--- _id: '11870' abstract: - lang: eng text: "We consider dynamic algorithms for maintaining Single-Source Reachability (SSR) and approximate Single-Source Shortest Paths (SSSP) on n-node m-edge directed graphs under edge deletions (decremental algorithms). The previous fastest algorithm for SSR and SSSP goes back three decades to Even and Shiloach (JACM 1981); it has O(1) query time and O(mn) total update time (i.e., linear amortized update time if all edges are deleted). This algorithm serves as a building block for several other dynamic algorithms. The question whether its total update time can be improved is a major, long standing, open problem.\r\n\r\nIn this paper, we answer this question affirmatively. We obtain a randomized algorithm which, in a simplified form, achieves an Õ(mn0.984) expected total update time for SSR and (1 + ε)-approximate SSSP, where Õ(·) hides poly log n. We also extend our algorithm to achieve roughly the same running time for Strongly Connected Components (SCC), improving the algorithm of Roditty and Zwick (FOCS 2002), and an algorithm that improves the Õ (mn log W)-time algorithm of Bernstein (STOC 2013) for approximating SSSP on weighted directed graphs, where the edge weights are integers from 1 to W. All our algorithms have constant query time in the worst case." article_number: 674 - 683 article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In: 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2014. doi:10.1145/2591796.2591869' apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In 46th Annual ACM Symposium on Theory of Computing. New York, NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2591796.2591869' chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” In 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2014. https://doi.org/10.1145/2591796.2591869. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs,” in 46th Annual ACM Symposium on Theory of Computing, New York, NY, United States, 2014. ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. 46th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 674–683.' mla: Henzinger, Monika H., et al. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” 46th Annual ACM Symposium on Theory of Computing, 674–683, Association for Computing Machinery, 2014, doi:10.1145/2591796.2591869. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 46th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2014. conference: end_date: 2014-06-03 location: New York, NY, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2014-05-31 date_created: 2022-08-16T09:41:57Z date_published: 2014-05-01T00:00:00Z date_updated: 2023-02-17T11:18:52Z day: '01' doi: 10.1145/2591796.2591869 extern: '1' external_id: arxiv: - '1504.07959' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.07959 month: '05' oa: 1 oa_version: Preprint publication: 46th Annual ACM Symposium on Theory of Computing publication_identifier: isbn: - 978-145032710-7 issn: - 0737-8017 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '11876' abstract: - lang: eng text: "We study dynamic (1 + ∊)-approximation algorithms for the single-source shortest paths problem in an unweighted undirected n-node m-edge graph under edge deletions. The fastest algorithm for this problem is an algorithm with O(n2+o(1)) total update time and constant query time by Bernstein and Roditty (SODA 2011). In this paper, we improve the total update time to O(n1.8+o(1) + m1+o(1)) while keeping the query time constant. This running time is essentially tight when m = Ω(n1.8) since we need Ω(m) time even in the static setting. For smaller values of m, the running time of our algorithm is subquadratic, and is the first that breaks through the quadratic time barrier.\r\n\r\nIn obtaining this result, we develop a fast algorithm for what we call center cover data structure. We also make non-trivial extensions to our previous techniques called lazy-update and monotone Even-Shiloach trees (ICALP 2013 and FOCS 2013). As by-products of our new techniques, we obtain two new results for the decremental all-pairs shortest-paths problem. Our first result is the first approximation algorithm whose total update time is faster than Õ(mn) for all values of m. Our second result is a new trade-off between the total update time and the additive approximation guarantee." article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Henzinger MH, Krinninger S, Nanongkai D. A subquadratic-time algorithm for decremental single-source shortest paths. In: 25th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:1053-1072. doi:10.1137/1.9781611973402.79' apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). A subquadratic-time algorithm for decremental single-source shortest paths. In 25th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1053–1072). Portland, OR, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973402.79' chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” In 25th Annual ACM-SIAM Symposium on Discrete Algorithms, 1053–72. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973402.79. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A subquadratic-time algorithm for decremental single-source shortest paths,” in 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Portland, OR, United States, 2014, pp. 1053–1072. ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. A subquadratic-time algorithm for decremental single-source shortest paths. 25th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1053–1072.' mla: Henzinger, Monika H., et al. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–72, doi:10.1137/1.9781611973402.79. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–1072. conference: end_date: 2014-01-07 location: Portland, OR, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2014-01-05 date_created: 2022-08-16T12:58:31Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-17T11:58:42Z day: '01' doi: 10.1137/1.9781611973402.79 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1137/1.9781611973402.79 month: '01' oa: 1 oa_version: Published Version page: 1053-1072 publication: 25th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-1-61197-340-2 isbn: - 978-1-61197-338-9 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: A subquadratic-time algorithm for decremental single-source shortest paths type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '11875' abstract: - lang: eng text: We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph in time per update. In particular, for minimum vertex cover we provide deterministic data structures for maintaining a (2 + ε) approximation in O(log n/ε2) amortized time per update. For maximum matching, we show how to maintain a (3 + e) approximation in O(m1/3/ε2) amortized time per update, and a (4 + ε) approximation in O(m1/3/ε2) worst-case time per update. Our data structure for fully dynamic minimum vertex cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld [13]. article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Giuseppe F. full_name: Italiano, Giuseppe F. last_name: Italiano citation: ama: 'Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. In: 26th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:785-804. doi:10.1137/1.9781611973730.54' apa: 'Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2014). Deterministic fully dynamic data structures for vertex cover and matching. In 26th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 785–804). San Diego, CA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973730.54' chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” In 26th Annual ACM-SIAM Symposium on Discrete Algorithms, 785–804. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973730.54. ieee: S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” in 26th Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2014, pp. 785–804. ista: 'Bhattacharya S, Henzinger MH, Italiano GF. 2014. Deterministic fully dynamic data structures for vertex cover and matching. 26th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 785–804.' mla: Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804, doi:10.1137/1.9781611973730.54. short: S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804. conference: end_date: 2015-01-06 location: San Diego, CA, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2015-01-04 date_created: 2022-08-16T12:36:42Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-21T16:32:06Z day: '01' doi: 10.1137/1.9781611973730.54 extern: '1' external_id: arxiv: - '1412.1318' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.1318 month: '01' oa: 1 oa_version: Preprint page: 785-804 publication: 26th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-1-61197-373-0 isbn: - 978-1-61197-374-7 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '11890' relation: later_version status: public scopus_import: '1' status: public title: Deterministic fully dynamic data structures for vertex cover and matching type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '119' abstract: - lang: eng text: Observations of flowing granular matter have suggested that same-material tribocharging depends on particle size, typically rendering large grains positive and small ones negative. Models assuming the transfer of trapped electrons can account for this trend, but have not been validated. Tracking individual grains in an electric field, we show quantitatively that charge is transferred based on size between materially identical grains. However, the surface density of trapped electrons, measured independently by thermoluminescence techniques, is orders of magnitude too small to account for the scale of charge transferred. This reveals that trapped electrons are not a necessary ingredient for same-material tribocharging. acknowledgement: This work was supported by the NSF through DMR-1309611. Access to the shared experimental facilities provided by the NSF-supported Chicago MRSEC (DMR-0820054) is gratefully acknowledged. S. L. F. and J. L. P. acknowledge funding from UIC NSF Grants No. 0850830 and No. 0602308. S. R. W. acknowledges support from a University of Chicago Millikan Fellowship and from Mrs. Joan Winstein through the Winstein Prize for Instrumentation. article_number: '218001' author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Victor full_name: Lee, Victor last_name: Lee - first_name: James full_name: Pierson, James last_name: Pierson - first_name: Steven full_name: Forman, Steven last_name: Forman - first_name: Heinrich full_name: Jaeger, Heinrich last_name: Jaeger citation: ama: Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 2014;112(21). doi:10.1103/PhysRevLett.112.218001 apa: Waitukaitis, S. R., Lee, V., Pierson, J., Forman, S., & Jaeger, H. (2014). Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.218001 chicago: Waitukaitis, Scott R, Victor Lee, James Pierson, Steven Forman, and Heinrich Jaeger. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.218001. ieee: S. R. Waitukaitis, V. Lee, J. Pierson, S. Forman, and H. Jaeger, “Size-dependent same-material tribocharging in insulating grains,” APS Physics, Physical Review Letters, vol. 112, no. 21. American Physical Society, 2014. ista: Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. 2014. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 112(21), 218001. mla: Waitukaitis, Scott R., et al. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters, vol. 112, no. 21, 218001, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.218001. short: S.R. Waitukaitis, V. Lee, J. Pierson, S. Forman, H. Jaeger, APS Physics, Physical Review Letters 112 (2014). date_created: 2018-12-11T11:44:44Z date_published: 2014-05-30T00:00:00Z date_updated: 2021-01-12T06:48:58Z day: '30' doi: 10.1103/PhysRevLett.112.218001 extern: '1' external_id: arxiv: - '1309.2578' intvolume: ' 112' issue: '21' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1309.2578 month: '05' oa: 1 oa_version: Submitted Version publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7935' quality_controlled: '1' status: public title: Size-dependent same-material tribocharging in insulating grains type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2014' ... --- _id: '11968' abstract: - lang: eng text: 'Membrane phospholipids typically contain fatty acids (FAs) of 16 and 18 carbon atoms. This particular chain length is evolutionarily highly conserved and presumably provides maximum stability and dynamic properties to biological membranes in response to nutritional or environmental cues. Here, we show that the relative proportion of C16 versus C18 FAs is regulated by the activity of acetyl-CoA carboxylase (Acc1), the first and rate-limiting enzyme of FA de novo synthesis. Acc1 activity is attenuated by AMPK/Snf1-dependent phosphorylation, which is required to maintain an appropriate acyl-chain length distribution. Moreover, we find that the transcriptional repressor Opi1 preferentially binds to C16 over C18 phosphatidic acid (PA) species: thus, C16-chain containing PA sequesters Opi1 more effectively to the ER, enabling AMPK/Snf1 control of PA acyl-chain length to determine the degree of derepression of Opi1 target genes. These findings reveal an unexpected regulatory link between the major energy-sensing kinase, membrane lipid composition, and transcription.' article_processing_charge: No article_type: original author: - first_name: Harald F. full_name: Hofbauer, Harald F. last_name: Hofbauer - first_name: Florian H. full_name: Schopf, Florian H. last_name: Schopf - first_name: Hannes full_name: Schleifer, Hannes last_name: Schleifer - first_name: Oskar L. full_name: Knittelfelder, Oskar L. last_name: Knittelfelder - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Gerald N. full_name: Rechberger, Gerald N. last_name: Rechberger - first_name: Heimo full_name: Wolinski, Heimo last_name: Wolinski - first_name: Maria L. full_name: Gaspar, Maria L. last_name: Gaspar - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe - first_name: Johannes full_name: Stadlmann, Johannes last_name: Stadlmann - first_name: Karl full_name: Mechtler, Karl last_name: Mechtler - first_name: Alexandra full_name: Zenz, Alexandra last_name: Zenz - first_name: Karl full_name: Lohner, Karl last_name: Lohner - first_name: Oksana full_name: Tehlivets, Oksana last_name: Tehlivets - first_name: Susan A. full_name: Henry, Susan A. last_name: Henry - first_name: Sepp D. full_name: Kohlwein, Sepp D. last_name: Kohlwein citation: ama: Hofbauer HF, Schopf FH, Schleifer H, et al. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 2014;29(6):P729-739. doi:10.1016/j.devcel.2014.04.025 apa: Hofbauer, H. F., Schopf, F. H., Schleifer, H., Knittelfelder, O. L., Pieber, B., Rechberger, G. N., … Kohlwein, S. D. (2014). Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2014.04.025 chicago: Hofbauer, Harald F., Florian H. Schopf, Hannes Schleifer, Oskar L. Knittelfelder, Bartholomäus Pieber, Gerald N. Rechberger, Heimo Wolinski, et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell. Elsevier, 2014. https://doi.org/10.1016/j.devcel.2014.04.025. ieee: H. F. Hofbauer et al., “Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids,” Developmental Cell, vol. 29, no. 6. Elsevier, pp. P729-739, 2014. ista: Hofbauer HF, Schopf FH, Schleifer H, Knittelfelder OL, Pieber B, Rechberger GN, Wolinski H, Gaspar ML, Kappe CO, Stadlmann J, Mechtler K, Zenz A, Lohner K, Tehlivets O, Henry SA, Kohlwein SD. 2014. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 29(6), P729-739. mla: Hofbauer, Harald F., et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell, vol. 29, no. 6, Elsevier, 2014, pp. P729-739, doi:10.1016/j.devcel.2014.04.025. short: H.F. Hofbauer, F.H. Schopf, H. Schleifer, O.L. Knittelfelder, B. Pieber, G.N. Rechberger, H. Wolinski, M.L. Gaspar, C.O. Kappe, J. Stadlmann, K. Mechtler, A. Zenz, K. Lohner, O. Tehlivets, S.A. Henry, S.D. Kohlwein, Developmental Cell 29 (2014) P729-739. date_created: 2022-08-25T08:42:42Z date_published: 2014-06-23T00:00:00Z date_updated: 2023-02-21T10:09:45Z day: '23' doi: 10.1016/j.devcel.2014.04.025 extern: '1' external_id: pmid: - '24960695' intvolume: ' 29' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2014.04.025 month: '06' oa: 1 oa_version: Published Version page: P729-739 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2014' ... --- _id: '11967' abstract: - lang: eng text: An experimentally easy to perform method for the generation of alumina-supported Fe3O4 nanoparticles [(6±1) nm size, 0.67 wt %]and the use of this material in hydrazine-mediated heterogeneously catalyzed reductions of nitroarenes to anilines under batch and continuous-flow conditions is presented. The bench-stable, reusable nano-Fe3O4@Al2O3 catalyst can selectively reduce functionalized nitroarenes at 1 mol % catalyst loading by using a 20 mol % excess of hydrazine hydrate in an elevated temperature regime (150 °C, reaction time 2–6 min in batch). For continuous-flow processing, the catalyst material is packed into dedicated cartridges and used in a commercially available high-temperature/-pressure flow device. In continuous mode, reaction times can be reduced to less than 1 min at 150 °C (30 bar back pressure) in a highly intensified process. The nano-Fe3O4@Al2O3 catalyst demonstrated stable reduction of nitrobenzene (0.5 M in MeOH) for more than 10 h on stream at a productivity of 30 mmol h−1 (0.72 mol per day). Importantly, virtually no leaching of the catalytically active material could be observed by inductively coupled plasma MS monitoring. article_processing_charge: No article_type: original author: - first_name: Mojtaba Mirhosseini full_name: Moghaddam, Mojtaba Mirhosseini last_name: Moghaddam - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Toma full_name: Glasnov, Toma last_name: Glasnov - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Moghaddam MM, Pieber B, Glasnov T, Kappe CO. Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. 2014;7(11):3122-3131. doi:10.1002/cssc.201402455 apa: Moghaddam, M. M., Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.201402455 chicago: Moghaddam, Mojtaba Mirhosseini, Bartholomäus Pieber, Toma Glasnov, and C. Oliver Kappe. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem. Wiley, 2014. https://doi.org/10.1002/cssc.201402455. ieee: M. M. Moghaddam, B. Pieber, T. Glasnov, and C. O. Kappe, “Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow,” ChemSusChem, vol. 7, no. 11. Wiley, pp. 3122–3131, 2014. ista: Moghaddam MM, Pieber B, Glasnov T, Kappe CO. 2014. Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. 7(11), 3122–3131. mla: Moghaddam, Mojtaba Mirhosseini, et al. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem, vol. 7, no. 11, Wiley, 2014, pp. 3122–31, doi:10.1002/cssc.201402455. short: M.M. Moghaddam, B. Pieber, T. Glasnov, C.O. Kappe, ChemSusChem 7 (2014) 3122–3131. date_created: 2022-08-25T08:36:54Z date_published: 2014-11-01T00:00:00Z date_updated: 2023-02-21T10:09:42Z day: '01' doi: 10.1002/cssc.201402455 extern: '1' external_id: pmid: - '25209099' intvolume: ' 7' issue: '11' language: - iso: eng month: '11' oa_version: None page: 3122-3131 pmid: 1 publication: ChemSusChem publication_identifier: eissn: - 1864-564X issn: - 1864-5631 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2014' ... --- _id: '11987' abstract: - lang: eng text: A method for the direct lithiation of terminal alkynes and heterocycles with subsequent carboxylation in a continuous flow format was developed. This method provides carboxylic acids at ambient conditions within less than five seconds with only little excess of the organometallic base and CO2. article_number: '13430' article_processing_charge: No article_type: letter_note author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Toma full_name: Glasnov, Toma last_name: Glasnov - first_name: C. O. full_name: Kappe, C. O. last_name: Kappe citation: ama: 'Pieber B, Glasnov T, Kappe CO. Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. 2014;4(26). doi:10.1039/c4ra01442a' apa: 'Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/c4ra01442a' chicago: 'Pieber, Bartholomäus, Toma Glasnov, and C. O. Kappe. “Flash Carboxylation: Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.” RSC Advances. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4ra01442a.' ieee: 'B. Pieber, T. Glasnov, and C. O. Kappe, “Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow,” RSC Advances, vol. 4, no. 26. Royal Society of Chemistry, 2014.' ista: 'Pieber B, Glasnov T, Kappe CO. 2014. Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. 4(26), 13430.' mla: 'Pieber, Bartholomäus, et al. “Flash Carboxylation: Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.” RSC Advances, vol. 4, no. 26, 13430, Royal Society of Chemistry, 2014, doi:10.1039/c4ra01442a.' short: B. Pieber, T. Glasnov, C.O. Kappe, RSC Advances 4 (2014). date_created: 2022-08-25T11:48:19Z date_published: 2014-03-03T00:00:00Z date_updated: 2023-02-21T10:10:31Z day: '03' doi: 10.1039/c4ra01442a extern: '1' intvolume: ' 4' issue: '26' language: - iso: eng month: '03' oa_version: None publication: RSC Advances publication_identifier: eissn: - 2046-2069 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: 'Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2014' ... --- _id: '1309' abstract: - lang: eng text: We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation display infinite speed of support propagation. We apply our method to the case of the quantum drift-diffusion equation which augments the DLSS equation with a drift term and possibly a second-order diffusion term. The proof is accomplished using weighted entropy estimates, Hardy's inequality and a family of singular weight functions to derive a differential inequality; the differential inequality shows exponential growth of the weighted entropy, with the growth constant blowing up very fast as the singularity of the weight becomes sharper. To the best of our knowledge, this is the first example of a nonnegativity-preserving higher-order parabolic equation displaying infinite speed of support propagation. author: - first_name: Julian L full_name: Julian Fischer id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0 apa: Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0 chicago: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0. ieee: J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models,” Nonlinear Differential Equations and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014. ista: Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 21(1), 27–50. mla: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0. short: J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014) 27–50. date_created: 2018-12-11T11:51:17Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:49:47Z day: '01' doi: 10.1007/s00030-013-0235-0 extern: 1 intvolume: ' 21' issue: '1' month: '01' page: 27 - 50 publication: Nonlinear Differential Equations and Applications publication_status: published publisher: Birkhäuser publist_id: '5960' quality_controlled: 0 status: public title: Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models type: journal_article volume: 21 year: '2014' ... --- _id: '1312' abstract: - lang: eng text: We derive upper bounds on the waiting time of solutions to the thin-film equation in the regime of weak slippage n ∈ [2, 32\11). In particular, we give sufficient conditions on the initial data for instantaneous forward motion of the free boundary. For n ∈ (2, 32\11), our estimates are sharp, for n = 2, they are sharp up to a logarithmic correction term. Note that the case n = 2 corresponds-with a grain of salt-to the assumption of the Navier slip condition at the fluid-solid interface. We also obtain results in the regime of strong slippage n ∈ (1,2); however, in this regime we expect them not to be optimal. Our method is based on weighted backward entropy estimates, Hardy's inequality and singular weight functions; we deduce a differential inequality which would enforce blowup of the weighted entropy if the contact line were to remain stationary for too long. author: - first_name: Julian L full_name: Julian Fischer id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: 'Fischer JL. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818. doi:10.1007/s00205-013-0690-0' apa: 'Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-013-0690-0' chicago: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis. Springer, 2014. https://doi.org/10.1007/s00205-013-0690-0.' ieee: 'J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation: The case of weak slippage,” Archive for Rational Mechanics and Analysis, vol. 211, no. 3. Springer, pp. 771–818, 2014.' ista: 'Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3), 771–818.' mla: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis, vol. 211, no. 3, Springer, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0.' short: J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818. date_created: 2018-12-11T11:51:18Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:49:48Z day: '01' doi: 10.1007/s00205-013-0690-0 extern: 1 intvolume: ' 211' issue: '3' month: '01' page: 771 - 818 publication: Archive for Rational Mechanics and Analysis publication_status: published publisher: Springer publist_id: '5959' quality_controlled: 0 status: public title: 'Upper bounds on waiting times for the Thin-film equation: The case of weak slippage' type: journal_article volume: 211 year: '2014' ... --- _id: '1375' abstract: - lang: eng text: 'We consider directed graphs where each edge is labeled with an integer weight and study the fundamental algorithmic question of computing the value of a cycle with minimum mean weight. Our contributions are twofold: (1) First we show that the algorithmic question is reducible to the problem of a logarithmic number of min-plus matrix multiplications of n×n-matrices, where n is the number of vertices of the graph. (2) Second, when the weights are nonnegative, we present the first (1+ε)-approximation algorithm for the problem and the running time of our algorithm is Õ(nωlog3(nW/ε)/ε),1 where O(nω) is the time required for the classic n×n-matrix multiplication and W is the maximum value of the weights. With an additional O(log(nW/ε)) factor in space a cycle with approximately optimal weight can be computed within the same time bound.' article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer - first_name: Michael full_name: Raskin, Michael last_name: Raskin citation: ama: Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. Approximating the minimum cycle mean. Theoretical Computer Science. 2014;547(C):104-116. doi:10.1016/j.tcs.2014.06.031 apa: Chatterjee, K., Henzinger, M. H., Krinninger, S., Loitzenbauer, V., & Raskin, M. (2014). Approximating the minimum cycle mean. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2014.06.031 chicago: Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, Veronika Loitzenbauer, and Michael Raskin. “Approximating the Minimum Cycle Mean.” Theoretical Computer Science. Elsevier, 2014. https://doi.org/10.1016/j.tcs.2014.06.031. ieee: K. Chatterjee, M. H. Henzinger, S. Krinninger, V. Loitzenbauer, and M. Raskin, “Approximating the minimum cycle mean,” Theoretical Computer Science, vol. 547, no. C. Elsevier, pp. 104–116, 2014. ista: Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. 2014. Approximating the minimum cycle mean. Theoretical Computer Science. 547(C), 104–116. mla: Chatterjee, Krishnendu, et al. “Approximating the Minimum Cycle Mean.” Theoretical Computer Science, vol. 547, no. C, Elsevier, 2014, pp. 104–16, doi:10.1016/j.tcs.2014.06.031. short: K. Chatterjee, M.H. Henzinger, S. Krinninger, V. Loitzenbauer, M. Raskin, Theoretical Computer Science 547 (2014) 104–116. date_created: 2018-12-11T11:51:40Z date_published: 2014-08-28T00:00:00Z date_updated: 2022-09-09T11:50:58Z day: '28' department: - _id: KrCh doi: 10.1016/j.tcs.2014.06.031 ec_funded: 1 external_id: arxiv: - '1307.4473' intvolume: ' 547' issue: C language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.4473 month: '08' oa: 1 oa_version: Preprint page: 104 - 116 project: - _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: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '5836' quality_controlled: '1' scopus_import: '1' status: public title: Approximating the minimum cycle mean type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 547 year: '2014' ... --- _id: '1392' abstract: - lang: eng text: Fault-tolerant distributed algorithms play an important role in ensuring the reliability of many software applications. In this paper we consider distributed algorithms whose computations are organized in rounds. To verify the correctness of such algorithms, we reason about (i) properties (such as invariants) of the state, (ii) the transitions controlled by the algorithm, and (iii) the communication graph. We introduce a logic that addresses these points, and contains set comprehensions with cardinality constraints, function symbols to describe the local states of each process, and a limited form of quantifier alternation to express the verification conditions. We show its use in automating the verification of consensus algorithms. In particular, we give a semi-decision procedure for the unsatisfiability problem of the logic and identify a decidable fragment. We successfully applied our framework to verify the correctness of a variety of consensus algorithms tolerant to both benign faults (message loss, process crashes) and value faults (message corruption). acknowledgement: Supported by the Vienna Science and Technology Fund (WWTF) through grant PROSEED. alternative_title: - LNCS author: - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - 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: Helmut full_name: Veith, Helmut last_name: Veith - first_name: Josef full_name: Widder, Josef last_name: Widder - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: 'Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. A logic-based framework for verifying consensus algorithms. In: Vol 8318. Springer; 2014:161-181. doi:10.1007/978-3-642-54013-4_10' apa: 'Dragoi, C., Henzinger, T. A., Veith, H., Widder, J., & Zufferey, D. (2014). A logic-based framework for verifying consensus algorithms (Vol. 8318, pp. 161–181). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54013-4_10' chicago: Dragoi, Cezara, Thomas A Henzinger, Helmut Veith, Josef Widder, and Damien Zufferey. “A Logic-Based Framework for Verifying Consensus Algorithms,” 8318:161–81. Springer, 2014. https://doi.org/10.1007/978-3-642-54013-4_10. ieee: 'C. Dragoi, T. A. Henzinger, H. Veith, J. Widder, and D. Zufferey, “A logic-based framework for verifying consensus algorithms,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA, 2014, vol. 8318, pp. 161–181.' ista: 'Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. 2014. A logic-based framework for verifying consensus algorithms. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 8318, 161–181.' mla: Dragoi, Cezara, et al. A Logic-Based Framework for Verifying Consensus Algorithms. Vol. 8318, Springer, 2014, pp. 161–81, doi:10.1007/978-3-642-54013-4_10. short: C. Dragoi, T.A. Henzinger, H. Veith, J. Widder, D. Zufferey, in:, Springer, 2014, pp. 161–181. conference: end_date: 2014-01-21 location: San Diego, USA name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' start_date: 2014-01-19 date_created: 2018-12-11T11:51:45Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:50:22Z day: '01' ddc: - '000' - '005' department: - _id: ToHe doi: 10.1007/978-3-642-54013-4_10 ec_funded: 1 file: - access_level: open_access checksum: bffa33d39be77df0da39defe97eabf84 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:06Z date_updated: 2020-07-14T12:44:48Z file_id: '4859' file_name: IST-2014-179-v1+1_vmcai14.pdf file_size: 444138 relation: main_file file_date_updated: 2020-07-14T12:44:48Z has_accepted_license: '1' intvolume: ' 8318' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 161 - 181 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Springer publist_id: '5817' pubrep_id: '179' quality_controlled: '1' scopus_import: 1 status: public title: A logic-based framework for verifying consensus algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8318 year: '2014' ... --- _id: '1393' abstract: - lang: eng text: 'Probabilistic programs are usual functional or imperative programs with two added constructs: (1) the ability to draw values at random from distributions, and (2) the ability to condition values of variables in a program via observations. Models from diverse application areas such as computer vision, coding theory, cryptographic protocols, biology and reliability analysis can be written as probabilistic programs. Probabilistic inference is the problem of computing an explicit representation of the probability distribution implicitly specified by a probabilistic program. Depending on the application, the desired output from inference may vary-we may want to estimate the expected value of some function f with respect to the distribution, or the mode of the distribution, or simply a set of samples drawn from the distribution. In this paper, we describe connections this research area called \Probabilistic Programming" has with programming languages and software engineering, and this includes language design, and the static and dynamic analysis of programs. We survey current state of the art and speculate on promising directions for future research.' article_processing_charge: No author: - first_name: Andrew full_name: Gordon, Andrew last_name: Gordon - 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: Aditya full_name: Nori, Aditya last_name: Nori - first_name: Sriram full_name: Rajamani, Sriram last_name: Rajamani citation: ama: 'Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: Proceedings of the on Future of Software Engineering. ACM; 2014:167-181. doi:10.1145/2593882.2593900' apa: 'Gordon, A., Henzinger, T. A., Nori, A., & Rajamani, S. (2014). Probabilistic programming. In Proceedings of the on Future of Software Engineering (pp. 167–181). Hyderabad, India: ACM. https://doi.org/10.1145/2593882.2593900' chicago: Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In Proceedings of the on Future of Software Engineering, 167–81. ACM, 2014. https://doi.org/10.1145/2593882.2593900. ieee: A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in Proceedings of the on Future of Software Engineering, Hyderabad, India, 2014, pp. 167–181. ista: 'Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming. Proceedings of the on Future of Software Engineering. FOSE: Future of Software Engineering, 167–181.' mla: Gordon, Andrew, et al. “Probabilistic Programming.” Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–81, doi:10.1145/2593882.2593900. short: A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181. conference: end_date: 2014-06-07 location: Hyderabad, India name: 'FOSE: Future of Software Engineering' start_date: 2014-05-31 date_created: 2018-12-11T11:51:45Z date_published: 2014-05-31T00:00:00Z date_updated: 2021-01-12T06:50:22Z day: '31' department: - _id: ToHe doi: 10.1145/2593882.2593900 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/2593882.2593900 month: '05' oa: 1 oa_version: Published Version page: 167 - 181 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the on Future of Software Engineering publication_status: published publisher: ACM publist_id: '5816' quality_controlled: '1' scopus_import: 1 status: public title: Probabilistic programming type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1404' abstract: - lang: eng text: "The co-evolution of hosts and pathogens is characterized by continuous adaptations of both parties. Pathogens of social insects need to adapt towards disease defences at two levels: 1) individual immunity of each colony member consisting of behavioural defence strategies as well as humoral and cellular immune responses and 2) social immunity that is collectively performed by all group members comprising behavioural, physiological and organisational defence strategies.\r\n\r\nTo disentangle the selection pressure on pathogens by the collective versus individual level of disease defence in social insects, we performed an evolution experiment using the Argentine Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution over 10 serial host passages to two different evolution host treatments: (1) only individual host immunity in a single host treatment, and (2) simultaneously acting individual and social immunity in a social host treatment, in which an exposed ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen evolution experiment, the 6 Metarhizium spp. strains were characterised concerning conidiospore size killing rates in singly and socially reared ants, their competitiveness under coinfecting conditions and their influence on ant behaviour. We analysed how the ancestral atrain mixture changed in conidiospere size, killing rate and strain composition dependent on host treatment (single or social hosts) during 10 passages and found that killing rate and conidiospere size of the pathogen increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting the evolved strain mixtures that evolved under either the single or social host treatment under both single and social current rearing conditions in a full factorial design experiment revealed that the additional collective defences in insect societies add new selection pressure for their coevolving pathogens that compromise their ability to adapt to its host at the group level. To our knowledge, this is the first study directly measuring the influence of social immunity on pathogen evolution." acknowledgement: This work was funded by the DFG and the ERC. alternative_title: - IST Austria Thesis author: - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock citation: ama: Stock M. Evolution of a fungal pathogen towards individual versus social immunity in ants. 2014. apa: Stock, M. (2014). Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria. chicago: Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants.” IST Austria, 2014. ieee: M. Stock, “Evolution of a fungal pathogen towards individual versus social immunity in ants,” IST Austria, 2014. ista: Stock M. 2014. Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria. mla: Stock, Miriam. Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants. IST Austria, 2014. short: M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants, IST Austria, 2014. date_created: 2018-12-11T11:51:49Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:50:30Z day: '01' department: - _id: SyCr language: - iso: eng month: '04' oa_version: None page: '101' publication_status: published publisher: IST Austria publist_id: '5803' status: public supervisor: - first_name: Sylvia M full_name: Cremer, Sylvia M id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: Evolution of a fungal pathogen towards individual versus social immunity in ants type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1516' abstract: - lang: eng text: "We present a rigorous derivation of the BCS gap equation for superfluid fermionic gases with point interactions. Our starting point is the BCS energy functional, whose minimizer we investigate in the limit when the range of the interaction potential goes to zero.