., Dietrich, D., & Bennett, M. (2017). Plant biology: Building barriers… in roots. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2017.01.060","ista":"von Wangenheim D, Goh T, Dietrich D, Bennett M. 2017. Plant biology: Building barriers… in roots. Current Biology. 27(5), R172–R174."},"main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/983","open_access":"1"}],"oa":1,"date_published":"2017-03-06T00:00:00Z","doi":"10.1016/j.cub.2017.01.060","day":"06","month":"03"},{"extern":1,"publist_id":"7290","abstract":[{"text":"The pituitary adenylyl cyclase-activating polypeptide (PACAP) and its G protein-coupled receptors, PAC1, VPAC1 and VPAC2 form a system involved in a variety of biological processes. Although some sympathetic stimulatory effects of this system have been reported, its central cardiovascular regulatory properties are poorly characterized. VPAC1 receptors are expressed in the nucleus ambiguus (nAmb), a key center controlling cardiac parasympathetic tone. In this study, we report that selective VPAC1 activation in rhodamine-labeled cardiac vagal preganglionic neurons of the rat nAmb produces inositol 1,4,5-trisphosphate receptor-mediated Ca2+ mobilization, membrane depolarization and activation of P/Q-type Ca2+ channels. In vivo, this pathway converges onto transient reduction in heart rate of conscious rats. Therefore we demonstrate a VPAC1-dependent mechanism in the central parasympathetic regulation of the heart rate, adding to the complexity of PACAP-mediated cardiovascular modulation.","lang":"eng"}],"type":"journal_article","volume":1657,"date_updated":"2021-01-12T08:01:26Z","date_created":"2018-12-11T11:46:59Z","author":[{"first_name":"Florin","last_name":"Gherghina","full_name":"Gherghina, Florin L"},{"full_name":"Tica, Andrei A","first_name":"Andrei","last_name":"Tica"},{"full_name":"Elena Deliu","last_name":"Deliu","first_name":"Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abood, Mary E","last_name":"Abood","first_name":"Mary"},{"last_name":"Brailoiu","first_name":"G.","full_name":"Brailoiu, G. Christina"},{"full_name":"Brǎiloiu, Eugen","last_name":"Brǎiloiu","first_name":"Eugen"}],"intvolume":" 1657","publisher":"Elsevier","publication_status":"published","title":"Effects of VPAC1 activation in nucleus ambiguus neurons","status":"public","acknowledgement":"This study was supported by startup funds from the Jefferson College of Pharmacy, and by the National Institutes of Health DA023204 (to M.E.A) and P30 DA 013429 to Center for Substance Abuse Research, Temple University.","_id":"529","year":"2017","month":"02","day":"15","doi":"10.1016/j.brainres.2016.12.026","date_published":"2017-02-15T00:00:00Z","page":"297 - 303","quality_controlled":0,"citation":{"short":"F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, E. Brǎiloiu, Brain Research 1657 (2017) 297–303.","mla":"Gherghina, Florin, et al. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” Brain Research, vol. 1657, Elsevier, 2017, pp. 297–303, doi:10.1016/j.brainres.2016.12.026.","chicago":"Gherghina, Florin, Andrei Tica, Elena Deliu, Mary Abood, G. Brailoiu, and Eugen Brǎiloiu. “Effects of VPAC1 Activation in Nucleus Ambiguus Neurons.” Brain Research. Elsevier, 2017. https://doi.org/10.1016/j.brainres.2016.12.026.","ama":"Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 2017;1657:297-303. doi:10.1016/j.brainres.2016.12.026","apa":"Gherghina, F., Tica, A., Deliu, E., Abood, M., Brailoiu, G., & Brǎiloiu, E. (2017). Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. Elsevier. https://doi.org/10.1016/j.brainres.2016.12.026","ieee":"F. Gherghina, A. Tica, E. Deliu, M. Abood, G. Brailoiu, and E. Brǎiloiu, “Effects of VPAC1 activation in nucleus ambiguus neurons,” Brain Research, vol. 1657. Elsevier, pp. 297–303, 2017.","ista":"Gherghina F, Tica A, Deliu E, Abood M, Brailoiu G, Brǎiloiu E. 2017. Effects of VPAC1 activation in nucleus ambiguus neurons. Brain Research. 1657, 297–303."},"publication":"Brain Research"},{"publication_identifier":{"issn":["01795376"]},"month":"06","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1602.07907","open_access":"1"}],"external_id":{"arxiv":["1602.07907"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00454-017-9900-0","publist_id":"7283","department":[{"_id":"UlWa"}],"publisher":"Springer","publication_status":"published","year":"2017","volume":58,"date_created":"2018-12-11T11:47:01Z","date_updated":"2023-02-21T17:01:34Z","related_material":{"record":[{"id":"1379","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Burton, Benjamin","last_name":"Burton","first_name":"Benjamin"},{"full_name":"De Mesmay, Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","last_name":"De Mesmay","first_name":"Arnaud N"},{"full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":1,"article_processing_charge":"No","day":"09","page":"871 - 888","article_type":"original","citation":{"ista":"Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.","ieee":"B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4. Springer, pp. 871–888, 2017.","apa":"Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9900-0","ama":"Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds. Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0","chicago":"Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer, 2017. https://doi.org/10.1007/s00454-017-9900-0.","mla":"Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.” Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017, pp. 871–88, doi:10.1007/s00454-017-9900-0.","short":"B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry 58 (2017) 871–888."},"publication":"Discrete & Computational Geometry","date_published":"2017-06-09T00:00:00Z","type":"journal_article","issue":"4","abstract":[{"text":"We investigate the complexity of finding an embedded non-orientable surface of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural question in low-dimensional topology, and as a first non-trivial instance of embeddability of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding to the relatively few hardness results that are currently known in 3-manifold topology. In addition, we show that the problem lies in NP when the Euler genus g is odd, and we give an explicit algorithm in this case.","lang":"eng"}],"intvolume":" 58","status":"public","title":"Finding non-orientable surfaces in 3-Manifolds","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"534","oa_version":"Preprint"},{"year":"2017","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Kainrath, Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","first_name":"Stephanie","last_name":"Kainrath"},{"full_name":"Stadler, Manuela","first_name":"Manuela","last_name":"Stadler"},{"orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart","first_name":"Eva","full_name":"Gschaider-Reichhart, Eva"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"volume":129,"date_created":"2018-12-11T11:47:02Z","date_updated":"2021-01-12T08:01:33Z","publist_id":"7279","ec_funded":1,"file_date_updated":"2020-07-14T12:46:39Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"},{"grant_number":"W1232-B24","_id":"255A6082-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Drug Targets"}],"quality_controlled":"1","doi":"10.1002/ange.201611998","language":[{"iso":"eng"}],"month":"05","_id":"538","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 129","title":"Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen","ddc":["571"],"status":"public","pubrep_id":"932","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":1668557,"access_level":"open_access","file_name":"IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf","checksum":"d66fee867e7cdbfa3fe276c2fb0778bb","date_updated":"2020-07-14T12:46:39Z","date_created":"2018-12-12T10:13:24Z","file_id":"5007","relation":"main_file"}],"type":"journal_article","issue":"16","abstract":[{"text":"Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren. Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität während der Embryonalentwicklung. ","lang":"ger"}],"citation":{"ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 2017;129(16):4679-4682. doi:10.1002/ange.201611998","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. 129(16), 4679–4682.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,” Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998","mla":"Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley, 2017, pp. 4679–82, doi:10.1002/ange.201611998.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie 129 (2017) 4679–4682.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998."},"publication":"Angewandte Chemie","page":"4679 - 4682","date_published":"2017-05-20T00:00:00Z","has_accepted_license":"1","day":"20"},{"department":[{"_id":"GaNo"}],"publisher":"Public Library of Science","publication_status":"published","year":"2017","volume":13,"date_created":"2018-12-11T11:47:03Z","date_updated":"2021-01-12T08:01:48Z","author":[{"first_name":"Kseniya","last_name":"Khamina","full_name":"Khamina, Kseniya"},{"full_name":"Lercher, Alexander","last_name":"Lercher","first_name":"Alexander"},{"full_name":"Caldera, Michael","first_name":"Michael","last_name":"Caldera"},{"last_name":"Schliehe","first_name":"Christopher","full_name":"Schliehe, Christopher"},{"first_name":"Bojan","last_name":"Vilagos","full_name":"Vilagos, Bojan"},{"first_name":"Mehmet","last_name":"Sahin","full_name":"Sahin, Mehmet"},{"first_name":"Lindsay","last_name":"Kosack","full_name":"Kosack, Lindsay"},{"first_name":"Anannya","last_name":"Bhattacharya","full_name":"Bhattacharya, Anannya"},{"first_name":"Peter","last_name":"Májek","full_name":"Májek, Peter"},{"first_name":"Alexey","last_name":"Stukalov","full_name":"Stukalov, Alexey"},{"full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87","first_name":"Roberto","last_name":"Sacco"},{"full_name":"James, Leo","last_name":"James","first_name":"Leo"},{"last_name":"Pinschewer","first_name":"Daniel","full_name":"Pinschewer, Daniel"},{"full_name":"Bennett, Keiryn","first_name":"Keiryn","last_name":"Bennett"},{"full_name":"Menche, Jörg","last_name":"Menche","first_name":"Jörg"},{"last_name":"Bergthaler","first_name":"Andreas","full_name":"Bergthaler, Andreas"}],"article_number":"e1006758","publist_id":"7276","file_date_updated":"2020-07-14T12:46:44Z","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1371/journal.ppat.1006758","publication_identifier":{"issn":["15537366"]},"month":"12","intvolume":" 13","title":"Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein","status":"public","ddc":["576","616"],"_id":"540","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:44Z","date_created":"2018-12-12T10:12:26Z","checksum":"1aa20f19a1e90664fadce6e7d5284fdc","file_id":"4944","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":4106772,"file_name":"IST-2018-931-v1+1_journal.ppat.1006758.pdf","access_level":"open_access"}],"pubrep_id":"931","type":"journal_article","issue":"12","abstract":[{"lang":"eng","text":"RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection. A major genetic determinant for its ability to persist maps to a single amino acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional consequences remain elusive. To unravel the L protein interactions with the host proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics. A subsequent mass-spectrometric analysis of L protein pulldowns from infected human cells revealed a comprehensive network of interacting host proteins. The obtained LCMV L protein interactome was bioinformatically integrated with known host protein interactors of RdRps from other RNA viruses, emphasizing interconnected modules of human proteins. Functional characterization of selected interactors highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors. To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired virus control in chronic infection. These results provide insights into the complex interactions of the arenavirus LCMV and other viral RdRps with the host proteome and contribute to a better molecular understanding of how chronic viruses interact with their host."}],"citation":{"ama":"Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 2017;13(12). doi:10.1371/journal.ppat.1006758","ista":"Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L, Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K, Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.","ieee":"K. Khamina et al., “Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol. 13, no. 12. Public Library of Science, 2017.","apa":"Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M., … Bergthaler, A. (2017). Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1006758","mla":"Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol. 13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.","short":"K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L. Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer, K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).","chicago":"Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe, Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758."},"publication":"PLoS Pathogens","date_published":"2017-12-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"01"},{"department":[{"_id":"KrCh"}],"publisher":"International Federation of Computational Logic","publication_status":"published","year":"2017","volume":13,"date_updated":"2023-02-23T12:26:16Z","date_created":"2018-12-11T11:46:38Z","related_material":{"record":[{"id":"1657","status":"public","relation":"earlier_version"},{"status":"public","relation":"earlier_version","id":"5429"},{"id":"5435","status":"public","relation":"earlier_version"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Křetínská, Zuzana","first_name":"Zuzana","last_name":"Křetínská"},{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"}],"article_number":"15","publist_id":"7355","ec_funded":1,"file_date_updated":"2020-07-14T12:46:33Z","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309","call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)"}],"quality_controlled":"1","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.23638/LMCS-13(2:15)2017","publication_identifier":{"issn":["18605974"]},"month":"07","intvolume":" 13","title":"Unifying two views on multiple mean-payoff objectives in Markov decision processes","status":"public","ddc":["004"],"_id":"466","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:18:32Z","date_updated":"2020-07-14T12:46:33Z","checksum":"bfa405385ec6229ad5ead89ab5751639","file_id":"5354","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":511832,"file_name":"IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf","access_level":"open_access"}],"pubrep_id":"957","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with multiple limit-average (or mean-payoff) objectives. There exist two different views: (i) the expectation semantics, where the goal is to optimize the expected mean-payoff objective, and (ii) the satisfaction semantics, where the goal is to maximize the probability of runs such that the mean-payoff value stays above a given vector. We consider optimization with respect to both objectives at once, thus unifying the existing semantics. Precisely, the goal is to optimize the expectation while ensuring the satisfaction constraint. Our problem captures the notion of optimization with respect to strategies that are risk-averse (i.e., ensure certain probabilistic guarantee). Our main results are as follows: First, we present algorithms for the decision problems which are always polynomial in the size of the MDP. We also show that an approximation of the Pareto-curve can be computed in time polynomial in the size of the MDP, and the approximation factor, but exponential in the number of dimensions. Second, we present a complete characterization of the strategy complexity (in terms of memory bounds and randomization) required to solve our problem. "}],"citation":{"ista":"Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 13(2), 15.","apa":"Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017","ieee":"K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple mean-payoff objectives in Markov decision processes,” Logical Methods in Computer Science, vol. 13, no. 2. International Federation of Computational Logic, 2017.","ama":"Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff objectives in Markov decision processes. Logical Methods in Computer Science. 2017;13(2). doi:10.23638/LMCS-13(2:15)2017","chicago":"Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(2:15)2017.","mla":"Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical Methods in Computer Science, vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017.","short":"K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science 13 (2017)."},"publication":"Logical Methods in Computer Science","date_published":"2017-07-03T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"03"},{"citation":{"apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata. ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.","ista":"Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 18(4), 31.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational Logic (TOCL) 18 (2017).","mla":"Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769."},"publication":"ACM Transactions on Computational Logic (TOCL)","date_published":"2017-12-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 18","status":"public","title":"Nested weighted automata","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"467","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata or in any other known decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata, which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in runtime verification. We establish an almost-complete decidability picture for the basic decision problems about nested weighted automata and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties."}],"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1606.03598","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1606.03598"]},"language":[{"iso":"eng"}],"doi":"10.1145/3152769","publication_identifier":{"issn":["15293785"]},"month":"12","publisher":"ACM","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","year":"2017","volume":18,"date_created":"2018-12-11T11:46:38Z","date_updated":"2023-02-23T12:26:19Z","related_material":{"record":[{"id":"1656","relation":"earlier_version","status":"public"},{"id":"5415","relation":"earlier_version","status":"public"},{"relation":"earlier_version","status":"public","id":"5436"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","first_name":"Jan"}],"article_number":"31","publist_id":"7354","ec_funded":1},{"type":"journal_article","issue":"3","abstract":[{"text":"The edit distance between two words w 1 , w 2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the edit distance from L 1 to L 2 is the minimal number k such that for every word from L 1 there exists a word in L 2 with edit distance at most k . We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1) deciding whether, for a given threshold k , the edit distance from a pushdown automaton to a finite automaton is at most k , and (2) deciding whether the edit distance from a pushdown automaton to a finite automaton is finite. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"465","intvolume":" 13","title":"Edit distance for pushdown automata","ddc":["004"],"status":"public","pubrep_id":"955","file":[{"content_type":"application/pdf","file_size":279071,"creator":"system","file_name":"IST-2015-321-v1+1_main.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:37Z","date_updated":"2020-07-14T12:46:33Z","checksum":"08041379ba408d40664f449eb5907a8f","relation":"main_file","file_id":"5090"},{"relation":"main_file","file_id":"5091","date_updated":"2020-07-14T12:46:33Z","date_created":"2018-12-12T10:14:38Z","checksum":"08041379ba408d40664f449eb5907a8f","file_name":"IST-2018-955-v1+1_2017_Chatterjee_Edit_distance.pdf","access_level":"open_access","file_size":279071,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","scopus_import":1,"has_accepted_license":"1","day":"13","citation":{"ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” Logical Methods in Computer Science, vol. 13, no. 3. International Federation of Computational Logic, 2017.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017). Edit distance for pushdown automata. Logical Methods in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for pushdown automata. Logical Methods in Computer Science. 13(3).","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods in Computer Science 13 (2017).","mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science, vol. 13, no. 3, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science. International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017."},"publication":"Logical Methods in Computer Science","date_published":"2017-09-13T00:00:00Z","ec_funded":1,"publist_id":"7356","file_date_updated":"2020-07-14T12:46:33Z","year":"2017","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"International Federation of Computational Logic","publication_status":"published","related_material":{"record":[{"id":"1610","status":"public","relation":"earlier_version"},{"id":"5438","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"volume":13,"date_created":"2018-12-11T11:46:37Z","date_updated":"2023-02-23T12:26:25Z","publication_identifier":{"issn":["18605974"]},"month":"09","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode"},"oa":1,"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"}],"quality_controlled":"1","doi":"10.23638/LMCS-13(3:23)2017","language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population. The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure. Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade. In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Cometswarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively. ","lang":"eng"}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"512","status":"public","title":"Amplification on undirected population structures: Comets beat stars","ddc":["004"],"intvolume":" 7","pubrep_id":"938","file":[{"file_name":"IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1536783,"creator":"system","relation":"main_file","file_id":"5357","date_created":"2018-12-12T10:18:35Z","date_updated":"2020-07-14T12:46:36Z","checksum":"7d05cbdd914e194a019c0f91fb64e9a8"}],"oa_version":"Published Version","scopus_import":1,"day":"06","article_processing_charge":"No","has_accepted_license":"1","publication":"Scientific Reports","citation":{"ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 2017;7(1). doi:10.1038/s41598-017-00107-w","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on undirected population structures: Comets beat stars. Scientific Reports. 7(1), 82.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification on undirected population structures: Comets beat stars. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification on undirected population structures: Comets beat stars,” Scientific Reports, vol. 7, no. 1. Nature Publishing Group, 2017.","mla":"Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing Group, 2017, doi:10.1038/s41598-017-00107-w.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports 7 (2017).","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.” Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w."},"date_published":"2017-03-06T00:00:00Z","article_number":"82","file_date_updated":"2020-07-14T12:46:36Z","publist_id":"7307","ec_funded":1,"year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Nature Publishing Group","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","first_name":"Andreas","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"related_material":{"record":[{"id":"5449","relation":"earlier_version","status":"public"}]},"date_updated":"2023-02-23T12:26:57Z","date_created":"2018-12-11T11:46:53Z","volume":7,"month":"03","publication_identifier":{"issn":["20452322"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"doi":"10.1038/s41598-017-00107-w","language":[{"iso":"eng"}]},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"27","citation":{"ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158118","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability for data-dependence and Alias analysis,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158118","ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and Alias analysis. Proceedings of the ACM on Programming Languages. 2(POPL), 30.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118."},"publication":"Proceedings of the ACM on Programming Languages","article_type":"original","date_published":"2017-12-27T00:00:00Z","type":"journal_article","issue":"POPL","abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graph where the edges are labeled with different types of opening and closing parentheses, and the reachability information is computed via paths whose parentheses are properly matched. We present new results for Dyck reachability problems with applications to alias analysis and data-dependence analysis. Our main contributions, that include improved upper bounds as well as lower bounds that establish optimality guarantees, are as follows: First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph with n nodes and m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)), where α(n) is the inverse Ackermann function, improving the previously known O(n2) time bound; (ii) a matching lower bound that shows that our algorithm is optimal wrt to worst-case complexity; and (iii) an optimal average-case upper bound of O(m) time, improving the previously known O(m · logn) bound. Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtain analysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is only linear, and only wrt the number of call sites. Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication, which is a long-standing open problem. Thus we establish that the existing combinatorial algorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the same hardness holds for graphs of constant treewidth. Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependence analysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform all existing methods on the two problems, over real-world benchmarks."}],"_id":"10416","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 2","title":"Optimal Dyck reachability for data-dependence and Alias analysis","status":"public","ddc":["000"],"oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2017_ACMProgLang_Chatterjee.pdf","content_type":"application/pdf","file_size":460188,"creator":"cchlebak","relation":"main_file","file_id":"10421","checksum":"faa3f7b3fe8aab84b50ed805c26a0ee5","success":1,"date_updated":"2021-12-07T08:06:28Z","date_created":"2021-12-07T08:06:28Z"}],"publication_identifier":{"eissn":["2475-1421"]},"month":"12","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["1910.00241"]},"oa":1,"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","doi":"10.1145/3158118","conference":{"name":"POPL: Programming Languages","end_date":"2018-01-13","start_date":"2018-01-07","location":"Los Angeles, CA, United States"},"language":[{"iso":"eng"}],"article_number":"30","ec_funded":1,"file_date_updated":"2021-12-07T08:06:28Z","year":"2017","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant (279307: Graph Games).\r\n","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5455"}]},"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Choudhary, Bhavya","last_name":"Choudhary","first_name":"Bhavya"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","full_name":"Pavlogiannis, Andreas"}],"volume":2,"date_updated":"2023-02-23T12:27:13Z","date_created":"2021-12-05T23:01:48Z"},{"day":"23","article_processing_charge":"No","has_accepted_license":"1","citation":{"ista":"Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability for data-dependence and alias analysis, IST Austria, 37p.","apa":"Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck reachability for data-dependence and alias analysis. IST Austria. https://doi.org/10.15479/AT:IST-2017-870-v1-1","ieee":"K. Chatterjee, B. Choudhary, and A. Pavlogiannis, Optimal Dyck reachability for data-dependence and alias analysis. IST Austria, 2017.","ama":"Chatterjee K, Choudhary B, Pavlogiannis A. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria; 2017. doi:10.15479/AT:IST-2017-870-v1-1","chicago":"Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-870-v1-1.","mla":"Chatterjee, Krishnendu, et al. Optimal Dyck Reachability for Data-Dependence and Alias Analysis. IST Austria, 2017, doi:10.15479/AT:IST-2017-870-v1-1.","short":"K. Chatterjee, B. Choudhary, A. Pavlogiannis, Optimal Dyck Reachability for Data-Dependence and Alias Analysis, IST Austria, 2017."},"page":"37","date_published":"2017-10-23T00:00:00Z","type":"technical_report","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"A fundamental algorithmic problem at the heart of static analysis is Dyck reachability. The input is a graphwhere the edges are labeled with different types of opening and closing parentheses, and the reachabilityinformation is computed via paths whose parentheses are properly matched. We present new results for Dyckreachability problems with applications to alias analysis and data-dependence analysis. Our main contributions,that include improved upper bounds as well as lower bounds that establish optimality guarantees, are asfollows:First, we consider Dyck reachability on bidirected graphs, which is the standard way of performing field-sensitive points-to analysis. Given a bidirected graph withnnodes andmedges, we present: (i) an algorithmwith worst-case running timeO(m+n·α(n)), whereα(n)is the inverse Ackermann function, improving thepreviously knownO(n2)time bound; (ii) a matching lower bound that shows that our algorithm is optimalwrt to worst-case complexity; and (iii) an optimal average-case upper bound ofO(m)time, improving thepreviously knownO(m·logn)bound.Second, we consider the problem of context-sensitive data-dependence analysis, where the task is to obtainanalysis summaries of library code in the presence of callbacks. Our algorithm preprocesses libraries in almostlinear time, after which the contribution of the library in the complexity of the client analysis is only linear,and only wrt the number of call sites.Third, we prove that combinatorial algorithms for Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained without obtaining sub-cubic combinatorial algorithms for Boolean MatrixMultiplication, which is a long-standing open problem. Thus we establish that the existing combinatorialalgorithms for Dyck reachability are (conditionally) optimal for general graphs. We also show that the samehardness holds for graphs of constant treewidth.Finally, we provide a prototype implementation of our algorithms for both alias analysis and data-dependenceanalysis. Our experimental evaluation demonstrates that the new algorithms significantly outperform allexisting methods on the two problems, over real-world benchmarks."}],"_id":"5455","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Optimal Dyck reachability for data-dependence and alias analysis","ddc":["000"],"status":"public","pubrep_id":"870","oa_version":"Published Version","file":[{"file_name":"IST-2017-870-v1+1_main.pdf","access_level":"open_access","file_size":960491,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5524","date_updated":"2020-07-14T12:46:59Z","date_created":"2018-12-12T11:54:02Z","checksum":"177a84a46e3ac17e87b31534ad16a4c9"}],"month":"10","publication_identifier":{"issn":["2664-1690"]},"oa":1,"doi":"10.15479/AT:IST-2017-870-v1-1","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:59Z","year":"2017","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IST Austria","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Choudhary, Bhavya","last_name":"Choudhary","first_name":"Bhavya"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"}],"related_material":{"record":[{"id":"10416","status":"public","relation":"later_version"}]},"date_created":"2018-12-12T11:39:26Z","date_updated":"2023-02-21T15:54:10Z"},{"date_published":"2017-06-26T00:00:00Z","oa":1,"publication_date":"2017-06-26","citation":{"ama":"Petritsch B. Implementing the Institutional Data Repository IST DataRep. IST Austria; 2017.","ista":"Petritsch B. 2017. Implementing the institutional data repository IST DataRep, IST Austria,p.","ieee":"B. Petritsch, Implementing the institutional data repository IST DataRep. IST Austria, 2017.","apa":"Petritsch, B. (2017). Implementing the institutional data repository IST DataRep. IST Austria.","mla":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017.","short":"B. Petritsch, Implementing the Institutional Data Repository IST DataRep, IST Austria, 2017.","chicago":"Petritsch, Barbara. Implementing the Institutional Data Repository IST DataRep. IST Austria, 2017."},"main_file_link":[{"url":"https://repository.ist.ac.at/id/eprint/724.","open_access":"1"}],"day":"26","month":"06","pubrep_id":"724","author":[{"full_name":"Barbara Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614","first_name":"Barbara","last_name":"Petritsch"}],"file":[{"creator":"system","file_size":3460985,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-724-v1+1_DataRep_Project_Report_2017.pdf","checksum":"6321792dcfa82bf490f17615a9b22355","date_created":"2018-12-12T11:53:22Z","date_updated":"2020-07-14T12:46:59Z","file_id":"5483","relation":"main_file"}],"date_updated":"2020-07-14T23:05:03Z","date_created":"2018-12-12T11:39:24Z","year":"2017","_id":"5450","department":[{"_id":"E-Lib"}],"publisher":"IST Austria","title":"Implementing the institutional data repository IST DataRep","status":"public","abstract":[{"lang":"eng","text":"In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep."}],"file_date_updated":"2020-07-14T12:46:59Z","extern":0,"type":"report"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence."}],"issue":"POPL","status":"public","title":"Data-centric dynamic partial order reduction","intvolume":" 2","_id":"10417","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","scopus_import":"1","day":"27","article_processing_charge":"No","article_type":"original","publication":"Proceedings of the ACM on Programming Languages","citation":{"short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2017).","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2017, doi:10.1145/3158119.","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158119.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2017;2(POPL). doi:10.1145/3158119","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31."},"date_published":"2017-12-27T00:00:00Z","article_number":"31","ec_funded":1,"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","year":"2017","date_created":"2021-12-05T23:01:49Z","date_updated":"2023-02-23T12:27:16Z","volume":2,"author":[{"last_name":"Chalupa","first_name":"Marek","full_name":"Chalupa, Marek"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"full_name":"Sinha, Nishant","first_name":"Nishant","last_name":"Sinha"},{"full_name":"Vaidya, Kapil","last_name":"Vaidya","first_name":"Kapil"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5448"},{"status":"public","relation":"earlier_version","id":"5456"}]},"month":"12","publication_identifier":{"eissn":["2475-1421"]},"quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"main_file_link":[{"url":"https://dl.acm.org/doi/10.1145/3158119","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1610.01188"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2018-01-13","location":"Los Angeles, CA, United States","start_date":"2018-01-07","name":"POPL: Programming Languages"},"doi":"10.1145/3158119"},{"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2017-872-v1-1","date_published":"2017-10-23T00:00:00Z","page":"36","citation":{"mla":"Chalupa, Marek, et al. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017, doi:10.15479/AT:IST-2017-872-v1-1.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2017.","chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. Data-Centric Dynamic Partial Order Reduction. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2017-872-v1-1.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-Centric Dynamic Partial Order Reduction. IST Austria; 2017. doi:10.15479/AT:IST-2017-872-v1-1","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric dynamic partial order reduction, IST Austria, 36p.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, Data-centric dynamic partial order reduction. IST Austria, 2017.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2017). Data-centric dynamic partial order reduction. IST Austria. https://doi.org/10.15479/AT:IST-2017-872-v1-1"},"oa":1,"publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","month":"10","day":"23","oa_version":"Published Version","file":[{"creator":"system","file_size":910347,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-872-v1+1_main.pdf","checksum":"d2635c4cf013000f0a1b09e80f9e4ab7","date_created":"2018-12-12T11:53:26Z","date_updated":"2020-07-14T12:46:59Z","file_id":"5487","relation":"main_file"}],"date_created":"2018-12-12T11:39:26Z","date_updated":"2023-02-23T12:26:54Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"10417"},{"status":"public","relation":"earlier_version","id":"5448"}]},"pubrep_id":"872","author":[{"last_name":"Chalupa","first_name":"Marek","full_name":"Chalupa, Marek"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722"},{"last_name":"Sinha","first_name":"Nishant","full_name":"Sinha, Nishant"},{"full_name":"Vaidya, Kapil","last_name":"Vaidya","first_name":"Kapil"}],"department":[{"_id":"KrCh"}],"publisher":"IST Austria","ddc":["000"],"publication_status":"published","status":"public","title":"Data-centric dynamic partial order reduction","year":"2017","_id":"5456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes."}],"file_date_updated":"2020-07-14T12:46:59Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report"},{"oa_version":"Published Version","file":[{"creator":"system","file_size":535077,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-924-v1+1_LIPIcs-MFCS-2017-61.pdf","checksum":"2eed5224c0e4e259484a1d71acb8ba6a","date_created":"2018-12-12T10:18:04Z","date_updated":"2020-07-14T12:47:00Z","file_id":"5322","relation":"main_file"}],"pubrep_id":"924","intvolume":" 83","title":"Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs","status":"public","ddc":["004"],"_id":"551","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. ","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2017-11-01T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Martin Nowak. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.61.","short":"K. Chatterjee, R. Ibsen-Jensen, M. Nowak, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. “Faster Monte Carlo Algorithms for Fixation Probability of the Moran Process on Undirected Graphs.” Leibniz International Proceedings in Informatics, vol. 83, 61, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.61.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and M. Nowak, “Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","apa":"Chatterjee, K., Ibsen-Jensen, R., & Nowak, M. (2017). Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.61","ista":"Chatterjee K, Ibsen-Jensen R, Nowak M. 2017. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 61.","ama":"Chatterjee K, Ibsen-Jensen R, Nowak M. Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.61"},"publication":"Leibniz International Proceedings in Informatics","has_accepted_license":"1","day":"01","scopus_import":1,"volume":83,"date_created":"2018-12-11T11:47:08Z","date_updated":"2021-01-12T08:02:34Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","year":"2017","publist_id":"7263","file_date_updated":"2020-07-14T12:47:00Z","article_number":"61","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.MFCS.2017.61","conference":{"start_date":"2017-08-21","location":"Aalborg, Denmark","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"isbn":["978-395977046-0"]},"month":"11"},{"year":"2017","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"volume":83,"date_created":"2018-12-11T11:47:08Z","date_updated":"2023-02-14T10:06:46Z","article_number":"39","ec_funded":1,"publist_id":"7262","file_date_updated":"2020-07-14T12:47:00Z","license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"quality_controlled":"1","doi":"10.4230/LIPIcs.MFCS.2017.39","conference":{"name":"MFCS: Mathematical Foundations of Computer Science (SG)","end_date":"2017-08-25","start_date":"2017-08-21","location":"Aalborg, Denmark"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-395977046-0"]},"month":"11","_id":"552","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 83","ddc":["004"],"status":"public","title":"Faster algorithms for mean-payoff parity games","pubrep_id":"923","file":[{"creator":"system","content_type":"application/pdf","file_size":610339,"file_name":"IST-2018-923-v1+1_LIPIcs-MFCS-2017-39.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:00Z","date_created":"2018-12-12T10:16:57Z","checksum":"c67f4866ddbfd555afef1f63ae9a8fc7","file_id":"5248","relation":"main_file"}],"oa_version":"Published Version","type":"conference","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective)."}],"citation":{"chicago":"Chatterjee, Krishnendu, Monika H Henzinger, and Alexander Svozil. “Faster Algorithms for Mean-Payoff Parity Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.39.","short":"K. Chatterjee, M.H. Henzinger, A. Svozil, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Mean-Payoff Parity Games.” Leibniz International Proceedings in Informatics, vol. 83, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.39.","ieee":"K. Chatterjee, M. H. Henzinger, and A. Svozil, “Faster algorithms for mean-payoff parity games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","apa":"Chatterjee, K., Henzinger, M. H., & Svozil, A. (2017). Faster algorithms for mean-payoff parity games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.39","ista":"Chatterjee K, Henzinger MH, Svozil A. 2017. Faster algorithms for mean-payoff parity games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 39.","ama":"Chatterjee K, Henzinger MH, Svozil A. Faster algorithms for mean-payoff parity games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.39"},"publication":"Leibniz International Proceedings in Informatics","date_published":"2017-11-01T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01"},{"date_published":"2017-11-01T00:00:00Z","publication":"Leibniz International Proceedings in Informatics","citation":{"mla":"Chatterjee, Krishnendu, et al. “Strategy Complexity of Concurrent Safety Games.” Leibniz International Proceedings in Informatics, vol. 83, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.55.","short":"K. Chatterjee, K. Hansen, R. Ibsen-Jensen, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Chatterjee, Krishnendu, Kristofer Hansen, and Rasmus Ibsen-Jensen. “Strategy Complexity of Concurrent Safety Games.” In Leibniz International Proceedings in Informatics, Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.55.","ama":"Chatterjee K, Hansen K, Ibsen-Jensen R. Strategy complexity of concurrent safety games. In: Leibniz International Proceedings in Informatics. Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.55","ista":"Chatterjee K, Hansen K, Ibsen-Jensen R. 2017. Strategy complexity of concurrent safety games. Leibniz International Proceedings in Informatics. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 55.","ieee":"K. Chatterjee, K. Hansen, and R. Ibsen-Jensen, “Strategy complexity of concurrent safety games,” in Leibniz International Proceedings in Informatics, Aalborg, Denmark, 2017, vol. 83.","apa":"Chatterjee, K., Hansen, K., & Ibsen-Jensen, R. (2017). Strategy complexity of concurrent safety games. In Leibniz International Proceedings in Informatics (Vol. 83). Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.55"},"day":"01","has_accepted_license":"1","scopus_import":1,"file":[{"relation":"main_file","file_id":"4753","checksum":"7101facb56ade363205c695d72dbd173","date_created":"2018-12-12T10:09:29Z","date_updated":"2020-07-14T12:47:00Z","access_level":"open_access","file_name":"IST-2018-922-v1+1_LIPIcs-MFCS-2017-55.pdf","file_size":549967,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","pubrep_id":"922","status":"public","title":"Strategy complexity of concurrent safety games","ddc":["004"],"intvolume":" 83","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"553","abstract":[{"lang":"eng","text":"We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. "}],"alternative_title":["LIPIcs"],"type":"conference","language":[{"iso":"eng"}],"conference":{"location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25","name":"MFCS: Mathematical Foundations of Computer Science (SG)"},"doi":"10.4230/LIPIcs.MFCS.2017.55","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://arxiv.org/abs/1506.02434","open_access":"1"}],"oa":1,"month":"11","publication_identifier":{"isbn":["978-395977046-0"]},"date_updated":"2021-01-12T08:02:35Z","date_created":"2018-12-11T11:47:08Z","volume":83,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Hansen","first_name":"Kristofer","full_name":"Hansen, Kristofer"},{"orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2017","file_date_updated":"2020-07-14T12:47:00Z","publist_id":"7261","article_number":"55"},{"author":[{"full_name":"Gerencser, Mate","first_name":"Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arnulf","last_name":"Jentzen","full_name":"Jentzen, Arnulf"},{"full_name":"Salimova, Diyora","last_name":"Salimova","first_name":"Diyora"}],"volume":473,"date_created":"2018-12-11T11:47:11Z","date_updated":"2021-01-12T08:03:04Z","year":"2017","department":[{"_id":"JaMa"}],"publisher":"Royal Society of London","publication_status":"published","publist_id":"7256","ec_funded":1,"article_number":"0104","doi":"10.1098/rspa.2017.0104","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1702.03229","open_access":"1"}],"oa":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"quality_controlled":"1","publication_identifier":{"issn":["13645021"]},"month":"11","oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"560","intvolume":" 473","title":"On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions","status":"public","issue":"2207","abstract":[{"text":"In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.","lang":"eng"}],"type":"journal_article","date_published":"2017-11-01T00:00:00Z","citation":{"chicago":"Gerencser, Mate, Arnulf Jentzen, and Diyora Salimova. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2017. https://doi.org/10.1098/rspa.2017.0104.","mla":"Gerencser, Mate, et al. “On Stochastic Differential Equations with Arbitrarily Slow Convergence Rates for Strong Approximation in Two Space Dimensions.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207, 0104, Royal Society of London, 2017, doi:10.1098/rspa.2017.0104.","short":"M. Gerencser, A. Jentzen, D. Salimova, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 473 (2017).","ista":"Gerencser M, Jentzen A, Salimova D. 2017. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 473(2207), 0104.","apa":"Gerencser, M., Jentzen, A., & Salimova, D. (2017). On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2017.0104","ieee":"M. Gerencser, A. Jentzen, and D. Salimova, “On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 473, no. 2207. Royal Society of London, 2017.","ama":"Gerencser M, Jentzen A, Salimova D. On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2017;473(2207). doi:10.1098/rspa.2017.0104"},"publication":"Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences","day":"01","scopus_import":1},{"author":[{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yau, Horng","last_name":"Yau","first_name":"Horng"}],"date_updated":"2022-05-24T06:57:28Z","date_created":"2018-12-11T11:47:13Z","volume":28,"year":"2017","publication_status":"published","publisher":"American Mathematical Society","department":[{"_id":"LaEr"}],"publist_id":"7247","ec_funded":1,"doi":"10.1090/cln/028","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"month":"01","publication_identifier":{"eisbn":["978-1-4704-4194-4"],"isbn":["9-781-4704-3648-3"]},"oa_version":"None","_id":"567","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A Dynamical Approach to Random Matrix Theory","status":"public","intvolume":" 28","abstract":[{"lang":"eng","text":"This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.\r\n"}],"type":"book","alternative_title":["Courant Lecture Notes"],"date_published":"2017-01-01T00:00:00Z","citation":{"ista":"Erdös L, Yau H. 2017. A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 226p.","ieee":"L. Erdös and H. Yau, A Dynamical Approach to Random Matrix Theory, vol. 28. American Mathematical Society, 2017.","apa":"Erdös, L., & Yau, H. (2017). A Dynamical Approach to Random Matrix Theory (Vol. 28). American Mathematical Society. https://doi.org/10.1090/cln/028","ama":"Erdös L, Yau H. A Dynamical Approach to Random Matrix Theory. Vol 28. American Mathematical Society; 2017. doi:10.1090/cln/028","chicago":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28. Courant Lecture Notes. American Mathematical Society, 2017. https://doi.org/10.1090/cln/028.","mla":"Erdös, László, and Horng Yau. A Dynamical Approach to Random Matrix Theory. Vol. 28, American Mathematical Society, 2017, doi:10.1090/cln/028.","short":"L. Erdös, H. Yau, A Dynamical Approach to Random Matrix Theory, American Mathematical Society, 2017."},"page":"226","day":"01","article_processing_charge":"No","series_title":"Courant Lecture Notes"},{"ec_funded":1,"publist_id":"7246","author":[{"id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek","first_name":"Peter","full_name":"Franek, Peter"},{"id":"33E21118-F248-11E8-B48F-1D18A9856A87","last_name":"Krcál","first_name":"Marek","full_name":"Krcál, Marek"}],"volume":19,"date_updated":"2021-01-12T08:03:12Z","date_created":"2018-12-11T11:47:14Z","year":"2017","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"publisher":"International Press","publication_status":"published","publication_identifier":{"issn":["15320073"]},"month":"01","doi":"10.4310/HHA.2017.v19.n2.a16","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1507.04310","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes (H2020)","_id":"2590DB08-B435-11E9-9278-68D0E5697425","grant_number":"701309"}],"quality_controlled":"1","issue":"2","abstract":[{"text":"We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"568","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 19","status":"public","title":"Persistence of zero sets","day":"01","scopus_import":1,"date_published":"2017-01-01T00:00:00Z","citation":{"ama":"Franek P, Krcál M. Persistence of zero sets. Homology, Homotopy and Applications. 2017;19(2):313-342. doi:10.4310/HHA.2017.v19.n2.a16","ista":"Franek P, Krcál M. 2017. Persistence of zero sets. Homology, Homotopy and Applications. 19(2), 313–342.","apa":"Franek, P., & Krcál, M. (2017). Persistence of zero sets. Homology, Homotopy and Applications. International Press. https://doi.org/10.4310/HHA.2017.v19.n2.a16","ieee":"P. Franek and M. Krcál, “Persistence of zero sets,” Homology, Homotopy and Applications, vol. 19, no. 2. International Press, pp. 313–342, 2017.","mla":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications, vol. 19, no. 2, International Press, 2017, pp. 313–42, doi:10.4310/HHA.2017.v19.n2.a16.","short":"P. Franek, M. Krcál, Homology, Homotopy and Applications 19 (2017) 313–342.","chicago":"Franek, Peter, and Marek Krcál. “Persistence of Zero Sets.” Homology, Homotopy and Applications. International Press, 2017. https://doi.org/10.4310/HHA.2017.v19.n2.a16."},"publication":"Homology, Homotopy and Applications","page":"313 - 342"},{"publist_id":"7244","ec_funded":1,"file_date_updated":"2020-07-14T12:47:10Z","article_number":"e28921","author":[{"first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"full_name":"Sarikas, Srdjan","last_name":"Sarikas","first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Acar, Hande","orcid":"0000-0003-1986-9753","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","last_name":"Acar","first_name":"Hande"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"}],"volume":6,"date_updated":"2021-01-12T08:03:15Z","date_created":"2018-12-11T11:47:14Z","year":"2017","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","publication_identifier":{"issn":["2050084X"]},"month":"11","doi":"10.7554/eLife.28921","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"quality_controlled":"1","abstract":[{"text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. ","lang":"eng"}],"type":"journal_article","pubrep_id":"918","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5096","checksum":"273ab17f33305e4eaafd911ff88e7c5b","date_created":"2018-12-12T10:14:42Z","date_updated":"2020-07-14T12:47:10Z","access_level":"open_access","file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","content_type":"application/pdf","file_size":8453470,"creator":"system"},{"date_created":"2018-12-12T10:14:43Z","date_updated":"2020-07-14T12:47:10Z","checksum":"b433f90576c7be597cd43367946f8e7f","file_id":"5097","relation":"main_file","creator":"system","file_size":1953221,"content_type":"application/pdf","file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","access_level":"open_access"}],"_id":"570","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 6","ddc":["576"],"title":"Regulatory network structure determines patterns of intermolecular epistasis","status":"public","has_accepted_license":"1","day":"13","scopus_import":1,"date_published":"2017-11-13T00:00:00Z","citation":{"mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.","short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921.","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017."},"publication":"eLife"},{"article_number":"e30867","file_date_updated":"2020-07-14T12:47:10Z","publist_id":"7245","year":"2017","publication_status":"published","department":[{"_id":"MiSi"}],"publisher":"eLife Sciences Publications","author":[{"full_name":"Spira, Felix","last_name":"Spira","first_name":"Felix"},{"full_name":"Cuylen Haering, Sara","first_name":"Sara","last_name":"Cuylen Haering"},{"first_name":"Shalin","last_name":"Mehta","full_name":"Mehta, Shalin"},{"first_name":"Matthias","last_name":"Samwer","full_name":"Samwer, Matthias"},{"orcid":"0000-0003-0666-8928","id":"35B76592-F248-11E8-B48F-1D18A9856A87","last_name":"Reversat","first_name":"Anne","full_name":"Reversat, Anne"},{"full_name":"Verma, Amitabh","last_name":"Verma","first_name":"Amitabh"},{"full_name":"Oldenbourg, Rudolf","last_name":"Oldenbourg","first_name":"Rudolf"},{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"full_name":"Gerlich, Daniel","first_name":"Daniel","last_name":"Gerlich"}],"date_created":"2018-12-11T11:47:14Z","date_updated":"2023-02-23T12:30:29Z","volume":6,"month":"11","publication_identifier":{"issn":["2050084X"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.7554/eLife.30867","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"569","title":"Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments","status":"public","ddc":["570"],"intvolume":" 6","pubrep_id":"919","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":9666973,"access_level":"open_access","file_name":"IST-2017-919-v1+1_elife-30867-figures-v1.pdf","checksum":"ba09c1451153d39e4f4b7cee013e314c","date_created":"2018-12-12T10:10:40Z","date_updated":"2020-07-14T12:47:10Z","file_id":"4829","relation":"main_file"},{"creator":"system","content_type":"application/pdf","file_size":5951246,"file_name":"IST-2017-919-v1+2_elife-30867-v1.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:10:41Z","checksum":"01eb51f1d6ad679947415a51c988e137","file_id":"4830","relation":"main_file"}],"scopus_import":1,"day":"06","has_accepted_license":"1","publication":"eLife","citation":{"ama":"Spira F, Cuylen Haering S, Mehta S, et al. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 2017;6. doi:10.7554/eLife.30867","ista":"Spira F, Cuylen Haering S, Mehta S, Samwer M, Reversat A, Verma A, Oldenbourg R, Sixt MK, Gerlich D. 2017. Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. eLife. 6, e30867.","apa":"Spira, F., Cuylen Haering, S., Mehta, S., Samwer, M., Reversat, A., Verma, A., … Gerlich, D. (2017). Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.30867","ieee":"F. Spira et al., “Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments,” eLife, vol. 6. eLife Sciences Publications, 2017.","mla":"Spira, Felix, et al. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife, vol. 6, e30867, eLife Sciences Publications, 2017, doi:10.7554/eLife.30867.","short":"F. Spira, S. Cuylen Haering, S. Mehta, M. Samwer, A. Reversat, A. Verma, R. Oldenbourg, M.K. Sixt, D. Gerlich, ELife 6 (2017).","chicago":"Spira, Felix, Sara Cuylen Haering, Shalin Mehta, Matthias Samwer, Anne Reversat, Amitabh Verma, Rudolf Oldenbourg, Michael K Sixt, and Daniel Gerlich. “Cytokinesis in Vertebrate Cells Initiates by Contraction of an Equatorial Actomyosin Network Composed of Randomly Oriented Filaments.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.30867."},"date_published":"2017-11-06T00:00:00Z"},{"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"571","intvolume":" 171","title":"Migrating platelets are mechano scavengers that collect and bundle bacteria","status":"public","issue":"6","abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface.","lang":"eng"}],"type":"journal_article","date_published":"2017-11-30T00:00:00Z","citation":{"chicago":"Gärtner, Florian R, Zerkah Ahmad, Gerhild Rosenberger, Shuxia Fan, Leo Nicolai, Benjamin Busch, Gökce Yavuz, et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.11.001.","short":"F.R. Gärtner, Z. Ahmad, G. Rosenberger, S. Fan, L. Nicolai, B. Busch, G. Yavuz, M. Luckner, H. Ishikawa Ankerhold, R. Hennel, A. Benechet, M. Lorenz, S. Chandraratne, I. Schubert, S. Helmer, B. Striednig, K. Stark, M. Janko, R. Böttcher, A. Verschoor, C. Leon, C. Gachet, T. Gudermann, M. Mederos Y Schnitzler, Z. Pincus, M. Iannacone, R. Haas, G. Wanner, K. Lauber, M.K. Sixt, S. Massberg, Cell Press 171 (2017) 1368–1382.","mla":"Gärtner, Florian R., et al. “Migrating Platelets Are Mechano Scavengers That Collect and Bundle Bacteria.” Cell Press, vol. 171, no. 6, Cell Press, 2017, pp. 1368–82, doi:10.1016/j.cell.2017.11.001.","apa":"Gärtner, F. R., Ahmad, Z., Rosenberger, G., Fan, S., Nicolai, L., Busch, B., … Massberg, S. (2017). Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. Cell Press. https://doi.org/10.1016/j.cell.2017.11.001","ieee":"F. R. Gärtner et al., “Migrating platelets are mechano scavengers that collect and bundle bacteria,” Cell Press, vol. 171, no. 6. Cell Press, pp. 1368–1382, 2017.","ista":"Gärtner FR, Ahmad Z, Rosenberger G, Fan S, Nicolai L, Busch B, Yavuz G, Luckner M, Ishikawa Ankerhold H, Hennel R, Benechet A, Lorenz M, Chandraratne S, Schubert I, Helmer S, Striednig B, Stark K, Janko M, Böttcher R, Verschoor A, Leon C, Gachet C, Gudermann T, Mederos Y Schnitzler M, Pincus Z, Iannacone M, Haas R, Wanner G, Lauber K, Sixt MK, Massberg S. 2017. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 171(6), 1368–1382.","ama":"Gärtner FR, Ahmad Z, Rosenberger G, et al. Migrating platelets are mechano scavengers that collect and bundle bacteria. Cell Press. 2017;171(6):1368-1382. doi:10.1016/j.cell.2017.11.001"},"publication":"Cell Press","page":"1368 - 1382","day":"30","scopus_import":1,"author":[{"full_name":"Gärtner, Florian R","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723"},{"first_name":"Zerkah","last_name":"Ahmad","full_name":"Ahmad, Zerkah"},{"full_name":"Rosenberger, Gerhild","first_name":"Gerhild","last_name":"Rosenberger"},{"full_name":"Fan, Shuxia","last_name":"Fan","first_name":"Shuxia"},{"full_name":"Nicolai, Leo","last_name":"Nicolai","first_name":"Leo"},{"first_name":"Benjamin","last_name":"Busch","full_name":"Busch, Benjamin"},{"full_name":"Yavuz, Gökce","last_name":"Yavuz","first_name":"Gökce"},{"last_name":"Luckner","first_name":"Manja","full_name":"Luckner, Manja"},{"first_name":"Hellen","last_name":"Ishikawa Ankerhold","full_name":"Ishikawa Ankerhold, Hellen"},{"last_name":"Hennel","first_name":"Roman","full_name":"Hennel, Roman"},{"full_name":"Benechet, Alexandre","last_name":"Benechet","first_name":"Alexandre"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"last_name":"Chandraratne","first_name":"Sue","full_name":"Chandraratne, Sue"},{"full_name":"Schubert, Irene","first_name":"Irene","last_name":"Schubert"},{"last_name":"Helmer","first_name":"Sebastian","full_name":"Helmer, Sebastian"},{"full_name":"Striednig, Bianca","last_name":"Striednig","first_name":"Bianca"},{"last_name":"Stark","first_name":"Konstantin","full_name":"Stark, Konstantin"},{"full_name":"Janko, Marek","last_name":"Janko","first_name":"Marek"},{"first_name":"Ralph","last_name":"Böttcher","full_name":"Böttcher, Ralph"},{"first_name":"Admar","last_name":"Verschoor","full_name":"Verschoor, Admar"},{"full_name":"Leon, Catherine","last_name":"Leon","first_name":"Catherine"},{"first_name":"Christian","last_name":"Gachet","full_name":"Gachet, Christian"},{"last_name":"Gudermann","first_name":"Thomas","full_name":"Gudermann, Thomas"},{"full_name":"Mederos Y Schnitzler, Michael","last_name":"Mederos Y Schnitzler","first_name":"Michael"},{"full_name":"Pincus, Zachary","last_name":"Pincus","first_name":"Zachary"},{"last_name":"Iannacone","first_name":"Matteo","full_name":"Iannacone, Matteo"},{"last_name":"Haas","first_name":"Rainer","full_name":"Haas, Rainer"},{"first_name":"Gerhard","last_name":"Wanner","full_name":"Wanner, Gerhard"},{"full_name":"Lauber, Kirsten","last_name":"Lauber","first_name":"Kirsten"},{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"first_name":"Steffen","last_name":"Massberg","full_name":"Massberg, Steffen"}],"volume":171,"date_updated":"2021-01-12T08:03:15Z","date_created":"2018-12-11T11:47:15Z","year":"2017","department":[{"_id":"MiSi"}],"publisher":"Cell Press","publication_status":"published","ec_funded":1,"publist_id":"7243","doi":"10.1016/j.cell.2017.11.001","language":[{"iso":"eng"}],"project":[{"_id":"260AA4E2-B435-11E9-9278-68D0E5697425","grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020"}],"quality_controlled":"1","publication_identifier":{"issn":["00928674"]},"month":"11"},{"publist_id":"7242","file_date_updated":"2020-07-14T12:47:10Z","article_number":"2587","author":[{"first_name":"Damilola","last_name":"Olatunji","full_name":"Olatunji, Damilola"},{"last_name":"Geelen","first_name":"Danny","full_name":"Geelen, Danny"},{"full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten","first_name":"Inge"}],"volume":18,"date_updated":"2021-01-12T08:03:16Z","date_created":"2018-12-11T11:47:15Z","year":"2017","department":[{"_id":"JiFr"}],"publisher":"MDPI","publication_status":"published","month":"12","doi":"10.3390/ijms18122587","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","issue":"12","abstract":[{"lang":"eng","text":"In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture."}],"type":"journal_article","pubrep_id":"917","file":[{"file_name":"IST-2017-917-v1+1_ijms-18-02587.pdf","access_level":"open_access","content_type":"application/pdf","file_size":920962,"creator":"system","relation":"main_file","file_id":"4718","date_updated":"2020-07-14T12:47:10Z","date_created":"2018-12-12T10:08:55Z","checksum":"82d51f11e493f7eec02976d9a9a9805e"}],"oa_version":"Published Version","_id":"572","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 18","ddc":["580"],"title":"Control of endogenous auxin levels in plant root development","status":"public","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2017-12-01T00:00:00Z","citation":{"ama":"Olatunji D, Geelen D, Verstraeten I. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 2017;18(12). doi:10.3390/ijms18122587","ista":"Olatunji D, Geelen D, Verstraeten I. 2017. Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. 18(12), 2587.","ieee":"D. Olatunji, D. Geelen, and I. Verstraeten, “Control of endogenous auxin levels in plant root development,” International Journal of Molecular Sciences, vol. 18, no. 12. MDPI, 2017.","apa":"Olatunji, D., Geelen, D., & Verstraeten, I. (2017). Control of endogenous auxin levels in plant root development. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms18122587","mla":"Olatunji, Damilola, et al. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences, vol. 18, no. 12, 2587, MDPI, 2017, doi:10.3390/ijms18122587.","short":"D. Olatunji, D. Geelen, I. Verstraeten, International Journal of Molecular Sciences 18 (2017).","chicago":"Olatunji, Damilola, Danny Geelen, and Inge Verstraeten. “Control of Endogenous Auxin Levels in Plant Root Development.” International Journal of Molecular Sciences. MDPI, 2017. https://doi.org/10.3390/ijms18122587."},"publication":"International Journal of Molecular Sciences"},{"month":"09","day":"01","publication_identifier":{"issn":["09249907"]},"language":[{"iso":"eng"}],"doi":"10.1007/s10851-017-0718-4","date_published":"2017-09-01T00:00:00Z","quality_controlled":"1","page":"69-83","publication":"Journal of Mathematical Imaging and Vision","citation":{"mla":"Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision, vol. 59, no. 1, Springer Nature, 2017, pp. 69–83, doi:10.1007/s10851-017-0718-4.","short":"R. Biswas, P. Bhowmick, Journal of Mathematical Imaging and Vision 59 (2017) 69–83.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On the Functionality and Usefulness of Quadraginta Octants of Naive Sphere.” Journal of Mathematical Imaging and Vision. Springer Nature, 2017. https://doi.org/10.1007/s10851-017-0718-4.","ama":"Biswas R, Bhowmick P. On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. 2017;59(1):69-83. doi:10.1007/s10851-017-0718-4","ista":"Biswas R, Bhowmick P. 2017. On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. 59(1), 69–83.","apa":"Biswas, R., & Bhowmick, P. (2017). On the functionality and usefulness of Quadraginta octants of naive sphere. Journal of Mathematical Imaging and Vision. Springer Nature. https://doi.org/10.1007/s10851-017-0718-4","ieee":"R. Biswas and P. Bhowmick, “On the functionality and usefulness of Quadraginta octants of naive sphere,” Journal of Mathematical Imaging and Vision, vol. 59, no. 1. Springer Nature, pp. 69–83, 2017."},"extern":"1","abstract":[{"text":"This paper presents a novel study on the functional gradation of coordinate planes in connection with the thinnest and tunnel-free (i.e., naive) discretization of sphere in the integer space. For each of the 48-symmetric quadraginta octants of naive sphere with integer radius and integer center, we show that the corresponding voxel set forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as its functional plane. We use this fundamental property to prove several other theoretical results for naive sphere. First, the quadraginta octants form symmetry groups and subgroups with certain equivalent topological properties. Second, a naive sphere is always unique and consists of fewest voxels. Third, it is efficiently constructible from its functional-plane projection. And finally, a special class of 4-symmetric discrete 3D circles can be constructed on a naive sphere based on back projection from the functional plane.","lang":"eng"}],"issue":"1","type":"journal_article","date_updated":"2021-01-12T08:03:34Z","date_created":"2019-01-08T20:42:08Z","volume":59,"oa_version":"None","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"publication_status":"published","title":"On the functionality and usefulness of Quadraginta octants of naive sphere","status":"public","publisher":"Springer Nature","intvolume":" 59","year":"2017","_id":"5800","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"On the polyhedra of graceful spheres and circular geodesics","publication_status":"published","status":"public","intvolume":" 216","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5799","year":"2017","date_updated":"2021-01-12T08:03:33Z","date_created":"2019-01-08T20:41:12Z","volume":216,"oa_version":"None","author":[{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"},{"last_name":"Brimkov","first_name":"Valentin E.","full_name":"Brimkov, Valentin E."}],"type":"journal_article","extern":"1","abstract":[{"lang":"eng","text":"We construct a polyhedral surface called a graceful surface, which provides best possible approximation to a given sphere regarding certain criteria. In digital geometry terms, the graceful surface is uniquely characterized by its minimality while guaranteeing the connectivity of certain discrete (polyhedral) curves defined on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva (1999) and shown to be useful for triangular mesh discretization through graceful planes and graceful lines. In this paper we extend the considerations to a nonlinear object such as a sphere. In particular, we investigate the properties of a discrete geodesic path between two voxels and show that discrete 3D circles, circular arcs, and Mobius triangles are all constructible on a graceful sphere, with guaranteed minimum thickness and the desired connectivity in the discrete topological space."}],"quality_controlled":"1","page":"362-375","publication":"Discrete Applied Mathematics","citation":{"chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics. Elsevier, 2017. https://doi.org/10.1016/j.dam.2015.11.017.","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, Discrete Applied Mathematics 216 (2017) 362–375.","mla":"Biswas, Ranita, et al. “On the Polyhedra of Graceful Spheres and Circular Geodesics.” Discrete Applied Mathematics, vol. 216, Elsevier, 2017, pp. 362–75, doi:10.1016/j.dam.2015.11.017.","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the polyhedra of graceful spheres and circular geodesics,” Discrete Applied Mathematics, vol. 216. Elsevier, pp. 362–375, 2017.","apa":"Biswas, R., Bhowmick, P., & Brimkov, V. E. (2017). On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2015.11.017","ista":"Biswas R, Bhowmick P, Brimkov VE. 2017. On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. 216, 362–375.","ama":"Biswas R, Bhowmick P, Brimkov VE. On the polyhedra of graceful spheres and circular geodesics. Discrete Applied Mathematics. 2017;216:362-375. doi:10.1016/j.dam.2015.11.017"},"language":[{"iso":"eng"}],"doi":"10.1016/j.dam.2015.11.017","date_published":"2017-01-10T00:00:00Z","day":"10","month":"01","publication_identifier":{"issn":["0166-218X"]}},{"language":[{"iso":"eng"}],"date_published":"2017-08-22T00:00:00Z","doi":"10.1007/978-3-319-66272-5_28","conference":{"start_date":"2017-09-19","location":"Vienna, Austria","end_date":"2017-09-21","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery"},"page":"347-359","quality_controlled":"1","citation":{"chicago":"Dwivedi, Shivam, Aniket Gupta, Siddhant Roy, Ranita Biswas, and Partha Bhowmick. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” In 20th IAPR International Conference, 10502:347–59. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_28.","mla":"Dwivedi, Shivam, et al. “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space.” 20th IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 347–59, doi:10.1007/978-3-319-66272-5_28.","short":"S. Dwivedi, A. Gupta, S. Roy, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 347–359.","ista":"Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. 2017. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 347–359.","apa":"Dwivedi, S., Gupta, A., Roy, S., Biswas, R., & Bhowmick, P. (2017). Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In 20th IAPR International Conference (Vol. 10502, pp. 347–359). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_28","ieee":"S. Dwivedi, A. Gupta, S. Roy, R. Biswas, and P. Bhowmick, “Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space,” in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502, pp. 347–359.","ama":"Dwivedi S, Gupta A, Roy S, Biswas R, Bhowmick P. Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space. In: 20th IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:347-359. doi:10.1007/978-3-319-66272-5_28"},"publication":"20th IAPR International Conference","article_processing_charge":"No","publication_identifier":{"isbn":["978-3-319-66271-8"],"eissn":["1611-3349"],"eisbn":["978-3-319-66272-5"],"issn":["0302-9743"]},"day":"22","month":"08","oa_version":"None","volume":10502,"date_updated":"2022-01-27T15:34:25Z","date_created":"2019-01-08T20:42:22Z","author":[{"full_name":"Dwivedi, Shivam","first_name":"Shivam","last_name":"Dwivedi"},{"full_name":"Gupta, Aniket","first_name":"Aniket","last_name":"Gupta"},{"full_name":"Roy, Siddhant","first_name":"Siddhant","last_name":"Roy"},{"full_name":"Biswas, Ranita","first_name":"Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"publisher":"Springer Nature","intvolume":" 10502","status":"public","publication_status":"published","title":"Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space","year":"2017","_id":"5801","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","abstract":[{"text":"Space filling circles and spheres have various applications in mathematical imaging and physical modeling. In this paper, we first show how the thinnest (i.e., 2-minimal) model of digital sphere can be augmented to a space filling model by fixing certain “simple voxels” and “filler voxels” associated with it. Based on elementary number-theoretic properties of such voxels, we design an efficient incremental algorithm for generation of these space filling spheres with successively increasing radius. The novelty of the proposed technique is established further through circular space filling on 3D digital plane. As evident from a preliminary set of experimental result, this can particularly be useful for parallel computing of 3D Voronoi diagrams in the digital space.","lang":"eng"}],"place":"Cham","alternative_title":["LNCS"],"type":"conference"},{"page":"93-104","publication":"Combinatorial image analysis","citation":{"apa":"Biswas, R., & Bhowmick, P. (2017). Construction of persistent Voronoi diagram on 3D digital plane. In Combinatorial image analysis (Vol. 10256, pp. 93–104). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-59108-7_8","ieee":"R. Biswas and P. Bhowmick, “Construction of persistent Voronoi diagram on 3D digital plane,” in Combinatorial image analysis, vol. 10256, Cham: Springer Nature, 2017, pp. 93–104.","ista":"Biswas R, Bhowmick P. 2017.Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial image analysis. LNCS, vol. 10256, 93–104.","ama":"Biswas R, Bhowmick P. Construction of persistent Voronoi diagram on 3D digital plane. In: Combinatorial Image Analysis. Vol 10256. Cham: Springer Nature; 2017:93-104. doi:10.1007/978-3-319-59108-7_8","chicago":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” In Combinatorial Image Analysis, 10256:93–104. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-59108-7_8.","short":"R. Biswas, P. Bhowmick, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2017, pp. 93–104.","mla":"Biswas, Ranita, and Partha Bhowmick. “Construction of Persistent Voronoi Diagram on 3D Digital Plane.” Combinatorial Image Analysis, vol. 10256, Springer Nature, 2017, pp. 93–104, doi:10.1007/978-3-319-59108-7_8."},"date_published":"2017-05-17T00:00:00Z","day":"17","article_processing_charge":"No","title":"Construction of persistent Voronoi diagram on 3D digital plane","status":"public","intvolume":" 10256","_id":"5803","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","alternative_title":["LNCS"],"type":"book_chapter","abstract":[{"lang":"eng","text":"Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept."}],"quality_controlled":"1","language":[{"iso":"eng"}],"conference":{"end_date":"2017-06-21","location":"Plovdiv, Bulgaria","start_date":"2017-06-19","name":"IWCIA: International Workshop on Combinatorial Image Analysis"},"doi":"10.1007/978-3-319-59108-7_8","month":"05","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-319-59107-0","978-3-319-59108-7"]},"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"Springer Nature","year":"2017","date_created":"2019-01-08T20:42:56Z","date_updated":"2022-01-28T07:48:24Z","volume":10256,"author":[{"full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","first_name":"Ranita"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"place":"Cham","extern":"1"},{"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-66272-5_31","date_published":"2017-08-22T00:00:00Z","conference":{"name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2017-09-21","start_date":"2017-09-19","location":"Vienna, Austria"},"page":"388-398","quality_controlled":"1","citation":{"apa":"Andres, E., Biswas, R., & Bhowmick, P. (2017). Digital primitives defined by weighted focal set. In 20th IAPR International Conference (Vol. 10502, pp. 388–398). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-66272-5_31","ieee":"E. Andres, R. Biswas, and P. Bhowmick, “Digital primitives defined by weighted focal set,” in 20th IAPR International Conference, Vienna, Austria, 2017, vol. 10502, pp. 388–398.","ista":"Andres E, Biswas R, Bhowmick P. 2017. Digital primitives defined by weighted focal set. 20th IAPR International Conference. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 10502, 388–398.","ama":"Andres E, Biswas R, Bhowmick P. Digital primitives defined by weighted focal set. In: 20th IAPR International Conference. Vol 10502. Cham: Springer Nature; 2017:388-398. doi:10.1007/978-3-319-66272-5_31","chicago":"Andres, Eric, Ranita Biswas, and Partha Bhowmick. “Digital Primitives Defined by Weighted Focal Set.” In 20th IAPR International Conference, 10502:388–98. Cham: Springer Nature, 2017. https://doi.org/10.1007/978-3-319-66272-5_31.","short":"E. Andres, R. Biswas, P. Bhowmick, in:, 20th IAPR International Conference, Springer Nature, Cham, 2017, pp. 388–398.","mla":"Andres, Eric, et al. “Digital Primitives Defined by Weighted Focal Set.” 20th IAPR International Conference, vol. 10502, Springer Nature, 2017, pp. 388–98, doi:10.1007/978-3-319-66272-5_31."},"publication":"20th IAPR International Conference","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-66272-5"],"eissn":["1611-3349"],"isbn":["978-3-319-66271-8"]},"article_processing_charge":"No","day":"22","month":"08","volume":10502,"oa_version":"None","date_created":"2019-01-08T20:42:39Z","date_updated":"2022-01-27T15:38:35Z","author":[{"full_name":"Andres, Eric","first_name":"Eric","last_name":"Andres"},{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"intvolume":" 10502","publisher":"Springer Nature","title":"Digital primitives defined by weighted focal set","publication_status":"published","status":"public","_id":"5802","year":"2017","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","extern":"1","abstract":[{"text":"This papers introduces a definition of digital primitives based on focal points and weighted distances (with positive weights). The proposed definition is applicable to general dimensions and covers in its gamut various regular curves and surfaces like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids, Cartesian k-ovals, etc. Several interesting properties are presented for this class of digital primitives such as space partitioning, topological separation, and connectivity properties. To demonstrate further the potential of this new way of defining digital primitives, we propose, as extension, another class of digital conics defined by focus-directrix combination.","lang":"eng"}],"place":"Cham","alternative_title":["LNCS"],"type":"conference"},{"type":"journal_article","issue":"14","publist_id":"7212","abstract":[{"text":"Bell correlations, indicating nonlocality in composite quantum systems, were until recently only seen in small systems. Here, we demonstrate Bell correlations in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective measurements as witnesses and are statistically significant to 124 standard deviations. The states are both generated and characterized using optical-cavity aided measurements.","lang":"eng"}],"extern":"1","_id":"593","year":"2017","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","intvolume":" 118","title":"Bell correlations in spin-squeezed states of 500 000 atoms","publication_status":"published","status":"public","author":[{"first_name":"Nils","last_name":"Engelsen","full_name":"Engelsen, Nils"},{"full_name":"Krishnakumar, Rajiv","last_name":"Krishnakumar","first_name":"Rajiv"},{"full_name":"Hosten, Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","first_name":"Onur","last_name":"Hosten"},{"last_name":"Kasevich","first_name":"Mark","full_name":"Kasevich, Mark"}],"volume":118,"oa_version":"None","date_created":"2018-12-11T11:47:23Z","date_updated":"2021-01-12T08:05:16Z","day":"03","month":"04","citation":{"ieee":"N. Engelsen, R. Krishnakumar, O. Hosten, and M. Kasevich, “Bell correlations in spin-squeezed states of 500 000 atoms,” Physical Review Letters, vol. 118, no. 14. American Physical Society, 2017.","apa":"Engelsen, N., Krishnakumar, R., Hosten, O., & Kasevich, M. (2017). Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.118.140401","ista":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. 2017. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 118(14).","ama":"Engelsen N, Krishnakumar R, Hosten O, Kasevich M. Bell correlations in spin-squeezed states of 500 000 atoms. Physical Review Letters. 2017;118(14). doi:10.1103/PhysRevLett.118.140401","chicago":"Engelsen, Nils, Rajiv Krishnakumar, Onur Hosten, and Mark Kasevich. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.118.140401.","short":"N. Engelsen, R. Krishnakumar, O. Hosten, M. Kasevich, Physical Review Letters 118 (2017).","mla":"Engelsen, Nils, et al. “Bell Correlations in Spin-Squeezed States of 500 000 Atoms.” Physical Review Letters, vol. 118, no. 14, American Physical Society, 2017, doi:10.1103/PhysRevLett.118.140401."},"publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.118.140401","date_published":"2017-04-03T00:00:00Z","language":[{"iso":"eng"}]},{"type":"journal_article","abstract":[{"text":"Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct “bendability” and “meltability” of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.","lang":"eng"}],"publist_id":"7204","issue":"1","extern":"1","_id":"600","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","title":"Structural basis of RNA polymerase I transcription initiation","publication_status":"published","status":"public","publisher":"Cell Press","intvolume":" 169","author":[{"full_name":"Engel, Christoph","last_name":"Engel","first_name":"Christoph"},{"first_name":"Tobias","last_name":"Gubbey","full_name":"Gubbey, Tobias"},{"full_name":"Neyer, Simon","first_name":"Simon","last_name":"Neyer"},{"full_name":"Sainsbury, Sarah","last_name":"Sainsbury","first_name":"Sarah"},{"first_name":"Christiane","last_name":"Oberthuer","full_name":"Oberthuer, Christiane"},{"full_name":"Baejen, Carlo","last_name":"Baejen","first_name":"Carlo"},{"orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","first_name":"Carrie A","full_name":"Bernecky, Carrie A"},{"full_name":"Cramer, Patrick","last_name":"Cramer","first_name":"Patrick"}],"date_updated":"2021-01-12T08:05:36Z","date_created":"2018-12-11T11:47:25Z","volume":169,"oa_version":"None","day":"23","month":"03","article_processing_charge":"No","publication_identifier":{"issn":["00928674"]},"publication":"Cell","citation":{"ama":"Engel C, Gubbey T, Neyer S, et al. Structural basis of RNA polymerase I transcription initiation. Cell. 2017;169(1):120-131.e22. doi:10.1016/j.cell.2017.03.003","ista":"Engel C, Gubbey T, Neyer S, Sainsbury S, Oberthuer C, Baejen C, Bernecky C, Cramer P. 2017. Structural basis of RNA polymerase I transcription initiation. Cell. 169(1), 120–131.e22.","apa":"Engel, C., Gubbey, T., Neyer, S., Sainsbury, S., Oberthuer, C., Baejen, C., … Cramer, P. (2017). Structural basis of RNA polymerase I transcription initiation. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.03.003","ieee":"C. Engel et al., “Structural basis of RNA polymerase I transcription initiation,” Cell, vol. 169, no. 1. Cell Press, p. 120–131.e22, 2017.","mla":"Engel, Christoph, et al. “Structural Basis of RNA Polymerase I Transcription Initiation.” Cell, vol. 169, no. 1, Cell Press, 2017, p. 120–131.e22, doi:10.1016/j.cell.2017.03.003.","short":"C. Engel, T. Gubbey, S. Neyer, S. Sainsbury, C. Oberthuer, C. Baejen, C. Bernecky, P. Cramer, Cell 169 (2017) 120–131.e22.","chicago":"Engel, Christoph, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, and Patrick Cramer. “Structural Basis of RNA Polymerase I Transcription Initiation.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.03.003."},"quality_controlled":"1","page":"120 - 131.e22","doi":"10.1016/j.cell.2017.03.003","date_published":"2017-03-23T00:00:00Z","language":[{"iso":"eng"}]},{"type":"conference","alternative_title":["Journal of Physics: Conference Series"],"issue":"1","abstract":[{"lang":"eng","text":"Tunneling of a particle through a potential barrier remains one of the most remarkable quantum phenomena. Owing to advances in laser technology, electric fields comparable to those electrons experience in atoms are readily generated and open opportunities to dynamically investigate the process of electron tunneling through the potential barrier formed by the superposition of both laser and atomic fields. Attosecond-time and angstrom-space resolution of the strong laser-field technique allow to address fundamental questions related to tunneling, which are still open and debated: Which time is spent under the barrier and what momentum is picked up by the particle in the meantime? In this combined experimental and theoretical study we demonstrate that for strong-field ionization the leading quantum mechanical Wigner treatment for the time resolved description of tunneling is valid. We achieve a high sensitivity on the tunneling barrier and unambiguously isolate its effects by performing a differential study of two systems with almost identical tunneling geometry. Moreover, working with a low frequency laser, we essentially limit the non-adiabaticity of the process as a major source of uncertainty. The agreement between experiment and theory implies two substantial corrections with respect to the widely employed quasiclassical treatment: In addition to a non-vanishing longitudinal momentum along the laser field-direction we provide clear evidence for a non-zero tunneling time delay. This addresses also the fundamental question how the transition occurs from the tunnel barrier to free space classical evolution of the ejected electron."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"313","intvolume":" 999","status":"public","title":"Experimental evidence for Wigner's tunneling time","ddc":["530"],"oa_version":"Published Version","file":[{"checksum":"6e70b525a84f6d5fb175c48e9f5cb59a","date_updated":"2020-07-14T12:46:00Z","date_created":"2019-01-22T08:34:10Z","file_id":"5871","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":949321,"access_level":"open_access","file_name":"2017_Physics_Camus.pdf"}],"scopus_import":1,"has_accepted_license":"1","day":"14","citation":{"mla":"Camus, Nicolas, et al. Experimental Evidence for Wigner’s Tunneling Time. Vol. 999, no. 1, 012004, American Physical Society, 2017, doi:10.1088/1742-6596/999/1/012004.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K. Hatsagortsyan, T. Pfeifer, C. Keitel, R. Moshammer, in:, American Physical Society, 2017.","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Hatsagortsyan, Thomas Pfeifer, Cristoph Keitel, and Robert Moshammer. “Experimental Evidence for Wigner’s Tunneling Time,” Vol. 999. American Physical Society, 2017. https://doi.org/10.1088/1742-6596/999/1/012004.","ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for Wigner’s tunneling time. In: Vol 999. American Physical Society; 2017. doi:10.1088/1742-6596/999/1/012004","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan K, Pfeifer T, Keitel C, Moshammer R. 2017. Experimental evidence for Wigner’s tunneling time. Annual International Laser Physics Workshop LPHYS, Journal of Physics: Conference Series, vol. 999, 012004.","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for Wigner’s tunneling time (Vol. 999). Presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation: American Physical Society. https://doi.org/10.1088/1742-6596/999/1/012004","ieee":"N. Camus et al., “Experimental evidence for Wigner’s tunneling time,” presented at the Annual International Laser Physics Workshop LPHYS, Kazan, Russian Federation, 2017, vol. 999, no. 1."},"date_published":"2017-07-14T00:00:00Z","article_number":"012004","publist_id":"7552","file_date_updated":"2020-07-14T12:46:00Z","year":"2017","publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"later_version","id":"6013"}]},"author":[{"first_name":"Nicolas","last_name":"Camus","full_name":"Camus, Nicolas"},{"full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","first_name":"Enderalp"},{"last_name":"Fechner","first_name":"Lutz","full_name":"Fechner, Lutz"},{"full_name":"Klaiber, Michael","first_name":"Michael","last_name":"Klaiber"},{"full_name":"Laux, Martin","first_name":"Martin","last_name":"Laux"},{"first_name":"Yonghao","last_name":"Mi","full_name":"Mi, Yonghao"},{"last_name":"Hatsagortsyan","first_name":"Karen","full_name":"Hatsagortsyan, Karen"},{"last_name":"Pfeifer","first_name":"Thomas","full_name":"Pfeifer, Thomas"},{"full_name":"Keitel, Cristoph","first_name":"Cristoph","last_name":"Keitel"},{"full_name":"Moshammer, Robert","last_name":"Moshammer","first_name":"Robert"}],"volume":999,"date_updated":"2023-02-23T12:36:07Z","date_created":"2018-12-11T11:45:46Z","publication_identifier":{"issn":["17426588"]},"month":"07","external_id":{"arxiv":["1611.03701"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1088/1742-6596/999/1/012004","conference":{"location":"Kazan, Russian Federation","start_date":"2017-08-17","end_date":"2017-08-21","name":"Annual International Laser Physics Workshop LPHYS"},"language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["20411723"]},"month":"06","doi":"10.1038/ncomms15741","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publist_id":"7203","file_date_updated":"2020-07-14T12:47:16Z","extern":"1","article_number":"15741","author":[{"full_name":"Xu, Youwei","last_name":"Xu","first_name":"Youwei"},{"last_name":"Bernecky","first_name":"Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","full_name":"Bernecky, Carrie A"},{"last_name":"Lee","first_name":"Chung","full_name":"Lee, Chung"},{"full_name":"Maier, Kerstin","first_name":"Kerstin","last_name":"Maier"},{"full_name":"Schwalb, Björn","first_name":"Björn","last_name":"Schwalb"},{"full_name":"Tegunov, Dimitri","last_name":"Tegunov","first_name":"Dimitri"},{"first_name":"Jürgen","last_name":"Plitzko","full_name":"Plitzko, Jürgen"},{"last_name":"Urlaub","first_name":"Henning","full_name":"Urlaub, Henning"},{"last_name":"Cramer","first_name":"Patrick","full_name":"Cramer, Patrick"}],"volume":8,"date_updated":"2021-01-12T08:05:40Z","date_created":"2018-12-11T11:47:25Z","year":"2017","publisher":"Nature Publishing Group","publication_status":"published","has_accepted_license":"1","article_processing_charge":"No","day":"06","date_published":"2017-06-06T00:00:00Z","citation":{"ieee":"Y. Xu et al., “Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex,” Nature Communications, vol. 8. Nature Publishing Group, 2017.","apa":"Xu, Y., Bernecky, C., Lee, C., Maier, K., Schwalb, B., Tegunov, D., … Cramer, P. (2017). Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms15741","ista":"Xu Y, Bernecky C, Lee C, Maier K, Schwalb B, Tegunov D, Plitzko J, Urlaub H, Cramer P. 2017. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 8, 15741.","ama":"Xu Y, Bernecky C, Lee C, et al. Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex. Nature Communications. 2017;8. doi:10.1038/ncomms15741","chicago":"Xu, Youwei, Carrie Bernecky, Chung Lee, Kerstin Maier, Björn Schwalb, Dimitri Tegunov, Jürgen Plitzko, Henning Urlaub, and Patrick Cramer. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/ncomms15741.","short":"Y. Xu, C. Bernecky, C. Lee, K. Maier, B. Schwalb, D. Tegunov, J. Plitzko, H. Urlaub, P. Cramer, Nature Communications 8 (2017).","mla":"Xu, Youwei, et al. “Architecture of the RNA Polymerase II-Paf1C-TFIIS Transcription Elongation Complex.” Nature Communications, vol. 8, 15741, Nature Publishing Group, 2017, doi:10.1038/ncomms15741."},"publication":"Nature Communications","abstract":[{"text":"The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. ","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"5865","checksum":"940742282a9a285dc4aeae0c2b5ebe96","date_created":"2019-01-21T14:48:10Z","date_updated":"2020-07-14T12:47:16Z","access_level":"open_access","file_name":"2017_NatureComm_Xu.pdf","content_type":"application/pdf","file_size":3018075,"creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"601","intvolume":" 8","title":"Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex","ddc":["570"],"status":"public"},{"article_number":"023201","related_material":{"record":[{"id":"313","relation":"earlier_version","status":"public"}]},"author":[{"full_name":"Camus, Nicolas","last_name":"Camus","first_name":"Nicolas"},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","first_name":"Enderalp","last_name":"Yakaboylu"},{"full_name":"Fechner, Lutz","last_name":"Fechner","first_name":"Lutz"},{"first_name":"Michael","last_name":"Klaiber","full_name":"Klaiber, Michael"},{"full_name":"Laux, Martin","last_name":"Laux","first_name":"Martin"},{"full_name":"Mi, Yonghao","last_name":"Mi","first_name":"Yonghao"},{"first_name":"Karen Z.","last_name":"Hatsagortsyan","full_name":"Hatsagortsyan, Karen Z."},{"first_name":"Thomas","last_name":"Pfeifer","full_name":"Pfeifer, Thomas"},{"first_name":"Christoph H.","last_name":"Keitel","full_name":"Keitel, Christoph H."