[{"external_id":{"isi":["000427798800005"]},"date_published":"2018-03-19T00:00:00Z","day":"19","author":[{"first_name":"Alexios","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis"},{"full_name":"Žnidarič, Marko","first_name":"Marko","last_name":"Žnidarič"},{"last_name":"Medvedyeva","first_name":"Mariya","full_name":"Medvedyeva, Mariya"},{"first_name":"Dmitry","full_name":"Abanin, Dmitry","last_name":"Abanin"},{"last_name":"Prosen","full_name":"Prosen, Tomaž","first_name":"Tomaž"},{"first_name":"Zlatko","full_name":"Papić, Zlatko","last_name":"Papić"}],"status":"public","oa_version":"Preprint","volume":97,"date_created":"2018-12-11T11:45:50Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1103/PhysRevB.97.104307","year":"2018","acknowledgement":"We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).","oa":1,"article_processing_charge":"No","title":"Slow dynamics in translation-invariant quantum lattice models","_id":"327","date_updated":"2023-09-18T09:31:46Z","department":[{"_id":"MaSe"}],"language":[{"iso":"eng"}],"publist_id":"7538","abstract":[{"lang":"eng","text":"Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations."}],"publication":"Physical Review B","scopus_import":"1","publisher":"American Physical Society","citation":{"ieee":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” Physical Review B, vol. 97, no. 10. American Physical Society, 2018.","ista":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307.","mla":"Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:10.1103/PhysRevB.97.104307.","short":"A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018).","ama":"Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307","apa":"Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307","chicago":"Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307."},"quality_controlled":"1","publication_status":"published","isi":1,"month":"03","article_number":"104307","intvolume":" 97","issue":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.05026"}],"type":"journal_article"},{"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.06271"}],"ec_funded":1,"acknowledged_ssus":[{"_id":"SSU"}],"issue":"12","article_number":"124501","intvolume":" 120","isi":1,"month":"03","publication_status":"published","citation":{"apa":"Choueiri, G. H., Lopez Alonso, J. M., & Hof, B. (2018). Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.124501","chicago":"Choueiri, George H, Jose M Lopez Alonso, and Björn Hof. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.124501.","ama":"Choueiri GH, Lopez Alonso JM, Hof B. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 2018;120(12). doi:10.1103/PhysRevLett.120.124501","short":"G.H. Choueiri, J.M. Lopez Alonso, B. Hof, Physical Review Letters 120 (2018).","mla":"Choueiri, George H., et al. “Exceeding the Asymptotic Limit of Polymer Drag Reduction.” Physical Review Letters, vol. 120, no. 12, 124501, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.124501.","ieee":"G. H. Choueiri, J. M. Lopez Alonso, and B. Hof, “Exceeding the asymptotic limit of polymer drag reduction,” Physical Review Letters, vol. 120, no. 12. American Physical Society, 2018.","ista":"Choueiri GH, Lopez Alonso JM, Hof B. 2018. Exceeding the asymptotic limit of polymer drag reduction. Physical Review Letters. 120(12), 124501."},"quality_controlled":"1","publisher":"American Physical Society","scopus_import":"1","publication":"Physical Review Letters","abstract":[{"text":"The drag of turbulent flows can be drastically decreased by adding small amounts of high molecular weight polymers. While drag reduction initially increases with polymer concentration, it eventually saturates to what is known as the maximum drag reduction (MDR) asymptote; this asymptote is generally attributed to the dynamics being reduced to a marginal yet persistent state of subdued turbulent motion. Contrary to this accepted view, we show that, for an appropriate choice of parameters, polymers can reduce the drag beyond the suggested asymptotic limit, eliminating turbulence and giving way to laminar flow. At higher polymer concentrations, however, the laminar state becomes unstable, resulting in a fluctuating flow with the characteristic drag of the MDR asymptote. Our findings indicate that the asymptotic state is hence dynamically disconnected from ordinary turbulence. © 2018 American Physical Society.","lang":"eng"}],"department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"publist_id":"7537","_id":"328","date_updated":"2023-10-10T13:27:44Z","article_processing_charge":"No","title":"Exceeding the asymptotic limit of polymer drag reduction","oa":1,"acknowledgement":"The authors thank Philipp Maier and the IST Austria workshop for their dedicated technical support.","year":"2018","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425"}],"doi":"10.1103/PhysRevLett.120.124501","volume":120,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:45:51Z","oa_version":"Preprint","author":[{"id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","last_name":"Choueiri","first_name":"George H","full_name":"Choueiri, George H"},{"orcid":"0000-0002-0384-2022","full_name":"Lopez Alonso, Jose M","first_name":"Jose M","last_name":"Lopez Alonso","id":"40770848-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof"}],"status":"public","day":"19","date_published":"2018-03-19T00:00:00Z","external_id":{"isi":["000427804000005"]}},{"publist_id":"8022","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"abstract":[{"text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.","lang":"eng"}],"scopus_import":"1","file":[{"access_level":"open_access","creator":"dernst","content_type":"application/pdf","checksum":"3334886c4b39678db4c4b74299ca14ba","file_id":"5692","relation":"main_file","date_updated":"2020-07-14T12:46:06Z","file_name":"2018_PeerJ_Bertl.pdf","file_size":1328344,"date_created":"2018-12-17T10:46:06Z"}],"publication":"PeerJ","file_date_updated":"2020-07-14T12:46:06Z","publisher":"PeerJ","quality_controlled":"1","citation":{"chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325.","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325.","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018."},"publication_status":"published","isi":1,"month":"10","intvolume":" 2018","article_number":"e5325","issue":"10","ddc":["576"],"type":"journal_article","external_id":{"pmid":["30294507"],"isi":["000447204400001"]},"date_published":"2018-10-01T00:00:00Z","day":"01","author":[{"full_name":"Bertl, Johanna","first_name":"Johanna","last_name":"Bertl"},{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","last_name":"Ringbauer","full_name":"Ringbauer, Harald","first_name":"Harald","orcid":"0000-0002-4884-9682"},{"last_name":"Blum","first_name":"Michaël","full_name":"Blum, Michaël"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:16Z","volume":2018,"doi":"10.7717/peerj.5325","pmid":1,"has_accepted_license":"1","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","year":"2018","oa":1,"article_processing_charge":"No","title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","date_updated":"2023-10-17T12:24:43Z","_id":"33"},{"oa_version":"None","citation":{"short":"E.M. Clarke, T.A. Henzinger, H. Veith, R. Bloem, Handbook of Model Checking, 1st ed., Springer Nature, Cham, 2018.","mla":"Clarke, Edmund M., et al. Handbook of Model Checking. 1st ed., Springer Nature, 2018, doi:10.1007/978-3-319-10575-8.","ista":"Clarke EM, Henzinger TA, Veith H, Bloem R. 2018. Handbook of Model Checking 1st ed., Cham: Springer Nature, XLVIII, 1212p.","ieee":"E. M. Clarke, T. A. Henzinger, H. Veith, and R. Bloem, Handbook of Model Checking, 1st ed. Cham: Springer Nature, 2018.","chicago":"Clarke, Edmund M., Thomas A Henzinger, Helmut Veith, and Roderick Bloem. Handbook of Model Checking. 1st ed. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-10575-8.","apa":"Clarke, E. M., Henzinger, T. A., Veith, H., & Bloem, R. (2018). Handbook of Model Checking (1st ed.). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-10575-8","ama":"Clarke EM, Henzinger TA, Veith H, Bloem R. Handbook of Model Checking. 1st ed. Cham: Springer Nature; 2018. doi:10.1007/978-3-319-10575-8"},"status":"public","quality_controlled":"1","author":[{"last_name":"Clarke","first_name":"Edmund M.","full_name":"Clarke, Edmund M."},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Veith","first_name":"Helmut","full_name":"Veith, Helmut"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"}],"doi":"10.1007/978-3-319-10575-8","date_created":"2018-12-11T12:02:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"This book first explores the origins of this idea, grounded in theoretical work on temporal logic and automata. The editors and authors are among the world's leading researchers in this domain, and they contributed 32 chapters representing a thorough view of the development and application of the technique. Topics covered include binary decision diagrams, symbolic model checking, satisfiability modulo theories, partial-order reduction, abstraction, interpolation, concurrency, security protocols, games, probabilistic model checking, and process algebra, and chapters on the transfer of theory to industrial practice, property specification languages for hardware, and verification of real-time systems and hybrid systems.\r\n\r\nThe book will be valuable for researchers and graduate students engaged with the development of formal methods and verification tools."}],"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publist_id":"3340","day":"08","publisher":"Springer Nature","scopus_import":"1","date_published":"2018-06-08T00:00:00Z","retracted":"1","article_processing_charge":"No","title":"Handbook of Model Checking","type":"book","_id":"3300","date_updated":"2025-07-24T09:25:31Z","place":"Cham","year":"2018","month":"06","page":"XLVIII, 1212","edition":"1","publication_identifier":{"eisbn":["978-3-319-10575-8"],"isbn":["978-3-319-10574-1"]}},{"day":"01","date_published":"2018-06-01T00:00:00Z","external_id":{"isi":["000492986200006"],"arxiv":["1710.00675"]},"volume":2018,"date_created":"2018-12-11T11:44:16Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chemlík","first_name":"Martin","full_name":"Chemlík, Martin"},{"first_name":"Ufuk","full_name":"Topcu, Ufuk","last_name":"Topcu"}],"status":"public","oa":1,"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"year":"2018","_id":"34","date_updated":"2023-09-19T14:44:14Z","conference":{"start_date":"2018-06-24","end_date":"2018-06-29","name":"ICAPS: International Conference on Automated Planning and Scheduling","location":"Delft, Netherlands"},"article_processing_charge":"No","title":"Sensor synthesis for POMDPs with reachability objectives","publisher":"AAAI Press","scopus_import":"1","abstract":[{"text":"Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies.","lang":"eng"}],"publist_id":"8021","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"publication_status":"published","citation":{"mla":"Chatterjee, Krishnendu, et al. Sensor Synthesis for POMDPs with Reachability Objectives. Vol. 2018, AAAI Press, 2018, pp. 47–55.","short":"K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55.","ieee":"K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.","ista":"Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. ICAPS: International Conference on Automated Planning and Scheduling, ICAPS, vol. 2018, 47–55.","apa":"Chatterjee, K., Chemlík, M., & Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands: AAAI Press.","chicago":"Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018.","ama":"Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: Vol 2018. AAAI Press; 2018:47-55."},"quality_controlled":"1","alternative_title":["ICAPS"],"ec_funded":1,"page":"47 - 55","intvolume":" 2018","isi":1,"month":"06","type":"conference","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1710.00675","open_access":"1"}]},{"article_processing_charge":"No","title":"Algorithms and conditional lower bounds for planning problems","_id":"35","date_updated":"2023-09-26T10:41:41Z","conference":{"name":"ICAPS: International Conference on Automated Planning and Scheduling","location":"Delft, Netherlands","start_date":"2018-06-24","end_date":"2018-06-29"},"related_material":{"record":[{"relation":"later_version","status":"public","id":"9293"}]},"year":"2018","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"oa":1,"oa_version":"None","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Dvorák, Wolfgang","first_name":"Wolfgang","last_name":"Dvorák"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Svozil, Alexander","first_name":"Alexander","last_name":"Svozil"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:17Z","external_id":{"isi":["000492986200007"],"arxiv":["1804.07031"]},"day":"01","date_published":"2018-06-01T00:00:00Z","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07031"}],"type":"conference","isi":1,"month":"06","ec_funded":1,"citation":{"ista":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. 