--- _id: '81' 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, alternative_title: - LNCS article_processing_charge: No author: - first_name: Adrian full_name: Elgyütt, Adrian id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87 last_name: Elgyütt - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: 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' 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' 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. 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.' 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. short: A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70. conference: end_date: 2018-09-06 location: Beijing, China name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' start_date: 2018-09-04 date_created: 2018-12-11T11:44:31Z date_published: 2018-08-26T00:00:00Z date_updated: 2023-09-13T08:58:34Z day: '26' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-00151-3_4 external_id: isi: - '000884993200004' file: - access_level: open_access checksum: e5d81c9b50a6bd9d8a2c16953aad7e23 content_type: application/pdf creator: dernst date_created: 2020-10-09T06:24:21Z date_updated: 2020-10-09T06:24:21Z file_id: '8638' file_name: 2018_LNCS_Elgyuett.pdf file_size: 537219 relation: main_file success: 1 file_date_updated: 2020-10-09T06:24:21Z has_accepted_license: '1' intvolume: ' 11022' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 53 - 70 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '7973' quality_controlled: '1' scopus_import: '1' status: public title: Monitoring temporal logic with clock variables type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11022 year: '2018' ... --- _id: '76' abstract: - lang: eng 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.' article_processing_charge: Yes (via OA deal) author: - first_name: Christoph full_name: Lenzen, Christoph last_name: Lenzen - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 citation: 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 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. ista: Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 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. short: C. Lenzen, J. Rybicki, Distributed Computing (2018). date_created: 2018-12-11T11:44:30Z date_published: 2018-09-12T00:00:00Z date_updated: 2023-09-13T09:01:06Z day: '12' ddc: - '000' department: - _id: DaAl doi: 10.1007/s00446-018-0342-6 external_id: isi: - '000475627800005' file: - access_level: open_access checksum: 872db70bba9b401500abe3c6ae2f1a61 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:21:22Z date_updated: 2020-07-14T12:48:01Z file_id: '5711' file_name: 2018_DistributedComputing_Lenzen.pdf file_size: 799337 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Distributed Computing publication_status: published publisher: Springer publist_id: '7978' quality_controlled: '1' scopus_import: '1' status: public title: Near-optimal self-stabilising counting and firing squads tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '530' 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. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham citation: 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' 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' 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.' 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.' 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.' short: 'H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.' date_created: 2018-12-11T11:46:59Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-13T08:59:00Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.comgeo.2017.06.014 ec_funded: 1 external_id: isi: - '000415778300010' file: - access_level: open_access checksum: 1c8d58cd489a66cd3e2064c1141c8c5e content_type: application/pdf creator: dernst date_created: 2019-02-12T06:47:52Z date_updated: 2020-07-14T12:46:38Z file_id: '5953' file_name: 2018_Edelsbrunner.pdf file_size: 708357 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' intvolume: ' 68' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Preprint page: 119 - 133 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '7289' quality_controlled: '1' scopus_import: '1' status: public title: 'Multiple covers with balls I: Inclusion–exclusion' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 68 year: '2018' ... --- _id: '307' abstract: - lang: eng 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. ' 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). article_number: ' 043812 ' article_processing_charge: No article_type: original author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alexander full_name: Makarov, Alexander last_name: Makarov - first_name: Vladimir full_name: Yudson, Vladimir last_name: Yudson citation: 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 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. 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. 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. 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. short: E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018). date_created: 2018-12-11T11:45:44Z date_published: 2018-04-09T00:00:00Z date_updated: 2023-09-13T09:00:41Z day: '09' department: - _id: JoFi doi: 10.1103/PhysRevA.97.043812 external_id: arxiv: - '1712.10127' isi: - '000429454000015' intvolume: ' 97' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.10127 month: '04' oa: 1 oa_version: Submitted Version publication: ' Physical Review A - Atomic, Molecular, and Optical Physics' publication_status: published publisher: American Physical Society publist_id: '7572' quality_controlled: '1' scopus_import: '1' status: public title: Nanoscopy of pairs of atoms by fluorescence in a magnetic field type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 97 year: '2018' ... --- _id: '279' abstract: - lang: eng 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.' article_number: '67' article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: 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 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 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. 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. 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. 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. short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018). date_created: 2018-12-11T11:45:35Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:32Z day: '31' ddc: - '570' department: - _id: FyKo doi: 10.1186/s13059-018-1434-0 ec_funded: 1 external_id: isi: - '000433986200001' file: - access_level: open_access checksum: f3e4922486bd9bf1483271bdbed394a7 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:05:01Z date_updated: 2020-07-14T12:45:47Z file_id: '5708' file_name: 2018_GenomeBiology_Zapata.pdf file_size: 1414722 relation: main_file file_date_updated: 2020-07-14T12:45:47Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Genome Biology publication_status: published publisher: BioMed Central publist_id: '7620' quality_controlled: '1' related_material: record: - id: '9811' relation: research_data status: public - id: '9812' relation: research_data status: public scopus_import: '1' status: public title: Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ...