[{"department":[{"_id":"ToHe"}],"file_date_updated":"2020-10-09T06:24:21Z","date_updated":"2023-09-13T08:58:34Z","ddc":["000"],"conference":{"end_date":"2018-09-06","location":"Beijing, China","start_date":"2018-09-04","name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"type":"conference","status":"public","_id":"81","volume":11022,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"8638","checksum":"e5d81c9b50a6bd9d8a2c16953aad7e23","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_LNCS_Elgyuett.pdf","date_created":"2020-10-09T06:24:21Z","creator":"dernst","file_size":537219,"date_updated":"2020-10-09T06:24:21Z"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 11022","month":"08","abstract":[{"lang":"eng","text":"We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,"}],"oa_version":"Submitted Version","external_id":{"isi":["000884993200004"]},"article_processing_charge":"No","publist_id":"7973","author":[{"first_name":"Adrian","id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","full_name":"Elgyütt, Adrian","last_name":"Elgyütt"},{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"title":"Monitoring temporal logic with clock variables","citation":{"chicago":"Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4.","ista":"Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.","mla":"Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4.","apa":"Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4","ama":"Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4","ieee":"A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.","short":"A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"page":"53 - 70","date_created":"2018-12-11T11:44:31Z","doi":"10.1007/978-3-030-00151-3_4","date_published":"2018-08-26T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","day":"26","oa":1,"quality_controlled":"1","publisher":"Springer"},{"quality_controlled":"1","publisher":"Springer","oa":1,"date_published":"2018-09-12T00:00:00Z","doi":"10.1007/s00446-018-0342-6","date_created":"2018-12-11T11:44:30Z","day":"12","publication":"Distributed Computing","isi":1,"has_accepted_license":"1","year":"2018","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"title":"Near-optimal self-stabilising counting and firing squads","author":[{"first_name":"Christoph","last_name":"Lenzen","full_name":"Lenzen, Christoph"},{"last_name":"Rybicki","full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel"}],"publist_id":"7978","external_id":{"isi":["000475627800005"]},"article_processing_charge":"Yes (via OA deal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing.","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6."},"month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.","lang":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5711","checksum":"872db70bba9b401500abe3c6ae2f1a61","file_size":799337,"date_updated":"2020-07-14T12:48:01Z","creator":"dernst","file_name":"2018_DistributedComputing_Lenzen.pdf","date_created":"2018-12-17T14:21:22Z"}],"language":[{"iso":"eng"}],"publication_status":"published","status":"public","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"76","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:48:01Z","ddc":["000"],"date_updated":"2023-09-13T09:01:06Z"},{"day":"01","publication":"Computational Geometry: Theory and Applications","has_accepted_license":"1","isi":1,"year":"2018","doi":"10.1016/j.comgeo.2017.06.014","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:46:59Z","page":"119 - 133","quality_controlled":"1","publisher":"Elsevier","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.","ista":"Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.","mla":"Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.","apa":"Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014","ama":"Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014","short":"H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.","ieee":"H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018."},"title":"Multiple covers with balls I: Inclusion–exclusion","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Iglesias Ham, Mabel","last_name":"Iglesias Ham","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7289","external_id":{"isi":["000415778300010"]},"article_processing_charge":"No","project":[{"_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493","name":"Topological Complex Systems"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1c8d58cd489a66cd3e2064c1141c8c5e","file_id":"5953","date_updated":"2020-07-14T12:46:38Z","file_size":708357,"creator":"dernst","date_created":"2019-02-12T06:47:52Z","file_name":"2018_Edelsbrunner.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":68,"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software."}],"month":"03","intvolume":" 68","scopus_import":"1","ddc":["000"],"date_updated":"2023-09-13T08:59:00Z","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:46:38Z","_id":"530","status":"public","type":"journal_article"},{"date_created":"2018-12-11T11:45:44Z","date_published":"2018-04-09T00:00:00Z","doi":"10.1103/PhysRevA.97.043812","publication":" Physical Review A - Atomic, Molecular, and Optical Physics","day":"09","year":"2018","isi":1,"oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE).","title":"Nanoscopy of pairs of atoms by fluorescence in a magnetic field","article_processing_charge":"No","external_id":{"arxiv":["1712.10127"],"isi":["000429454000015"]},"publist_id":"7572","author":[{"full_name":"Redchenko, Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","first_name":"Elena"},{"full_name":"Makarov, Alexander","last_name":"Makarov","first_name":"Alexander"},{"first_name":"Vladimir","full_name":"Yudson, Vladimir","last_name":"Yudson"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812.","chicago":"Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812.","ama":"Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812","apa":"Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812","short":"E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018).","ieee":"E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018.","mla":"Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812."},"article_number":" 043812 ","issue":"4","volume":97,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 97","month":"04","main_file_link":[{"url":"https://arxiv.org/abs/1712.10127","open_access":"1"}],"scopus_import":"1","oa_version":"Submitted Version","abstract":[{"text":"Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. ","lang":"eng"}],"department":[{"_id":"JoFi"}],"date_updated":"2023-09-13T09:00:41Z","status":"public","type":"journal_article","article_type":"original","_id":"307"},{"article_number":"67","project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"335980","name":"Systematic investigation of epistasis in molecular evolution"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0.","short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0."},"title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","article_processing_charge":"No","external_id":{"isi":["000433986200001"]},"author":[{"last_name":"Zapata","full_name":"Zapata, Luis","first_name":"Luis"},{"last_name":"Pich","full_name":"Pich, Oriol","first_name":"Oriol"},{"first_name":"Luis","full_name":"Serrano, Luis","last_name":"Serrano"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"last_name":"Ossowski","full_name":"Ossowski, Stephan","first_name":"Stephan"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"publist_id":"7620","oa":1,"publisher":"BioMed Central","quality_controlled":"1","publication":"Genome Biology","day":"31","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:45:35Z","date_published":"2018-05-31T00:00:00Z","doi":"10.1186/s13059-018-1434-0","_id":"279","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-09-13T09:01:32Z","file_date_updated":"2020-07-14T12:45:47Z","department":[{"_id":"FyKo"}],"oa_version":"Published Version","abstract":[{"text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.","lang":"eng"}],"intvolume":" 19","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":1414722,"date_updated":"2020-07-14T12:45:47Z","file_name":"2018_GenomeBiology_Zapata.pdf","date_created":"2018-12-17T14:05:01Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5708","checksum":"f3e4922486bd9bf1483271bdbed394a7"}],"publication_status":"published","ec_funded":1,"volume":19,"related_material":{"record":[{"status":"public","id":"9811","relation":"research_data"},{"status":"public","id":"9812","relation":"research_data"}]}}]