2018. Algorithms and conditional lower bounds for planning problems. 28th International Conference on Automated Planning and Scheduling . ICAPS: International Conference on Automated Planning and Scheduling.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and A. Svozil, “Algorithms and conditional lower bounds for planning problems,” in 28th International Conference on Automated Planning and Scheduling , Delft, Netherlands, 2018.","mla":"Chatterjee, Krishnendu, et al. “Algorithms and Conditional Lower Bounds for Planning Problems.” 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, A. Svozil, in:, 28th International Conference on Automated Planning and Scheduling , AAAI Press, 2018.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Svozil A. Algorithms and conditional lower bounds for planning problems. In: 28th International Conference on Automated Planning and Scheduling . AAAI Press; 2018.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., & Svozil, A. (2018). Algorithms and conditional lower bounds for planning problems. In 28th International Conference on Automated Planning and Scheduling . Delft, Netherlands: AAAI Press.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Alexander Svozil. “Algorithms and Conditional Lower Bounds for Planning Problems.” In 28th International Conference on Automated Planning and Scheduling . AAAI Press, 2018."},"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"We consider planning problems for graphs, Markov decision processes (MDPs), and games on graphs. While graphs represent the most basic planning model, MDPs represent interaction with nature and games on graphs represent interaction with an adversarial environment. We consider two planning problems where there are k different target sets, and the problems are as follows: (a) the coverage problem asks whether there is a plan for each individual target set; and (b) the sequential target reachability problem asks whether the targets can be reached in sequence. For the coverage problem, we present a linear-time algorithm for graphs, and quadratic conditional lower bound for MDPs and games on graphs. For the sequential target problem, we present a linear-time algorithm for graphs, a sub-quadratic algorithm for MDPs, and a quadratic conditional lower bound for games on graphs. Our results with conditional lower bounds establish (i) model-separation results showing that for the coverage problem MDPs and games on graphs are harder than graphs and for the sequential reachability problem games on graphs are harder than MDPs and graphs; and (ii) objective-separation results showing that for MDPs the coverage problem is harder than the sequential target problem."}],"language":[{"iso":"eng"}],"publist_id":"8020","department":[{"_id":"KrCh"}],"publisher":"AAAI Press","scopus_import":"1","publication":"28th International Conference on Automated Planning and Scheduling "},{"article_processing_charge":"No","title":"Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms","date_updated":"2023-09-19T10:00:46Z","_id":"36","acknowledgement":"TZ is supported by a grant from the Chinese Scholarship Council.","year":"2018","has_accepted_license":"1","oa":1,"oa_version":"Published Version","author":[{"last_name":"Vu","full_name":"Vu, Lam","first_name":"Lam"},{"last_name":"Zhu","full_name":"Zhu, Tingting","first_name":"Tingting"},{"full_name":"Verstraeten, Inge","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","last_name":"Verstraeten"},{"last_name":"Van De Cotte","first_name":"Brigitte","full_name":"Van De Cotte, Brigitte"},{"last_name":"Gevaert","first_name":"Kris","full_name":"Gevaert, Kris"},{"last_name":"De Smet","first_name":"Ive","full_name":"De Smet, Ive"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1093/jxb/ery204","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:17Z","volume":69,"external_id":{"isi":["000443568700010"]},"day":"31","date_published":"2018-08-31T00:00:00Z","ddc":["581"],"type":"journal_article","intvolume":" 69","month":"08","isi":1,"page":"4609 - 4624","issue":"19","quality_controlled":"1","citation":{"short":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624.","mla":"Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204.","ieee":"L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018.","ista":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624.","apa":"Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204","chicago":"Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204.","ama":"Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204"},"publication_status":"published","abstract":[{"text":"Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.","lang":"eng"}],"publist_id":"8019","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"publisher":"Oxford University Press","file_date_updated":"2020-07-14T12:46:13Z","file":[{"file_name":"2018_JournalExperimBotany_Vu.pdf","date_updated":"2020-07-14T12:46:13Z","date_created":"2018-12-18T09:47:51Z","file_size":3359316,"relation":"main_file","file_id":"5741","creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"34cb0a1611588b75bd6f4913fb4e30f1"}],"publication":"Journal of Experimental Botany","scopus_import":"1"},{"type":"book_chapter","ddc":["570"],"ec_funded":1,"page":"47 - 63","month":"10","intvolume":" 1863","publication_status":"published","citation":{"mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4.","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4"},"quality_controlled":"1","series_title":"MIMB","alternative_title":["Methods in Molecular Biology"],"file_date_updated":"2020-10-13T14:20:37Z","scopus_import":"1","file":[{"content_type":"application/pdf","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","creator":"dernst","access_level":"open_access","file_id":"8656","relation":"main_file","date_created":"2020-10-13T14:20:37Z","success":1,"file_size":4906815,"file_name":"2018_MIMB_Zagorski.pdf","date_updated":"2020-10-13T14:20:37Z"}],"publication":"Morphogen Gradients ","publisher":"Springer Nature","department":[{"_id":"AnKi"}],"publist_id":"8018","language":[{"iso":"eng"}],"abstract":[{"text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube.","lang":"eng"}],"_id":"37","date_updated":"2021-01-12T07:49:03Z","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","article_processing_charge":"No","publication_identifier":{"isbn":["978-1-4939-8771-9"],"issn":["1064-3745"]},"oa":1,"has_accepted_license":"1","year":"2018","project":[{"grant_number":"680037","call_identifier":"H2020","name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"volume":1863,"date_created":"2018-12-11T11:44:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-1-4939-8772-6_4","status":"public","author":[{"first_name":"Marcin P","full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski"},{"last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","full_name":"Kicheva, Anna"}],"oa_version":"Submitted Version","date_published":"2018-10-16T00:00:00Z","day":"16"},{"ddc":["570"],"type":"journal_article","intvolume":" 115","month":"10","isi":1,"page":"11006 - 11011","issue":"43","quality_controlled":"1","citation":{"short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_status":"published","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"publist_id":"8017","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","scopus_import":"1","file_date_updated":"2020-07-14T12:46:16Z","publication":"PNAS","file":[{"file_id":"5683","content_type":"application/pdf","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","access_level":"open_access","creator":"dernst","date_created":"2018-12-17T08:44:03Z","file_size":1911302,"date_updated":"2020-07-14T12:46:16Z","file_name":"11006.full.pdf","relation":"main_file"}],"article_processing_charge":"No","title":"Selection and gene flow shape genomic islands that control floral guides","date_updated":"2023-09-18T08:36:49Z","_id":"38","acknowledgement":" ERC Grant 201252 (to N.H.B.)","year":"2018","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["00278424"]},"oa_version":"Published Version","author":[{"last_name":"Tavares","full_name":"Tavares, Hugo","first_name":"Hugo"},{"first_name":"Annabel","full_name":"Whitley, Annabel","last_name":"Whitley"},{"orcid":"0000-0002-4014-8478","first_name":"David","full_name":"Field, David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bradley","full_name":"Bradley, Desmond","first_name":"Desmond"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"last_name":"Elleouet","full_name":"Elleouet, Joane","first_name":"Joane"},{"first_name":"Monique","full_name":"Burrus, Monique","last_name":"Burrus"},{"full_name":"Andalo, Christophe","first_name":"Christophe","last_name":"Andalo"},{"full_name":"Li, Miaomiao","first_name":"Miaomiao","last_name":"Li"},{"first_name":"Qun","full_name":"Li, Qun","last_name":"Li"},{"last_name":"Xue","full_name":"Xue, Yongbiao","first_name":"Yongbiao"},{"first_name":"Alexandra B","full_name":"Rebocho, Alexandra B","last_name":"Rebocho"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","doi":"10.1073/pnas.1801832115","pmid":1,"date_created":"2018-12-11T11:44:18Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":115,"external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"day":"23","date_published":"2018-10-23T00:00:00Z"},{"isi":1,"month":"03","intvolume":" 10","pubrep_id":"999","issue":"3","page":"928 - 938","ddc":["576"],"type":"journal_article","language":[{"iso":"eng"}],"publist_id":"7445","department":[{"_id":"FyKo"}],"abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"scopus_import":"1","publication":"Genome Biology and Evolution","file_date_updated":"2020-07-14T12:46:16Z","file":[{"file_id":"4667","access_level":"open_access","creator":"system","checksum":"458a7c2c2e79528567edfeb0f326cbe0","content_type":"application/pdf","date_updated":"2020-07-14T12:46:16Z","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","file_size":691602,"date_created":"2018-12-12T10:08:07Z","relation":"main_file"}],"publisher":"Oxford University Press","quality_controlled":"1","citation":{"short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938.","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049"},"publication_status":"published","has_accepted_license":"1","year":"2018","acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","oa":1,"article_processing_charge":"No","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","date_updated":"2023-09-11T13:56:52Z","_id":"384","external_id":{"isi":["000429483700022"]},"date_published":"2018-03-01T00:00:00Z","day":"01","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"first_name":"Peter","full_name":"Hönigschmid, Peter","last_name":"Hönigschmid"},{"last_name":"Bykova","first_name":"Nadya","full_name":"Bykova, Nadya"},{"first_name":"René","full_name":"Schneider, René","last_name":"Schneider"},{"full_name":"Ivankov, Dmitry","first_name":"Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Frishman","first_name":"Dmitrij","full_name":"Frishman, Dmitrij"}],"status":"public","oa_version":"Published Version","date_created":"2018-12-11T11:46:10Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":10,"doi":"10.1093/gbe/evy049"},{"scopus_import":"1","publication":"Genetics","publisher":"Genetics Society of America","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"abstract":[{"text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.","lang":"eng"}],"publication_status":"published","article_type":"original","quality_controlled":"1","citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018."