},{"first_name":"Robert","last_name":"Moshammer","full_name":"Moshammer, Robert"}],"volume":119,"date_updated":"2023-02-23T11:13:36Z","date_created":"2019-02-14T15:24:13Z","year":"2017","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"07","doi":"10.1103/PhysRevLett.119.023201","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1611.03701"}],"oa":1,"external_id":{"arxiv":["1611.03701"]},"quality_controlled":"1","issue":"2","abstract":[{"lang":"eng","text":"The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”"}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6013","intvolume":" 119","status":"public","title":"Experimental evidence for quantum tunneling time","day":"14","scopus_import":1,"date_published":"2017-07-14T00:00:00Z","citation":{"ama":"Camus N, Yakaboylu E, Fechner L, et al. Experimental evidence for quantum tunneling time. Physical Review Letters. 2017;119(2). doi:10.1103/PhysRevLett.119.023201","apa":"Camus, N., Yakaboylu, E., Fechner, L., Klaiber, M., Laux, M., Mi, Y., … Moshammer, R. (2017). Experimental evidence for quantum tunneling time. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.119.023201","ieee":"N. Camus et al., “Experimental evidence for quantum tunneling time,” Physical Review Letters, vol. 119, no. 2. American Physical Society, 2017.","ista":"Camus N, Yakaboylu E, Fechner L, Klaiber M, Laux M, Mi Y, Hatsagortsyan KZ, Pfeifer T, Keitel CH, Moshammer R. 2017. Experimental evidence for quantum tunneling time. Physical Review Letters. 119(2), 023201.","short":"N. Camus, E. Yakaboylu, L. Fechner, M. Klaiber, M. Laux, Y. Mi, K.Z. Hatsagortsyan, T. Pfeifer, C.H. Keitel, R. Moshammer, Physical Review Letters 119 (2017).","mla":"Camus, Nicolas, et al. “Experimental Evidence for Quantum Tunneling Time.” Physical Review Letters, vol. 119, no. 2, 023201, American Physical Society, 2017, doi:10.1103/PhysRevLett.119.023201.","chicago":"Camus, Nicolas, Enderalp Yakaboylu, Lutz Fechner, Michael Klaiber, Martin Laux, Yonghao Mi, Karen Z. Hatsagortsyan, Thomas Pfeifer, Christoph H. Keitel, and Robert Moshammer. “Experimental Evidence for Quantum Tunneling Time.” Physical Review Letters. American Physical Society, 2017. https://doi.org/10.1103/PhysRevLett.119.023201."},"publication":"Physical Review Letters"},{"abstract":[{"text":"During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.","lang":"eng"}],"publist_id":"7202","issue":"10","extern":"1","type":"journal_article","author":[{"full_name":"Bernecky, Carrie A","first_name":"Carrie A","last_name":"Bernecky","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036"},{"full_name":"Plitzko, Jürgen","first_name":"Jürgen","last_name":"Plitzko"},{"full_name":"Cramer, Patrick","last_name":"Cramer","first_name":"Patrick"}],"date_updated":"2021-01-12T08:05:47Z","date_created":"2018-12-11T11:47:26Z","oa_version":"None","volume":24,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"603","year":"2017","title":"Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp","status":"public","publication_status":"published","publisher":"Nature Publishing Group","intvolume":" 24","month":"10","day":"05","article_processing_charge":"No","publication_identifier":{"issn":["15459993"]},"date_published":"2017-10-05T00:00:00Z","doi":"10.1038/nsmb.3465","language":[{"iso":"eng"}],"publication":"Nature Structural and Molecular Biology","citation":{"ama":"Bernecky C, Plitzko J, Cramer P. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and Molecular Biology. 2017;24(10):809-815. doi:10.1038/nsmb.3465","ista":"Bernecky C, Plitzko J, Cramer P. 2017. Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and Molecular Biology. 24(10), 809–815.","apa":"Bernecky, C., Plitzko, J., & Cramer, P. (2017). Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb.3465","ieee":"C. Bernecky, J. Plitzko, and P. Cramer, “Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp,” Nature Structural and Molecular Biology, vol. 24, no. 10. Nature Publishing Group, pp. 809–815, 2017.","mla":"Bernecky, Carrie, et al. “Structure of a Transcribing RNA Polymerase II-DSIF Complex Reveals a Multidentate DNA-RNA Clamp.” Nature Structural and Molecular Biology, vol. 24, no. 10, Nature Publishing Group, 2017, pp. 809–15, doi:10.1038/nsmb.3465.","short":"C. Bernecky, J. Plitzko, P. Cramer, Nature Structural and Molecular Biology 24 (2017) 809–815.","chicago":"Bernecky, Carrie, Jürgen Plitzko, and Patrick Cramer. “Structure of a Transcribing RNA Polymerase II-DSIF Complex Reveals a Multidentate DNA-RNA Clamp.” Nature Structural and Molecular Biology. Nature Publishing Group, 2017. https://doi.org/10.1038/nsmb.3465."},"quality_controlled":"1","page":"809 - 815"},{"month":"11","publication_identifier":{"isbn":["978-331970499-9"]},"quality_controlled":"1","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/536"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"TCC: Theory of Cryptography Conference","end_date":"2017-11-15","start_date":"2017-11-12","location":"Baltimore, MD, United States"},"doi":"10.1007/978-3-319-70500-2_3","publist_id":"7200","ec_funded":1,"publication_status":"published","editor":[{"last_name":"Kalai","first_name":"Yael","full_name":"Kalai, Yael"},{"first_name":"Leonid","last_name":"Reyzin","full_name":"Reyzin, Leonid"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"year":"2017","date_created":"2018-12-11T11:47:27Z","date_updated":"2021-01-12T08:05:53Z","volume":10677,"author":[{"full_name":"Brody, Joshua","last_name":"Brody","first_name":"Joshua"},{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"first_name":"Sebastian","last_name":"Faust","full_name":"Faust, Sebastian"},{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak"}],"scopus_import":1,"day":"05","page":"56 - 81","citation":{"ista":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. 2017. Position based cryptography and multiparty communication complexity. TCC: Theory of Cryptography Conference, LNCS, vol. 10677, 56–81.","ieee":"J. Brody, S. Dziembowski, S. Faust, and K. Z. Pietrzak, “Position based cryptography and multiparty communication complexity,” presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States, 2017, vol. 10677, pp. 56–81.","apa":"Brody, J., Dziembowski, S., Faust, S., & Pietrzak, K. Z. (2017). Position based cryptography and multiparty communication complexity. In Y. Kalai & L. Reyzin (Eds.) (Vol. 10677, pp. 56–81). Presented at the TCC: Theory of Cryptography Conference, Baltimore, MD, United States: Springer. https://doi.org/10.1007/978-3-319-70500-2_3","ama":"Brody J, Dziembowski S, Faust S, Pietrzak KZ. Position based cryptography and multiparty communication complexity. In: Kalai Y, Reyzin L, eds. Vol 10677. Springer; 2017:56-81. doi:10.1007/978-3-319-70500-2_3","chicago":"Brody, Joshua, Stefan Dziembowski, Sebastian Faust, and Krzysztof Z Pietrzak. “Position Based Cryptography and Multiparty Communication Complexity.” edited by Yael Kalai and Leonid Reyzin, 10677:56–81. Springer, 2017. https://doi.org/10.1007/978-3-319-70500-2_3.","mla":"Brody, Joshua, et al. Position Based Cryptography and Multiparty Communication Complexity. Edited by Yael Kalai and Leonid Reyzin, vol. 10677, Springer, 2017, pp. 56–81, doi:10.1007/978-3-319-70500-2_3.","short":"J. Brody, S. Dziembowski, S. Faust, K.Z. Pietrzak, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 56–81."},"date_published":"2017-11-05T00:00:00Z","alternative_title":["LNCS"],"type":"conference","abstract":[{"text":"Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes.","lang":"eng"}],"title":"Position based cryptography and multiparty communication complexity","status":"public","intvolume":" 10677","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"605","oa_version":"Submitted Version"},{"date_created":"2018-12-11T11:47:27Z","date_updated":"2021-01-12T08:05:50Z","volume":11,"author":[{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail"},{"full_name":"Schmidt, Richard","first_name":"Richard","last_name":"Schmidt"}],"publication_status":"published","editor":[{"first_name":"Oliver","last_name":"Dulieu","full_name":"Dulieu, Oliver"},{"first_name":"Andreas","last_name":"Osterwalder","full_name":"Osterwalder, Andreas"}],"department":[{"_id":"MiLe"}],"publisher":"The Royal Society of Chemistry","year":"2017","publist_id":"7201","language":[{"iso":"eng"}],"doi":"10.1039/9781782626800-00444","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.06753","open_access":"1"}],"month":"12","publication_identifier":{"issn":["20413181"]},"oa_version":"Submitted Version","status":"public","title":"Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets","intvolume":" 11","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"604","abstract":[{"lang":"eng","text":"In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies."}],"alternative_title":["Theoretical and Computational Chemistry Series"],"type":"book_chapter","date_published":"2017-12-14T00:00:00Z","page":"444 - 495","publication":"Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero ","citation":{"chicago":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” In Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , edited by Oliver Dulieu and Andreas Osterwalder, 11:444–95. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry, 2017. https://doi.org/10.1039/9781782626800-00444.","short":"M. Lemeshko, R. Schmidt, in:, O. Dulieu, A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , The Royal Society of Chemistry, 2017, pp. 444–495.","mla":"Lemeshko, Mikhail, and Richard Schmidt. “Molecular Impurities Interacting with a Many-Particle Environment: From Ultracold Gases to Helium Nanodroplets.” Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , edited by Oliver Dulieu and Andreas Osterwalder, vol. 11, The Royal Society of Chemistry, 2017, pp. 444–95, doi:10.1039/9781782626800-00444.","apa":"Lemeshko, M., & Schmidt, R. (2017). Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In O. Dulieu & A. Osterwalder (Eds.), Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero (Vol. 11, pp. 444–495). The Royal Society of Chemistry. https://doi.org/10.1039/9781782626800-00444","ieee":"M. Lemeshko and R. Schmidt, “Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets,” in Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero , vol. 11, O. Dulieu and A. Osterwalder, Eds. The Royal Society of Chemistry, 2017, pp. 444–495.","ista":"Lemeshko M, Schmidt R. 2017.Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Theoretical and Computational Chemistry Series, vol. 11, 444–495.","ama":"Lemeshko M, Schmidt R. Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets. In: Dulieu O, Osterwalder A, eds. Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero . Vol 11. Theoretical and Computational Chemistry Series. The Royal Society of Chemistry; 2017:444-495. doi:10.1039/9781782626800-00444"},"day":"14","series_title":"Theoretical and Computational Chemistry Series","scopus_import":1},{"publication_identifier":{"issn":["1046-2023"]},"day":"01","month":"01","date_published":"2017-01-01T00:00:00Z","doi":"10.1016/j.ymeth.2016.09.013","language":[{"iso":"eng"}],"citation":{"apa":"Balta, E., Stopp, J. A., Castelletti, L., Kirchgessner, H., Samstag, Y., & Wabnitz, G. H. (2017). Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. Methods. Elsevier. https://doi.org/10.1016/j.ymeth.2016.09.013","ieee":"E. Balta, J. A. Stopp, L. Castelletti, H. Kirchgessner, Y. Samstag, and G. H. Wabnitz, “Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy,” Methods, vol. 112, no. 1. Elsevier, pp. 25–38, 2017.","ista":"Balta E, Stopp JA, Castelletti L, Kirchgessner H, Samstag Y, Wabnitz GH. 2017. Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. Methods. 112(1), 25–38.","ama":"Balta E, Stopp JA, Castelletti L, Kirchgessner H, Samstag Y, Wabnitz GH. Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy. Methods. 2017;112(1):25-38. doi:10.1016/j.ymeth.2016.09.013","chicago":"Balta, Emre, Julian A Stopp, Laura Castelletti, Henning Kirchgessner, Yvonne Samstag, and Guido H. Wabnitz. “Qualitative and Quantitative Analysis of PMN/T-Cell Interactions by InFlow and Super-Resolution Microscopy.” Methods. Elsevier, 2017. https://doi.org/10.1016/j.ymeth.2016.09.013.","short":"E. Balta, J.A. Stopp, L. Castelletti, H. Kirchgessner, Y. Samstag, G.H. Wabnitz, Methods 112 (2017) 25–38.","mla":"Balta, Emre, et al. “Qualitative and Quantitative Analysis of PMN/T-Cell Interactions by InFlow and Super-Resolution Microscopy.” Methods, vol. 112, no. 1, Elsevier, 2017, pp. 25–38, doi:10.1016/j.ymeth.2016.09.013."},"external_id":{"pmid":["27693880"]},"publication":"Methods","page":"25-38","quality_controlled":"1","issue":"1","abstract":[{"text":"Neutrophils or polymorphonuclear cells (PMN) eliminate bacteria via phagocytosis and/or NETosis. Apartfrom these conventional roles, PMN also have immune-regulatory functions. They can transdifferentiateand upregulate MHCII as well as ligands for costimulatory receptors which enables them to behave asantigen presenting cells (APC). The initial step for activating T-cells is the formation of an immunesynapse between T-cells and antigen-presenting cells. However, the immune synapse that develops atthe PMN/T-cell contact zone is as yet hardly investigated due to the non-availability of methods foranalysis of large number of PMN interactions. In order to overcome these obstacles, we introduce herea workflow to analyse the immune synapse of primary human PMN and T-cells using multispectral imag-ing flow cytometry (InFlow microscopy) and super-resolution microscopy. For that purpose, we used CD3and CD66b as the lineage markers for T-cells and PMN, respectively. Thereafter, we applied and criticallydiscussed various ‘‘masks” for identification of T-cell PMN interactions. Using this approach, we foundthat a small fraction of transdifferentiated PMN (CD66b+CD86high) formed stable PMN/T-cell conjugates.Interestingly, while both CD3 and CD66b accumulation in the immune synapse was dependent on thematuration state of the PMN, only CD3 accumulation was greatly enhanced by the presence of superanti-gen. The actin cytoskeleton was weakly rearranged at the PMN side on the immune synapse upon contactwith a T-cell in the presence of superantigen. A more detailed analysis using super-resolution microscopy(structured-illumination microscopy, SIM) confirmed this finding. Together, we present an InFlow micro-scopy based approach for the large scale analysis of PMN/T-cell interactions and – combined with SIM – apossibility for an in-depth analysis of protein translocation at the site of interactions.","lang":"eng"}],"extern":"1","type":"journal_article","related_material":{"link":[{"relation":"supplementary_material","url":"http://dx.doi.org/10.1016/j.ymeth.2016.09.013"}]},"author":[{"full_name":"Balta, Emre","last_name":"Balta","first_name":"Emre"},{"full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A"},{"full_name":"Castelletti, Laura","last_name":"Castelletti","first_name":"Laura"},{"full_name":"Kirchgessner, Henning","last_name":"Kirchgessner","first_name":"Henning"},{"first_name":"Yvonne","last_name":"Samstag","full_name":"Samstag, Yvonne"},{"full_name":"Wabnitz, Guido H.","first_name":"Guido H.","last_name":"Wabnitz"}],"volume":112,"oa_version":"None","date_updated":"2021-01-12T08:05:57Z","date_created":"2019-02-26T13:45:17Z","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6059","year":"2017","publisher":"Elsevier","intvolume":" 112","publication_status":"published","status":"public","title":"Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy"},{"date_published":"2017-11-05T00:00:00Z","page":"493 - 526","citation":{"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.","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.","short":"J.F. Alwen, B. Tackmann, in:, Y. Kalai, L. Reyzin (Eds.), Springer, 2017, pp. 493–526.","ista":"Alwen JF, Tackmann B. 2017. Moderately hard functions: Definition, instantiations, and applications. TCC: Theory of Cryptography, LNCS, vol. 10677, 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","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.","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"},"day":"05","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 10677","title":"Moderately hard functions: Definition, instantiations, and applications","status":"public","_id":"609","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-70500-2_17","conference":{"name":"TCC: Theory of Cryptography","location":"Baltimore, MD, United States","start_date":"2017-11-12","end_date":"2017-11-15"},"quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2017/945","open_access":"1"}],"oa":1,"publication_identifier":{"isbn":["978-331970499-9"]},"month":"11","volume":10677,"date_updated":"2021-01-12T08:06:04Z","date_created":"2018-12-11T11:47:28Z","author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F","full_name":"Alwen, Joel F"},{"first_name":"Björn","last_name":"Tackmann","full_name":"Tackmann, Björn"}],"publisher":"Springer","department":[{"_id":"KrPi"}],"editor":[{"full_name":"Kalai, Yael","last_name":"Kalai","first_name":"Yael"},{"first_name":"Leonid","last_name":"Reyzin","full_name":"Reyzin, Leonid"}],"publication_status":"published","year":"2017","publist_id":"7196"},{"ec_funded":1,"publist_id":"7194","date_created":"2018-12-11T11:47:29Z","date_updated":"2023-02-23T10:02:13Z","volume":222,"author":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"first_name":"Isaac","last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac"},{"last_name":"Paták","first_name":"Pavel","full_name":"Paták, Pavel"},{"full_name":"Patakova, Zuzana","last_name":"Patakova","first_name":"Zuzana","orcid":"0000-0002-3975-1683","id":"48B57058-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tancer, Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1191-6714","first_name":"Martin","last_name":"Tancer"},{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli"}],"related_material":{"record":[{"id":"1511","status":"public","relation":"earlier_version"}]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer","year":"2017","acknowledgement":"The work by Z. P. was partially supported by the Israel Science Foundation grant ISF-768/12. The work by Z. P. and M. T. was partially supported by the project CE-ITI (GACR P202/12/G061) of the Czech Science Foundation and by the ERC Advanced Grant No. 267165. Part of the research work of M.T. was conducted at IST Austria, supported by an IST Fellowship. The research of P. P. was supported by the ERC Advanced grant no. 320924. The work by I. M. and U. W. was supported by the Swiss National Science Foundation (grants SNSF-200020-138230 and SNSF-PP00P2-138948). The collaboration between U. W. and X. G. was partially supported by the LabEx Bézout (ANR-10-LABX-58).","month":"10","language":[{"iso":"eng"}],"doi":"10.1007/s11856-017-1607-7","quality_controlled":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.09063"}],"oa":1,"abstract":[{"lang":"eng","text":"The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition."}],"issue":"2","type":"journal_article","oa_version":"Preprint","title":"On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result","status":"public","intvolume":" 222","_id":"610","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","scopus_import":1,"date_published":"2017-10-01T00:00:00Z","page":"841 - 866","publication":"Israel Journal of Mathematics","citation":{"ieee":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result,” Israel Journal of Mathematics, vol. 222, no. 2. Springer, pp. 841–866, 2017.","apa":"Goaoc, X., Mabillard, I., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2017). On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-017-1607-7","ista":"Goaoc X, Mabillard I, Paták P, Patakova Z, Tancer M, Wagner U. 2017. On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result. Israel Journal of Mathematics. 222(2), 841–866.","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","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.","short":"X. Goaoc, I. Mabillard, P. Paták, Z. Patakova, M. Tancer, U. Wagner, Israel Journal of Mathematics 222 (2017) 841–866.","mla":"Goaoc, Xavier, et al. “On Generalized Heawood Inequalities for Manifolds: A van Kampen–Flores Type Nonembeddability Result.” Israel Journal of Mathematics, vol. 222, no. 2, Springer, 2017, pp. 841–66, doi:10.1007/s11856-017-1607-7."}},{"quality_controlled":"1","external_id":{"pmid":["28373553"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1618934114","publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"04","publisher":"National Academy of Sciences","publication_status":"published","pmid":1,"year":"2017","volume":114,"date_created":"2019-03-19T13:46:36Z","date_updated":"2021-01-12T08:06:11Z","author":[{"full_name":"Fenk, Lorenz A.","first_name":"Lorenz A.","last_name":"Fenk"},{"last_name":"de Bono","first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario"}],"extern":"1","file_date_updated":"2020-07-14T12:47:20Z","page":"4195-4200","citation":{"chicago":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1618934114.","short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) 4195–4200.","mla":"Fenk, Lorenz A., and Mario de Bono. “Memory of Recent Oxygen Experience Switches Pheromone Valence InCaenorhabditis Elegans.” Proceedings of the National Academy of Sciences, vol. 114, no. 16, National Academy of Sciences, 2017, pp. 4195–200, doi:10.1073/pnas.1618934114.","apa":"Fenk, L. A., & de Bono, M. (2017). Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1618934114","ieee":"L. A. Fenk and M. de Bono, “Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans,” Proceedings of the National Academy of Sciences, vol. 114, no. 16. National Academy of Sciences, pp. 4195–4200, 2017.","ista":"Fenk LA, de Bono M. 2017. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(16), 4195–4200.","ama":"Fenk LA, de Bono M. Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans. Proceedings of the National Academy of Sciences. 2017;114(16):4195-4200. doi:10.1073/pnas.1618934114"},"publication":"Proceedings of the National Academy of Sciences","date_published":"2017-04-18T00:00:00Z","has_accepted_license":"1","day":"18","intvolume":" 114","status":"public","ddc":["570"],"title":"Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans","_id":"6115","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"kschuh","file_size":1217696,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_PNAS_Fenk.pdf","checksum":"1801bc8319b752fa17598004ec375279","date_updated":"2020-07-14T12:47:20Z","date_created":"2019-03-19T14:00:42Z","file_id":"6116","relation":"main_file"}],"type":"journal_article","issue":"16","abstract":[{"text":"Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.","lang":"eng"}]},{"page":"43-48","publication":"Nature","citation":{"ama":"Chen C, Itakura E, Nelson GM, et al. IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. Nature. 2017;542(7639):43-48. doi:10.1038/nature20818","ista":"Chen C, Itakura E, Nelson GM, Sheng M, Laurent P, Fenk LA, Butcher RA, Hegde RS, de Bono M. 2017. IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. Nature. 542(7639), 43–48.","apa":"Chen, C., Itakura, E., Nelson, G. M., Sheng, M., Laurent, P., Fenk, L. A., … de Bono, M. (2017). IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses. Nature. Springer Nature. https://doi.org/10.1038/nature20818","ieee":"C. Chen et al., “IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses,” Nature, vol. 542, no. 7639. Springer Nature, pp. 43–48, 2017.","mla":"Chen, Changchun, et al. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans Sensory Responses.” Nature, vol. 542, no. 7639, Springer Nature, 2017, pp. 43–48, doi:10.1038/nature20818.","short":"C. Chen, E. Itakura, G.M. Nelson, M. Sheng, P. Laurent, L.A. Fenk, R.A. Butcher, R.S. Hegde, M. de Bono, Nature 542 (2017) 43–48.","chicago":"Chen, Changchun, Eisuke Itakura, Geoffrey M. Nelson, Ming Sheng, Patrick Laurent, Lorenz A. Fenk, Rebecca A. Butcher, Ramanujan S. Hegde, and Mario de Bono. “IL-17 Is a Neuromodulator of Caenorhabditis Elegans Sensory Responses.” Nature. Springer Nature, 2017. https://doi.org/10.1038/nature20818."},"date_published":"2017-02-02T00:00:00Z","day":"02","status":"public","title":"IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses","intvolume":" 542","_id":"6117","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates responses to pathogens or tissue damage, and drives autoimmune diseases. Little is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter their response properties and contribution to behaviour. Using unbiased genetic screens, we delineate an IL-17 signalling pathway and show that it acts in the RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to input from oxygen sensors, and renders sustained escape from 21% oxygen transient and contingent on additional stimuli. Over-activating IL-17 receptors abnormally heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in adults can rescue mutant defects within 6 h. These findings reveal a non-immunological role of IL-17 modulating circuit function and behaviour."}],"issue":"7639","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/28099418"}],"external_id":{"pmid":[" 28099418"]},"language":[{"iso":"eng"}],"doi":"10.1038/nature20818","month":"02","publication_identifier":{"issn":["0028-0836","1476-4687"]},"publication_status":"published","publisher":"Springer Nature","year":"2017","pmid":1,"date_updated":"2021-01-12T08:06:12Z","date_created":"2019-03-19T14:06:41Z","volume":542,"author":[{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"},{"full_name":"Itakura, Eisuke","first_name":"Eisuke","last_name":"Itakura"},{"full_name":"Nelson, Geoffrey M.","last_name":"Nelson","first_name":"Geoffrey M."},{"first_name":"Ming","last_name":"Sheng","full_name":"Sheng, Ming"},{"last_name":"Laurent","first_name":"Patrick","full_name":"Laurent, Patrick"},{"first_name":"Lorenz A.","last_name":"Fenk","full_name":"Fenk, Lorenz A."},{"last_name":"Butcher","first_name":"Rebecca A.","full_name":"Butcher, Rebecca A."},{"first_name":"Ramanujan S.","last_name":"Hegde","full_name":"Hegde, Ramanujan S."},{"first_name":"Mario","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"}],"extern":"1"},{"department":[{"_id":"NiBa"}],"publisher":"American Association for the Advancement of Science","intvolume":" 358","title":"Evolution of flower color pattern through selection on regulatory small RNAs","publication_status":"published","status":"public","year":"2017","_id":"611","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":358,"date_updated":"2021-01-12T08:06:10Z","date_created":"2018-12-11T11:47:29Z","author":[{"first_name":"Desmond","last_name":"Bradley","full_name":"Bradley, Desmond"},{"first_name":"Ping","last_name":"Xu","full_name":"Xu, Ping"},{"first_name":"Irina","last_name":"Mohorianu","full_name":"Mohorianu, Irina"},{"last_name":"Whibley","first_name":"Annabel","full_name":"Whibley, Annabel"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"first_name":"Hugo","last_name":"Tavares","full_name":"Tavares, Hugo"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"last_name":"Copsey","first_name":"Lucy","full_name":"Copsey, Lucy"},{"full_name":"Carpenter, Rosemary","last_name":"Carpenter","first_name":"Rosemary"},{"full_name":"Li, Miaomiao","first_name":"Miaomiao","last_name":"Li"},{"full_name":"Li, Qun","first_name":"Qun","last_name":"Li"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"first_name":"Tamas","last_name":"Dalmay","full_name":"Dalmay, Tamas"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"type":"journal_article","publist_id":"7193","issue":"6365","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."}],"page":"925 - 928","quality_controlled":"1","citation":{"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.","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.","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao3526","ieee":"D. Bradley et al., “Evolution of flower color pattern through selection on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017.","ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","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"},"publication":"Science","language":[{"iso":"eng"}],"doi":"10.1126/science.aao3526","date_published":"2017-11-17T00:00:00Z","scopus_import":1,"publication_identifier":{"issn":["00368075"]},"month":"11","day":"17"},{"has_accepted_license":"1","day":"06","citation":{"chicago":"Oda, Shigekazu, Yu Toyoshima, and Mario de Bono. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2017. https://doi.org/10.1073/pnas.1614596114.","mla":"Oda, Shigekazu, et al. “Modulation of Sensory Information Processing by a Neuroglobin in Caenorhabditis Elegans.” Proceedings of the National Academy of Sciences, vol. 114, no. 23, National Academy of Sciences, 2017, pp. E4658–65, doi:10.1073/pnas.1614596114.","short":"S. Oda, Y. Toyoshima, M. de Bono, Proceedings of the National Academy of Sciences 114 (2017) E4658–E4665.","ista":"Oda S, Toyoshima Y, de Bono M. 2017. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 114(23), E4658–E4665.","apa":"Oda, S., Toyoshima, Y., & de Bono, M. (2017). Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1614596114","ieee":"S. Oda, Y. Toyoshima, and M. de Bono, “Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans,” Proceedings of the National Academy of Sciences, vol. 114, no. 23. National Academy of Sciences, pp. E4658–E4665, 2017.","ama":"Oda S, Toyoshima Y, de Bono M. Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans. Proceedings of the National Academy of Sciences. 2017;114(23):E4658-E4665. doi:10.1073/pnas.1614596114"},"publication":"Proceedings of the National Academy of Sciences","page":"E4658-E4665","date_published":"2017-06-06T00:00:00Z","type":"journal_article","issue":"23","_id":"6113","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 114","status":"public","ddc":["570"],"title":"Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-19T13:42:58Z","checksum":"9e42ce47090ecdad7d76f2dbdebb924e","relation":"main_file","file_id":"6114","file_size":1469622,"content_type":"application/pdf","creator":"kschuh","file_name":"2017_PNAS_Oda.pdf","access_level":"open_access"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"month":"06","external_id":{"pmid":["28536200"]},"oa":1,"quality_controlled":"1","doi":"10.1073/pnas.1614596114","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:19Z","extern":"1","pmid":1,"year":"2017","publisher":"National Academy of Sciences","publication_status":"published","author":[{"first_name":"Shigekazu","last_name":"Oda","full_name":"Oda, Shigekazu"},{"full_name":"Toyoshima, Yu","first_name":"Yu","last_name":"Toyoshima"},{"full_name":"de Bono, Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","last_name":"de Bono"}],"volume":114,"date_updated":"2021-01-12T08:06:11Z","date_created":"2019-03-19T13:29:51Z"},{"date_published":"2017-12-01T00:00:00Z","publication":"Nature Communications","citation":{"mla":"Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.","short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).","chicago":"Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01683-1.","ama":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-01683-1","ista":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.","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","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."},"day":"01","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":1,"pubrep_id":"911","file":[{"file_id":"5190","relation":"main_file","checksum":"44bb5d0229926c23a9955d9fe0f9723f","date_updated":"2020-07-14T12:47:20Z","date_created":"2018-12-12T10:16:05Z","access_level":"open_access","file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf","creator":"system","file_size":1951699,"content_type":"application/pdf"}],"oa_version":"Published Version","_id":"613","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Shaping bacterial population behavior through computer interfaced control of individual cells","ddc":["576","579"],"intvolume":" 8","abstract":[{"text":"Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior.","lang":"eng"}],"issue":"1","type":"journal_article","doi":"10.1038/s41467-017-01683-1","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"month":"12","publication_identifier":{"issn":["20411723"]},"author":[{"full_name":"Chait, Remy P","first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187"},{"full_name":"Ruess, Jakob","last_name":"Ruess","first_name":"Jakob","orcid":"0000-0003-1615-3282","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bergmiller","first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"date_updated":"2021-01-12T08:06:15Z","date_created":"2018-12-11T11:47:30Z","volume":8,"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).","year":"2017","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:20Z","ec_funded":1,"publist_id":"7191","article_number":"1535"},{"oa_version":"Submitted Version","status":"public","title":"Universality for random matrix flows with time dependent density","intvolume":" 53","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"615","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."}],"issue":"4","type":"journal_article","date_published":"2017-11-01T00:00:00Z","page":"1606 - 1656","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","citation":{"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","ista":"Erdös L, Schnelli K. 2017. Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. 53(4), 1606–1656.","ieee":"L. Erdös and K. Schnelli, “Universality for random matrix flows with time dependent density,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4. Institute of Mathematical Statistics, pp. 1606–1656, 2017.","apa":"Erdös, L., & Schnelli, K. (2017). Universality for random matrix flows with time dependent density. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/16-AIHP765","mla":"Erdös, László, and Kevin Schnelli. “Universality for Random Matrix Flows with Time Dependent Density.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 53, no. 4, Institute of Mathematical Statistics, 2017, pp. 1606–56, doi:10.1214/16-AIHP765.","short":"L. Erdös, K. Schnelli, Annales de l’institut Henri Poincare (B) Probability and Statistics 53 (2017) 1606–1656.","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."},"day":"01","scopus_import":1,"date_updated":"2021-01-12T08:06:22Z","date_created":"2018-12-11T11:47:30Z","volume":53,"author":[{"full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schnelli","first_name":"Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}],"publication_status":"published","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","year":"2017","publist_id":"7189","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1214/16-AIHP765","quality_controlled":"1","project":[{"name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1504.00650","open_access":"1"}],"month":"11","publication_identifier":{"issn":["02460203"]}},{"date_published":"2017-06-02T00:00:00Z","citation":{"mla":"Franke, Frederik, et al. “Environmental Temperature Variation Influences Fitness Trade-Offs in a Fish-Tapeworm Association .” Parasites & Vectors, vol. 10, no. 252, 52, BioMed Central, 2017, doi:10.1186/s13071-017-2192-7.","short":"F. Franke, S. Armitage, M. Kutzer, J. Kurtz, J. Scharsack, Parasites & Vectors 10 (2017).","chicago":"Franke, Frederik, Sophie Armitage, Megan Kutzer, Joachim Kurtz, and Jörn Scharsack. “Environmental Temperature Variation Influences Fitness Trade-Offs in a Fish-Tapeworm Association .” Parasites & Vectors. BioMed Central, 2017. https://doi.org/10.1186/s13071-017-2192-7.","ama":"Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . Parasites & Vectors. 2017;10(252). doi:10.1186/s13071-017-2192-7","ista":"Franke F, Armitage S, Kutzer M, Kurtz J, Scharsack J. 2017. Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . Parasites & Vectors. 10(252), 52.","ieee":"F. Franke, S. Armitage, M. Kutzer, J. Kurtz, and J. Scharsack, “Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association ,” Parasites & Vectors, vol. 10, no. 252. BioMed Central, 2017.","apa":"Franke, F., Armitage, S., Kutzer, M., Kurtz, J., & Scharsack, J. (2017). Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association . Parasites & Vectors. BioMed Central. https://doi.org/10.1186/s13071-017-2192-7"},"publication":"Parasites & Vectors","has_accepted_license":"1","day":"02","file":[{"file_size":671807,"content_type":"application/pdf","creator":"dernst","file_name":"2017_Parasites_Franke.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:22Z","date_created":"2019-01-21T13:45:36Z","checksum":"742943377a38ee208108705b8e2f4dbf","relation":"main_file","file_id":"5864"}],"oa_version":"Published Version","intvolume":" 10","title":"Environmental temperature variation influences fitness trade-offs in a fish-tapeworm association ","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"618","issue":"252","abstract":[{"text":"Background: Increasing temperatures are predicted to strongly impact host-parasite interactions, but empirical tests are rare. Host species that are naturally exposed to a broad temperature spectrum offer the possibility to investigate the effects of elevated temperatures on hosts and parasites. Using three-spined sticklebacks, Gasterosteus aculeatus L., and tapeworms, Schistocephalus solidus (Müller, 1776), originating from a cold and a warm water site of a volcanic lake, we subjected sympatric and allopatric host-parasite combinations to cold and warm conditions in a fully crossed design. We predicted that warm temperatures would promote the development of the parasites, while the hosts might benefit from cooler temperatures. We further expected adaptations to the local temperature and mutual adaptations of local host-parasite pairs. Results: Overall, S. solidus parasites grew faster at warm temperatures and stickleback hosts at cold temperatures. On a finer scale, we observed that parasites were able to exploit their hosts more efficiently at the parasite’s temperature of origin. In contrast, host tolerance towards parasite infection was higher when sticklebacks were infected with parasites at the parasite’s ‘foreign’ temperature. Cold-origin sticklebacks tended to grow faster and parasite infection induced a stronger immune response. Conclusions: Our results suggest that increasing environmental temperatures promote the parasite rather than the host and that host tolerance is dependent on the interaction between parasite infection and temperature. Sticklebacks might use tolerance mechanisms towards parasite infection in combination with their high plasticity towards temperature changes to cope with increasing parasite infection pressures and rising temperatures.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1186/s13071-017-2192-7","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["17563305"]},"month":"06","volume":10,"date_updated":"2021-01-12T08:06:35Z","date_created":"2018-12-11T11:47:31Z","author":[{"first_name":"Frederik","last_name":"Franke","full_name":"Franke, Frederik"},{"full_name":"Armitage, Sophie","first_name":"Sophie","last_name":"Armitage"},{"full_name":"Kutzer, Megan","last_name":"Kutzer","first_name":"Megan","orcid":"0000-0002-8696-6978","id":"29D0B332-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kurtz","first_name":"Joachim","full_name":"Kurtz, Joachim"},{"last_name":"Scharsack","first_name":"Jörn","full_name":"Scharsack, Jörn"}],"publisher":"BioMed Central","publication_status":"published","year":"2017","extern":"1","publist_id":"7186","file_date_updated":"2020-07-14T12:47:22Z","article_number":"52"},{"type":"book_chapter","alternative_title":["ADVSANAT"],"abstract":[{"lang":"eng","text":"Genetic factors might be largely responsible for the development of autism spectrum disorder (ASD) that alone or in combination with specific environmental risk factors trigger the pathology. Multiple mutations identified in ASD patients that impair synaptic function in the central nervous system are well studied in animal models. How these mutations might interact with other risk factors is not fully understood though. Additionally, how systems outside of the brain are altered in the context of ASD is an emerging area of research. Extracerebral influences on the physiology could begin in utero and contribute to changes in the brain and in the development of other body systems and further lead to epigenetic changes. Therefore, multiple recent studies have aimed at elucidating the role of gene-environment interactions in ASD. Here we provide an overview on the extracerebral systems that might play an important associative role in ASD and review evidence regarding the potential roles of inflammation, trace metals, metabolism, genetic susceptibility, enteric nervous system function and the microbiota of the gastrointestinal (GI) tract on the development of endophenotypes in animal models of ASD. By influencing environmental conditions, it might be possible to reduce or limit the severity of ASD pathology."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"623","title":"Extracerebral dysfunction in animal models of autism spectrum disorder","status":"public","intvolume":" 224","oa_version":"None","scopus_import":1,"series_title":"Advances in Anatomy Embryology and Cell Biology","day":"28","publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","citation":{"ista":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. 2017.Extracerebral dysfunction in animal models of autism spectrum disorder. In: Translational Anatomy and Cell Biology of Autism Spectrum Disorder. ADVSANAT, vol. 224, 159–187.","apa":"Hill Yardin, E., Mckeown, S., Novarino, G., & Grabrucker, A. (2017). Extracerebral dysfunction in animal models of autism spectrum disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 159–187). Springer. https://doi.org/10.1007/978-3-319-52498-6_9","ieee":"E. Hill Yardin, S. Mckeown, G. Novarino, and A. Grabrucker, “Extracerebral dysfunction in animal models of autism spectrum disorder,” in Translational Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 159–187.","ama":"Hill Yardin E, Mckeown S, Novarino G, Grabrucker A. Extracerebral dysfunction in animal models of autism spectrum disorder. In: Schmeisser M, Boekers T, eds. Translational Anatomy and Cell Biology of Autism Spectrum Disorder. Vol 224. Advances in Anatomy Embryology and Cell Biology. Springer; 2017:159-187. doi:10.1007/978-3-319-52498-6_9","chicago":"Hill Yardin, Elisa, Sonja Mckeown, Gaia Novarino, and Andreas Grabrucker. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” In Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, 224:159–87. Advances in Anatomy Embryology and Cell Biology. Springer, 2017. https://doi.org/10.1007/978-3-319-52498-6_9.","mla":"Hill Yardin, Elisa, et al. “Extracerebral Dysfunction in Animal Models of Autism Spectrum Disorder.” Translational Anatomy and Cell Biology of Autism Spectrum Disorder, edited by Michael Schmeisser and Tobias Boekers, vol. 224, Springer, 2017, pp. 159–87, doi:10.1007/978-3-319-52498-6_9.","short":"E. Hill Yardin, S. Mckeown, G. Novarino, A. Grabrucker, in:, M. Schmeisser, T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder, Springer, 2017, pp. 159–187."},"page":"159 - 187","date_published":"2017-05-28T00:00:00Z","publist_id":"7177","year":"2017","publication_status":"published","department":[{"_id":"GaNo"}],"editor":[{"full_name":"Schmeisser, Michael","first_name":"Michael","last_name":"Schmeisser"},{"full_name":"Boekers, Tobias","last_name":"Boekers","first_name":"Tobias"}],"publisher":"Springer","author":[{"full_name":"Hill Yardin, Elisa","first_name":"Elisa","last_name":"Hill Yardin"},{"first_name":"Sonja","last_name":"Mckeown","full_name":"Mckeown, Sonja"},{"full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"},{"full_name":"Grabrucker, Andreas","first_name":"Andreas","last_name":"Grabrucker"}],"date_updated":"2021-01-12T08:06:46Z","date_created":"2018-12-11T11:47:33Z","volume":224,"month":"05","publication_identifier":{"issn":["03015556"],"isbn":["978-3-319-52496-2"]},"quality_controlled":"1","doi":"10.1007/978-3-319-52498-6_9","language":[{"iso":"eng"}]},{"scopus_import":1,"day":"01","has_accepted_license":"1","page":"50 - 73","publication":"Theoretical Population Biology","citation":{"mla":"Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology, vol. 118, Academic Press, 2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73.","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.","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","ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” Theoretical Population Biology, vol. 118. Academic Press, pp. 50–73, 2017."},"date_published":"2017-12-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","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."}],"title":"The infinitesimal model: Definition derivation and implications","status":"public","ddc":["576"],"intvolume":" 118","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"626","file":[{"file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1133924,"creator":"system","relation":"main_file","file_id":"4964","date_updated":"2020-07-14T12:47:25Z","date_created":"2018-12-12T10:12:45Z","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8"}],"oa_version":"Published Version","pubrep_id":"908","month":"12","publication_identifier":{"issn":["00405809"]},"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.06.001","file_date_updated":"2020-07-14T12:47:25Z","ec_funded":1,"publist_id":"7169","publication_status":"published","publisher":"Academic Press","department":[{"_id":"NiBa"}],"year":"2017","date_created":"2018-12-11T11:47:34Z","date_updated":"2021-01-12T08:06:50Z","volume":118,"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"},{"first_name":"Amandine","last_name":"Véber","full_name":"Véber, Amandine"}]},{"alternative_title":["LNCS"],"type":"book_chapter","abstract":[{"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.","lang":"eng"}],"ddc":["000"],"title":"The cost of exactness in quantitative reachability","status":"public","intvolume":" 10460","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"625","file":[{"file_id":"7048","relation":"main_file","checksum":"b2402766ec02c79801aac634bd8f9f6c","date_updated":"2020-07-14T12:47:25Z","date_created":"2019-11-19T08:06:50Z","access_level":"open_access","file_name":"2017_ModelsAlgorithms_Chatterjee.pdf","creator":"dernst","content_type":"application/pdf","file_size":192826}],"oa_version":"Submitted Version","series_title":"Theoretical Computer Science and General Issues","scopus_import":"1","day":"25","article_processing_charge":"No","has_accepted_license":"1","page":"367 - 381","publication":"Models, Algorithms, Logics and Tools","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.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, R. Mardare (Eds.), Models, Algorithms, Logics and Tools, Springer, 2017, pp. 367–381.","mla":"Chatterjee, Krishnendu, et al. “The Cost of Exactness in Quantitative Reachability.” Models, Algorithms, Logics and Tools, edited by Luca Aceto et al., vol. 10460, Springer, 2017, pp. 367–81, doi:10.1007/978-3-319-63121-9_18.