--- _id: '184' abstract: - lang: eng text: We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. acknowledgement: 'Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.' alternative_title: - Leibniz International Proceedings in Information, LIPIcs author: - first_name: Xavier full_name: Goaoc, Xavier last_name: Goaoc - first_name: Pavel full_name: Paták, Pavel last_name: Paták - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41' apa: 'Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41' chicago: Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41. ieee: 'X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.' ista: 'Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.' mla: Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41. short: X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16. conference: end_date: 2018-06-14 location: Budapest, Hungary name: 'SoCG: Symposium on Computational Geometry' start_date: 2018-06-11 date_created: 2018-12-11T11:45:04Z date_published: 2018-06-11T00:00:00Z date_updated: 2023-09-06T11:10:57Z day: '11' ddc: - '516' - '000' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2018.41 file: - access_level: open_access checksum: d12bdd60f04a57307867704b5f930afd content_type: application/pdf creator: dernst date_created: 2018-12-17T16:35:02Z date_updated: 2020-07-14T12:45:18Z file_id: '5725' file_name: 2018_LIPIcs_Goaoc.pdf file_size: 718414 relation: main_file file_date_updated: 2020-07-14T12:45:18Z has_accepted_license: '1' intvolume: ' 99' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 41:1 - 41:16 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7736' quality_controlled: '1' related_material: record: - id: '7108' relation: later_version status: public scopus_import: 1 status: public title: Shellability is NP-complete 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2018' ... --- _id: '285' abstract: - lang: eng text: In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)). acknowledgement: Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program). alternative_title: - LIPIcs article_number: '46' article_processing_charge: No author: - first_name: Kristóf full_name: Huszár, Kristóf id: 33C26278-F248-11E8-B48F-1D18A9856A87 last_name: Huszár orcid: 0000-0002-5445-5057 - first_name: Jonathan full_name: Spreer, Jonathan last_name: Spreer - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46' apa: 'Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46' chicago: Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46. ieee: 'K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.' ista: 'Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.' mla: Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46. short: K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-06-14 location: Budapest, Hungary name: 'SoCG: Symposium on Computational Geometry' start_date: 2018-06-11 date_created: 2018-12-11T11:45:37Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-06T11:13:41Z day: '01' ddc: - '516' - '000' department: - _id: UlWa doi: 10.4230/LIPIcs.SoCG.2018.46 external_id: arxiv: - '1712.00434' file: - access_level: open_access checksum: 530d084116778135d5bffaa317479cac content_type: application/pdf creator: dernst date_created: 2018-12-17T15:32:38Z date_updated: 2020-07-14T12:45:51Z file_id: '5713' file_name: 2018_LIPIcs_Huszar.pdf file_size: 642522 relation: main_file file_date_updated: 2020-07-14T12:45:51Z has_accepted_license: '1' intvolume: ' 99' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7614' quality_controlled: '1' related_material: record: - id: '7093' relation: later_version status: public scopus_import: 1 status: public title: On the treewidth of triangulated 3-manifolds 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2018' ... --- _id: '13059' abstract: - lang: eng text: "This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee)." article_processing_charge: No author: - first_name: Edgar full_name: Garriga, Edgar last_name: Garriga - first_name: Paolo full_name: di Tommaso, Paolo last_name: di Tommaso - first_name: Cedrik full_name: Magis, Cedrik last_name: Magis - first_name: Ionas full_name: Erb, Ionas last_name: Erb - first_name: Leila full_name: Mansouri, Leila last_name: Mansouri - first_name: Athanasios full_name: Baltzis, Athanasios last_name: Baltzis - first_name: Hafid full_name: Laayouni, Hafid last_name: Laayouni - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Evan full_name: Floden, Evan last_name: Floden - first_name: Cedric full_name: Notredame, Cedric last_name: Notredame citation: ama: Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846 apa: Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846 chicago: Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846. ieee: E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018. ista: Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846. mla: Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846. short: E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018). date_created: 2023-05-23T16:08:20Z date_published: 2018-12-07T00:00:00Z date_updated: 2023-09-06T14:32:51Z day: '07' ddc: - '570' department: - _id: FyKo doi: 10.5281/ZENODO.2025846 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.3271452 month: '12' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '7181' relation: used_in_publication status: public status: public title: Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method 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: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '49' abstract: - lang: eng text: Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hannes full_name: Watzinger, Hannes id: 35DF8E50-F248-11E8-B48F-1D18A9856A87 last_name: Watzinger citation: ama: Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033 apa: Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033 chicago: Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033. ieee: H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018. ista: Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. mla: Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033. short: H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:21Z date_published: 2018-07-30T00:00:00Z date_updated: 2023-09-07T12:27:43Z day: '30' ddc: - '530' degree_awarded: PhD department: - _id: GeKa doi: 10.15479/AT:ISTA:th_1033 file: - access_level: open_access checksum: b653b5216251f938ddbeafd1de88667c content_type: application/pdf creator: dernst date_created: 2019-04-09T07:13:28Z date_updated: 2020-07-14T12:46:35Z file_id: '6249' file_name: 2018_Thesis_Watzinger.pdf file_size: 85539748 relation: main_file - access_level: closed checksum: 39bcf8de7ac5b1bb516b11ce2f966785 content_type: application/zip creator: dernst date_created: 2019-04-09T07:13:27Z date_updated: 2020-07-14T12:46:35Z file_id: '6250' file_name: 2018_Thesis_Watzinger_source.zip file_size: 21830697 relation: source_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '77' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8005' pubrep_id: '1033' status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Ge hut wires - from growth to hole spin resonance 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '201' abstract: - lang: eng text: 'We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham citation: ama: Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026 apa: Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026 chicago: Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026. ieee: M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018. ista: Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria. mla: Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026. short: M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:45:10Z date_published: 2018-06-11T00:00:00Z date_updated: 2023-09-07T12:25:32Z day: '11' ddc: - '514' - '516' degree_awarded: PhD department: - _id: HeEd doi: 10.15479/AT:ISTA:th_1026 file: - access_level: closed checksum: dd699303623e96d1478a6ae07210dd05 content_type: application/zip creator: kschuh date_created: 2019-02-05T07:43:31Z date_updated: 2020-07-14T12:45:24Z file_id: '5918' file_name: IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip file_size: 11827713 relation: source_file - access_level: open_access checksum: ba163849a190d2b41d66fef0e4983294 content_type: application/pdf creator: kschuh date_created: 2019-02-05T07:43:45Z date_updated: 2020-07-14T12:45:24Z file_id: '5919' file_name: IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf file_size: 4783846 relation: main_file file_date_updated: 2020-07-14T12:45:24Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '171' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7712' pubrep_id: '1026' status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Multiple covers with balls type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '68' abstract: - lang: eng text: The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alexander full_name: Zimin, Alexander id: 37099E9C-F248-11E8-B48F-1D18A9856A87 last_name: Zimin citation: ama: Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048 apa: Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048 chicago: Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048. ieee: A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018. ista: Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria. mla: Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048. short: A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:27Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-07T12:29:07Z day: '01' ddc: - '004' - '519' degree_awarded: PhD department: - _id: ChLa doi: 10.15479/AT:ISTA:TH1048 ec_funded: 1 file: - access_level: open_access checksum: e849dd40a915e4d6c5572b51b517f098 content_type: application/pdf creator: dernst date_created: 2019-04-09T07:32:47Z date_updated: 2020-07-14T12:47:40Z file_id: '6253' file_name: 2018_Thesis_Zimin.pdf file_size: 1036137 relation: main_file - access_level: closed checksum: da092153cec55c97461bd53c45c5d139 content_type: application/zip creator: dernst date_created: 2019-04-09T07:32:47Z date_updated: 2020-07-14T12:47:40Z file_id: '6254' file_name: 2018_Thesis_Zimin_Source.zip file_size: 637490 relation: source_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '92' project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7986' pubrep_id: '1048' status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Learning from dependent data type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '83' abstract: - lang: eng text: "A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hamza M full_name: Abusalah, Hamza M id: 40297222-F248-11E8-B48F-1D18A9856A87 last_name: Abusalah citation: ama: Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046 apa: Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046 chicago: Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046. ieee: H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018. ista: Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. mla: Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046. short: H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:32Z date_published: 2018-09-05T00:00:00Z date_updated: 2023-09-07T12:30:23Z day: '05' ddc: - '004' degree_awarded: PhD department: - _id: KrPi doi: 10.15479/AT:ISTA:TH_1046 ec_funded: 1 file: - access_level: open_access checksum: c4b5f7d111755d1396787f41886fc674 content_type: application/pdf creator: dernst date_created: 2019-04-09T06:43:41Z date_updated: 2020-07-14T12:48:11Z file_id: '6245' file_name: 2018_Thesis_Abusalah.pdf file_size: 876241 relation: main_file - access_level: closed checksum: 0f382ac56b471c48fd907d63eb87dafe content_type: application/x-gzip creator: dernst date_created: 2019-04-09T06:43:41Z date_updated: 2020-07-14T12:48:11Z file_id: '6246' file_name: 2018_Thesis_Abusalah_source.tar.gz file_size: 2029190 relation: source_file file_date_updated: 2020-07-14T12:48:11Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '59' project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7971' pubrep_id: '1046' related_material: record: - id: '1229' relation: part_of_dissertation status: public - id: '1235' relation: part_of_dissertation status: public - id: '1236' relation: part_of_dissertation status: public - id: '559' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: Proof systems for sustainable decentralized cryptocurrencies type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '197' abstract: - lang: eng text: Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task. acknowledgement: I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alexander full_name: Kolesnikov, Alexander id: 2D157DB6-F248-11E8-B48F-1D18A9856A87 last_name: Kolesnikov citation: ama: Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:10.15479/AT:ISTA:th_1021 apa: Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021 chicago: Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1021. ieee: A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018. ista: Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. mla: Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021. short: A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:45:09Z date_published: 2018-05-25T00:00:00Z date_updated: 2023-09-07T12:51:46Z day: '25' ddc: - '004' degree_awarded: PhD department: - _id: ChLa doi: 10.15479/AT:ISTA:th_1021 ec_funded: 1 file: - access_level: open_access checksum: bc678e02468d8ebc39dc7267dfb0a1c4 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:57Z date_updated: 2020-07-14T12:45:22Z file_id: '5113' file_name: IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf file_size: 12918758 relation: main_file - access_level: closed checksum: bc66973b086da5a043f1162dcfb1fde4 content_type: application/zip creator: dernst date_created: 2019-04-05T09:34:49Z date_updated: 2020-07-14T12:45:22Z file_id: '6225' file_name: 2018_Thesis_Kolesnikov_source.zip file_size: 55973760 relation: source_file file_date_updated: 2020-07-14T12:45:22Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '113' project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7718' pubrep_id: '1021' status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '6774' abstract: - lang: eng text: "A central problem of algebraic topology is to understand the homotopy groups \ \U0001D70B\U0001D451(\U0001D44B) of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group \U0001D70B1(\U0001D44B) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with \U0001D70B1(\U0001D44B) \ trivial), compute the higher homotopy group \U0001D70B\U0001D451(\U0001D44B) \ for any given \U0001D451≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of \U0001D70B\U0001D451(\U0001D44B) , \U0001D451≥2 \ as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of \U0001D70B\U0001D451(\U0001D44B) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere \U0001D446\U0001D451 to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes \U0001D70B\U0001D451(\U0001D44B) \ and represents its elements as simplicial maps from a suitable triangulation of the d-sphere \U0001D446\U0001D451 to X. For fixed d, the algorithm runs in time exponential in size(\U0001D44B) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed \U0001D451≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of \U0001D70B\U0001D451(\U0001D44B) , the size of the triangulation of \U0001D446\U0001D451 on which the map is defined, is exponential in size(\U0001D44B) ." article_type: original author: - first_name: Marek full_name: Filakovský, Marek id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87 last_name: Filakovský - first_name: Peter full_name: Franek, Peter id: 473294AE-F248-11E8-B48F-1D18A9856A87 last_name: Franek orcid: 0000-0001-8878-8397 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Stephan Y full_name: Zhechev, Stephan Y id: 3AA52972-F248-11E8-B48F-1D18A9856A87 last_name: Zhechev citation: ama: Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2018;2(3-4):177-231. doi:10.1007/s41468-018-0021-5 apa: Filakovský, M., Franek, P., Wagner, U., & Zhechev, S. Y. (2018). Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. Springer. https://doi.org/10.1007/s41468-018-0021-5 chicago: Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology. Springer, 2018. https://doi.org/10.1007/s41468-018-0021-5. ieee: M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial representatives of homotopy group elements,” Journal of Applied and Computational Topology, vol. 2, no. 3–4. Springer, pp. 177–231, 2018. ista: Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4), 177–231. mla: Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology, vol. 2, no. 3–4, Springer, 2018, pp. 177–231, doi:10.1007/s41468-018-0021-5. short: M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231. date_created: 2019-08-08T06:47:40Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-09-07T13:10:36Z day: '01' ddc: - '514' department: - _id: UlWa doi: 10.1007/s41468-018-0021-5 file: - access_level: open_access checksum: cf9e7fcd2a113dd4828774fc75cdb7e8 content_type: application/pdf creator: dernst date_created: 2019-08-08T06:55:21Z date_updated: 2020-07-14T12:47:40Z file_id: '6775' file_name: 2018_JourAppliedComputTopology_Filakovsky.pdf file_size: 1056278 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 2' issue: 3-4 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 177-231 project: - _id: 25F8B9BC-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M01980 name: Robust invariants of Nonlinear Systems - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Journal of Applied and Computational Topology publication_identifier: eissn: - 2367-1734 issn: - 2367-1726 publication_status: published publisher: Springer quality_controlled: '1' related_material: record: - id: '6681' relation: dissertation_contains status: public status: public title: Computing simplicial representatives of homotopy group elements 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2018' ... --- _id: '133' abstract: - lang: eng text: Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs. alternative_title: - LIPIcs article_number: '21' author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer - 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: 'Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.21' apa: 'Kragl, B., Qadeer, S., & Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21' chicago: Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21. ieee: 'B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.' ista: 'Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.' mla: Kragl, Bernhard, et al. Synchronizing the Asynchronous. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.21. short: B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-09-07 location: Beijing, China name: 'CONCUR: International Conference on Concurrency Theory' start_date: 2018-09-04 date_created: 2018-12-11T11:44:48Z date_published: 2018-08-13T00:00:00Z date_updated: 2023-09-07T13:18:00Z day: '13' ddc: - '000' department: - _id: ToHe doi: 10.4230/LIPIcs.CONCUR.2018.21 file: - access_level: open_access checksum: c90895f4c5fafc18ddc54d1c8848077e content_type: application/pdf creator: system date_created: 2018-12-12T10:18:46Z date_updated: 2020-07-14T12:44:44Z file_id: '5368' file_name: IST-2018-853-v2+2_concur2018.pdf file_size: 745438 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 118' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication_identifier: issn: - '18688969' publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7790' pubrep_id: '1039' quality_controlled: '1' related_material: record: - id: '6426' relation: earlier_version status: public - id: '8332' relation: dissertation_contains status: public scopus_import: 1 status: public title: Synchronizing the asynchronous 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 118 year: '2018' ... --- _id: '187' abstract: - lang: eng text: 'Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. ' acknowledgement: This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF). alternative_title: - LIPIcs article_number: '34' author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 citation: ama: 'Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.34' apa: 'Edelsbrunner, H., & Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.34' chicago: Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.34. ieee: 'H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.' ista: 'Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.' mla: Edelsbrunner, Herbert, and Georg F. Osang. The Multi-Cover Persistence of Euclidean Balls. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.34. short: H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. conference: end_date: 2018-06-14 location: Budapest, Hungary name: 'SoCG: Symposium on Computational Geometry' start_date: 2018-06-11 date_created: 2018-12-11T11:45:05Z date_published: 2018-06-11T00:00:00Z date_updated: 2023-09-07T13:29:00Z day: '11' ddc: - '516' department: - _id: HeEd doi: 10.4230/LIPIcs.SoCG.2018.34 file: - access_level: open_access checksum: d8c0533ad0018eb4ed1077475eb8fc18 content_type: application/pdf creator: dernst date_created: 2018-12-18T09:27:22Z date_updated: 2020-07-14T12:45:19Z file_id: '5738' file_name: 2018_LIPIcs_Edelsbrunner_Osang.pdf file_size: 528018 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 99' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7732' quality_controlled: '1' related_material: record: - id: '9317' relation: later_version status: public - id: '9056' relation: dissertation_contains status: public scopus_import: 1 status: public title: The multi-cover persistence of Euclidean balls 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 99 year: '2018' ... --- _id: '692' abstract: - lang: eng text: We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X citation: ama: Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 2018;194(1):55-64. doi:10.1007/s10711-017-0265-6 apa: Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6 chicago: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6. ieee: A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018. ista: Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 194(1), 55–64. mla: Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6. short: A. Akopyan, Geometriae Dedicata 194 (2018) 55–64. date_created: 2018-12-11T11:47:57Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-08T11:40:29Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1007/s10711-017-0265-6 ec_funded: 1 external_id: isi: - '000431418800004' file: - access_level: open_access checksum: 1febcfc1266486053a069e3425ea3713 content_type: application/pdf creator: kschuh date_created: 2020-01-03T11:35:08Z date_updated: 2020-07-14T12:47:44Z file_id: '7222' file_name: 2018_Springer_Akopyan.pdf file_size: 1140860 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 194' isi: 1 issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 55 - 64 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Geometriae Dedicata publication_status: published publisher: Springer publist_id: '7014' quality_controlled: '1' scopus_import: '1' status: public title: 3-Webs generated by confocal conics and circles 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: 194 year: '2018' ... --- _id: '77' abstract: - lang: eng text: Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices. acknowledged_ssus: - _id: M-Shop - _id: NanoFab article_processing_charge: Yes article_type: original author: - first_name: Hannes full_name: Watzinger, Hannes id: 35DF8E50-F248-11E8-B48F-1D18A9856A87 last_name: Watzinger - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka - first_name: Lada full_name: Vukusic, Lada id: 31E9F056-F248-11E8-B48F-1D18A9856A87 last_name: Vukusic orcid: 0000-0003-2424-8636 - first_name: Fei full_name: Gao, Fei last_name: Gao - first_name: Ting full_name: Wang, Ting last_name: Wang - first_name: Friedrich full_name: Schäffler, Friedrich last_name: Schäffler - first_name: Jian full_name: Zhang, Jian last_name: Zhang - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4 apa: Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4 chicago: Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4. ieee: H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications, vol. 9, no. 3902. Nature Publishing Group, 2018. ista: Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902). mla: Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4. short: H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018). date_created: 2018-12-11T11:44:30Z date_published: 2018-09-25T00:00:00Z date_updated: 2023-09-08T11:44:02Z day: '25' ddc: - '530' department: - _id: GeKa doi: 10.1038/s41467-018-06418-4 ec_funded: 1 external_id: isi: - '000445560800010' file: - access_level: open_access checksum: e7148c10a64497e279c4de570b6cc544 content_type: application/pdf creator: dernst date_created: 2018-12-17T10:28:30Z date_updated: 2020-07-14T12:48:02Z file_id: '5687' file_name: 2018_NatureComm_Watzinger.pdf file_size: 1063469 relation: main_file file_date_updated: 2020-07-14T12:48:02Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '3902 ' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25517E86-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335497' name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires - _id: 2552F888-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y00715 name: Loch Spin-Qubits und Majorana-Fermionen in Germanium publication: Nature Communications publication_status: published publisher: Nature Publishing Group quality_controlled: '1' related_material: record: - id: '7977' relation: popular_science - id: '7996' relation: dissertation_contains status: public scopus_import: '1' status: public title: A germanium hole spin qubit 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: 9 year: '2018' ... --- _id: '401' 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. article_number: '1210' article_processing_charge: No author: - first_name: Xiang full_name: Qin, Xiang last_name: Qin - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Thomas full_name: Mangeat, Thomas last_name: Mangeat - first_name: Chang full_name: Liu, Chang last_name: Liu - first_name: Pralay full_name: Majumder, Pralay last_name: Majumder - first_name: Jjiaying full_name: Liu, Jjiaying last_name: Liu - first_name: Valerie full_name: Choesmel Cadamuro, Valerie last_name: Choesmel Cadamuro - first_name: Jocelyn full_name: Mcdonald, Jocelyn last_name: Mcdonald - first_name: Yinyao full_name: Liu, Yinyao last_name: Liu - first_name: Bin full_name: Yi, Bin last_name: Yi - first_name: Xiaobo full_name: Wang, Xiaobo last_name: Wang citation: 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. ieee: X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018. 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. 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). date_created: 2018-12-11T11:46:16Z date_published: 2018-03-23T00:00:00Z date_updated: 2023-09-08T11:41:45Z day: '23' ddc: - '539' - '570' department: - _id: EdHa doi: 10.1038/s41467-018-03574-5 external_id: isi: - '000428165400009' file: - access_level: open_access checksum: 87a427bc2e8724be3dd22a4efdd21a33 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:45Z date_updated: 2020-07-14T12:46:22Z file_id: '4902' file_name: IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf file_size: 3780491 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '7427' pubrep_id: '996' quality_controlled: '1' scopus_import: '1' status: public title: A biochemical network controlling basal myosin oscillation 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: 9 year: '2018' ... --- _id: '318' abstract: - lang: eng text: The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides. acknowledgement: Short Survey article_processing_charge: No author: - first_name: Alessandra M full_name: Casano, Alessandra M id: 3DBA3F4E-F248-11E8-B48F-1D18A9856A87 last_name: Casano orcid: 0000-0002-6009-6804 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Casano AM, Sixt MK. A fat lot of good for wound healing. Developmental Cell. 2018;44(4):405-406. doi:10.1016/j.devcel.2018.02.009 apa: Casano, A. M., & Sixt, M. K. (2018). A fat lot of good for wound healing. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.02.009 chicago: Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.02.009. ieee: A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” Developmental Cell, vol. 44, no. 4. Cell Press, pp. 405–406, 2018. ista: Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406. mla: Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:10.1016/j.devcel.2018.02.009. short: A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406. date_created: 2018-12-11T11:45:47Z date_published: 2018-02-26T00:00:00Z date_updated: 2023-09-08T11:42:28Z day: '26' department: - _id: MiSi doi: 10.1016/j.devcel.2018.02.009 external_id: isi: - '000426150700002' pmid: - '29486189' intvolume: ' 44' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/29486189 month: '02' oa: 1 oa_version: Published Version page: 405 - 406 pmid: 1 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '7547' quality_controlled: '1' scopus_import: '1' status: public title: A fat lot of good for wound healing type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 44 year: '2018' ... --- _id: '410' abstract: - lang: eng text: Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods. article_number: '5184' article_processing_charge: No author: - first_name: Javier full_name: Masís, Javier last_name: Masís - first_name: David full_name: Mankus, David last_name: Mankus - first_name: Steffen full_name: Wolff, Steffen last_name: Wolff - first_name: Grigori full_name: Guitchounts, Grigori last_name: Guitchounts - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 - first_name: David full_name: Cox, David last_name: Cox citation: ama: Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-23247-z apa: Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-23247-z chicago: Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-23247-z. ieee: J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018. ista: Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184. mla: Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:10.1038/s41598-018-23247-z. short: J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018). date_created: 2018-12-11T11:46:19Z date_published: 2018-03-26T00:00:00Z date_updated: 2023-09-08T11:48:39Z day: '26' ddc: - '571' - '572' department: - _id: MaJö doi: 10.1038/s41598-018-23247-z external_id: isi: - '000428234100005' file: - access_level: open_access checksum: 653fcb852f899c75b00ceee2a670d738 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:42Z date_updated: 2020-07-14T12:46:23Z file_id: '4831' file_name: IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf file_size: 2359430 relation: main_file file_date_updated: 2020-07-14T12:46:23Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '7419' pubrep_id: '994' quality_controlled: '1' scopus_import: '1' status: public title: A micro-CT-based method for quantitative brain lesion characterization and electrode localization 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: 8 year: '2018' ... --- _id: '277' abstract: - lang: eng text: 'Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions.' article_processing_charge: No article_type: original author: - first_name: Ladislav full_name: Dokládal, Ladislav last_name: Dokládal - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: David full_name: Honys, David last_name: Honys - first_name: Nikoleta full_name: Dupláková, Nikoleta last_name: Dupláková - first_name: Lan full_name: Lee, Lan last_name: Lee - first_name: Stanton full_name: Gelvin, Stanton last_name: Gelvin - first_name: Eva full_name: Sýkorová, Eva last_name: Sýkorová citation: ama: Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 2018;97(5):407-420. doi:10.1007/s11103-018-0747-4 apa: Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., & Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-018-0747-4 chicago: Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology. Springer, 2018. https://doi.org/10.1007/s11103-018-0747-4. ieee: L. Dokládal et al., “An armadillo-domain protein participates in a telomerase interaction network,” Plant Molecular Biology, vol. 97, no. 5. Springer, pp. 407–420, 2018. ista: Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420. mla: Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:10.1007/s11103-018-0747-4. short: L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420. date_created: 2018-12-11T11:45:34Z date_published: 2018-06-12T00:00:00Z date_updated: 2023-09-08T13:21:05Z day: '12' ddc: - '580' department: - _id: EvBe doi: 10.1007/s11103-018-0747-4 external_id: isi: - '000438981700009' file: - access_level: open_access checksum: 451ae47616e6af2533099f596b2a47fb content_type: application/pdf creator: dernst date_created: 2020-05-14T12:23:08Z date_updated: 2020-07-14T12:45:45Z file_id: '7834' file_name: 2018_PlantMolecBio_Dokladal.pdf file_size: 1150679 relation: main_file file_date_updated: 2020-07-14T12:45:45Z has_accepted_license: '1' intvolume: ' 97' isi: 1 issue: '5' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 407 - 420 publication: Plant Molecular Biology publication_status: published publisher: Springer publist_id: '7625' quality_controlled: '1' scopus_import: '1' status: public title: An armadillo-domain protein participates in a telomerase interaction network type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 97 year: '2018' ... --- _id: '299' abstract: - lang: eng text: We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. alternative_title: - LNCS article_processing_charge: No author: - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Olivier full_name: Lebeltel, Olivier last_name: Lebeltel - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Dogan full_name: Ulus, Dogan last_name: Ulus citation: ama: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In: Beyer D, Huisman M, eds. Vol 10806. Springer; 2018:303-319. doi:10.1007/978-3-319-89963-3_18' apa: 'Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2018). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In D. Beyer & M. Huisman (Eds.) (Vol. 10806, pp. 303–319). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89963-3_18' chicago: 'Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” edited by Dirk Beyer and Marieke Huisman, 10806:303–19. Springer, 2018. https://doi.org/10.1007/978-3-319-89963-3_18.' ieee: 'D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10806, pp. 303–319.' ista: 'Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2018. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10806, 303–319.' mla: 'Nickovic, Dejan, et al. AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic. Edited by Dirk Beyer and Marieke Huisman, vol. 10806, Springer, 2018, pp. 303–19, doi:10.1007/978-3-319-89963-3_18.' short: D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, in:, D. Beyer, M. Huisman (Eds.), Springer, 2018, pp. 303–319. conference: end_date: 2018-04-20 location: Thessaloniki, Greece name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2018-04-14 date_created: 2018-12-11T11:45:41Z date_published: 2018-04-14T00:00:00Z date_updated: 2023-09-08T11:52:02Z day: '14' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-89963-3_18 editor: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Marieke full_name: Huisman, Marieke last_name: Huisman external_id: isi: - '00445822600018' file: - access_level: open_access checksum: e11db3b9c8e27a1c7d1c738cc5e4d25a content_type: application/pdf creator: dernst date_created: 2019-02-06T07:33:05Z date_updated: 2020-07-14T12:45:58Z file_id: '5928' file_name: 2018_LNCS_Nickovic.pdf file_size: 3267209 relation: main_file file_date_updated: 2020-07-14T12:45:58Z has_accepted_license: '1' intvolume: ' 10806' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 303 - 319 publication_status: published publisher: Springer publist_id: '7582' quality_controlled: '1' related_material: record: - id: '10861' relation: later_version status: public scopus_import: '1' status: public title: 'AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic' 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: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10806 year: '2018' ... --- _id: '413' abstract: - lang: eng text: Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk. article_processing_charge: No author: - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Sina full_name: Metzler, Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler orcid: 0000-0002-9547-2494 - first_name: Katharina full_name: Seif, Katharina id: 90F7894A-02CF-11E9-976E-E38CFE5CBC1D last_name: Seif - first_name: Elisabeth full_name: Naderlinger, Elisabeth id: 31757262-F248-11E8-B48F-1D18A9856A87 last_name: Naderlinger - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 2018;115(11):2782-2787. doi:10.1073/pnas.1713501115 apa: Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V., & Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713501115 chicago: Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713501115. ieee: M. Konrad et al., “Ants avoid superinfections by performing risk-adjusted sanitary care,” PNAS, vol. 115, no. 11. National Academy of Sciences, pp. 2782–2787, 2018. ista: Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11), 2782–2787. mla: Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS, vol. 115, no. 11, National Academy of Sciences, 2018, pp. 2782–87, doi:10.1073/pnas.1713501115. short: M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S. Cremer, PNAS 115 (2018) 2782–2787. date_created: 2018-12-11T11:46:20Z date_published: 2018-03-13T00:00:00Z date_updated: 2023-09-08T13:22:21Z day: '13' department: - _id: SyCr doi: 10.1073/pnas.1713501115 ec_funded: 1 external_id: isi: - '000427245400069' pmid: - '29463746' intvolume: ' 115' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/29463746 month: '03' oa: 1 oa_version: Published Version page: 2782 - 2787 pmid: 1 project: - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '7416' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/ scopus_import: '1' status: public title: Ants avoid superinfections by performing risk-adjusted sanitary care type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '195' abstract: - lang: eng text: We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases. article_number: '045402' article_processing_charge: No author: - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 2018;98(4). doi:10.1103/PhysRevB.98.045402 apa: Yakaboylu, E., & Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.98.045402 chicago: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.045402. ieee: E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4. American Physical Society, 2018. ista: Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402. mla: Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:10.1103/PhysRevB.98.045402. short: E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018). date_created: 2018-12-11T11:45:08Z date_published: 2018-07-15T00:00:00Z date_updated: 2023-09-08T13:22:57Z day: '15' department: - _id: MiLe doi: 10.1103/PhysRevB.98.045402 ec_funded: 1 external_id: arxiv: - '1712.00308' isi: - '000436939100007' intvolume: ' 98' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.00308 month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Anyonic statistics of quantum impurities in two dimensions type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 98 year: '2018' ... --- _id: '144' abstract: - lang: eng text: The task of a monitor is to watch, at run-time, the execution of a reactive system, and signal the occurrence of a safety violation in the observed sequence of events. While finite-state monitors have been studied extensively, in practice, monitoring software also makes use of unbounded memory. We define a model of automata equipped with integer-valued registers which can execute only a bounded number of instructions between consecutive events, and thus can form the theoretical basis for the study of infinite-state monitors. We classify these register monitors according to the number k of available registers, and the type of register instructions. In stark contrast to the theory of computability for register machines, we prove that for every k 1, monitors with k + 1 counters (with instruction set 〈+1, =〉) are strictly more expressive than monitors with k counters. We also show that adder monitors (with instruction set 〈1, +, =〉) are strictly more expressive than counter monitors, but are complete for monitoring all computable safety -languages for k = 6. Real-time monitors are further required to signal the occurrence of a safety violation as soon as it occurs. The expressiveness hierarchy for counter monitors carries over to real-time monitors. We then show that 2 adders cannot simulate 3 counters in real-time. Finally, we show that real-time adder monitors with inequalities are as expressive as real-time Turing machines. alternative_title: - ACM/IEEE Symposium on Logic in Computer Science article_processing_charge: No author: - 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 - first_name: Ege full_name: Saraç, Ege last_name: Saraç citation: ama: 'Ferrere T, Henzinger TA, Saraç E. A theory of register monitors. In: Vol Part F138033. IEEE; 2018:394-403. doi:10.1145/3209108.3209194' apa: 'Ferrere, T., Henzinger, T. A., & Saraç, E. (2018). A theory of register monitors (Vol. Part F138033, pp. 394–403). Presented at the LICS: Logic in Computer Science, Oxford, UK: IEEE. https://doi.org/10.1145/3209108.3209194' chicago: Ferrere, Thomas, Thomas A Henzinger, and Ege Saraç. “A Theory of Register Monitors,” Part F138033:394–403. IEEE, 2018. https://doi.org/10.1145/3209108.3209194. ieee: 'T. Ferrere, T. A. Henzinger, and E. Saraç, “A theory of register monitors,” presented at the LICS: Logic in Computer Science, Oxford, UK, 2018, vol. Part F138033, pp. 394–403.' ista: 'Ferrere T, Henzinger TA, Saraç E. 2018. A theory of register monitors. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. Part F138033, 394–403.' mla: Ferrere, Thomas, et al. A Theory of Register Monitors. Vol. Part F138033, IEEE, 2018, pp. 394–403, doi:10.1145/3209108.3209194. short: T. Ferrere, T.A. Henzinger, E. Saraç, in:, IEEE, 2018, pp. 394–403. conference: end_date: 2018-07-12 location: Oxford, UK name: 'LICS: Logic in Computer Science' start_date: 2018-07-09 date_created: 2018-12-11T11:44:52Z date_published: 2018-07-09T00:00:00Z date_updated: 2023-09-08T11:49:13Z day: '09' department: - _id: ToHe doi: 10.1145/3209108.3209194 external_id: isi: - '000545262800041' isi: 1 language: - iso: eng month: '07' oa_version: None page: 394 - 403 publication_status: published publisher: IEEE publist_id: '7779' quality_controlled: '1' scopus_import: '1' status: public title: A theory of register monitors type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: Part F138033 year: '2018' ... --- _id: '203' abstract: - lang: eng text: Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses. article_processing_charge: No author: - first_name: Mohamad full_name: Abbas, Mohamad id: 47E8FC1C-F248-11E8-B48F-1D18A9856A87 last_name: Abbas - first_name: García J full_name: Hernández, García J last_name: Hernández - first_name: Stephan full_name: Pollmann, Stephan last_name: Pollmann - first_name: Sophia L full_name: Samodelov, Sophia L last_name: Samodelov - first_name: Martina full_name: Kolb, Martina last_name: Kolb - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ulrich Z full_name: Hammes, Ulrich Z last_name: Hammes - first_name: Matias D full_name: Zurbriggen, Matias D last_name: Zurbriggen - first_name: Miguel full_name: Blázquez, Miguel last_name: Blázquez - first_name: David full_name: Alabadí, David last_name: Alabadí citation: ama: Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115 apa: Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115 chicago: Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115. ieee: M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018. ista: Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869. mla: Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115. short: M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869. date_created: 2018-12-11T11:45:11Z date_published: 2018-06-26T00:00:00Z date_updated: 2023-09-08T13:24:40Z day: '26' department: - _id: JiFr doi: 10.1073/pnas.1806565115 ec_funded: 1 external_id: isi: - '000436245000096' intvolume: ' 115' isi: 1 issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: http://eprints.nottingham.ac.uk/52388/ month: '06' oa: 1 oa_version: None page: 6864-6869 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '7710' quality_controlled: '1' scopus_import: '1' status: public title: Auxin methylation is required for differential growth in Arabidopsis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '399' 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. 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). article_number: '10007' article_processing_charge: No article_type: original author: - first_name: Marcin M full_name: Napiórkowski, Marcin M id: 4197AD04-F248-11E8-B48F-1D18A9856A87 last_name: Napiórkowski - first_name: Robin full_name: Reuvers, Robin last_name: Reuvers - first_name: Jan full_name: Solovej, Jan last_name: Solovej 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. 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. 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. 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. short: M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018). date_created: 2018-12-11T11:46:15Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-08T13:30:51Z day: '01' department: - _id: RoSe doi: 10.1209/0295-5075/121/10007 external_id: arxiv: - '1706.01822' isi: - '000460003000003' intvolume: ' 121' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.01822 month: '01' oa: 1 oa_version: Preprint project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: EPL publication_status: published publisher: IOP Publishing Ltd. publist_id: '7432' quality_controlled: '1' scopus_import: '1' status: public title: Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 121 year: '2018' ... --- _id: '5830' abstract: - lang: eng text: CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants. article_processing_charge: No author: - first_name: Luosha full_name: Zhang, Luosha last_name: Zhang - first_name: Xiong full_name: Shi, Xiong last_name: Shi - first_name: Yutao full_name: Zhang, Yutao last_name: Zhang - first_name: Jiajing full_name: Wang, Jiajing last_name: Wang - first_name: Jingwei full_name: Yang, Jingwei last_name: Yang - first_name: Takashi full_name: Ishida, Takashi last_name: Ishida - first_name: Wenqian full_name: Jiang, Wenqian last_name: Jiang - first_name: Xiangyu full_name: Han, Xiangyu last_name: Han - first_name: Jingke full_name: Kang, Jingke last_name: Kang - first_name: Xuening full_name: Wang, Xuening last_name: Wang - first_name: Lixia full_name: Pan, Lixia last_name: Pan - first_name: Shuo full_name: Lv, Shuo last_name: Lv - first_name: Bing full_name: Cao, Bing last_name: Cao - first_name: Yonghong full_name: Zhang, Yonghong last_name: Zhang - first_name: Jinbin full_name: Wu, Jinbin last_name: Wu - first_name: Huibin full_name: Han, Huibin id: 31435098-F248-11E8-B48F-1D18A9856A87 last_name: Han - first_name: Zhubing full_name: Hu, Zhubing last_name: Hu - first_name: Langjun full_name: Cui, Langjun last_name: Cui - first_name: Shinichiro full_name: Sawa, Shinichiro last_name: Sawa - first_name: Junmin full_name: He, Junmin last_name: He - first_name: Guodong full_name: Wang, Guodong last_name: Wang citation: ama: Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475 apa: Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475 chicago: Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475. ieee: L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018. ista: Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. mla: Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475. short: L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018). date_created: 2019-01-13T22:59:11Z date_published: 2018-10-31T00:00:00Z date_updated: 2023-09-11T12:43:31Z day: '31' department: - _id: JiFr doi: 10.1111/pce.13475 external_id: isi: - '000459014800021' pmid: - '30378140' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30378140 month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Plant Cell and Environment publication_identifier: issn: - '01407791' publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '288' abstract: - lang: eng text: Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer. article_processing_charge: No article_type: original author: - first_name: Anna full_name: Lilja, Anna last_name: Lilja - first_name: Veronica full_name: Rodilla, Veronica last_name: Rodilla - first_name: Mathilde full_name: Huyghe, Mathilde last_name: Huyghe - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Camille full_name: Landragin, Camille last_name: Landragin - first_name: Olivier full_name: Renaud, Olivier last_name: Renaud - first_name: Olivier full_name: Leroy, Olivier last_name: Leroy - first_name: Steffen full_name: Rulands, Steffen last_name: Rulands - first_name: Benjamin full_name: Simons, Benjamin last_name: Simons - first_name: Silvia full_name: Fré, Silvia last_name: Fré citation: ama: Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687. doi:10.1038/s41556-018-0108-1 apa: Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1 chicago: Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1. ieee: A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018. ista: Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687. mla: Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1. short: A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687. date_created: 2018-12-11T11:45:38Z date_published: 2018-05-21T00:00:00Z date_updated: 2023-09-11T12:44:08Z day: '21' department: - _id: EdHa doi: 10.1038/s41556-018-0108-1 external_id: isi: - '000433237300003' pmid: - '29784917' intvolume: ' 20' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964 month: '05' oa: 1 oa_version: Submitted Version page: 677 - 687 pmid: 1 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '7594' quality_controlled: '1' scopus_import: '1' status: public title: Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 20 year: '2018' ... --- _id: '304' abstract: - lang: eng text: "Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods.\r\nAs a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications.\r\n \r\nIn this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process.\r\nThis requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure.\r\nMany of these components should be re-usable for the design of other optical structures at this scale.\r\n \r\nWe show initial results of material samples fabricated based on our designs.\r\nWhile these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications." acknowledgement: This work was in part supported by King Abdullah University of Science and Technology Baseline Funding. alternative_title: - ACM Transactions on Graphics article_number: '159' article_processing_charge: No author: - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Wolfgang full_name: Heidrich, Wolfgang last_name: Heidrich - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376 apa: Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201376 chicago: Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201376. ieee: T. Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural color for additive manufacturing,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018. ista: Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159. mla: Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4, 159, ACM, 2018, doi:10.1145/3197517.3201376. short: T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018). date_created: 2018-12-11T11:45:43Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-11T12:46:13Z day: '01' ddc: - '000' - '535' - '680' department: - _id: BeBi doi: 10.1145/3197517.3201376 ec_funded: 1 external_id: isi: - '000448185000120' file: - access_level: open_access checksum: dcdcc955a4c1c6d2599aeebb97d2e7b9 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:14Z date_updated: 2020-07-14T12:45:59Z file_id: '5334' file_name: IST-2018-1024-v1+1_NanoStructColor-Auzinger-paper.pdf file_size: 10751684 relation: main_file - access_level: open_access checksum: cae52b3a8d5e97be84771cd61ea2f75e content_type: application/pdf creator: system date_created: 2018-12-12T10:18:15Z date_updated: 2020-07-14T12:45:59Z file_id: '5335' file_name: IST-2018-1024-v1+2_NanoStructColor-Auzinger-supplemental.pdf file_size: 20755095 relation: main_file - access_level: open_access checksum: 76dd90648f75779d3f64e324b6daaffe content_type: image/jpeg creator: system date_created: 2018-12-12T10:18:16Z date_updated: 2020-07-14T12:45:59Z file_id: '5336' file_name: IST-2018-1024-v1+3_NanoStructColor-Auzinger-image.jpg file_size: 2186944 relation: main_file - access_level: open_access checksum: c3a5b775a0ecdb20ccefb8d9646ec140 content_type: application/x-7z-compressed creator: system date_created: 2018-12-12T10:18:17Z date_updated: 2020-07-14T12:45:59Z file_id: '5337' file_name: IST-2018-1024-v1+4_NanoStructColor-Auzinger-blueprint.7z file_size: 2734352 relation: main_file - access_level: open_access checksum: dcdcc955a4c1c6d2599aeebb97d2e7b9 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:18Z date_updated: 2020-07-14T12:45:59Z file_id: '5338' file_name: IST-2018-1024-v2+1_NanoStructColor-Auzinger-paper.pdf file_size: 10751684 relation: main_file - access_level: open_access checksum: 76dd90648f75779d3f64e324b6daaffe content_type: image/jpeg creator: system date_created: 2018-12-12T10:18:19Z date_updated: 2020-07-14T12:45:59Z file_id: '5339' file_name: IST-2018-1024-v2+3_NanoStructColor-Auzinger-image.jpg file_size: 2186944 relation: main_file - access_level: open_access checksum: c3a5b775a0ecdb20ccefb8d9646ec140 content_type: application/x-7z-compressed creator: system date_created: 2018-12-12T10:18:20Z date_updated: 2020-07-14T12:45:59Z file_id: '5340' file_name: IST-2018-1024-v2+4_NanoStructColor-Auzinger-blueprint.7z file_size: 2734352 relation: main_file - access_level: open_access checksum: 667e91b686db41e44d855a4fb2137402 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:21Z date_updated: 2020-07-14T12:45:59Z file_id: '5341' file_name: IST-2018-1024-v2+5_NanoStructColor-Auzinger-supplemental.pdf file_size: 20755762 relation: main_file - access_level: open_access checksum: dcdcc955a4c1c6d2599aeebb97d2e7b9 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:22Z date_updated: 2020-07-14T12:45:59Z file_id: '5342' file_name: IST-2018-1024-v3+1_NanoStructColor-Auzinger-paper.pdf file_size: 10751684 relation: main_file - access_level: open_access checksum: 76dd90648f75779d3f64e324b6daaffe content_type: image/jpeg creator: system date_created: 2018-12-12T10:18:22Z date_updated: 2020-07-14T12:45:59Z file_id: '5343' file_name: IST-2018-1024-v3+3_NanoStructColor-Auzinger-image.jpg file_size: 2186944 relation: main_file - access_level: open_access checksum: c3a5b775a0ecdb20ccefb8d9646ec140 content_type: application/x-7z-compressed creator: system date_created: 2018-12-12T10:18:23Z date_updated: 2020-07-14T12:45:59Z file_id: '5344' file_name: IST-2018-1024-v3+4_NanoStructColor-Auzinger-blueprint.7z file_size: 2734352 relation: main_file - access_level: open_access checksum: 667e91b686db41e44d855a4fb2137402 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:24Z date_updated: 2020-07-14T12:45:59Z file_id: '5345' file_name: IST-2018-1024-v3+5_NanoStructColor-Auzinger-supplemental.pdf file_size: 20755762 relation: main_file - access_level: open_access checksum: 72dce35388fb1aa7953df4d9ae3d02f1 content_type: application/vnd.openxmlformats-officedocument.presentationml.presentation creator: system date_created: 2018-12-12T10:18:25Z date_updated: 2020-07-14T12:45:59Z file_id: '5346' file_name: IST-2018-1024-v3+6_NanoStructColor-Auzinger-presentation.pptx file_size: 69698068 relation: main_file file_date_updated: 2020-07-14T12:45:59Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Transactions on Graphics publication_status: published publisher: ACM pubrep_id: '1028' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/color-effects-from-transparent-3d-printed-nanostructures/ scopus_import: '1' status: public title: Computational design of nanostructural color for additive manufacturing type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '12' abstract: - lang: eng text: Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects. article_number: '135' article_processing_charge: No author: - first_name: Kazutaka full_name: Nakashima, Kazutaka last_name: Nakashima - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Emmanuel full_name: Iarussi, Emmanuel id: 33F19F16-F248-11E8-B48F-1D18A9856A87 last_name: Iarussi - first_name: Ran full_name: Zhang, Ran id: 4DDBCEB0-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0002-3808-281X - first_name: Takeo full_name: Igarashi, Takeo last_name: Igarashi - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: 'Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341' apa: 'Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341' chicago: 'Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341.' ieee: 'K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018.' ista: 'Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.' mla: 'Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol. 37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341.' short: K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018). date_created: 2018-12-11T11:44:09Z date_published: 2018-08-04T00:00:00Z date_updated: 2023-09-11T12:48:09Z day: '04' ddc: - '004' - '516' - '670' department: - _id: BeBi doi: 10.1145/3197517.3201341 ec_funded: 1 external_id: isi: - '000448185000096' file: - access_level: open_access checksum: 6a5368bc86c4e1a9fcfe588fd1f14ee8 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:38Z date_updated: 2020-07-14T12:44:38Z file_id: '5360' file_name: IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf file_size: 104225664 relation: main_file - access_level: open_access checksum: 3861e693ba47c51f3ec7b7867d573a61 content_type: application/zip creator: system date_created: 2018-12-12T10:18:39Z date_updated: 2020-07-14T12:44:38Z file_id: '5361' file_name: IST-2018-1037-v1+2_CoreCavity-Supplemental.zip file_size: 377743553 relation: main_file - access_level: open_access checksum: 490040c685ed869536e2a18f5a906b94 content_type: video/vnd.objectvideo creator: system date_created: 2018-12-12T10:18:41Z date_updated: 2020-07-14T12:44:38Z file_id: '5362' file_name: IST-2018-1037-v1+3_CoreCavity-Video.mp4 file_size: 162634396 relation: main_file - access_level: open_access checksum: be7fc8b229adda727419b6504b3b9352 content_type: image/jpeg creator: system date_created: 2018-12-12T10:18:42Z date_updated: 2020-07-14T12:44:38Z file_id: '5363' file_name: IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg file_size: 527972 relation: main_file file_date_updated: 2020-07-14T12:44:38Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design publication: ACM Transaction on Graphics publication_status: published publisher: ACM publist_id: '8044' pubrep_id: '1037' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/ scopus_import: '1' status: public title: 'CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '454' abstract: - lang: eng text: Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games. acknowledgement: "This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson." article_number: '555' article_processing_charge: No author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: David full_name: Rand, David last_name: Rand - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02721-8 apa: Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., & Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02721-8 chicago: Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-017-02721-8. ieee: J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018. ista: Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555. mla: Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:10.1038/s41467-017-02721-8. short: J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018). date_created: 2018-12-11T11:46:34Z date_published: 2018-02-07T00:00:00Z date_updated: 2023-09-11T12:51:03Z day: '07' ddc: - '004' department: - _id: KrCh doi: 10.1038/s41467-017-02721-8 ec_funded: 1 external_id: isi: - '000424318200001' file: - access_level: open_access checksum: b6b90367545b4c615891c960ab0567f1 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:18Z date_updated: 2020-07-14T12:46:31Z file_id: '4741' file_name: IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf file_size: 843646 relation: main_file file_date_updated: 2020-07-14T12:46:31Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '7368' pubrep_id: '964' quality_controlled: '1' scopus_import: '1' status: public title: Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness 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: 9 year: '2018' ... --- _id: '320' abstract: - lang: eng text: 'Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. ' article_processing_charge: Yes (in subscription journal) author: - first_name: Hua full_name: Hu, Hua id: 4AC0145C-F248-11E8-B48F-1D18A9856A87 last_name: Hu - first_name: Fabian full_name: Roth, Fabian last_name: Roth - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 2018;98(1):156-165. doi:10.1016/j.neuron.2018.02.024 apa: Hu, H., Roth, F., Vandael, D. H., & Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.02.024 chicago: Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.02.024. ieee: H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” Neuron, vol. 98, no. 1. Elsevier, pp. 156–165, 2018. ista: Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165. mla: Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:10.1016/j.neuron.2018.02.024. short: H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165. date_created: 2018-12-11T11:45:48Z date_published: 2018-04-04T00:00:00Z date_updated: 2023-09-11T12:45:10Z day: '04' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuron.2018.02.024 ec_funded: 1 external_id: isi: - '000429192100016' file: - access_level: open_access checksum: 76070f3729f9c603e1080d0151aa2b11 content_type: application/pdf creator: dernst date_created: 2018-12-17T10:37:50Z date_updated: 2020-07-14T12:46:03Z file_id: '5690' file_name: 2018_Neuron_Hu.pdf file_size: 3180444 relation: main_file file_date_updated: 2020-07-14T12:46:03Z has_accepted_license: '1' intvolume: ' 98' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 156 - 165 project: - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize publication: Neuron publication_status: published publisher: Elsevier publist_id: '7545' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/ scopus_import: '1' status: public title: Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons 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: 98 year: '2018' ... --- _id: '423' abstract: - lang: eng text: Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity. acknowledgement: "We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions." article_number: e32035 article_processing_charge: No author: - first_name: Pavel full_name: Payne, Pavel id: 35F78294-F248-11E8-B48F-1D18A9856A87 last_name: Payne orcid: 0000-0002-2711-9453 - first_name: Lukas full_name: Geyrhofer, Lukas last_name: Geyrhofer - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035 apa: Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035 chicago: Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035. ieee: P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018. ista: Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035. mla: Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035. short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018). date_created: 2018-12-11T11:46:23Z date_published: 2018-03-09T00:00:00Z date_updated: 2023-09-11T12:49:17Z day: '09' ddc: - '576' department: - _id: NiBa - _id: JoBo doi: 10.7554/eLife.32035 ec_funded: 1 external_id: isi: - '000431035800001' file: - access_level: open_access checksum: 447cf6e680bdc3c01062a8737d876569 content_type: application/pdf creator: dernst date_created: 2018-12-17T10:36:07Z date_updated: 2020-07-14T12:46:25Z file_id: '5689' file_name: 2018_eLife_Payne.pdf file_size: 3533881 relation: main_file file_date_updated: 2020-07-14T12:46:25Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 2578D616-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '648440' name: Selective Barriers to Horizontal Gene Transfer publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '7400' quality_controlled: '1' related_material: record: - id: '9840' relation: research_data status: public scopus_import: '1' status: public title: CRISPR-based herd immunity can limit phage epidemics in bacterial populations 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: 7 year: '2018' ... --- _id: '5791' abstract: - lang: eng text: Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths. alternative_title: - LNCS article_processing_charge: No author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Csaba D. full_name: Tóth, Csaba D. last_name: Tóth citation: ama: 'Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16' apa: 'Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16' chicago: Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16. ieee: R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241. ista: Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241. mla: Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16. short: R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241. conference: end_date: 2018-09-28 location: Barcelona, Spain name: Graph Drawing and Network Visualization start_date: 2018-09-26 date_created: 2018-12-30T22:59:15Z date_published: 2018-12-18T00:00:00Z date_updated: 2023-09-11T12:49:55Z day: '18' department: - _id: UlWa doi: 10.1007/978-3-030-04414-5_16 external_id: arxiv: - '1808.07608' isi: - '000672802500016' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.07608 month: '12' oa: 1 oa_version: Preprint page: 229-241 publication_identifier: isbn: - '9783030044138' publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Crossing minimization in perturbed drawings type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: '11282 ' year: '2018' ... --- _id: '291' abstract: - lang: eng text: Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions. article_number: '054401' article_processing_charge: No author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 2018;3(5). doi:10.1103/PhysRevFluids.3.054401 apa: Budanur, N. B., & Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.054401 chicago: Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.054401. ieee: N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” Physical Review Fluids, vol. 3, no. 5. American Physical Society, 2018. ista: Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401. mla: Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.054401. short: N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018). date_created: 2018-12-11T11:45:39Z date_published: 2018-05-30T00:00:00Z date_updated: 2023-09-11T12:45:44Z day: '30' department: - _id: BjHo doi: 10.1103/PhysRevFluids.3.054401 external_id: arxiv: - '1802.01918' isi: - '000433426200001' intvolume: ' 3' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.01918 month: '05' oa: 1 oa_version: Preprint publication: Physical Review Fluids publication_status: published publisher: American Physical Society publist_id: '7590' quality_controlled: '1' scopus_import: '1' status: public title: Complexity of the laminar-turbulent boundary in pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 3 year: '2018' ... --- _id: '58' abstract: - lang: eng text: 'Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks.' article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Erel full_name: Segal Halevi, Erel last_name: Segal Halevi citation: ama: Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X apa: Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M110407X chicago: Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X. ieee: A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,” SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial and Applied Mathematics , pp. 2242–2257, 2018. ista: Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 32(3), 2242–2257. mla: Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X. short: A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018) 2242–2257. date_created: 2018-12-11T11:44:24Z date_published: 2018-09-06T00:00:00Z date_updated: 2023-09-11T12:48:39Z day: '06' department: - _id: HeEd doi: 10.1137/16M110407X ec_funded: 1 external_id: arxiv: - '1604.00960' isi: - '000450810500036' intvolume: ' 32' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.00960 month: '09' oa: 1 oa_version: Preprint page: 2242 - 2257 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: SIAM Journal on Discrete Mathematics publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '7996' quality_controlled: '1' scopus_import: '1' status: public title: Counting blanks in polygonal arrangements type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2018' ... --- _id: '9840' abstract: - lang: eng text: Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity. article_processing_charge: No author: - first_name: Pavel full_name: Payne, Pavel id: 35F78294-F248-11E8-B48F-1D18A9856A87 last_name: Payne orcid: 0000-0002-2711-9453 - first_name: Lukas full_name: Geyrhofer, Lukas last_name: Geyrhofer - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jonathan P full_name: Bollback, Jonathan P id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44' apa: 'Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44' chicago: 'Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44.' ieee: 'P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.' ista: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.' mla: 'Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.' short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018). date_created: 2021-08-09T13:10:02Z date_published: 2018-03-12T00:00:00Z date_updated: 2023-09-11T12:49:17Z day: '12' department: - _id: NiBa - _id: JoBo doi: 10.5061/dryad.42n44 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.42n44 month: '03' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '423' relation: used_in_publication status: public status: public title: 'Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '616' abstract: - lang: eng text: Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − "destructive disinfection" − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation. article_number: e32073 article_processing_charge: Yes author: - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Florian full_name: Wiesenhofer, Florian id: 39523C54-F248-11E8-B48F-1D18A9856A87 last_name: Wiesenhofer - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Thomas full_name: Schmitt, Thomas last_name: Schmitt - first_name: Mark full_name: Brown, Mark last_name: Brown - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 2018;7. doi:10.7554/eLife.32073 apa: Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt, T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073 chicago: Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse, Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073. ieee: C. Pull et al., “Destructive disinfection of infected brood prevents systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences Publications, 2018. ista: Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 7, e32073. mla: Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife Sciences Publications, 2018, doi:10.7554/eLife.32073. short: C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt, M. Brown, S. Cremer, ELife 7 (2018). date_created: 2018-12-11T11:47:31Z date_published: 2018-01-09T00:00:00Z date_updated: 2023-09-11T12:54:26Z day: '09' ddc: - '570' - '590' department: - _id: SyCr doi: 10.7554/eLife.32073 ec_funded: 1 external_id: isi: - '000419601300001' file: - access_level: open_access checksum: 540f941e8d3530a9441e4affd94f07d7 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:43Z date_updated: 2020-07-14T12:47:20Z file_id: '4832' file_name: IST-2018-978-v1+1_elife-32073-v1.pdf file_size: 1435585 relation: main_file file_date_updated: 2020-07-14T12:47:20Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' - _id: 25DDF0F0-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '302004' name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach' publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '7188' pubrep_id: '978' quality_controlled: '1' related_material: record: - id: '819' relation: dissertation_contains status: public scopus_import: '1' status: public title: Destructive disinfection of infected brood prevents systemic disease spread in ant colonies 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: 7 year: '2018' ... --- _id: '132' abstract: - lang: eng text: Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments. acknowledgement: E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support. article_processing_charge: No article_type: original author: - first_name: Magdalena full_name: Sznurkowska, Magdalena last_name: Sznurkowska - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Roberta full_name: Azzarelli, Roberta last_name: Azzarelli - first_name: Steffen full_name: Rulands, Steffen last_name: Rulands - first_name: Sonia full_name: Nestorowa, Sonia last_name: Nestorowa - first_name: Christopher full_name: Hindley, Christopher last_name: Hindley - first_name: Jennifer full_name: Nichols, Jennifer last_name: Nichols - first_name: Berthold full_name: Göttgens, Berthold last_name: Göttgens - first_name: Meritxell full_name: Huch, Meritxell last_name: Huch - first_name: Anna full_name: Philpott, Anna last_name: Philpott - first_name: Benjamin full_name: Simons, Benjamin last_name: Simons citation: ama: Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028 apa: Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028 chicago: Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028. ieee: M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018. ista: Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375. mla: Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028. short: M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375. date_created: 2018-12-11T11:44:48Z date_published: 2018-08-06T00:00:00Z date_updated: 2023-09-11T12:52:41Z day: '06' ddc: - '570' department: - _id: EdHa doi: 10.1016/j.devcel.2018.06.028 external_id: isi: - '000441327300012' file: - access_level: open_access checksum: 78d2062b9e3c3b90fe71545aeb6d2f65 content_type: application/pdf creator: dernst date_created: 2018-12-17T10:49:49Z date_updated: 2020-07-14T12:44:43Z file_id: '5694' file_name: 2018_DevelopmentalCell_Sznurkowska.pdf file_size: 8948384 relation: main_file file_date_updated: 2020-07-14T12:44:43Z has_accepted_license: '1' intvolume: ' 46' isi: 1 issue: '3' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 360 - 375 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '7791' quality_controlled: '1' scopus_import: '1' status: public title: Defining lineage potential and fate behavior of precursors during pancreas development 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: 46 year: '2018' ... --- _id: '42' abstract: - lang: eng text: Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield. acknowledgement: This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204). article_processing_charge: No author: - first_name: Mara full_name: Cucinotta, Mara last_name: Cucinotta - first_name: Silvia full_name: Manrique, Silvia last_name: Manrique - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Lucia full_name: Colombo, Lucia last_name: Colombo citation: ama: Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176. doi:10.1093/jxb/ery281 apa: Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery281 chicago: Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281. ieee: M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018. ista: Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176. mla: Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281. short: M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176. date_created: 2018-12-11T11:44:19Z date_published: 2018-07-26T00:00:00Z date_updated: 2023-09-11T12:52:03Z day: '26' ddc: - '575' department: - _id: EvBe doi: 10.1093/jxb/ery281 external_id: isi: - '000448163900015' file: - access_level: open_access checksum: ca3b6711040b1662488aeb3d1f961f13 content_type: application/pdf creator: dernst date_created: 2018-12-17T10:44:16Z date_updated: 2020-07-14T12:46:25Z file_id: '5691' file_name: 2018_JournalExperimBotany_Cucinotta.pdf file_size: 1292128 relation: main_file file_date_updated: 2020-07-14T12:46:25Z has_accepted_license: '1' intvolume: ' 69' isi: 1 issue: '21' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 5169 - 5176 publication: Journal of Experimental Botany publication_status: published publisher: Oxford University Press publist_id: '8012' quality_controlled: '1' scopus_import: '1' status: public title: Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis 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: 69 year: '2018' ... --- _id: '407' abstract: - lang: eng text: Isoprenoid cytokinins play a number of crucial roles in the regulation of plant growth and development. To study cytokinin receptor properties in plants, we designed and prepared fluorescent derivatives of 6-[(3-methylbut-2-en-1-yl)amino]purine (N6-isopentenyladenine, iP) with several fluorescent labels attached to the C2 or N9 atom of the purine moiety via a 2- or 6-carbon linker. The fluorescent labels included dansyl (DS), fluorescein (FC), 7-nitrobenzofurazan (NBD), rhodamine B (RhoB), coumarin (Cou), 7-(diethylamino)coumarin (DEAC) and cyanine 5 dye (Cy5). All prepared compounds were screened for affinity for the Arabidopsis thaliana cytokinin receptor (CRE1/AHK4). Although the attachment of the fluorescent labels to iP via the linkers mostly disrupted binding to the receptor, several fluorescent derivatives interacted well. For this reason, three derivatives, two rhodamine B and one 4-chloro-7-nitrobenzofurazan labeled iP were tested for their interaction with CRE1/AHK4 and Zea mays cytokinin receptors in detail. We further showed that the three derivatives were able to activate transcription of cytokinin response regulator ARR5 in Arabidopsis seedlings. The activity of fluorescently labeled cytokinins was compared with corresponding 6-dimethylaminopurine fluorescently labeled negative controls. Selected rhodamine B C2-labeled compounds 17, 18 and 4-chloro-7-nitrobenzofurazan N9-labeled compound 28 and their respective negative controls (19, 20 and 29, respectively) were used for in planta staining experiments in Arabidopsis thaliana cell suspension culture using live cell confocal microscopy. acknowledgement: "This work was supported by the Ministry of Education Youth and Sports, Czech Republic (grant LO1204 from the National Program of Sustainability I and Agricultural Research ) and by Czech Science Foundation grants 16-04184S , 501/10/1450 and 13-39982S and by IGA projects IGA_PrF_2018_033 and IGA_PrF_2018_023 . We would like to thank Jarmila Balonová, Olga Hustáková and Miroslava Šubová for their skillful technical assistance and Mgr. Tomáš Pospíšil, Ph.D. for his measurement of 1 H NMR and analysis of some 2D NMR spectral data. \r\n" article_processing_charge: No author: - first_name: Karolina full_name: Kubiasová, Karolina last_name: Kubiasová - first_name: Václav full_name: Mik, Václav last_name: Mik - first_name: Jaroslav full_name: Nisler, Jaroslav last_name: Nisler - first_name: Martin full_name: Hönig, Martin last_name: Hönig - first_name: Alexandra full_name: Husičková, Alexandra last_name: Husičková - first_name: Lukáš full_name: Spíchal, Lukáš last_name: Spíchal - first_name: Zuzana full_name: Pěkná, Zuzana last_name: Pěkná - first_name: Olga full_name: Šamajová, Olga last_name: Šamajová - first_name: Karel full_name: Doležal, Karel last_name: Doležal - first_name: Ondřej full_name: Plíhal, Ondřej last_name: Plíhal - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Lucie full_name: Plíhalová, Lucie last_name: Plíhalová citation: ama: Kubiasová K, Mik V, Nisler J, et al. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 2018;150:1-11. doi:10.1016/j.phytochem.2018.02.015 apa: Kubiasová, K., Mik, V., Nisler, J., Hönig, M., Husičková, A., Spíchal, L., … Plíhalová, L. (2018). Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. Elsevier. https://doi.org/10.1016/j.phytochem.2018.02.015 chicago: Kubiasová, Karolina, Václav Mik, Jaroslav Nisler, Martin Hönig, Alexandra Husičková, Lukáš Spíchal, Zuzana Pěkná, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry. Elsevier, 2018. https://doi.org/10.1016/j.phytochem.2018.02.015. ieee: K. Kubiasová et al., “Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins,” Phytochemistry, vol. 150. Elsevier, pp. 1–11, 2018. ista: Kubiasová K, Mik V, Nisler J, Hönig M, Husičková A, Spíchal L, Pěkná Z, Šamajová O, Doležal K, Plíhal O, Benková E, Strnad M, Plíhalová L. 2018. Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins. Phytochemistry. 150, 1–11. mla: Kubiasová, Karolina, et al. “Design, Synthesis and Perception of Fluorescently Labeled Isoprenoid Cytokinins.” Phytochemistry, vol. 150, Elsevier, 2018, pp. 1–11, doi:10.1016/j.phytochem.2018.02.015. short: K. Kubiasová, V. Mik, J. Nisler, M. Hönig, A. Husičková, L. Spíchal, Z. Pěkná, O. Šamajová, K. Doležal, O. Plíhal, E. Benková, M. Strnad, L. Plíhalová, Phytochemistry 150 (2018) 1–11. date_created: 2018-12-11T11:46:18Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-11T12:53:11Z day: '01' department: - _id: EvBe doi: 10.1016/j.phytochem.2018.02.015 external_id: isi: - '000435623400001' intvolume: ' 150' isi: 1 language: - iso: eng month: '06' oa_version: None page: 1-11 publication: Phytochemistry publication_status: published publisher: Elsevier publist_id: '7422' quality_controlled: '1' scopus_import: '1' status: public title: Design, synthesis and perception of fluorescently labeled isoprenoid cytokinins type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 150 year: '2018' ... --- _id: '46' abstract: - lang: eng text: We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase. acknowledgement: F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award. article_number: '161122' article_processing_charge: No article_type: original author: - first_name: Daniel full_name: Hetterich, Daniel last_name: Hetterich - first_name: Norman full_name: Yao, Norman last_name: Yao - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Frank full_name: Pollmann, Frank last_name: Pollmann - first_name: Björn full_name: Trauzettel, Björn last_name: Trauzettel citation: ama: Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. Physical Review B. 2018;98(16). doi:10.1103/PhysRevB.98.161122 apa: Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., & Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.161122 chicago: Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.161122. ieee: D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” Physical Review B, vol. 98, no. 16. American Physical Society, 2018. ista: Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122. mla: Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:10.1103/PhysRevB.98.161122. short: D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018). date_created: 2018-12-11T11:44:20Z date_published: 2018-10-15T00:00:00Z date_updated: 2023-09-11T12:55:03Z day: '15' department: - _id: MaSe doi: 10.1103/PhysRevB.98.161122 external_id: arxiv: - '1806.08316' isi: - '000448596500002' intvolume: ' 98' isi: 1 issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.08316 month: '10' oa: 1 oa_version: Preprint publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '8008' quality_controlled: '1' scopus_import: '1' status: public title: Detection and characterization of many-body localization in central spin models type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 98 year: '2018' ... --- _id: '308' abstract: - lang: eng text: Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo. acknowledged_ssus: - _id: SSU article_processing_charge: No article_type: original author: - first_name: Aparna full_name: Ratheesh, Aparna id: 2F064CFE-F248-11E8-B48F-1D18A9856A87 last_name: Ratheesh orcid: 0000-0001-7190-0776 - first_name: Julia full_name: Biebl, Julia id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87 last_name: Biebl - first_name: Michael full_name: Smutny, Michael last_name: Smutny - first_name: Jana full_name: Veselá, Jana id: 433253EE-F248-11E8-B48F-1D18A9856A87 last_name: Veselá - first_name: Ekaterina full_name: Papusheva, Ekaterina id: 41DB591E-F248-11E8-B48F-1D18A9856A87 last_name: Papusheva - first_name: Gabriel full_name: Krens, Gabriel id: 2B819732-F248-11E8-B48F-1D18A9856A87 last_name: Krens orcid: 0000-0003-4761-5996 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Attila full_name: György, Attila id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87 last_name: György orcid: 0000-0002-1819-198X - first_name: Alessandra M full_name: Casano, Alessandra M id: 3DBA3F4E-F248-11E8-B48F-1D18A9856A87 last_name: Casano orcid: 0000-0002-6009-6804 - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 citation: ama: Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002 apa: Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002 chicago: Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002. ieee: A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018. ista: Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346. mla: Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002. short: A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346. date_created: 2018-12-11T11:45:44Z date_published: 2018-05-07T00:00:00Z date_updated: 2023-09-11T13:22:13Z day: '07' department: - _id: DaSi - _id: CaHe - _id: Bio - _id: EM-Fac - _id: MiSi doi: 10.1016/j.devcel.2018.04.002 ec_funded: 1 external_id: isi: - '000432461400009' pmid: - '29738712' intvolume: ' 45' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2018.04.002 month: '05' oa: 1 oa_version: Published Version page: 331 - 346 pmid: 1 project: - _id: 253B6E48-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29638 name: Drosophila TNFa´s Funktion in Immunzellen - _id: 2536F660-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '334077' name: Investigating the role of transporters in invasive migration through junctions publication: Developmental Cell publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/ scopus_import: '1' status: public title: Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 45 year: '2018' ... --- _id: '17' abstract: - lang: eng text: Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow. article_number: '103302 ' article_processing_charge: No author: - first_name: Atul full_name: Varshney, Atul id: 2A2006B2-F248-11E8-B48F-1D18A9856A87 last_name: Varshney orcid: 0000-0002-3072-5999 - first_name: Victor full_name: Steinberg, Victor last_name: Steinberg citation: ama: Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302 apa: Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103302 chicago: Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103302. ieee: A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018. ista: Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302. mla: Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302. short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018). date_created: 2018-12-11T11:44:11Z date_published: 2018-10-15T00:00:00Z date_updated: 2023-09-11T12:59:28Z day: '15' ddc: - '532' department: - _id: BjHo doi: 10.1103/PhysRevFluids.3.103302 ec_funded: 1 external_id: isi: - '000447311500001' file: - access_level: open_access checksum: e1445be33e8165114e96246275600750 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:14Z date_updated: 2020-07-14T12:45:12Z file_id: '4800' file_name: IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf file_size: 1409040 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 3' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Fluids publication_status: published publisher: American Physical Society publist_id: '8038' pubrep_id: '1061' quality_controlled: '1' scopus_import: '1' status: public title: Drag enhancement and drag reduction in viscoelastic flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 3 year: '2018' ... --- _id: '281' abstract: - lang: eng text: 'Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.' acknowledgement: This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.). article_processing_charge: No article_type: original author: - first_name: Alejandro full_name: Granados, Alejandro last_name: Granados - first_name: Julian full_name: Pietsch, Julian last_name: Pietsch - first_name: Sarah A full_name: Cepeda Humerez, Sarah A id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87 last_name: Cepeda Humerez - first_name: Isebail full_name: Farquhar, Isebail last_name: Farquhar - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Peter full_name: Swain, Peter last_name: Swain citation: ama: Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115 apa: Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115 chicago: Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115. ieee: A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018. ista: Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093. mla: Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115. short: A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093. date_created: 2018-12-11T11:45:35Z date_published: 2018-06-05T00:00:00Z date_updated: 2023-09-11T12:58:24Z day: '05' department: - _id: GaTk doi: 10.1073/pnas.1716659115 external_id: isi: - '000434114900071' pmid: - '29784812' intvolume: ' 115' isi: 1 issue: '23' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/early/2017/09/21/192039 month: '06' oa: 1 oa_version: Preprint page: 6088 - 6093 pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '7618' quality_controlled: '1' related_material: record: - id: '6473' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Distributed and dynamic intracellular organization of extracellular information type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '620' abstract: - lang: eng text: Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis. article_number: jcs207696 article_processing_charge: No author: - first_name: Wataru full_name: Yamamoto, Wataru last_name: Yamamoto - first_name: Suguru full_name: Wada, Suguru last_name: Wada - first_name: Makoto full_name: Nagano, Makoto last_name: Nagano - first_name: Kaito full_name: Aoshima, Kaito last_name: Aoshima - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Junko full_name: Toshima, Junko last_name: Toshima - first_name: Jiro full_name: Toshima, Jiro last_name: Toshima citation: ama: Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696 apa: Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696 chicago: Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696. ieee: W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018. ista: Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696. mla: Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696. short: W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018). date_created: 2018-12-11T11:47:32Z date_published: 2018-01-04T00:00:00Z date_updated: 2023-09-11T12:57:13Z day: '04' department: - _id: DaSi doi: 10.1242/jcs.207696 external_id: isi: - '000424786900012' pmid: - '29192062' intvolume: ' 131' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/29192062 month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '7184' quality_controlled: '1' scopus_import: '1' status: public title: Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 131 year: '2018' ... --- _id: '182' abstract: - lang: eng text: We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice. alternative_title: - HSCC Proceedings article_processing_charge: No author: - first_name: Alexey full_name: Bakhirkin, Alexey last_name: Bakhirkin - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Oded full_name: Maler, Oded last_name: Maler citation: ama: 'Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: Proceedings of the 21st International Conference on Hybrid Systems. ACM; 2018:177-186. doi:10.1145/3178126.3178132' apa: 'Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification for STL. In Proceedings of the 21st International Conference on Hybrid Systems (pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132' chicago: Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In Proceedings of the 21st International Conference on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132. ieee: A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in Proceedings of the 21st International Conference on Hybrid Systems, Porto, Portugal, 2018, pp. 177–186. ista: 'Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186.' mla: Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86, doi:10.1145/3178126.3178132. short: A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186. conference: end_date: 2018-04-13 location: Porto, Portugal name: 'HSCC: Hybrid Systems: Computation and Control' start_date: 2018-04-11 date_created: 2018-12-11T11:45:04Z date_published: 2018-04-11T00:00:00Z date_updated: 2023-09-11T13:30:51Z day: '11' ddc: - '000' department: - _id: ToHe doi: 10.1145/3178126.3178132 external_id: isi: - '000474781600020' file: - access_level: open_access checksum: 81eabc96430e84336ea88310ac0a1ad0 content_type: application/pdf creator: dernst date_created: 2020-05-14T12:18:29Z date_updated: 2020-07-14T12:45:17Z file_id: '7833' file_name: 2018_HSCC_Bakhirkin.pdf file_size: 5900421 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 177 - 186 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the 21st International Conference on Hybrid Systems publication_identifier: isbn: - '978-1-4503-5642-8 ' publication_status: published publisher: ACM publist_id: '7739' quality_controlled: '1' scopus_import: '1' status: public title: Efficient parametric identification for STL type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '143' abstract: - lang: eng text: 'Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis.' alternative_title: - ACM/IEEE Symposium on Logic in Computer Science article_processing_charge: No author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny - first_name: Dominik full_name: Velan, Dominik last_name: Velan - first_name: Florian full_name: Zuleger, Florian last_name: Zuleger citation: ama: 'Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:10.1145/3209108.3209191' apa: 'Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191' chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191. ieee: 'T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.' ista: 'Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.' mla: Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191. short: T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194. conference: end_date: 2018-07-12 location: Oxford, United Kingdom name: 'LICS: Logic in Computer Science' start_date: 2018-07-09 date_created: 2018-12-11T11:44:51Z date_published: 2018-07-09T00:00:00Z date_updated: 2023-09-11T13:23:42Z day: '09' department: - _id: KrCh doi: 10.1145/3209108.3209191 ec_funded: 1 external_id: isi: - '000545262800020' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.10985 month: '07' oa: 1 oa_version: Preprint page: 185 - 194 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_identifier: isbn: - 978-1-4503-5583-4 publication_status: published publisher: IEEE publist_id: '7780' quality_controlled: '1' scopus_import: '1' status: public title: Efficient algorithms for asymptotic bounds on termination time in VASS type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: F138033 year: '2018' ... --- _id: '273' abstract: - lang: eng text: The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time. article_processing_charge: No author: - first_name: Pritish full_name: Mohapatra, Pritish last_name: Mohapatra - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek - first_name: C V full_name: Jawahar, C V last_name: Jawahar - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: M Pawan full_name: Kumar, M Pawan last_name: Kumar citation: ama: 'Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389' apa: 'Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389' chicago: Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389. ieee: P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp. 3693–3701. ista: 'Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.' mla: Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389. short: P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701. conference: end_date: 2018-06-22 location: Salt Lake City, UT, USA name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2018-06-18 date_created: 2018-12-11T11:45:33Z date_published: 2018-06-28T00:00:00Z date_updated: 2023-09-11T13:24:43Z day: '28' department: - _id: VlKo doi: 10.1109/cvpr.2018.00389 ec_funded: 1 external_id: arxiv: - '1604.08269' isi: - '000457843603087' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1604.08269 month: '06' oa: 1 oa_version: Preprint page: 3693-3701 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition publication_identifier: isbn: - '9781538664209' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Efficient optimization for rank-based loss functions type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '289' abstract: - lang: eng text: We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry. acknowledgement: The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256. article_number: '167601' article_processing_charge: No article_type: original author: - first_name: Alexander full_name: Zibrov, Alexander last_name: Zibrov - first_name: Rao full_name: Peng, Rao id: 47C23AC6-02D0-11E9-BD0E-99399A5D3DEB last_name: Peng orcid: 0000-0003-1250-0021 - first_name: Carlos full_name: Kometter, Carlos last_name: Kometter - first_name: Jia full_name: Li, Jia last_name: Li - first_name: Cory full_name: Dean, Cory last_name: Dean - first_name: Takashi full_name: Taniguchi, Takashi last_name: Taniguchi - first_name: Kenji full_name: Watanabe, Kenji last_name: Watanabe - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Andrea full_name: Young, Andrea last_name: Young citation: ama: Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.167601 apa: Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.167601 chicago: Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.167601. ieee: A. Zibrov et al., “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018. ista: Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601. mla: Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.167601. short: A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018). date_created: 2018-12-11T11:45:38Z date_published: 2018-10-19T00:00:00Z date_updated: 2023-09-11T13:39:50Z day: '19' department: - _id: MaSe doi: 10.1103/PhysRevLett.121.167601 external_id: arxiv: - '1805.01038' isi: - '000447307500007' intvolume: ' 121' isi: 1 issue: '16' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.01038 month: '10' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 121 year: '2018' ... --- _id: '287' abstract: - lang: eng text: In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy. acknowledgement: The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22. article_processing_charge: No author: - first_name: Vahid full_name: Salari, Vahid last_name: Salari - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Michal full_name: Cifra, Michal last_name: Cifra - first_name: Christoph full_name: Simon, Christoph last_name: Simon - first_name: Felix full_name: Scholkmann, Felix last_name: Scholkmann - first_name: Zahra full_name: Alirezaei, Zahra last_name: Alirezaei - first_name: Jack full_name: Tuszynski, Jack last_name: Tuszynski citation: ama: Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 2018;23(8):1391-1406. doi:10.2741/4651 apa: Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers in Bioscience. https://doi.org/10.2741/4651 chicago: Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark. Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651. ieee: V. Salari et al., “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018. ista: Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406. mla: Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651. short: V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406. date_created: 2018-12-11T11:45:37Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-11T13:38:14Z day: '01' department: - _id: JoFi doi: 10.2741/4651 ec_funded: 1 external_id: isi: - '000439042800001' pmid: - '29293441' intvolume: ' 23' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.bioscience.org/2018/v23/af/4651/fulltext.htm month: '03' oa: 1 oa_version: Submitted Version page: 1391 - 1406 pmid: 1 project: - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM' publication: Frontiers in Bioscience - Landmark publication_status: published publisher: Frontiers in Bioscience quality_controlled: '1' scopus_import: '1' status: public title: Electromagnetic fields and optomechanics In cancer diagnostics and treatment type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 23 year: '2018' ... --- _id: '425' abstract: - lang: eng text: 'We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \ X with length bounded by a computable function of the number of tetrahedra of X.' article_number: '5' article_processing_charge: No article_type: original author: - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Eric full_name: Sedgwick, Eric last_name: Sedgwick - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632 apa: Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632 chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632. ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018. ista: Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5. mla: Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632. short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018). date_created: 2018-12-11T11:46:24Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-11T13:38:49Z day: '01' department: - _id: UlWa doi: 10.1145/3078632 ec_funded: 1 external_id: arxiv: - '1402.0815' isi: - '000425685900006' intvolume: ' 65' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1402.0815 month: '01' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '7398' quality_controlled: '1' related_material: record: - id: '2157' relation: earlier_version status: public scopus_import: '1' status: public title: Embeddability in the 3-Sphere is decidable type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 65 year: '2018' ... --- _id: '564' abstract: - lang: eng text: "Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population." article_processing_charge: No article_type: original author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007 apa: Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007 chicago: Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007. ieee: N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018. ista: Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127. mla: Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007. short: N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127. date_created: 2018-12-11T11:47:12Z date_published: 2018-07-01T00:00:00Z date_updated: 2023-09-11T13:41:22Z day: '01' ddc: - '519' - '576' department: - _id: NiBa doi: 10.1016/j.tpb.2017.11.007 ec_funded: 1 external_id: isi: - '000440392900014' file: - access_level: open_access checksum: 0b96f6db47e3e91b5e7d103b847c239d content_type: application/pdf creator: nbarton date_created: 2019-12-21T09:36:39Z date_updated: 2020-07-14T12:47:09Z file_id: '7199' file_name: bartonetheridge.pdf file_size: 2287682 relation: main_file file_date_updated: 2020-07-14T12:47:09Z has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '7' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '07' oa: 1 oa_version: Submitted Version page: 110-127 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Theoretical Population Biology publication_status: published publisher: Academic Press publist_id: '7250' quality_controlled: '1' related_material: record: - id: '9842' relation: research_data status: public scopus_import: '1' status: public title: Establishment in a new habitat by polygenic adaptation tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 122 year: '2018' ...