},"issue":"4","page":"1411-1427","month":"12","isi":1,"intvolume":" 210","type":"journal_article","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}],"date_published":"2018-12-04T00:00:00Z","day":"04","external_id":{"isi":["000452315900021"]},"date_created":"2018-12-11T11:44:18Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":210,"doi":"10.1534/genetics.118.301429","author":[{"last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"status":"public","oa_version":"Preprint","publication_identifier":{"issn":["00166731"]},"oa":1,"year":"2018","date_updated":"2023-09-18T08:10:29Z","_id":"39","article_processing_charge":"No","title":"Replicability of introgression under linked, polygenic selection"},{"month":"03","pubrep_id":"992","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"EM-Fac"},{"_id":"Bio"}],"page":"88","ddc":["570","616"],"type":"dissertation","language":[{"iso":"eng"}],"department":[{"_id":"GaNo"}],"publist_id":"7434","abstract":[{"lang":"eng","text":"Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurological conditions. Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental disorders (e.g. autism spectrum disorder, intellectual disability, epilepsy) remains a great challenge. Recent advancements in geno mics, like whole-exome or whole-genome sequencing, have enabled scientists to identify numerous mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that were discovered, the etiological variability and the heterogeneous phenotypic outcomes, the need for genotype -along with phenotype- based diagnosis of individual patients becomes a requisite. Driven by this rationale, in a previous study our group described mutations, identified via whole - exome sequencing, in the gene BCKDK – encoding for a key regulator of branched chain amin o acid (BCAA) catabolism - as a cause of ASD. Following up on the role of BCAAs, in the study described here we show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid transporter localized mainly at the blood brain barrier (BBB), has an essential role in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal mRNA translation and severe neurolo gical abnormalities. Additionally, deletion of Slc7a5 from the neural progenitor cell population leads to microcephaly. Interestingly, we demonstrate that BCAA intracerebroventricular administration ameliorates abnormal behaviors in adult mutant mice. Furthermore, whole - exome sequencing of patients diagnosed with neurological dis o r ders helped us identify several patients with autistic traits, microcephaly and motor delay carrying deleterious homozygous mutations in the SLC7A5 gene. In conclusion, our data elucidate a neurological syndrome defined by SLC7A5 mutations and support an essential role for t he BCAA s in human bra in function. Together with r ecent studies (described in chapter two) that have successfully made the transition into clinical practice, our findings on the role of B CAAs might have a crucial impact on the development of novel individualized therapeutic strategies for ASD. 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Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_992"},"publication_status":"published","supervisor":[{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","project":[{"call_identifier":"FWF","grant_number":"F03523","_id":"25473368-B435-11E9-9278-68D0E5697425","name":"Transmembrane Transporters in Health and Disease"}],"year":"2018","publication_identifier":{"issn":["2663-337X"]},"oa":1,"article_processing_charge":"No","title":"The branched chain amino acids in autism spectrum disorders ","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1183"}]},"date_updated":"2023-09-07T12:38:59Z","_id":"395","date_published":"2018-03-01T00:00:00Z","day":"01","author":[{"full_name":"Tarlungeanu, Dora-Clara","first_name":"Dora-Clara","last_name":"Tarlungeanu","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa_version":"Published Version","date_created":"2018-12-11T11:46:14Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.15479/AT:ISTA:th_992"},{"publication_status":"published","citation":{"ama":"Arbel Raviv M, Brown TA. Harnessing epoch-based reclamation for efficient range queries. In: Vol 53. ACM; 2018:14-27. doi:10.1145/3178487.3178489","chicago":"Arbel Raviv, Maya, and Trevor A Brown. “Harnessing Epoch-Based Reclamation for Efficient Range Queries,” 53:14–27. ACM, 2018. https://doi.org/10.1145/3178487.3178489.","apa":"Arbel Raviv, M., & Brown, T. A. (2018). Harnessing epoch-based reclamation for efficient range queries (Vol. 53, pp. 14–27). Presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria: ACM. https://doi.org/10.1145/3178487.3178489","ista":"Arbel Raviv M, Brown TA. 2018. Harnessing epoch-based reclamation for efficient range queries. PPoPP: Principles and Practice of Parallel Programming, PPoPP, vol. 53, 14–27.","ieee":"M. Arbel Raviv and T. A. Brown, “Harnessing epoch-based reclamation for efficient range queries,” presented at the PPoPP: Principles and Practice of Parallel Programming, Vienna, Austria, 2018, vol. 53, no. 1, pp. 14–27.","short":"M. Arbel Raviv, T.A. Brown, in:, ACM, 2018, pp. 14–27.","mla":"Arbel Raviv, Maya, and Trevor A. Brown. Harnessing Epoch-Based Reclamation for Efficient Range Queries. Vol. 53, no. 1, ACM, 2018, pp. 14–27, doi:10.1145/3178487.3178489."},"quality_controlled":"1","alternative_title":["PPoPP"],"publisher":"ACM","scopus_import":"1","abstract":[{"lang":"eng","text":"Concurrent sets with range query operations are highly desirable in applications such as in-memory databases. However, few set implementations offer range queries. Known techniques for augmenting data structures with range queries (or operations that can be used to build range queries) have numerous problems that limit their usefulness. For example, they impose high overhead or rely heavily on garbage collection. In this work, we show how to augment data structures with highly efficient range queries, without relying on garbage collection. We identify a property of epoch-based memory reclamation algorithms that makes them ideal for implementing range queries, and produce three algorithms, which use locks, transactional memory and lock-free techniques, respectively. Our algorithms are applicable to more data structures than previous work, and are shown to be highly efficient on a large scale Intel system. "}],"language":[{"iso":"eng"}],"publist_id":"7430","department":[{"_id":"DaAl"}],"type":"conference","page":"14 - 27","issue":"1","intvolume":" 53","month":"02","isi":1,"doi":"10.1145/3178487.3178489","volume":53,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:14Z","oa_version":"None","status":"public","author":[{"first_name":"Maya","full_name":"Arbel Raviv, Maya","last_name":"Arbel