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “The cost of exactness in quantitative reachability,” in Models, Algorithms, Logics and Tools, vol. 10460, L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, and R. Mardare, Eds. Springer, 2017, pp. 367–381.","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2017). The cost of exactness in quantitative reachability. In L. Aceto, G. Bacci, A. Ingólfsdóttir, A. Legay, & R. Mardare (Eds.), Models, Algorithms, Logics and Tools (Vol. 10460, pp. 367–381). Springer. https://doi.org/10.1007/978-3-319-63121-9_18","ista":"Chatterjee K, Doyen L, Henzinger TA. 2017.The cost of exactness in quantitative reachability. In: Models, Algorithms, Logics and Tools. LNCS, vol. 10460, 367–381.","ama":"Chatterjee K, Doyen L, Henzinger TA. The cost of exactness in quantitative reachability. In: Aceto L, Bacci G, Ingólfsdóttir A, Legay A, Mardare R, eds. Models, Algorithms, Logics and Tools. Vol 10460. Theoretical Computer Science and General Issues. Springer; 2017:367-381. doi:10.1007/978-3-319-63121-9_18"},"date_published":"2017-07-25T00:00:00Z","file_date_updated":"2020-07-14T12:47:25Z","publist_id":"7170","ec_funded":1,"publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"editor":[{"last_name":"Aceto","first_name":"Luca","full_name":"Aceto, Luca"},{"full_name":"Bacci, Giorgio","first_name":"Giorgio","last_name":"Bacci"},{"first_name":"Anna","last_name":"Ingólfsdóttir","full_name":"Ingólfsdóttir, Anna"},{"full_name":"Legay, Axel","first_name":"Axel","last_name":"Legay"},{"first_name":"Radu","last_name":"Mardare","full_name":"Mardare, Radu"}],"year":"2017","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.","date_created":"2018-12-11T11:47:34Z","date_updated":"2022-05-23T08:54:02Z","volume":10460,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"month":"07","publication_identifier":{"isbn":["978-3-319-63120-2"],"issn":["0302-9743"]},"quality_controlled":"1","project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-63121-9_18"},{"type":"journal_article","issue":"9","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"}],"_id":"624","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2017","status":"public","title":"MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations","ddc":["579"],"pubrep_id":"909","oa_version":"Published Version","file":[{"creator":"system","content_type":"application/pdf","file_size":682064,"access_level":"open_access","file_name":"IST-2017-909-v1+1_peerj-3830.pdf","checksum":"3d79ae6b6eabc90b0eaaed82ff3493b0","date_created":"2018-12-12T10:11:51Z","date_updated":"2020-07-14T12:47:24Z","file_id":"4908","relation":"main_file"}],"scopus_import":1,"has_accepted_license":"1","day":"21","citation":{"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","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.","ieee":"N. Nikolic, Z. Didara, and I. Moll, “MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations,” PeerJ, vol. 2017, no. 9. PeerJ, 2017.","apa":"Nikolic, N., Didara, Z., & Moll, I. (2017). MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations. PeerJ. PeerJ. https://doi.org/10.7717/peerj.3830","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).","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."},"publication":"PeerJ","date_published":"2017-09-21T00:00:00Z","article_number":"3830","publist_id":"7172","file_date_updated":"2020-07-14T12:47:24Z","acknowledgement":"Austrian Science Fund (FWF): M1697, P22249; Swiss National Science Foundation (SNF): 145706; European Commission;FWF Special Research Program: RNA-REG F43","year":"2017","department":[{"_id":"CaGu"}],"publisher":"PeerJ","publication_status":"published","author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9068-6090","first_name":"Nela","last_name":"Nikolic","full_name":"Nikolic, Nela"},{"last_name":"Didara","first_name":"Zrinka","full_name":"Didara, Zrinka"},{"last_name":"Moll","first_name":"Isabella","full_name":"Moll, Isabella"}],"volume":2017,"date_updated":"2021-01-12T08:06:48Z","date_created":"2018-12-11T11:47:33Z","publication_identifier":{"issn":["21678359"]},"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.7717/peerj.3830","language":[{"iso":"eng"}]},{"year":"2017","publisher":"Springer","editor":[{"full_name":"Majumdar, Rupak","first_name":"Rupak","last_name":"Majumdar"},{"full_name":"Kunčak, Viktor","first_name":"Viktor","last_name":"Kunčak"}],"department":[{"_id":"KrCh"}],"publication_status":"published","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"full_name":"Murhekar, Aniket","first_name":"Aniket","last_name":"Murhekar"}],"volume":10426,"date_updated":"2021-01-12T08:06:55Z","date_created":"2018-12-11T11:47:35Z","ec_funded":1,"publist_id":"7166","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00314"}],"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"quality_controlled":"1","doi":"10.1007/978-3-319-63387-9_6","conference":{"name":"CAV: Computer Aided Verification","location":"Heidelberg, Germany","start_date":"2017-07-24","end_date":"2017-07-28"},"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331963386-2"]},"month":"01","_id":"628","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 10426","status":"public","title":"Automated recurrence analysis for almost linear expected runtime bounds","oa_version":"Submitted Version","type":"conference","alternative_title":["LNCS"],"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"}],"citation":{"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.","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.","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","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.","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"},"page":"118 - 139","date_published":"2017-01-01T00:00:00Z","scopus_import":1,"day":"01"},{"publist_id":"7165","pmid":1,"year":"2017","publisher":"Springer","department":[{"_id":"MaLo"}],"publication_status":"published","author":[{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"full_name":"Zieske, Katja","last_name":"Zieske","first_name":"Katja"},{"full_name":"Schwille, Petra","first_name":"Petra","last_name":"Schwille"}],"volume":84,"date_updated":"2021-01-12T08:06:57Z","date_created":"2018-12-11T11:47:35Z","publication_identifier":{"eisbn":["978-3-319-53047-5"]},"month":"05","external_id":{"pmid":["28500535"]},"quality_controlled":"1","doi":"10.1007/978-3-319-53047-5_15","language":[{"iso":"eng"}],"type":"book_chapter","abstract":[{"text":"Even simple cells like bacteria have precisely regulated cellular anatomies, which allow them to grow, divide and to respond to internal or external cues with high fidelity. How spatial and temporal intracellular organization in prokaryotic cells is achieved and maintained on the basis of locally interacting proteins still remains largely a mystery. Bulk biochemical assays with purified components and in vivo experiments help us to approach key cellular processes from two opposite ends, in terms of minimal and maximal complexity. However, to understand how cellular phenomena emerge, that are more than the sum of their parts, we have to assemble cellular subsystems step by step from the bottom up. Here, we review recent in vitro reconstitution experiments with proteins of the bacterial cell division machinery and illustrate how they help to shed light on fundamental cellular mechanisms that constitute spatiotemporal order and regulate cell division.","lang":"eng"}],"_id":"629","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 84","title":"Reconstitution of protein dynamics involved in bacterial cell division","status":"public","oa_version":"None","scopus_import":1,"series_title":"Sub-Cellular Biochemistry","day":"13","citation":{"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","ieee":"M. Loose, K. Zieske, and P. Schwille, “Reconstitution of protein dynamics involved in bacterial cell division,” in Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp. 419–444.","ista":"Loose M, Zieske K, Schwille P. 2017.Reconstitution of protein dynamics involved in bacterial cell division. In: Prokaryotic Cytoskeletons. vol. 84, 419–444.","short":"M. Loose, K. Zieske, P. Schwille, in:, Prokaryotic Cytoskeletons, Springer, 2017, pp. 419–444.","mla":"Loose, Martin, et al. “Reconstitution of Protein Dynamics Involved in Bacterial Cell Division.” Prokaryotic Cytoskeletons, vol. 84, Springer, 2017, pp. 419–44, doi:10.1007/978-3-319-53047-5_15.","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."},"publication":"Prokaryotic Cytoskeletons","page":"419 - 444","date_published":"2017-05-13T00:00:00Z"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:47:27Z","publist_id":"7164","publication_status":"published","publisher":"IOS Press","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"year":"2017","date_created":"2018-12-11T11:47:36Z","date_updated":"2021-01-12T08:06:59Z","volume":236,"author":[{"full_name":"Sauermann, Stefan","first_name":"Stefan","last_name":"Sauermann"},{"first_name":"Veronika","last_name":"David","full_name":"David, Veronika"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Egelkraut","first_name":"Reinhard","full_name":"Egelkraut, Reinhard"},{"full_name":"Frohner, Matthias","first_name":"Matthias","last_name":"Frohner"},{"first_name":"Birgit","last_name":"Pohn","full_name":"Pohn, Birgit"},{"last_name":"Urbauer","first_name":"Philipp","full_name":"Urbauer, Philipp"},{"last_name":"Mense","first_name":"Alexander","full_name":"Mense, Alexander"}],"month":"01","publication_identifier":{"isbn":["978-161499758-0"]},"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"language":[{"iso":"eng"}],"conference":{"name":"eHealth: Health Informatics Meets eHealth","location":"Vienna, Austria","start_date":"2017-05-23","end_date":"2017-05-24"},"doi":"10.3233/978-1-61499-759-7-356","alternative_title":["Studies in Health Technology and Informatics"],"type":"conference","abstract":[{"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.","lang":"eng"}],"status":"public","ddc":["005"],"title":"Biosignals standards and FHIR: The way to go","intvolume":" 236","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"630","oa_version":"Published Version","file":[{"creator":"system","file_size":443635,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-906-v1+1_SHTI236-0356.pdf","checksum":"1254dcc5b04a996d97fad9a726b42727","date_created":"2018-12-12T10:11:56Z","date_updated":"2020-07-14T12:47:27Z","file_id":"4913","relation":"main_file"}],"pubrep_id":"906","scopus_import":1,"day":"01","has_accepted_license":"1","page":"356 - 362","citation":{"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.","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.","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","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.","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.","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"},"date_published":"2017-01-01T00:00:00Z"},{"intvolume":" 145","title":"A note on 2D focusing many boson systems","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"632","oa_version":"Submitted Version","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We consider a 2D quantum system of N bosons in a trapping potential |x|s, interacting via a pair potential of the form N2β−1 w(Nβ x). We show that for all 0 < β < (s + 1)/(s + 2), the leading order behavior of ground states of the many-body system is described in the large N limit by the corresponding cubic nonlinear Schrödinger energy functional. Our result covers the focusing case (w < 0) where even the stability of the many-body system is not obvious. This answers an open question mentioned by X. Chen and J. Holmer for harmonic traps (s = 2). Together with the BBGKY hierarchy approach used by these authors, our result implies the convergence of the many-body quantum dynamics to the focusing NLS equation with harmonic trap for all 0 < β < 3/4. "}],"page":"2441 - 2454","citation":{"ama":"Lewin M, Nam P, Rougerie N. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 2017;145(6):2441-2454. doi:10.1090/proc/13468","ista":"Lewin M, Nam P, Rougerie N. 2017. A note on 2D focusing many boson systems. Proceedings of the American Mathematical Society. 145(6), 2441–2454.","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.","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","mla":"Lewin, Mathieu, et al. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society, vol. 145, no. 6, American Mathematical Society, 2017, pp. 2441–54, doi:10.1090/proc/13468.","short":"M. Lewin, P. Nam, N. Rougerie, Proceedings of the American Mathematical Society 145 (2017) 2441–2454.","chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “A Note on 2D Focusing Many Boson Systems.” Proceedings of the American Mathematical Society. American Mathematical Society, 2017. https://doi.org/10.1090/proc/13468."},"publication":"Proceedings of the American Mathematical Society","date_published":"2017-01-01T00:00:00Z","scopus_import":1,"day":"01","department":[{"_id":"RoSe"}],"publisher":"American Mathematical Society","publication_status":"published","year":"2017","volume":145,"date_created":"2018-12-11T11:47:36Z","date_updated":"2021-01-12T08:07:03Z","author":[{"first_name":"Mathieu","last_name":"Lewin","full_name":"Lewin, Mathieu"},{"full_name":"Nam, Phan","last_name":"Nam","first_name":"Phan","id":"404092F4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicolas","last_name":"Rougerie","full_name":"Rougerie, Nicolas"}],"publist_id":"7160","ec_funded":1,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1509.09045"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1090/proc/13468","month":"01"},{"publist_id":"7156","author":[{"full_name":"Schroeder, Jan","first_name":"Jan","last_name":"Schroeder"},{"last_name":"Deliu","first_name":"Elena","orcid":"0000-0002-7370-5293","id":"37A40D7E-F248-11E8-B48F-1D18A9856A87","full_name":"Deliu, Elena"},{"orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia"},{"full_name":"Schmeisser, Michael","last_name":"Schmeisser","first_name":"Michael"}],"date_updated":"2021-01-12T08:07:08Z","date_created":"2018-12-11T11:47:37Z","volume":224,"year":"2017","publication_status":"published","publisher":"Springer","editor":[{"first_name":"Michael","last_name":"Schmeisser","full_name":"Schmeisser, Michael"},{"last_name":"Boekers","first_name":"Tobias","full_name":"Boekers, Tobias"}],"department":[{"_id":"GaNo"}],"month":"05","publication_identifier":{"eisbn":["978-3-319-52498-6"]},"doi":"10.1007/978-3-319-52498-6_10","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"grant_number":"F03523","_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease","call_identifier":"FWF"}],"abstract":[{"text":"As autism spectrum disorder (ASD) is largely regarded as a neurodevelopmental condition, long-time consensus was that its hallmark features are irreversible. However, several studies from recent years using defined mouse models of ASD have provided clear evidence that in mice neurobiological and behavioural alterations can be ameliorated or even reversed by genetic restoration or pharmacological treatment either before or after symptom onset. Here, we review findings on genetic and pharmacological reversibility of phenotypes in mouse models of ASD. Our review should give a comprehensive overview on both aspects and encourage future studies to better understand the underlying molecular mechanisms that might be translatable from animals to humans.","lang":"eng"}],"type":"book_chapter","alternative_title":["ADVSANAT"],"oa_version":"None","_id":"634","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder","intvolume":" 224","day":"28","scopus_import":1,"series_title":"Advances in Anatomy Embryology and Cell Biology","date_published":"2017-05-28T00:00:00Z","publication":"Translational Anatomy and Cell Biology of Autism Spectrum Disorder","citation":{"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","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.","apa":"Schroeder, J., Deliu, E., Novarino, G., & Schmeisser, M. (2017). Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder. In M. Schmeisser & T. Boekers (Eds.), Translational Anatomy and Cell Biology of Autism Spectrum Disorder (Vol. 224, pp. 189–211). Springer. https://doi.org/10.1007/978-3-319-52498-6_10","ieee":"J. Schroeder, E. Deliu, G. Novarino, and M. Schmeisser, “Genetic and pharmacological reversibility of phenotypes in mouse models of autism spectrum disorder,” in Translational Anatomy and Cell Biology of Autism Spectrum Disorder, vol. 224, M. Schmeisser and T. Boekers, Eds. Springer, 2017, pp. 189–211.","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.","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.","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."},"page":"189 - 211"},{"abstract":[{"lang":"eng","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."}],"type":"conference","alternative_title":["LNCS"],"oa_version":"None","_id":"633","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10381","title":"Challenges and tool implementation of hybrid rapidly exploring random trees","status":"public","day":"01","scopus_import":1,"date_published":"2017-01-01T00:00:00Z","citation":{"short":"S. Bak, S. Bogomolov, T.A. Henzinger, A. Kumar, in:, A. Abate, S. Bodo (Eds.), Springer, 2017, pp. 83–89.","mla":"Bak, Stanley, et al. Challenges and Tool Implementation of Hybrid Rapidly Exploring Random Trees. Edited by Alessandro Abate and Sylvie Bodo, vol. 10381, Springer, 2017, pp. 83–89, doi:10.1007/978-3-319-63501-9_6.","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.","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","ieee":"S. Bak, S. Bogomolov, T. A. Henzinger, and A. Kumar, “Challenges and tool implementation of hybrid rapidly exploring random trees,” presented at the NSV: Numerical Software Verification, Heidelberg, Germany, 2017, vol. 10381, pp. 83–89.","apa":"Bak, S., Bogomolov, S., Henzinger, T. A., & Kumar, A. (2017). Challenges and tool implementation of hybrid rapidly exploring random trees. In A. Abate & S. Bodo (Eds.) (Vol. 10381, pp. 83–89). Presented at the NSV: Numerical Software Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63501-9_6","ista":"Bak S, Bogomolov S, Henzinger TA, Kumar A. 2017. Challenges and tool implementation of hybrid rapidly exploring random trees. NSV: Numerical Software Verification, LNCS, vol. 10381, 83–89."},"page":"83 - 89","publist_id":"7159","author":[{"full_name":"Bak, Stanley","first_name":"Stanley","last_name":"Bak"},{"full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","first_name":"Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Kumar, Aviral","first_name":"Aviral","last_name":"Kumar"}],"volume":10381,"date_updated":"2021-01-12T08:07:06Z","date_created":"2018-12-11T11:47:37Z","year":"2017","publisher":"Springer","department":[{"_id":"ToHe"}],"editor":[{"first_name":"Alessandro","last_name":"Abate","full_name":"Abate, Alessandro"},{"full_name":"Bodo, Sylvie","first_name":"Sylvie","last_name":"Bodo"}],"publication_status":"published","publication_identifier":{"isbn":["978-331963500-2"]},"month":"01","doi":"10.1007/978-3-319-63501-9_6","conference":{"end_date":"2017-07-23","start_date":"2017-07-22","location":"Heidelberg, Germany","name":"NSV: Numerical Software Verification"},"language":[{"iso":"eng"}],"project":[{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"quality_controlled":"1"},{"author":[{"full_name":"Alwen, Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","first_name":"Joel F","last_name":"Alwen"},{"first_name":"Binchi","last_name":"Chen","full_name":"Chen, Binchi"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Reyzin, Leonid","last_name":"Reyzin","first_name":"Leonid"},{"first_name":"Stefano","last_name":"Tessaro","full_name":"Tessaro, Stefano"}],"date_created":"2018-12-11T11:47:37Z","date_updated":"2021-01-12T08:07:10Z","volume":10212,"year":"2017","publication_status":"published","publisher":"Springer","editor":[{"full_name":"Coron, Jean-Sébastien","first_name":"Jean-Sébastien","last_name":"Coron"},{"full_name":"Buus Nielsen, Jesper","first_name":"Jesper","last_name":"Buus Nielsen"}],"department":[{"_id":"KrPi"}],"publist_id":"7154","ec_funded":1,"conference":{"start_date":"2017-04-30","location":"Paris, France","end_date":"2017-05-04","name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques"},"doi":"10.1007/978-3-319-56617-7_2","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/989"}],"oa":1,"quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"month":"01","publication_identifier":{"isbn":["978-331956616-0"]},"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"635","title":"Scrypt is maximally memory hard","status":"public","intvolume":" 10212","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"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2017-01-01T00:00:00Z","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.","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.","chicago":"Alwen, Joel F, Binchi Chen, Krzysztof Z Pietrzak, Leonid Reyzin, and Stefano Tessaro. “Scrypt Is Maximally Memory Hard.” edited by Jean-Sébastien Coron and Jesper Buus Nielsen, 10212:33–62. Springer, 2017. https://doi.org/10.1007/978-3-319-56617-7_2.","ama":"Alwen JF, Chen B, Pietrzak KZ, Reyzin L, Tessaro S. Scrypt is maximally memory hard. In: Coron J-S, Buus Nielsen J, eds. Vol 10212. Springer; 2017:33-62. doi:10.1007/978-3-319-56617-7_2","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.","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","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."},"page":"33 - 62","day":"01","scopus_import":1},{"day":"03","scopus_import":1,"date_published":"2017-08-03T00:00:00Z","page":"189 - 206","citation":{"chicago":"Bakhirkin, Alexey, Thomas Ferrere, Oded Maler, and Dogan Ulus. “On the Quantitative Semantics of Regular Expressions over Real-Valued Signals.” edited by Alessandro Abate and Gilles Geeraerts, 10419:189–206. Springer, 2017. https://doi.org/10.1007/978-3-319-65765-3_11.","short":"A. Bakhirkin, T. Ferrere, O. Maler, D. Ulus, in:, A. Abate, G. Geeraerts (Eds.), Springer, 2017, pp. 189–206.","mla":"Bakhirkin, Alexey, et al. On the Quantitative Semantics of Regular Expressions over Real-Valued Signals. Edited by Alessandro Abate and Gilles Geeraerts, vol. 10419, Springer, 2017, pp. 189–206, doi:10.1007/978-3-319-65765-3_11.","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","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.","ista":"Bakhirkin A, Ferrere T, Maler O, Ulus D. 2017. On the quantitative semantics of regular expressions over real-valued signals. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 189–206.","ama":"Bakhirkin A, Ferrere T, Maler O, Ulus D. On the quantitative semantics of regular expressions over real-valued signals. In: Abate A, Geeraerts G, eds. Vol 10419. Springer; 2017:189-206. doi:10.1007/978-3-319-65765-3_11"},"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"}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","title":"On the quantitative semantics of regular expressions over real-valued signals","status":"public","intvolume":" 10419","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"636","month":"08","publication_identifier":{"isbn":["978-331965764-6"]},"language":[{"iso":"eng"}],"conference":{"start_date":"2017-09-05","location":"Berlin, Germany","end_date":"2017-09-07","name":"FORMATS: Formal Modelling and Analysis of Timed Systems"},"doi":"10.1007/978-3-319-65765-3_11","quality_controlled":"1","project":[{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01552132"}],"publist_id":"7152","date_updated":"2021-01-12T08:07:14Z","date_created":"2018-12-11T11:47:38Z","volume":10419,"author":[{"last_name":"Bakhirkin","first_name":"Alexey","full_name":"Bakhirkin, Alexey"},{"full_name":"Ferrere, Thomas","last_name":"Ferrere","first_name":"Thomas","orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"first_name":"Dogan","last_name":"Ulus","full_name":"Ulus, Dogan"}],"publication_status":"published","editor":[{"full_name":"Abate, Alessandro","first_name":"Alessandro","last_name":"Abate"},{"full_name":"Geeraerts, Gilles","first_name":"Gilles","last_name":"Geeraerts"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","year":"2017"},{"language":[{"iso":"eng"}],"conference":{"name":"NSV: Numerical Software Verification","start_date":"2016-07-17","location":"Toronto, ON, Canada","end_date":"2016-07-18"},"date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-54292-8","quality_controlled":"1","citation":{"chicago":"Bogomolov, Sergiy, Matthieu Martel, and Pavithra Prabhakar, eds. Numerical Software Verification. Vol. 10152. LNCS. Springer, 2017. https://doi.org/10.1007/978-3-319-54292-8.","mla":"Bogomolov, Sergiy, et al., editors. Numerical Software Verification. Vol. 10152, Springer, 2017, doi:10.1007/978-3-319-54292-8.","short":"S. Bogomolov, M. Martel, P. Prabhakar, eds., Numerical Software Verification, Springer, 2017.","ista":"Bogomolov S, Martel M, Prabhakar P eds. 2017. Numerical Software Verification, Springer,p.","apa":"Bogomolov, S., Martel, M., & Prabhakar, P. (Eds.). (2017). Numerical Software Verification (Vol. 10152). Presented at the NSV: Numerical Software Verification, Toronto, ON, Canada: Springer. https://doi.org/10.1007/978-3-319-54292-8","ieee":"S. Bogomolov, M. Martel, and P. Prabhakar, Eds., Numerical Software Verification, vol. 10152. Springer, 2017.","ama":"Bogomolov S, Martel M, Prabhakar P, eds. Numerical Software Verification. Vol 10152. Springer; 2017. doi:10.1007/978-3-319-54292-8"},"month":"01","day":"01","publication_identifier":{"issn":["0302-9743"],"eisbn":["978-3-319-54292-8"]},"article_processing_charge":"No","series_title":"LNCS","date_created":"2018-12-11T11:47:38Z","date_updated":"2022-05-24T07:09:52Z","volume":10152,"oa_version":"None","status":"public","title":"Numerical Software Verification","publication_status":"published","editor":[{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy"},{"first_name":"Matthieu","last_name":"Martel","full_name":"Martel, Matthieu"},{"first_name":"Pavithra","last_name":"Prabhakar","full_name":"Prabhakar, Pavithra"}],"intvolume":" 10152","department":[{"_id":"ToHe"}],"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"638","year":"2017","abstract":[{"lang":"eng","text":"This book constitutes the refereed proceedings of the 9th InternationalWorkshop on Numerical Software Verification, NSV 2016, held in Toronto, ON, Canada in July 2011 - colocated with CAV 2016, the 28th International Conference on Computer Aided Verification.\r\nThe NSV workshop is dedicated to the development of logical and mathematical techniques for the reasoning about programmability and reliability."}],"publist_id":"7150","type":"conference_editor"},{"date_published":"2017-04-01T00:00:00Z","page":"3 - 32","citation":{"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.","mla":"Alwen, Joel F., et al. Depth-Robust Graphs and Their Cumulative Memory Complexity. Edited by Jean-Sébastien Coron and Jesper Buus Nielsen, vol. 10212, Springer, 2017, pp. 3–32, doi:10.1007/978-3-319-56617-7_1.","short":"J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, J.-S. Coron, J. Buus Nielsen (Eds.), Springer, 2017, pp. 3–32.","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.","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","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.","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"},"day":"01","scopus_import":1,"oa_version":"Submitted Version","status":"public","title":"Depth-robust graphs and their cumulative memory complexity","intvolume":" 10212","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"640","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"}],"alternative_title":["LNCS"],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","start_date":"2017-04-30","location":"Paris, France","end_date":"2017-05-04"},"doi":"10.1007/978-3-319-56617-7_1","quality_controlled":"1","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"url":"https://eprint.iacr.org/2016/875","open_access":"1"}],"oa":1,"month":"04","publication_identifier":{"isbn":["978-331956616-0"]},"date_created":"2018-12-11T11:47:39Z","date_updated":"2021-01-12T08:07:22Z","volume":10212,"author":[{"id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","first_name":"Joel F","full_name":"Alwen, Joel F"},{"first_name":"Jeremiah","last_name":"Blocki","full_name":"Blocki, Jeremiah"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer","editor":[{"full_name":"Coron, Jean-Sébastien","first_name":"Jean-Sébastien","last_name":"Coron"},{"full_name":"Buus Nielsen, Jesper","last_name":"Buus Nielsen","first_name":"Jesper"}],"year":"2017","publist_id":"7148","ec_funded":1},{"scopus_import":1,"day":"01","month":"01","publication_identifier":{"isbn":["978-331958770-7"]},"quality_controlled":"1","page":"323 - 334","citation":{"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","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.","ieee":"V. Trajkovska, P. Swoboda, F. Åström, and S. Petra, “Graphical model parameter learning by inverse linear programming,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 323–334.","apa":"Trajkovska, V., Swoboda, P., Åström, F., & Petra, S. (2017). Graphical model parameter learning by inverse linear programming. In F. Lauze, Y. Dong, & A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 323–334). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. https://doi.org/10.1007/978-3-319-58771-4_26","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.","short":"V. Trajkovska, P. Swoboda, F. Åström, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 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."},"language":[{"iso":"eng"}],"conference":{"name":"SSVM: Scale Space and Variational Methods in Computer Vision","start_date":"2017-06-04","location":"Kolding, Denmark","end_date":"2017-06-08"},"date_published":"2017-01-01T00:00:00Z","doi":"10.1007/978-3-319-58771-4_26","alternative_title":["LNCS"],"type":"conference","abstract":[{"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.","lang":"eng"}],"publist_id":"7147","status":"public","publication_status":"published","title":"Graphical model parameter learning by inverse linear programming","department":[{"_id":"VlKo"}],"publisher":"Springer","intvolume":" 10302","editor":[{"full_name":"Lauze, François","first_name":"François","last_name":"Lauze"},{"first_name":"Yiqiu","last_name":"Dong","full_name":"Dong, Yiqiu"},{"last_name":"Bjorholm Dahl","first_name":"Anders","full_name":"Bjorholm Dahl, Anders"}],"_id":"641","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2017","date_created":"2018-12-11T11:47:39Z","date_updated":"2021-01-12T08:07:23Z","volume":10302,"oa_version":"None","author":[{"full_name":"Trajkovska, Vera","first_name":"Vera","last_name":"Trajkovska"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul"},{"first_name":"Freddie","last_name":"Åström","full_name":"Åström, Freddie"},{"full_name":"Petra, Stefanie","first_name":"Stefanie","last_name":"Petra"}]},{"day":"04","month":"08","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2017-08-04T00:00:00Z","doi":"10.15479/AT:IST-2018-853-v2-2","page":"28","citation":{"ama":"Henzinger TA, Kragl B, Qadeer S. Synchronizing the Asynchronous. IST Austria; 2017. doi:10.15479/AT:IST-2018-853-v2-2","ieee":"T. A. Henzinger, B. Kragl, and S. Qadeer, Synchronizing the asynchronous. IST Austria, 2017.","apa":"Henzinger, T. A., Kragl, B., & Qadeer, S. (2017). Synchronizing the asynchronous. IST Austria. https://doi.org/10.15479/AT:IST-2018-853-v2-2","ista":"Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST Austria, 28p.","short":"T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST Austria, 2017.","mla":"Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria, 2017, doi:10.15479/AT:IST-2018-853-v2-2.","chicago":"Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. Synchronizing the Asynchronous. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2018-853-v2-2."},"oa":1,"file_date_updated":"2020-07-14T12:47:30Z","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."}],"alternative_title":["IST Austria Technical Report"],"type":"technical_report","date_created":"2019-05-13T08:15:55Z","date_updated":"2023-02-21T16:59:21Z","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-13T08:14:44Z","checksum":"b48d42725182d7ca10107a118815f4cf","file_id":"6431","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":971347,"file_name":"main(1).pdf","access_level":"open_access"}],"author":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","first_name":"Bernhard"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"133"}]},"publication_status":"published","ddc":["000"],"status":"public","title":"Synchronizing the asynchronous","department":[{"_id":"ToHe"}],"publisher":"IST Austria","_id":"6426","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017"},{"quality_controlled":"1","external_id":{"pmid":["28847140"]},"language":[{"iso":"eng"}],"doi":"10.4077/CJP.2017.BAF469","publication_identifier":{"issn":["03044920"]},"month":"08","department":[{"_id":"RySh"}],"publisher":"Chinese Physiological Society","publication_status":"published","pmid":1,"year":"2017","volume":60,"date_created":"2018-12-11T11:47:40Z","date_updated":"2021-01-12T08:07:28Z","author":[{"full_name":"Sun, Wuping","last_name":"Sun","first_name":"Wuping"},{"last_name":"Zhai","first_name":"Ming-Zhu","id":"34009CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Zhai, Ming-Zhu"},{"full_name":"Zhou, Qian","first_name":"Qian","last_name":"Zhou"},{"full_name":"Qian, Chengrui","last_name":"Qian","first_name":"Chengrui"},{"last_name":"Jiang","first_name":"Changyu","full_name":"Jiang, Changyu"}],"publist_id":"7142","page":"207 - 214","article_type":"original","citation":{"short":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology 60 (2017) 207–214.","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.","chicago":"Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469.","ama":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469","apa":"Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469","ieee":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp. 207–214, 2017.","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."},"publication":"Chinese Journal of Physiology","date_published":"2017-08-31T00:00:00Z","scopus_import":1,"article_processing_charge":"No","day":"31","intvolume":" 60","status":"public","ddc":["570"],"title":"Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats","_id":"643","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","issue":"4","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"}]},{"date_published":"2017-01-01T00:00:00Z","page":"2373 - 2397","citation":{"mla":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation, vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201.","short":"M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.","chicago":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” Mathematics of Computation. American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201.","ama":"Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397. doi:10.1090/mcom/3201","ista":"Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 86(307), 2373–2397.","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"},"publication":"Mathematics of Computation","day":"01","scopus_import":1,"oa_version":"Submitted Version","intvolume":" 86","status":"public","title":"Localization errors in solving stochastic partial differential equations in the whole space","_id":"642","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"307","abstract":[{"lang":"eng","text":"Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1090/mcom/3201","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1508.05535","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["00255718"]},"month":"01","volume":86,"date_created":"2018-12-11T11:47:40Z","date_updated":"2021-01-12T08:07:26Z","author":[{"first_name":"Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate"},{"full_name":"Gyöngy, István","last_name":"Gyöngy","first_name":"István"}],"department":[{"_id":"JaMa"}],"publisher":"American Mathematical Society","publication_status":"published","year":"2017","publist_id":"7144"},{"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"645","intvolume":" 10426","status":"public","title":"Value iteration for long run average reward in markov decision processes","abstract":[{"text":"Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2017-07-13T00:00:00Z","citation":{"chicago":"Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer, 2017. https://doi.org/10.1007/978-3-319-63387-9_10.","mla":"Ashok, Pranav, et al. Value Iteration for Long Run Average Reward in Markov Decision Processes. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 201–21, doi:10.1007/978-3-319-63387-9_10.","short":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221.","ista":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration for long run average reward in markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 10426, 201–221.","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","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.","ama":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration for long run average reward in markov decision processes. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:201-221. doi:10.1007/978-3-319-63387-9_10"},"page":"201 - 221","day":"13","scopus_import":1,"author":[{"full_name":"Ashok, Pranav","first_name":"Pranav","last_name":"Ashok"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"},{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"full_name":"Meggendorfer, Tobias","first_name":"Tobias","last_name":"Meggendorfer"}],"volume":10426,"date_updated":"2021-01-12T08:07:32Z","date_created":"2018-12-11T11:47:41Z","year":"2017","department":[{"_id":"KrCh"}],"publisher":"Springer","editor":[{"last_name":"Majumdar","first_name":"Rupak","full_name":"Majumdar, Rupak"},{"first_name":"Viktor","last_name":"Kunčak","full_name":"Kunčak, Viktor"}],"publication_status":"published","ec_funded":1,"publist_id":"7135","doi":"10.1007/978-3-319-63387-9_10","conference":{"location":"Heidelberg, Germany","start_date":"2017-07-24","end_date":"2017-07-28","name":"CAV: Computer Aided Verification"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02326"}],"oa":1,"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-331963386-2"]},"month":"07"},{"volume":46,"date_created":"2018-12-11T11:47:40Z","date_updated":"2023-02-23T10:07:49Z","related_material":{"record":[{"id":"1637","relation":"other","status":"public"}]},"author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"},{"full_name":"Krokhin, Andrei","first_name":"Andrei","last_name":"Krokhin"},{"full_name":"Rolinek, Michal","first_name":"Michal","last_name":"Rolinek","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"publisher":"SIAM","department":[{"_id":"VlKo"}],"publication_status":"published","year":"2017","publist_id":"7138","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1137/16M1091836","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1502.07327","open_access":"1"}],"oa":1,"month":"06","oa_version":"Preprint","intvolume":" 46","status":"public","title":"The complexity of general-valued CSPs","_id":"644","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"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.","lang":"eng"}],"type":"journal_article","date_published":"2017-06-29T00:00:00Z","page":"1087 - 1110","citation":{"short":"V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017) 1087–1110.","mla":"Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:10.1137/16M1091836.","chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs.” SIAM Journal on Computing. SIAM, 2017. https://doi.org/10.1137/16M1091836.","ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. SIAM Journal on Computing. 2017;46(3):1087-1110. doi:10.1137/16M1091836","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.","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","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued CSPs. SIAM Journal on Computing. 46(3), 1087–1110."},"publication":"SIAM Journal on Computing","day":"29","scopus_import":1},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"646","title":"A novel convex relaxation for non binary discrete tomography","status":"public","intvolume":" 10302","oa_version":"Submitted Version","type":"conference","alternative_title":["LNCS"],"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."}],"citation":{"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.","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","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.","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","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.","short":"J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 235–246.","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."},"page":"235 - 246","date_published":"2017-06-01T00:00:00Z","scopus_import":1,"day":"01","year":"2017","publication_status":"published","publisher":"Springer","department":[{"_id":"VlKo"}],"editor":[{"full_name":"Lauze, François","last_name":"Lauze","first_name":"François"},{"first_name":"Yiqiu","last_name":"Dong","full_name":"Dong, Yiqiu"},{"last_name":"Bjorholm Dahl","first_name":"Anders","full_name":"Bjorholm Dahl, Anders"}],"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"},{"last_name":"Petra","first_name":"Stefanie","full_name":"Petra, Stefanie"}],"date_updated":"2021-01-12T08:07:34Z","date_created":"2018-12-11T11:47:41Z","volume":10302,"publist_id":"7132","ec_funded":1,"main_file_link":[{"url":"https://arxiv.org/abs/1703.03769","open_access":"1"}],"oa":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"conference":{"location":"Kolding, Denmark","start_date":"2017-06-04","end_date":"2017-06-08","name":"SSVM: Scale Space and Variational Methods in Computer Vision"},"doi":"10.1007/978-3-319-58771-4_19","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"isbn":["978-331958770-7"]}},{"date_published":"2017-04-01T00:00:00Z","citation":{"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.","mla":"Skórski, Maciej. On the Complexity of Breaking Pseudoentropy. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:10.1007/978-3-319-55911-7_43.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.","ista":"Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 600–613.","apa":"Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger & S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. https://doi.org/10.1007/978-3-319-55911-7_43","ieee":"M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 600–613.","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"},"page":"600 - 613","day":"01","scopus_import":1,"oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"648","intvolume":" 10185","status":"public","title":"On the complexity of breaking pseudoentropy","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"}],"type":"conference","alternative_title":["LNCS"],"doi":"10.1007/978-3-319-55911-7_43","conference":{"end_date":"2017-04-22","location":"Bern, Switzerland","start_date":"2017-04-20","name":"TAMC: Theory and Applications of Models of Computation"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/1186.pdf"}],"oa":1,"quality_controlled":"1","publication_identifier":{"isbn":["978-331955910-0"]},"month":"04","author":[{"full_name":"Skórski, Maciej","last_name":"Skórski","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"volume":10185,"date_created":"2018-12-11T11:47:42Z","date_updated":"2021-01-12T08:07:39Z","year":"2017","publisher":"Springer","editor":[{"last_name":"Jäger","first_name":"Gerhard","full_name":"Jäger, Gerhard"},{"full_name":"Steila, Silvia","first_name":"Silvia","last_name":"Steila"}],"department":[{"_id":"KrPi"}],"publication_status":"published","publist_id":"7125"},{"author":[{"full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0845-1338"}],"volume":2184,"date_updated":"2022-05-24T07:01:33Z","date_created":"2018-12-11T11:47:42Z","year":"2017","publisher":"Springer","department":[{"_id":"JaMa"}],"editor":[{"first_name":"Laurent","last_name":"Najman","full_name":"Najman, Laurent"},{"first_name":"Pascal","last_name":"Romon","full_name":"Romon, Pascal"}],"publication_status":"published","publist_id":"7123","doi":"10.1007/978-3-319-58002-9_5","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-3-319-58001-2"],"eissn":["978-3-319-58002-9"]},"month":"10","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"649","intvolume":" 2184","status":"public","title":"Entropic Ricci curvature for discrete spaces","abstract":[{"lang":"eng","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."}],"type":"book_chapter","date_published":"2017-10-05T00:00:00Z","citation":{"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","ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.","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","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.","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."},"publication":"Modern Approaches to Discrete Curvature","page":"159 - 174","article_processing_charge":"No","day":"05","scopus_import":"1","series_title":"Lecture Notes in Mathematics"},{"publication_status":"published","publisher":"Springer","editor":[{"full_name":"Jäger, Gerhard","last_name":"Jäger","first_name":"Gerhard"},{"full_name":"Steila, Silvia","last_name":"Steila","first_name":"Silvia"}],"department":[{"_id":"KrPi"}],"year":"2017","date_created":"2018-12-11T11:47:42Z","date_updated":"2021-01-12T08:07:46Z","volume":10185,"author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"publist_id":"7119","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/965.pdf"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2017-04-22","start_date":"2017-04-20","location":"Bern, Switzerland","name":"TAMC: Theory and Applications of Models of Computation"},"doi":"10.1007/978-3-319-55911-7_42","month":"01","publication_identifier":{"issn":["03029743"]},"status":"public","title":"A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds","intvolume":" 10185","_id":"650","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","alternative_title":["LNCS"],"type":"conference","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"}],"page":"586 - 599","citation":{"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","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","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.","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.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599.","mla":"Skórski, Maciej. A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 586–99, doi:10.1007/978-3-319-55911-7_42.","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."},"date_published":"2017-01-01T00:00:00Z","scopus_import":1,"day":"01"}]