Raviv"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Trevor A","full_name":"Brown, Trevor A"}],"day":"10","date_published":"2018-02-10T00:00:00Z","external_id":{"isi":["000446161100002"]},"_id":"397","date_updated":"2023-09-11T14:10:25Z","conference":{"start_date":"2018-02-24","end_date":"2018-02-28","name":"PPoPP: Principles and Practice of Parallel Programming","location":"Vienna, Austria"},"title":"Harnessing epoch-based reclamation for efficient range queries","article_processing_charge":"No","publication_identifier":{"isbn":["978-1-4503-4982-6"]},"year":"2018"},{"month":"05","isi":1,"year":"2018","intvolume":" 13","page":"e568-e578","title":"Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device","article_processing_charge":"No","date_updated":"2023-09-11T14:12:33Z","_id":"398","type":"journal_article","external_id":{"isi":["000432942700070"]},"department":[{"_id":"BeBi"}],"publist_id":"7431","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Objective: To report long-term results after Pipeline Embolization Device (PED) implantation, characterize complex and standard aneurysms comprehensively, and introduce a modified flow disruption scale. Methods: We retrospectively reviewed a consecutive series of 40 patients harboring 59 aneurysms treated with 54 PEDs. Aneurysm complexity was assessed using our proposed classification. Immediate angiographic results were analyzed using previously published grading scales and our novel flow disruption scale. Results: According to our new definition, 46 (78%) aneurysms were classified as complex. Most PED interventions were performed in the paraophthalmic and cavernous internal carotid artery segments. Excellent neurologic outcome (modified Rankin Scale 0 and 1) was observed in 94% of patients. Our data showed low permanent procedure-related mortality (0%) and morbidity (3%) rates. Long-term angiographic follow-up showed complete occlusion in 81% and near-total obliteration in a further 14%. Complete obliteration after deployment of a single PED was achieved in all standard aneurysms with 1-year follow-up. Our new scale was an independent predictor of aneurysm occlusion in a multivariable analysis. All aneurysms with a high flow disruption grade showed complete occlusion at follow-up regardless of PED number or aneurysm complexity. Conclusions: Treatment with the PED should be recognized as a primary management strategy for a highly selected cohort with predominantly complex intracranial aneurysms. We further show that a priori assessment of aneurysm complexity and our new postinterventional angiographic flow disruption scale predict occlusion probability and may help to determine the adequate number of per-aneurysm devices."}],"date_published":"2018-05-01T00:00:00Z","scopus_import":"1","publication":"World Neurosurgery","day":"01","publisher":"Elsevier","quality_controlled":"1","author":[{"first_name":"Philippe","full_name":"Dodier, Philippe","last_name":"Dodier"},{"last_name":"Frischer","full_name":"Frischer, Josa","first_name":"Josa"},{"first_name":"Wei","full_name":"Wang, Wei","last_name":"Wang"},{"orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas","first_name":"Thomas","last_name":"Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mallouhi","first_name":"Ammar","full_name":"Mallouhi, Ammar"},{"last_name":"Serles","full_name":"Serles, Wolfgang","first_name":"Wolfgang"},{"full_name":"Gruber, Andreas","first_name":"Andreas","last_name":"Gruber"},{"last_name":"Knosp","full_name":"Knosp, Engelbert","first_name":"Engelbert"},{"full_name":"Bavinzski, Gerhard","first_name":"Gerhard","last_name":"Bavinzski"}],"status":"public","citation":{"ista":"Dodier P, Frischer J, Wang W, Auzinger T, Mallouhi A, Serles W, Gruber A, Knosp E, Bavinzski G. 2018. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 13, e568–e578.","ieee":"P. Dodier et al., “Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device,” World Neurosurgery, vol. 13. Elsevier, pp. e568–e578, 2018.","mla":"Dodier, Philippe, et al. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery, vol. 13, Elsevier, 2018, pp. e568–78, doi:10.1016/j.wneu.2018.02.096.","short":"P. Dodier, J. Frischer, W. Wang, T. Auzinger, A. Mallouhi, W. Serles, A. Gruber, E. Knosp, G. Bavinzski, World Neurosurgery 13 (2018) e568–e578.","ama":"Dodier P, Frischer J, Wang W, et al. Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. 2018;13:e568-e578. doi:10.1016/j.wneu.2018.02.096","apa":"Dodier, P., Frischer, J., Wang, W., Auzinger, T., Mallouhi, A., Serles, W., … Bavinzski, G. (2018). Immediate flow disruption as a prognostic factor after flow diverter treatment long term experience with the pipeline embolization device. World Neurosurgery. Elsevier. https://doi.org/10.1016/j.wneu.2018.02.096","chicago":"Dodier, Philippe, Josa Frischer, Wei Wang, Thomas Auzinger, Ammar Mallouhi, Wolfgang Serles, Andreas Gruber, Engelbert Knosp, and Gerhard Bavinzski. “Immediate Flow Disruption as a Prognostic Factor after Flow Diverter Treatment Long Term Experience with the Pipeline Embolization Device.” World Neurosurgery. Elsevier, 2018. https://doi.org/10.1016/j.wneu.2018.02.096."},"oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","date_created":"2018-12-11T11:46:15Z","volume":13,"doi":"10.1016/j.wneu.2018.02.096"},{"publication_status":"published","article_type":"original","quality_controlled":"1","citation":{"ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007."},"scopus_import":"1","publication":"EPL","publisher":"IOP Publishing Ltd.","publist_id":"7432","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm."}],"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1706.01822","open_access":"1"}],"arxiv":1,"issue":"1","month":"01","isi":1,"intvolume":" 121","article_number":"10007","date_created":"2018-12-11T11:46:15Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":121,"doi":"10.1209/0295-5075/121/10007","author":[{"full_name":"Napiórkowski, Marcin M","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski"},{"last_name":"Reuvers","full_name":"Reuvers, Robin","first_name":"Robin"},{"last_name":"Solovej","full_name":"Solovej, Jan","first_name":"Jan"}],"status":"public","oa_version":"Preprint","date_published":"2018-01-01T00:00:00Z","day":"01","external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"date_updated":"2023-09-08T13:30:51Z","_id":"399","article_processing_charge":"No","title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","oa":1,"acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","project":[{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF"}],"year":"2018"},{"scopus_import":"1","file":[{"file_id":"5216","access_level":"open_access","creator":"system","checksum":"7a2243668f215821bc6aecad0320079a","content_type":"application/pdf","date_updated":"2020-07-14T12:46:22Z","file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","file_size":22803163,"date_created":"2018-12-12T10:16:28Z","relation":"main_file"}],"file_date_updated":"2020-07-14T12:46:22Z","publication":"ACM Trans. Graph.","publisher":"ACM","department":[{"_id":"BeBi"}],"publist_id":"8053","language":[{"iso":"eng"}],"abstract":[{"text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","citation":{"ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89.","mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. 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(Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"department":[{"_id":"NiBa"}],"publist_id":"8014","language":[{"iso":"eng"}],"publisher":"Wiley","file":[{"content_type":"application/pdf","access_level":"open_access","creator":"apreinsp","file_id":"6652","relation":"main_file","date_created":"2019-07-19T06:54:46Z","file_size":295452,"date_updated":"2020-07-14T12:46:22Z","file_name":"2018_MolecularEcology_BartonNick.pdf"}],"scopus_import":"1","file_date_updated":"2020-07-14T12:46:22Z","publication":"Molecular Ecology","quality_controlled":"1","citation":{"chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018."},"article_type":"letter_note","publication_status":"published","year":"2018","has_accepted_license":"1","oa":1,"publication_identifier":{"issn":["1365294X"]},"title":"The consequences of an introgression event","article_processing_charge":"Yes (via OA deal)","date_updated":"2023-09-19T10:06:08Z","_id":"40","related_material":{"record":[{"id":"9805","status":"public","relation":"research_data"}]},"external_id":{"pmid":["30599087"],"isi":["000454600500001"]},"day":"31","date_published":"2018-12-31T00:00:00Z","oa_version":"Published Version","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"doi":"10.1111/mec.14950","pmid":1,"date_created":"2018-12-11T11:44:18Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":27},{"ddc":["510"],"type":"journal_article","issue":"5","page":"1507 - 1527","ec_funded":1,"isi":1,"month":"05","intvolume":" 19","pubrep_id":"1011","publication_status":"published","quality_controlled":"1","citation":{"ama":"Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7","apa":"Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7","chicago":"Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7.","ieee":"A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018.","ista":"Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527.","short":"A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527.","mla":"Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7."},"scopus_import":"1","file_date_updated":"2020-07-14T12:46:22Z","publication":"Annales Henri Poincare","file":[{"relation":"main_file","file_size":582680,"date_created":"2018-12-12T10:12:47Z","file_name":"IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf","date_updated":"2020-07-14T12:46:22Z","checksum":"04d2c9bd7cbf3ca1d7acaaf4e7dca3e5","content_type":"application/pdf","creator":"system","access_level":"open_access","file_id":"4966"}],"publisher":"Springer","publist_id":"7429","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"abstract":[{"text":"We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case.","lang":"eng"}],"date_updated":"2023-09-15T12:04:15Z","_id":"400","title":"Persistence of translational symmetry in the BCS model with radial pair interaction","article_processing_charge":"Yes (via OA deal)","oa":1,"has_accepted_license":"1","project":[{"name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","grant_number":"694227","call_identifier":"H2020"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"year":"2018","date_created":"2018-12-11T11:46:15Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":19,"doi":"10.1007/s00023-018-0665-7","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"orcid":"0000-0003-3146-6746","first_name":"Andreas","full_name":"Deuchert, Andreas","last_name":"Deuchert","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Geisinge, Alissa","first_name":"Alissa","last_name":"Geisinge"},{"first_name":"Christian","full_name":"Hainzl, Christian","last_name":"Hainzl"},{"full_name":"Loss, Michael","first_name":"Michael","last_name":"Loss"}],"status":"public","oa_version":"Published Version","date_published":"2018-05-01T00:00:00Z","day":"01","external_id":{"isi":["000429799900008"]}},{"file":[{"creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"87a427bc2e8724be3dd22a4efdd21a33","file_id":"4902","relation":"main_file","file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","date_updated":"2020-07-14T12:46:22Z","date_created":"2018-12-12T10:11:45Z","file_size":3780491}],"scopus_import":"1","file_date_updated":"2020-07-14T12:46:22Z","publication":"Nature Communications","publisher":"Nature Publishing Group","language":[{"iso":"eng"}],"publist_id":"7427","department":[{"_id":"EdHa"}],"abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation."}],"publication_status":"published","quality_controlled":"1","citation":{"ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:10.1038/s41467-018-03574-5.","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).","ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5","apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5","chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-03574-5."},"issue":"1","month":"03","isi":1,"intvolume":" 9","pubrep_id":"996","article_number":"1210","ddc":["539","570"],"type":"journal_article","date_published":"2018-03-23T00:00:00Z","day":"23","external_id":{"isi":["000428165400009"]},"date_created":"2018-12-11T11:46:16Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":9,"doi":"10.1038/s41467-018-03574-5","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Qin, Xiang","first_name":"Xiang","last_name":"Qin"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"},{"full_name":"Mangeat, Thomas","first_name":"Thomas","last_name":"Mangeat"},{"last_name":"Liu","first_name":"Chang","full_name":"Liu, Chang"},{"last_name":"Majumder","first_name":"Pralay","full_name":"Majumder, Pralay"},{"last_name":"Liu","first_name":"Jjiaying","full_name":"Liu, Jjiaying"},{"full_name":"Choesmel Cadamuro, Valerie","first_name":"Valerie","last_name":"Choesmel Cadamuro"},{"last_name":"Mcdonald","first_name":"Jocelyn","full_name":"Mcdonald, Jocelyn"},{"first_name":"Yinyao","full_name":"Liu, Yinyao","last_name":"Liu"},{"full_name":"Yi, Bin","first_name":"Bin","last_name":"Yi"},{"last_name":"Wang","first_name":"Xiaobo","full_name":"Wang, Xiaobo"}],"oa_version":"Published Version","oa":1,"has_accepted_license":"1","year":"2018","date_updated":"2023-09-08T11:41:45Z","_id":"401","article_processing_charge":"No","title":"A biochemical network controlling basal myosin oscillation"},{"oa":1,"year":"2018","acknowledgement":"M.B. was supported by the Cell Communication in Health and Disease graduate study program of the Austrian Science Fund (FWF) and the Medical University of Vienna. M.S. was supported by the European Research Council (grant ERC GA 281556) and an FWF START award.\r\nWe thank C. Moussion for establishing the intralymphatic injection at IST Austria and for providing anti-PNAd hybridoma supernatant, R. Förster and A. Braun for sharing the intralymphatic injection technology, K. Vaahtomeri for the lentiviral constructs, M. Hons for establishing in vivo multiphoton imaging, the Sixt lab for intellectual input, M. Schunn for help with the design of the in vivo experiments, F. Langer for technical assistance with the in vivo experiments, the bioimaging facility of IST Austria for support, and R. Efferl for providing the CT26 cell line.","project":[{"_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and transduction of leukocytes (FWF)","call_identifier":"FWF","grant_number":"Y 564-B12"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","call_identifier":"FP7","grant_number":"281556"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6947"}]},"_id":"402","date_updated":"2024-03-25T23:30:05Z","article_processing_charge":"No","title":"Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice","date_published":"2018-03-23T00:00:00Z","day":"23","external_id":{"isi":["000428043600047"],"pmid":["29567714"]},"volume":359,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:16Z","doi":"10.1126/science.aal3662","pmid":1,"status":"public","author":[{"last_name":"Brown","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87","full_name":"Brown, Markus","first_name":"Markus"},{"first_name":"Frank P","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","last_name":"Assen"},{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","first_name":"Alexander F","last_name":"Leithner","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Abe, Jun","first_name":"Jun","last_name":"Abe"},{"last_name":"Schachner","full_name":"Schachner, Helga","first_name":"Helga"},{"last_name":"Asfour","full_name":"Asfour, Gabriele","first_name":"Gabriele"},{"last_name":"Bagó Horváth","full_name":"Bagó Horváth, Zsuzsanna","first_name":"Zsuzsanna"},{"first_name":"Jens","full_name":"Stein, Jens","last_name":"Stein"},{"first_name":"Pavel","full_name":"Uhrin, Pavel","last_name":"Uhrin"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"}],"oa_version":"Published Version","issue":"6382","ec_funded":1,"page":"1408 - 1411","acknowledged_ssus":[{"_id":"Bio"}],"month":"03","isi":1,"intvolume":" 359","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.aal3662"}],"publication":"Science","scopus_import":"1","publisher":"American Association for the Advancement of Science","department":[{"_id":"MiSi"}],"language":[{"iso":"eng"}],"publist_id":"7428","abstract":[{"text":"During metastasis, malignant cells escape the primary tumor, intravasate lymphatic vessels, and reach draining sentinel lymph nodes before they colonize distant organs via the blood circulation. Although lymph node metastasis in cancer patients correlates with poor prognosis, evidence is lacking as to whether and how tumor cells enter the bloodstream via lymph nodes. To investigate this question, we delivered carcinoma cells into the lymph nodes of mice by microinfusing the cells into afferent lymphatic vessels. We found that tumor cells rapidly infiltrated the lymph node parenchyma, invaded blood vessels, and seeded lung metastases without involvement of the thoracic duct. These results suggest that the lymph node blood vessels can serve as an exit route for systemic dissemination of cancer cells in experimental mouse models. Whether this form of tumor cell spreading occurs in cancer patients remains to be determined.","lang":"eng"}],"publication_status":"published","article_type":"original","citation":{"ama":"Brown M, Assen FP, Leithner AF, et al. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 2018;359(6382):1408-1411. doi:10.1126/science.aal3662","apa":"Brown, M., Assen, F. P., Leithner, A. F., Abe, J., Schachner, H., Asfour, G., … Kerjaschki, D. (2018). Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aal3662","chicago":"Brown, Markus, Frank P Assen, Alexander F Leithner, Jun Abe, Helga Schachner, Gabriele Asfour, Zsuzsanna Bagó Horváth, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aal3662.","ista":"Brown M, Assen FP, Leithner AF, Abe J, Schachner H, Asfour G, Bagó Horváth Z, Stein J, Uhrin P, Sixt MK, Kerjaschki D. 2018. Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice. Science. 359(6382), 1408–1411.","ieee":"M. Brown et al., “Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice,” Science, vol. 359, no. 6382. American Association for the Advancement of Science, pp. 1408–1411, 2018.","short":"M. Brown, F.P. Assen, A.F. Leithner, J. Abe, H. Schachner, G. Asfour, Z. Bagó Horváth, J. Stein, P. Uhrin, M.K. Sixt, D. Kerjaschki, Science 359 (2018) 1408–1411.","mla":"Brown, Markus, et al. “Lymph Node Blood Vessels Provide Exit Routes for Metastatic Tumor Cell Dissemination in Mice.” Science, vol. 359, no. 6382, American Association for the Advancement of Science, 2018, pp. 1408–11, doi:10.1126/science.aal3662."},"quality_controlled":"1"}]