\r\n" article_processing_charge: No author: - first_name: Gerhard full_name: Bräunlich, Gerhard last_name: Bräunlich - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Bräunlich G, Hainzl C, Seiringer R. On the BCS gap equation for superfluid fermionic gases. In: Proceedings of the QMath12 Conference. World Scientific Publishing; 2014:127-137. doi:10.1142/9789814618144_0007' apa: 'Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). On the BCS gap equation for superfluid fermionic gases. In Proceedings of the QMath12 Conference (pp. 127–137). Berlin, Germany: World Scientific Publishing. https://doi.org/10.1142/9789814618144_0007' chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “On the BCS Gap Equation for Superfluid Fermionic Gases.” In Proceedings of the QMath12 Conference, 127–37. World Scientific Publishing, 2014. https://doi.org/10.1142/9789814618144_0007. ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “On the BCS gap equation for superfluid fermionic gases,” in Proceedings of the QMath12 Conference, Berlin, Germany, 2014, pp. 127–137. ista: 'Bräunlich G, Hainzl C, Seiringer R. 2014. On the BCS gap equation for superfluid fermionic gases. Proceedings of the QMath12 Conference. QMath: Mathematical Results in Quantum Physics, 127–137.' mla: Bräunlich, Gerhard, et al. “On the BCS Gap Equation for Superfluid Fermionic Gases.” Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–37, doi:10.1142/9789814618144_0007. short: G. Bräunlich, C. Hainzl, R. Seiringer, in:, Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–137. conference: end_date: 2013-09-13 location: Berlin, Germany name: 'QMath: Mathematical Results in Quantum Physics' start_date: 2013-09-10 date_created: 2018-12-11T11:52:28Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:51:19Z day: '01' department: - _id: RoSe doi: 10.1142/9789814618144_0007 external_id: arxiv: - '1403.2563' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.2563 month: '01' oa: 1 oa_version: Preprint page: 127 - 137 publication: Proceedings of the QMath12 Conference publication_status: published publisher: World Scientific Publishing publist_id: '5661' quality_controlled: '1' status: public title: On the BCS gap equation for superfluid fermionic gases type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1629' abstract: - lang: eng text: We propose a method for propagating edit operations in 2D vector graphics, based on geometric relationship functions. These functions quantify the geometric relationship of a point to a polygon, such as the distance to the boundary or the direction to the closest corner vertex. The level sets of the relationship functions describe points with the same relationship to a polygon. For a given query point, we first determine a set of relationships to local features, construct all level sets for these relationships, and accumulate them. The maxima of the resulting distribution are points with similar geometric relationships. We show extensions to handle mirror symmetries, and discuss the use of relationship functions as local coordinate systems. Our method can be applied, for example, to interactive floorplan editing, and it is especially useful for large layouts, where individual edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds of objects by propagating relatively few edit operations. article_number: '15' author: - first_name: Paul full_name: Guerrero, Paul last_name: Guerrero - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer - first_name: Peter full_name: Wonka, Peter last_name: Wonka citation: ama: Guerrero P, Jeschke S, Wimmer M, Wonka P. Edit propagation using geometric relationship functions. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2591010 apa: Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2014). Edit propagation using geometric relationship functions. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2591010 chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Edit Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics. ACM, 2014. https://doi.org/10.1145/2591010. ieee: P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Edit propagation using geometric relationship functions,” ACM Transactions on Graphics, vol. 33, no. 2. ACM, 2014. ista: Guerrero P, Jeschke S, Wimmer M, Wonka P. 2014. Edit propagation using geometric relationship functions. ACM Transactions on Graphics. 33(2), 15. mla: Guerrero, Paul, et al. “Edit Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics, vol. 33, no. 2, 15, ACM, 2014, doi:10.1145/2591010. short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, ACM Transactions on Graphics 33 (2014). date_created: 2018-12-11T11:53:08Z date_published: 2014-03-01T00:00:00Z date_updated: 2021-01-12T06:52:06Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2591010 file: - access_level: open_access checksum: 7f91e588a4e888610313b98271e6418e content_type: application/pdf creator: system date_created: 2018-12-12T10:11:22Z date_updated: 2020-07-14T12:45:07Z file_id: '4876' file_name: IST-2016-577-v1+1_2014.TOG.Paul.EditingPropagation.final.pdf file_size: 9832561 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 33' issue: '2' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '5526' pubrep_id: '577' quality_controlled: '1' status: public title: Edit propagation using geometric relationship functions type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2014' ... --- _id: '10793' abstract: - lang: eng text: "The Hanani–Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this classical result to clustered graphs with two disjoint clusters, and show that a straightforward extension of our result to flat clustered graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give a new and short proof for a related result by Di Battista and Frati based on the matroid intersection algorithm." 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: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Igor full_name: Malinović, Igor last_name: Malinović - first_name: Dömötör full_name: Pálvölgyi, Dömötör last_name: Pálvölgyi citation: ama: 'Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited. In: International Symposium on Graph Drawing. Vol 8871. Cham: Springer Nature; 2014:428-436. doi:10.1007/978-3-662-45803-7_36' apa: 'Fulek, R., Kynčl, J., Malinović, I., & Pálvölgyi, D. (2014). Clustered planarity testing revisited. In International Symposium on Graph Drawing (Vol. 8871, pp. 428–436). Cham: Springer Nature. https://doi.org/10.1007/978-3-662-45803-7_36' chicago: 'Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” In International Symposium on Graph Drawing, 8871:428–36. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-662-45803-7_36.' ieee: R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing revisited,” in International Symposium on Graph Drawing, 2014, vol. 8871, pp. 428–436. ista: Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436. mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” International Symposium on Graph Drawing, vol. 8871, Springer Nature, 2014, pp. 428–36, doi:10.1007/978-3-662-45803-7_36. short: R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436. date_created: 2022-02-25T10:32:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T10:08:04Z day: '01' department: - _id: UlWa doi: 10.1007/978-3-662-45803-7_36 external_id: arxiv: - '1305.4519' intvolume: ' 8871' language: - iso: eng month: '01' oa_version: Preprint page: 428-436 place: Cham publication: International Symposium on Graph Drawing publication_identifier: issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '1642' relation: later_version status: public scopus_import: '1' status: public title: Clustered planarity testing revisited type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8871 year: '2014' ... --- _id: '1643' abstract: - lang: eng text: We extend the notion of verifiable random functions (VRF) to constrained VRFs, which generalize the concept of constrained pseudorandom functions, put forward by Boneh and Waters (Asiacrypt’13), and independently by Kiayias et al. (CCS’13) and Boyle et al. (PKC’14), who call them delegatable PRFs and functional PRFs, respectively. In a standard VRF the secret key sk allows one to evaluate a pseudorandom function at any point of its domain; in addition, it enables computation of a non-interactive proof that the function value was computed correctly. In a constrained VRF from the key sk one can derive constrained keys skS for subsets S of the domain, which allow computation of function values and proofs only at points in S. After formally defining constrained VRFs, we derive instantiations from the multilinear-maps-based constrained PRFs by Boneh and Waters, yielding a VRF with constrained keys for any set that can be decided by a polynomial-size circuit. Our VRFs have the same function values as the Boneh-Waters PRFs and are proved secure under the same hardness assumption, showing that verifiability comes at no cost. Constrained (functional) VRFs were stated as an open problem by Boyle et al. alternative_title: - LNCS author: - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer citation: ama: 'Fuchsbauer G. Constrained Verifiable Random Functions . In: Abdalla M, De Prisco R, eds. SCN 2014. Vol 8642. Springer; 2014:95-114. doi:10.1007/978-3-319-10879-7_7' apa: 'Fuchsbauer, G. (2014). Constrained Verifiable Random Functions . In M. Abdalla & R. De Prisco (Eds.), SCN 2014 (Vol. 8642, pp. 95–114). Amalfi, Italy: Springer. https://doi.org/10.1007/978-3-319-10879-7_7' chicago: Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” In SCN 2014, edited by Michel Abdalla and Roberto De Prisco, 8642:95–114. Springer, 2014. https://doi.org/10.1007/978-3-319-10879-7_7. ieee: G. Fuchsbauer, “Constrained Verifiable Random Functions ,” in SCN 2014, Amalfi, Italy, 2014, vol. 8642, pp. 95–114. ista: 'Fuchsbauer G. 2014. Constrained Verifiable Random Functions . SCN 2014. SCN: Security and Cryptography for Networks, LNCS, vol. 8642, 95–114.' mla: Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” SCN 2014, edited by Michel Abdalla and Roberto De Prisco, vol. 8642, Springer, 2014, pp. 95–114, doi:10.1007/978-3-319-10879-7_7. short: G. Fuchsbauer, in:, M. Abdalla, R. De Prisco (Eds.), SCN 2014, Springer, 2014, pp. 95–114. conference: end_date: 2014-09-05 location: Amalfi, Italy name: 'SCN: Security and Cryptography for Networks' start_date: 2014-09-03 date_created: 2018-12-11T11:53:13Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:52:12Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-10879-7_7 ec_funded: 1 editor: - first_name: Michel full_name: Abdalla, Michel last_name: Abdalla - first_name: Roberto full_name: De Prisco, Roberto last_name: De Prisco intvolume: ' 8642' language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2014/537 month: '01' oa: 1 oa_version: Submitted Version page: 95 - 114 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: SCN 2014 publication_status: published publisher: Springer publist_id: '5509' scopus_import: 1 status: public title: 'Constrained Verifiable Random Functions ' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8642 year: '2014' ... --- _id: '1702' abstract: - lang: eng text: In this paper we present INTERHORN, a solver for recursion-free Horn clauses. The main application domain of INTERHORN lies in solving interpolation problems arising in software verification. We show how a range of interpolation problems, including path, transition, nested, state/transition and well-founded interpolation can be handled directly by INTERHORN. By detailing these interpolation problems and their Horn clause representations, we hope to encourage the emergence of a common back-end interpolation interface useful for diverse verification tools. alternative_title: - EPTCS author: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Corneliu full_name: Popeea, Corneliu last_name: Popeea - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko citation: ama: 'Gupta A, Popeea C, Rybalchenko A. Generalised interpolation by solving recursion free-horn clauses. In: Electronic Proceedings in Theoretical Computer Science, EPTCS. Vol 169. Open Publishing; 2014:31-38. doi:10.4204/EPTCS.169.5' apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2014). Generalised interpolation by solving recursion free-horn clauses. In Electronic Proceedings in Theoretical Computer Science, EPTCS (Vol. 169, pp. 31–38). Vienna, Austria: Open Publishing. https://doi.org/10.4204/EPTCS.169.5' chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” In Electronic Proceedings in Theoretical Computer Science, EPTCS, 169:31–38. Open Publishing, 2014. https://doi.org/10.4204/EPTCS.169.5. ieee: A. Gupta, C. Popeea, and A. Rybalchenko, “Generalised interpolation by solving recursion free-horn clauses,” in Electronic Proceedings in Theoretical Computer Science, EPTCS, Vienna, Austria, 2014, vol. 169, pp. 31–38. ista: 'Gupta A, Popeea C, Rybalchenko A. 2014. Generalised interpolation by solving recursion free-horn clauses. Electronic Proceedings in Theoretical Computer Science, EPTCS. HCVS: Horn Clauses for Verification and Synthesis, EPTCS, vol. 169, 31–38.' mla: Gupta, Ashutosh, et al. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” Electronic Proceedings in Theoretical Computer Science, EPTCS, vol. 169, Open Publishing, 2014, pp. 31–38, doi:10.4204/EPTCS.169.5. short: A. Gupta, C. Popeea, A. Rybalchenko, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing, 2014, pp. 31–38. conference: end_date: 2014-07-17 location: Vienna, Austria name: 'HCVS: Horn Clauses for Verification and Synthesis' start_date: 2014-07-17 date_created: 2018-12-11T11:53:33Z date_published: 2014-12-02T00:00:00Z date_updated: 2021-01-12T06:52:38Z day: '02' department: - _id: ToHe doi: 10.4204/EPTCS.169.5 intvolume: ' 169' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1303.7378v2 month: '12' oa: 1 oa_version: Submitted Version page: 31 - 38 publication: Electronic Proceedings in Theoretical Computer Science, EPTCS publication_status: published publisher: Open Publishing publist_id: '5435' quality_controlled: '1' status: public title: Generalised interpolation by solving recursion free-horn clauses type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 169 year: '2014' ... --- _id: '1708' abstract: - lang: eng text: It has been long argued that, because of inherent ambiguity and noise, the brain needs to represent uncertainty in the form of probability distributions. The neural encoding of such distributions remains however highly controversial. Here we present a novel circuit model for representing multidimensional real-valued distributions using a spike based spatio-temporal code. Our model combines the computational advantages of the currently competing models for probabilistic codes and exhibits realistic neural responses along a variety of classic measures. Furthermore, the model highlights the challenges associated with interpreting neural activity in relation to behavioral uncertainty and points to alternative population-level approaches for the experimental validation of distributed representations. author: - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: 'Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032.' apa: 'Savin, C., & Denève, S. (2014). Spatio-temporal representations of uncertainty in spiking neural networks (Vol. 3, pp. 2024–2032). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.' chicago: Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing Systems, 2014. ieee: 'C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in spiking neural networks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2014, vol. 3, no. January, pp. 2024–2032.' ista: 'Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in spiking neural networks. NIPS: Neural Information Processing Systems vol. 3, 2024–2032.' mla: Savin, Cristina, and Sophie Denève. Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks. Vol. 3, no. January, Neural Information Processing Systems, 2014, pp. 2024–32. short: C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032. conference: end_date: 2014-12-13 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2014-12-08 date_created: 2018-12-11T11:53:35Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:52:40Z day: '01' department: - _id: GaTk intvolume: ' 3' issue: January language: - iso: eng main_file_link: - url: http://papers.nips.cc/paper/5343-spatio-temporal-representations-of-uncertainty-in-spiking-neural-networks.pdf month: '01' oa_version: None page: 2024 - 2032 publication_status: published publisher: Neural Information Processing Systems publist_id: '5427' quality_controlled: '1' scopus_import: 1 status: public title: Spatio-temporal representations of uncertainty in spiking neural networks type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2014' ... --- _id: '1761' abstract: - lang: eng text: Metal silicides formed by means of thermal annealing processes are employed as contact materials in microelectronics. Control of the structure of silicide/silicon interfaces becomes a critical issue when the characteristic size of the device is reduced below a few tens of nanometers. Here, we report on silicide clustering occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling spectroscopy. Our results provide evidence for the segregation of a PtSi cluster with a diameter of a few nanometers from the silicide contact. The cluster acts as a metallic quantum dot giving rise to distinct signatures of quantum transport through its discrete energy states. acknowledgement: This work was supported by the Agence Nationale de la Recherche and by the EU through the ERC Starting Grant HybridNano author: - first_name: Massimo full_name: Mongillo, Massimo last_name: Mongillo - first_name: Panayotis full_name: Spathis, Panayotis N last_name: Spathis - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi - first_name: Pascal full_name: Gentile, Pascal last_name: Gentile - first_name: Riccardo full_name: Rurali, Riccardo last_name: Rurali - first_name: Xavier full_name: Cartoixà, Xavier last_name: Cartoixà citation: ama: Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025 apa: Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali, R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025 chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi, Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X. American Physical Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025. ieee: M. Mongillo et al., “PtSi clustering in silicon probed by transport spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society, 2014. ista: Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 3(4). mla: Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025. short: M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali, X. Cartoixà, Physical Review X 3 (2014). date_created: 2018-12-11T11:53:52Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:02Z day: '01' doi: 10.1103/PhysRevX.3.041025 extern: 1 intvolume: ' 3' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.5413 month: '01' oa: 1 publication: Physical Review X publication_status: published publisher: American Physical Society publist_id: '5363' quality_controlled: 0 status: public title: PtSi clustering in silicon probed by transport spectroscopy type: journal_article volume: 3 year: '2014' ... --- _id: '1791' abstract: - lang: eng text: Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways. acknowledgement: This work was supported by the National Institutes of Health R01NS41537. G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini Fellowship, and A.G.F. by the Brain Behavior Research Foundation author: - first_name: Seungtae full_name: Baek, SeungTae last_name: Baek - first_name: Géraldine full_name: Kerjan, Géraldine last_name: Kerjan - first_name: Stephanie full_name: Bielas, Stephanie L last_name: Bielas - first_name: Jieun full_name: Lee, Jieun last_name: Lee - first_name: Ali full_name: Fenstermaker, Ali G last_name: Fenstermaker - first_name: Gaia full_name: Gaia Novarino id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Joseph full_name: Gleeson, Joseph G last_name: Gleeson citation: ama: Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036 apa: Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G., & Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.036 chicago: Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker, Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036. ieee: S. Baek et al., “Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron, vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014. ista: Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J. 2014. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262. mla: Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036. short: S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson, Neuron 82 (2014) 1255–1262. date_created: 2018-12-11T11:54:01Z date_published: 2014-06-18T00:00:00Z date_updated: 2021-01-12T06:53:13Z day: '18' doi: 10.1016/j.neuron.2014.04.036 extern: 1 intvolume: ' 82' issue: '6' month: '06' page: 1255 - 1262 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5322' quality_controlled: 0 status: public title: Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation type: journal_article volume: 82 year: '2014' ... --- _id: '1806' abstract: - lang: eng text: The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants. author: - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8' apa: Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8 chicago: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8. ieee: P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170. ista: 'Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.' mla: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8. short: P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170. date_created: 2018-12-11T11:54:07Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:53:19Z day: '01' department: - _id: JiFr doi: 10.1007/978-3-7091-1526-8_8 editor: - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 language: - iso: eng month: '04' oa_version: None page: 143 - 170 publication: Auxin and Its Role in Plant Development publication_status: published publisher: Springer publist_id: '5304' quality_controlled: '1' scopus_import: 1 status: public title: Auxin on the road navigated by cellular PIN polarity type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1816' abstract: - lang: eng text: Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques. acknowledgement: 'Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.' author: - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Peter full_name: Meerwald, Peter last_name: Meerwald - first_name: Roland full_name: Kwitt, Roland last_name: Kwitt citation: ama: Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 2014;24(1):61-86. doi:10.1142/S0218195914500034 apa: Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034 chicago: Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034. ieee: S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” International Journal of Computational Geometry and Applications, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014. ista: Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86. mla: Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034. short: S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86. date_created: 2018-12-11T11:54:10Z date_published: 2014-03-16T00:00:00Z date_updated: 2021-01-12T06:53:23Z day: '16' ddc: - '000' department: - _id: HeEd doi: 10.1142/S0218195914500034 file: - access_level: open_access checksum: be45c133ab4d43351260e21beaa8f4b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:43Z date_updated: 2020-07-14T12:45:17Z file_id: '4704' file_name: IST-2016-443-v1+1_S0218195914500034.pdf file_size: 991734 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 24' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 61 - 86 publication: International Journal of Computational Geometry and Applications publication_status: published publisher: World Scientific Publishing publist_id: '5290' pubrep_id: '443' quality_controlled: '1' scopus_import: 1 status: public title: Topology-preserving watermarking of vector graphics 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1821' abstract: - lang: eng text: We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end. article_number: '1.4881536' author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536 apa: Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4881536 chicago: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4881536. ieee: R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014. ista: Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536. mla: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:10.1063/1.4881536. short: R. Seiringer, Journal of Mathematical Physics 55 (2014). date_created: 2018-12-11T11:54:11Z date_published: 2014-06-26T00:00:00Z date_updated: 2021-01-12T06:53:25Z day: '26' ddc: - '510' - '530' department: - _id: RoSe doi: 10.1063/1.4881536 file: - access_level: open_access checksum: ed0efc93c10f1341155f0316af617b82 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:49Z date_updated: 2020-07-14T12:45:17Z file_id: '5172' file_name: IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf file_size: 269171 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 55' issue: '7' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '5285' pubrep_id: '532' quality_controlled: '1' scopus_import: 1 status: public title: Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ... --- _id: '1822' article_number: '075101' author: - first_name: Vojkan full_name: Jakšić, Vojkan last_name: Jakšić - first_name: Claude full_name: Pillet, Claude last_name: Pillet - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4884877 apa: Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877 chicago: Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877. ieee: V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014. ista: Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101. mla: Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877. short: V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014). date_created: 2018-12-11T11:54:12Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:53:25Z day: '01' department: - _id: RoSe doi: 10.1063/1.4884877 intvolume: ' 55' issue: '7' language: - iso: eng month: '07' oa_version: None publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '5284' quality_controlled: '1' scopus_import: 1 status: public title: Introduction type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ... --- _id: '1829' abstract: - lang: eng text: Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements. alternative_title: - Springer Tracts in Advanced Robotics author: - first_name: Katharina full_name: Muelling, Katharina last_name: Muelling - first_name: Oliver full_name: Kroemer, Oliver last_name: Kroemer - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf citation: ama: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills. Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3' apa: Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.), Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3 chicago: Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf. “Movement Templates for Learning of Hitting and Batting.” In Learning Motor Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3. ieee: K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates for learning of hitting and batting,” in Learning Motor Skills, vol. 97, J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82. ista: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in Advanced Robotics, vol. 97, 69–82.' mla: Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol. 97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3. short: K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82. date_created: 2018-12-11T11:54:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:28Z day: '01' department: - _id: ChLa doi: 10.1007/978-3-319-03194-1_3 editor: - first_name: Jens full_name: Kober, Jens last_name: Kober - first_name: Jan full_name: Peters, Jan last_name: Peters intvolume: ' 97' language: - iso: eng month: '01' oa_version: None page: 69 - 82 publication: Learning Motor Skills publication_status: published publisher: Springer publist_id: '5274' quality_controlled: '1' scopus_import: 1 series_title: From Algorithms to Robot Experiments status: public title: Movement templates for learning of hitting and batting type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2014' ... --- _id: '1844' abstract: - lang: eng text: 'Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.' author: - first_name: Valeria full_name: Risso, Valeria last_name: Risso - first_name: Fadia full_name: Manssour Triedo, Fadia last_name: Manssour Triedo - first_name: Asuncion full_name: Delgado Delgado, Asuncion last_name: Delgado Delgado - first_name: Rocio full_name: Arco, Rocio last_name: Arco - first_name: Alicia full_name: Barroso Deljesús, Alicia last_name: Barroso Deljesús - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Raquel full_name: Godoy Ruiz, Raquel last_name: Godoy Ruiz - first_name: Josè full_name: Gavira, Josè last_name: Gavira - first_name: Eric full_name: Gaucher, Eric last_name: Gaucher - first_name: Beatriz full_name: Ibarra Molero, Beatriz last_name: Ibarra Molero - first_name: Jose full_name: Sánchez Ruiz, Jose last_name: Sánchez Ruiz citation: ama: Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 2014;32(2):440-455. doi:10.1093/molbev/msu312 apa: Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu312 chicago: Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312. ieee: V. Risso et al., “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 440–455, 2014. ista: Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455. mla: Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312. short: V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455. date_created: 2018-12-11T11:54:19Z date_published: 2014-11-12T00:00:00Z date_updated: 2021-01-12T06:53:34Z day: '12' ddc: - '571' department: - _id: HaJa doi: 10.1093/molbev/msu312 file: - access_level: open_access checksum: 06215318e66be8f3e0c33abb07e9d3da content_type: application/pdf creator: system date_created: 2018-12-12T10:16:56Z date_updated: 2020-07-14T12:45:19Z file_id: '5247' file_name: IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf file_size: 1545246 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 32' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '11' oa: 1 oa_version: Published Version page: 440 - 455 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '5257' pubrep_id: '430' quality_controlled: '1' scopus_import: 1 status: public title: Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2014' ... --- _id: '1842' abstract: - lang: eng text: We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices. acknowledgement: Marek Krčál was supported by the ERC Advanced Grant No. 267165. author: - first_name: Josef full_name: Cibulka, Josef last_name: Cibulka - first_name: Pu full_name: Gao, Pu last_name: Gao - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál - first_name: Tomáš full_name: Valla, Tomáš last_name: Valla - first_name: Pavel full_name: Valtr, Pavel last_name: Valtr citation: ama: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79. doi:10.1007/s00454-014-9646-x apa: Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x chicago: Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x. ieee: J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey number of outerplanar graphs,” Discrete & Computational Geometry, vol. 53, no. 1. Springer, pp. 64–79, 2014. ista: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79. mla: Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014, pp. 64–79, doi:10.1007/s00454-014-9646-x. short: J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational Geometry 53 (2014) 64–79. date_created: 2018-12-11T11:54:18Z date_published: 2014-11-14T00:00:00Z date_updated: 2021-01-12T06:53:33Z day: '14' department: - _id: UlWa - _id: HeEd doi: 10.1007/s00454-014-9646-x intvolume: ' 53' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1310.7004 month: '11' oa: 1 oa_version: Submitted Version page: 64 - 79 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5260' scopus_import: 1 status: public title: On the geometric ramsey number of outerplanar graphs type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2014' ... --- _id: '1854' abstract: - lang: eng text: In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. author: - first_name: Paul full_name: Guerrero, Paul last_name: Guerrero - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke citation: ama: Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509 apa: Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12509 chicago: Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509. ieee: P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” Computer Graphics Forum, vol. 34, no. 1. Wiley, pp. 239–252, 2014. ista: Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252. mla: Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:10.1111/cgf.12509. short: P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252. date_created: 2018-12-11T11:54:22Z date_published: 2014-11-05T00:00:00Z date_updated: 2021-01-12T06:53:38Z day: '05' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12509 file: - access_level: open_access checksum: 91946bfc509c77f5fd3151a3ff2b2c8f content_type: application/pdf creator: system date_created: 2018-12-12T10:15:58Z date_updated: 2020-07-14T12:45:19Z file_id: '5182' file_name: IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf file_size: 24817484 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 34' issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 239 - 252 publication: Computer Graphics Forum publication_status: published publisher: Wiley publist_id: '5246' pubrep_id: '574' quality_controlled: '1' scopus_import: 1 status: public title: Partial shape matching using transformation parameter similarity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2014' ... --- _id: '1852' abstract: - lang: eng text: To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner. acknowledgement: 'This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ' author: - first_name: Massimiliano full_name: Sassi, Massimiliano last_name: Sassi - first_name: Olivier full_name: Ali, Olivier last_name: Ali - first_name: Frédéric full_name: Boudon, Frédéric last_name: Boudon - first_name: Gladys full_name: Cloarec, Gladys last_name: Cloarec - first_name: Ursula full_name: Abad, Ursula last_name: Abad - first_name: Coralie full_name: Cellier, Coralie last_name: Cellier - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Benjamin full_name: Gilles, Benjamin last_name: Gilles - first_name: Pascale full_name: Milani, Pascale last_name: Milani - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Teva full_name: Vernoux, Teva last_name: Vernoux - first_name: Christophe full_name: Godin, Christophe last_name: Godin - first_name: Olivier full_name: Hamant, Olivier last_name: Hamant - first_name: Jan full_name: Traas, Jan last_name: Traas citation: ama: Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036 apa: Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036 chicago: Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036. ieee: M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” Current Biology, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014. ista: Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342. mla: Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036. short: M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342. date_created: 2018-12-11T11:54:22Z date_published: 2014-10-06T00:00:00Z date_updated: 2021-01-12T06:53:37Z day: '06' department: - _id: JiFr doi: 10.1016/j.cub.2014.08.036 intvolume: ' 24' issue: '19' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01074821 month: '10' oa: 1 oa_version: Submitted Version page: 2335 - 2342 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5248' quality_controlled: '1' scopus_import: 1 status: public title: An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1853' abstract: - lang: eng text: Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques. author: - first_name: Susmit full_name: Jha, Susmit last_name: Jha - first_name: Stavros full_name: Tripakis, Stavros last_name: Tripakis - first_name: Sanjit full_name: Seshia, Sanjit last_name: Seshia - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120' apa: 'Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120' chicago: Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. https://doi.org/10.1109/IOT.2014.7030120. ieee: 'S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure localization in wireless sensor networks,” presented at the IOT: Internet of Things, Cambridge, USA, 2014, pp. 85–90.' ista: 'Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.' mla: Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120. short: S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90. conference: end_date: 2014-10-08 location: Cambridge, USA name: 'IOT: Internet of Things' start_date: 2014-10-06 date_created: 2018-12-11T11:54:22Z date_published: 2014-02-03T00:00:00Z date_updated: 2021-01-12T06:53:38Z day: '03' department: - _id: KrCh doi: 10.1109/IOT.2014.7030120 language: - iso: eng month: '02' oa_version: None page: 85 - 90 publication_status: published publisher: IEEE publist_id: '5247' quality_controlled: '1' status: public title: Game theoretic secure localization in wireless sensor networks type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1862' abstract: - lang: eng text: The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses. acknowledgement: We thank R. Dixit for performing complementary experiments, D. W. Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively, E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J. Leung for text optimization. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007, to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT) (to H.R.). This work benefited from the facilities and expertise of the Imagif Cell Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil Général de l’Essonne. article_processing_charge: No article_type: original author: - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Laurie full_name: Grandont, Laurie last_name: Grandont - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Sébastien full_name: Paque, Sébastien last_name: Paque - first_name: Anas full_name: Abuzeineh, Anas last_name: Abuzeineh - first_name: Hana full_name: Rakusova, Hana id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA last_name: Rakusova - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Catherine full_name: Perrot Rechenmann, Catherine last_name: Perrot Rechenmann - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 2014;516(729):90-93. doi:10.1038/nature13889 apa: Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., … Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13889 chicago: Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque, Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13889. ieee: X. Chen et al., “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” Nature, vol. 516, no. 729. Nature Publishing Group, pp. 90–93, 2014. ista: Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 516(729), 90–93. mla: Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:10.1038/nature13889. short: X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova, E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93. date_created: 2018-12-11T11:54:25Z date_published: 2014-12-04T00:00:00Z date_updated: 2022-05-23T08:26:44Z day: '04' department: - _id: JiFr - _id: Bio - _id: EvBe doi: 10.1038/nature13889 ec_funded: 1 external_id: pmid: - '25409144' intvolume: ' 516' issue: '729' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/ month: '12' oa: 1 oa_version: Submitted Version page: 90 - 93 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Nature Publishing Group publist_id: '5237' quality_controlled: '1' scopus_import: '1' status: public title: Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 516 year: '2014' ... --- _id: '1869' abstract: - lang: eng text: Boolean controllers for systems with complex datapaths are often very difficult to implement correctly, in particular when concurrency is involved. Yet, in many instances it is easy to formally specify correctness. For example, the specification for the controller of a pipelined processor only has to state that the pipelined processor gives the same results as a non-pipelined reference design. This makes such controllers a good target for automated synthesis. However, an efficient abstraction for the complex datapath elements is needed, as a bit-precise description is often infeasible. We present Suraq, the first controller synthesis tool which uses uninterpreted functions for the abstraction. Quantified firstorder formulas (with specific quantifier structure) serve as the specification language from which Suraq synthesizes Boolean controllers. Suraq transforms the specification into an unsatisfiable SMT formula, and uses Craig interpolation to compute its results. Using Suraq, we were able to synthesize a controller (consisting of two Boolean signals) for a five-stage pipelined DLX processor in roughly one hour and 15 minutes. acknowledgement: The work presented in this paper was supported in part by the European Research Council (ERC) under grant agreement QUAINT (I774-N23) alternative_title: - LNCS author: - first_name: Georg full_name: Hofferek, Georg last_name: Hofferek - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta citation: ama: 'Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted functions. In: Yahav E, ed. HVC 2014. Vol 8855. Springer; 2014:68-74. doi:10.1007/978-3-319-13338-6_6' apa: 'Hofferek, G., & Gupta, A. (2014). Suraq - a controller synthesis tool using uninterpreted functions. In E. Yahav (Ed.), HVC 2014 (Vol. 8855, pp. 68–74). Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-13338-6_6' chicago: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” In HVC 2014, edited by Eran Yahav, 8855:68–74. Springer, 2014. https://doi.org/10.1007/978-3-319-13338-6_6. ieee: G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted functions,” in HVC 2014, Haifa, Israel, 2014, vol. 8855, pp. 68–74. ista: 'Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.' mla: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” HVC 2014, edited by Eran Yahav, vol. 8855, Springer, 2014, pp. 68–74, doi:10.1007/978-3-319-13338-6_6. short: G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp. 68–74. conference: end_date: 2014-11-20 location: Haifa, Israel name: 'HVC: Haifa Verification Conference' start_date: 2014-11-18 date_created: 2018-12-11T11:54:27Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:44Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-319-13338-6_6 ec_funded: 1 editor: - first_name: Eran full_name: Yahav, Eran last_name: Yahav intvolume: ' 8855' language: - iso: eng month: '01' oa_version: None page: 68 - 74 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: HVC 2014 publication_status: published publisher: Springer publist_id: '5228' quality_controlled: '1' status: public title: Suraq - a controller synthesis tool using uninterpreted functions type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8855 year: '2014' ... --- _id: '1872' abstract: - lang: eng text: Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover. acknowledgement: This research was supported in part by the Austrian National Research Network RiSE (S11410-N23). alternative_title: - LNCS author: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Laura full_name: Kovács, Laura last_name: Kovács - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Andrei full_name: Voronkov, Andrei last_name: Voronkov citation: ama: 'Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: Cassez F, Raskin J-F, eds. ATVA 2014. Vol 8837. Springer; 2014:185-200. doi:10.1007/978-3-319-11936-6_14' apa: 'Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis and proving identity. In F. Cassez & J.-F. Raskin (Eds.), ATVA 2014 (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14' chicago: Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In ATVA 2014, edited by Franck Cassez and Jean-François Raskin, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14. ieee: A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in ATVA 2014, Sydney, Australia, 2014, vol. 8837, pp. 185–200. ista: 'Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 185–200.' mla: Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” ATVA 2014, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14. short: A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin (Eds.), ATVA 2014, Springer, 2014, pp. 185–200. conference: end_date: 2014-11-07 location: Sydney, Australia name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2014-11-03 date_created: 2018-12-11T11:54:28Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:45Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-11936-6_14 ec_funded: 1 editor: - first_name: Franck full_name: Cassez, Franck last_name: Cassez - first_name: Jean-François full_name: Raskin, Jean-François last_name: Raskin file: - access_level: open_access checksum: af4bd3fc1f4c93075e4dc5cbf625fe7b content_type: application/pdf creator: system date_created: 2018-12-12T10:10:15Z date_updated: 2020-07-14T12:45:19Z file_id: '4801' file_name: IST-2016-641-v1+1_atva2014.pdf file_size: 244294 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 8837' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 185 - 200 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: ATVA 2014 publication_status: published publisher: Springer publist_id: '5226' pubrep_id: '641' quality_controlled: '1' scopus_import: 1 status: public title: Extensional crisis and proving identity type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8837 year: '2014' ... --- _id: '1870' abstract: - lang: eng text: We investigate the problem of checking if a finite-state transducer is robust to uncertainty in its input. Our notion of robustness is based on the analytic notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions. We show that K-robustness is undecidable even for deterministic transducers. We identify a class of functional transducers, which admits a polynomial time automata-theoretic decision procedure for K-robustness. This class includes Mealy machines and functional letter-to-letter transducers. We also study K-robustness of nondeterministic transducers. Since a nondeterministic transducer generates a set of output words for each input word, we quantify output perturbation using setsimilarity functions. We show that K-robustness of nondeterministic transducers is undecidable, even for letter-to-letter transducers. We identify a class of set-similarity functions which admit decidable K-robustness of letter-to-letter transducers. alternative_title: - LIPIcs author: - 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: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta citation: ama: 'Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers. In: Leibniz International Proceedings in Informatics, LIPIcs. Vol 29. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:10.4230/LIPIcs.FSTTCS.2014.431' apa: 'Henzinger, T. A., Otop, J., & Samanta, R. (2014). Lipschitz robustness of finite-state transducers. In Leibniz International Proceedings in Informatics, LIPIcs (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431' chicago: Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Finite-State Transducers.” In Leibniz International Proceedings in Informatics, LIPIcs, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431. ieee: T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state transducers,” in Leibniz International Proceedings in Informatics, LIPIcs, Delhi, India, 2014, vol. 29, pp. 431–443. ista: 'Henzinger TA, Otop J, Samanta R. 2014. Lipschitz robustness of finite-state transducers. Leibniz International Proceedings in Informatics, LIPIcs. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 29, 431–443.' mla: Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.” Leibniz International Proceedings in Informatics, LIPIcs, vol. 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:10.4230/LIPIcs.FSTTCS.2014.431. short: T.A. Henzinger, J. Otop, R. Samanta, in:, Leibniz International Proceedings in Informatics, LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–443. conference: end_date: 2014-12-17 location: Delhi, India name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science' start_date: 2014-12-15 date_created: 2018-12-11T11:54:27Z date_published: 2014-12-01T00:00:00Z date_updated: 2021-01-12T06:53:45Z day: '01' ddc: - '004' department: - _id: ToHe doi: 10.4230/LIPIcs.FSTTCS.2014.431 file: - access_level: open_access checksum: 7b1aff1710a8bffb7080ec07f62d9a17 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:11Z date_updated: 2020-07-14T12:45:19Z file_id: '4734' file_name: IST-2017-804-v1+1_37.pdf file_size: 562151 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 29' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 431 - 443 publication: Leibniz International Proceedings in Informatics, LIPIcs publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5227' pubrep_id: '804' quality_controlled: '1' status: public title: Lipschitz robustness of finite-state transducers 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2014' ... --- _id: '1875' abstract: - lang: eng text: We present a formal framework for repairing infinite-state, imperative, sequential programs, with (possibly recursive) procedures and multiple assertions; the framework can generate repaired programs by modifying the original erroneous program in multiple program locations, and can ensure the readability of the repaired program using user-defined expression templates; the framework also generates a set of inductive assertions that serve as a proof of correctness of the repaired program. As a step toward integrating programmer intent and intuition in automated program repair, we present a cost-aware formulation - given a cost function associated with permissible statement modifications, the goal is to ensure that the total program modification cost does not exceed a given repair budget. As part of our predicate abstractionbased solution framework, we present a sound and complete algorithm for repair of Boolean programs. We have developed a prototype tool based on SMT solving and used it successfully to repair diverse errors in benchmark C programs. alternative_title: - LNCS author: - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta - first_name: Oswaldo full_name: Olivo, Oswaldo last_name: Olivo - first_name: Emerson full_name: Allen, Emerson last_name: Allen citation: ama: 'Samanta R, Olivo O, Allen E. Cost-aware automatic program repair. In: Müller-Olm M, Seidl H, eds. Vol 8723. Springer; 2014:268-284. doi:10.1007/978-3-319-10936-7_17' apa: 'Samanta, R., Olivo, O., & Allen, E. (2014). Cost-aware automatic program repair. In M. Müller-Olm & H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented at the SAS: Static Analysis Symposium, Munich, Germany: Springer. https://doi.org/10.1007/978-3-319-10936-7_17' chicago: Samanta, Roopsha, Oswaldo Olivo, and Emerson Allen. “Cost-Aware Automatic Program Repair.” edited by Markus Müller-Olm and Helmut Seidl, 8723:268–84. Springer, 2014. https://doi.org/10.1007/978-3-319-10936-7_17. ieee: 'R. Samanta, O. Olivo, and E. Allen, “Cost-aware automatic program repair,” presented at the SAS: Static Analysis Symposium, Munich, Germany, 2014, vol. 8723, pp. 268–284.' ista: 'Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS: Static Analysis Symposium, LNCS, vol. 8723, 268–284.' mla: Samanta, Roopsha, et al. Cost-Aware Automatic Program Repair. Edited by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84, doi:10.1007/978-3-319-10936-7_17. short: R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer, 2014, pp. 268–284. conference: end_date: 2014-09-14 location: Munich, Germany name: 'SAS: Static Analysis Symposium' start_date: 2014-09-11 date_created: 2018-12-11T11:54:29Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T06:53:46Z day: '01' ddc: - '000' - '005' department: - _id: ToHe doi: 10.1007/978-3-319-10936-7_17 editor: - first_name: Markus full_name: Müller-Olm, Markus last_name: Müller-Olm - first_name: Helmut full_name: Seidl, Helmut last_name: Seidl file: - access_level: open_access checksum: 78ec4ea1bdecc676cd3e8cad35c6182c content_type: application/pdf creator: system date_created: 2018-12-12T10:07:51Z date_updated: 2020-07-14T12:45:19Z file_id: '4650' file_name: IST-2014-313-v1+1_SOE.SAS14.pdf file_size: 409485 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 8723' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 268 - 284 publication_status: published publisher: Springer publist_id: '5221' pubrep_id: '313' quality_controlled: '1' scopus_import: 1 status: public title: Cost-aware automatic program repair type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8723 year: '2014' ... --- _id: '1876' abstract: - lang: eng text: We study densities of functionals over uniformly bounded triangulations of a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay triangulation if this is the case for finite sets. article_processing_charge: No article_type: original author: - first_name: Nikolai full_name: Dolbilin, Nikolai last_name: Dolbilin - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Alexey full_name: Glazyrin, Alexey last_name: Glazyrin - first_name: Oleg full_name: Musin, Oleg last_name: Musin citation: ama: Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 2014;14(3):491-504. doi:10.17323/1609-4514-2014-14-3-491-504 apa: Dolbilin, N., Edelsbrunner, H., Glazyrin, A., & Musin, O. (2014). Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-3-491-504 chicago: Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-3-491-504. ieee: N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations of delaunay sets,” Moscow Mathematical Journal, vol. 14, no. 3. Independent University of Moscow, pp. 491–504, 2014. ista: Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504. mla: Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal, vol. 14, no. 3, Independent University of Moscow, 2014, pp. 491–504, doi:10.17323/1609-4514-2014-14-3-491-504. short: N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical Journal 14 (2014) 491–504. date_created: 2018-12-11T11:54:29Z date_published: 2014-07-01T00:00:00Z date_updated: 2022-03-03T11:47:09Z day: '01' department: - _id: HeEd doi: 10.17323/1609-4514-2014-14-3-491-504 external_id: arxiv: - '1211.7053' intvolume: ' 14' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1211.7053 month: '07' oa: 1 oa_version: Submitted Version page: 491 - 504 publication: Moscow Mathematical Journal publication_identifier: issn: - '16093321' publication_status: published publisher: Independent University of Moscow publist_id: '5220' quality_controlled: '1' scopus_import: '1' status: public title: Functionals on triangulations of delaunay sets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '1877' abstract: - lang: eng text: During inflammation, lymph nodes swell with an influx of immune cells. New findings identify a signalling pathway that induces relaxation in the contractile cells that give structure to these organs. article_type: letter_note author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 citation: ama: 'Sixt MK, Vaahtomeri K. Physiology: Relax and come in. Nature. 2014;514(7523):441-442. doi:10.1038/514441a' apa: 'Sixt, M. K., & Vaahtomeri, K. (2014). Physiology: Relax and come in. Nature. Springer Nature. https://doi.org/10.1038/514441a' chicago: 'Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature. Springer Nature, 2014. https://doi.org/10.1038/514441a.' ieee: 'M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” Nature, vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.' ista: 'Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523), 441–442.' mla: 'Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature, vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:10.1038/514441a.' short: M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442. date_created: 2018-12-11T11:54:30Z date_published: 2014-10-23T00:00:00Z date_updated: 2021-01-12T06:53:47Z day: '23' department: - _id: MiSi doi: 10.1038/514441a intvolume: ' 514' issue: '7523' language: - iso: eng month: '10' oa_version: None page: 441 - 442 publication: Nature publication_status: published publisher: Springer Nature publist_id: '5219' quality_controlled: '1' scopus_import: 1 status: public title: 'Physiology: Relax and come in' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 514 year: '2014' ... --- _id: '1886' abstract: - lang: eng text: 'Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability.' article_number: e03722 author: - first_name: Ann full_name: Hermundstad, Ann last_name: Hermundstad - first_name: John full_name: Briguglio, John last_name: Briguglio - first_name: Mary full_name: Conte, Mary last_name: Conte - first_name: Jonathan full_name: Victor, Jonathan last_name: Victor - first_name: Vijay full_name: Balasubramanian, Vijay last_name: Balasubramanian - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722 apa: Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkačik, G. (2014). Variance predicts salience in central sensory processing. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722 chicago: Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722. ieee: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 2014. ista: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722. mla: Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722. short: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014). date_created: 2018-12-11T11:54:32Z date_published: 2014-11-14T00:00:00Z date_updated: 2021-01-12T06:53:50Z day: '14' ddc: - '570' department: - _id: GaTk doi: 10.7554/eLife.03722 file: - access_level: open_access checksum: 766ac8999ac6e3364f10065a06024b8f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:04Z date_updated: 2020-07-14T12:45:20Z file_id: '4922' file_name: IST-2016-420-v1+1_e03722.full.pdf file_size: 5117086 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' issue: November language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '5209' pubrep_id: '420' quality_controlled: '1' scopus_import: 1 status: public title: Variance predicts salience in central sensory processing 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1890' abstract: - lang: eng text: To search for a target in a complex environment is an everyday behavior that ends with finding the target. When we search for two identical targets, however, we must continue the search after finding the first target and memorize its location. We used fixation-related potentials to investigate the neural correlates of different stages of the search, that is, before and after finding the first target. Having found the first target influenced subsequent distractor processing. Compared to distractor fixations before the first target fixation, a negative shift was observed for three subsequent distractor fixations. These results suggest that processing a target in continued search modulates the brain's response, either transiently by reflecting temporary working memory processes or permanently by reflecting working memory retention. acknowledgement: 'Funded by Austrian Science Fund (FWF) Grant Number: P 22189-B18; European Union within the 6th Framework Programme Grant Number: 517590; State government of Styria Grant Number: PN 4055' author: - first_name: Christof full_name: Körner, Christof last_name: Körner - first_name: Verena full_name: Braunstein, Verena last_name: Braunstein - first_name: Matthias full_name: Stangl, Matthias last_name: Stangl - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Christa full_name: Neuper, Christa last_name: Neuper - first_name: Anja full_name: Ischebeck, Anja last_name: Ischebeck citation: ama: 'Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 2014;51(4):385-395. doi:10.1111/psyp.12062' apa: 'Körner, C., Braunstein, V., Stangl, M., Schlögl, A., Neuper, C., & Ischebeck, A. (2014). Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. Wiley-Blackwell. https://doi.org/10.1111/psyp.12062' chicago: 'Körner, Christof, Verena Braunstein, Matthias Stangl, Alois Schlögl, Christa Neuper, and Anja Ischebeck. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/psyp.12062.' ieee: 'C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, and A. Ischebeck, “Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection,” Psychophysiology, vol. 51, no. 4. Wiley-Blackwell, pp. 385–395, 2014.' ista: 'Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. 2014. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 51(4), 385–395.' mla: 'Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology, vol. 51, no. 4, Wiley-Blackwell, 2014, pp. 385–95, doi:10.1111/psyp.12062.' short: C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck, Psychophysiology 51 (2014) 385–395. date_created: 2018-12-11T11:54:34Z date_published: 2014-02-11T00:00:00Z date_updated: 2021-01-12T06:53:52Z day: '11' ddc: - '000' department: - _id: ScienComp - _id: PeJo doi: 10.1111/psyp.12062 file: - access_level: open_access checksum: 4255b6185e774acce1d99f8e195c564d content_type: application/pdf creator: system date_created: 2018-12-12T10:16:44Z date_updated: 2020-07-14T12:45:20Z file_id: '5233' file_name: IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf file_size: 543243 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 51' issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 385 - 395 publication: Psychophysiology publication_status: published publisher: Wiley-Blackwell publist_id: '5205' pubrep_id: '442' scopus_import: 1 status: public title: 'Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection' 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2014' ... --- _id: '1892' abstract: - lang: eng text: Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in Lamprologus callipterus. acknowledgement: "This research was supported by grants of the Swiss National Science Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet for field assistance, Dolores Schütz for vital help in the field and with the manuscript, David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture and Livestock of Zambia, for permission and support." article_number: '20140253' article_processing_charge: No article_type: original author: - first_name: Sabine full_name: Ocana, Sabine last_name: Ocana - first_name: Patrick full_name: Meidl, Patrick id: 4709BCE6-F248-11E8-B48F-1D18A9856A87 last_name: Meidl - first_name: Danielle full_name: Bonfils, Danielle last_name: Bonfils - first_name: Michael full_name: Taborsky, Michael last_name: Taborsky citation: ama: Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.0253 apa: Ocana, S., Meidl, P., Bonfils, D., & Taborsky, M. (2014). Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.0253 chicago: Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253. ieee: S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. The Royal Society, 2014. ista: Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20140253. mla: Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:10.1098/rspb.2014.0253. short: S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014). date_created: 2018-12-11T11:54:34Z date_published: 2014-11-07T00:00:00Z date_updated: 2022-06-07T09:12:32Z day: '07' department: - _id: CampIT doi: 10.1098/rspb.2014.0253 external_id: pmid: - '25232141' intvolume: ' 281' issue: '1794' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/ month: '11' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: The Royal Society publist_id: '5203' quality_controlled: '1' scopus_import: '1' status: public title: Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 281 year: '2014' ... --- _id: '1891' abstract: - lang: eng text: We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single-molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single-molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force-extension patterns of the guest protein. We study examples of such systems within a coarse-grained structure-based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force-displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single-molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure. acknowledgement: Grant Nr. 2011/01/N/ST3/02475 author: - first_name: Mateusz full_name: Chwastyk, Mateusz last_name: Chwastyk - first_name: Albert full_name: Galera Prat, Albert last_name: Galera Prat - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Àngel full_name: Gómez Sicilia, Àngel last_name: Gómez Sicilia - first_name: Mariano full_name: Carrión Vázquez, Mariano last_name: Carrión Vázquez - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak citation: ama: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726. doi:10.1002/prot.24436' apa: 'Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.24436' chicago: 'Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia, Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.' ieee: 'M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein nanomechanics,” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.' ista: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726.' mla: 'Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.' short: 'M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.' date_created: 2018-12-11T11:54:34Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-01-12T06:53:52Z day: '01' department: - _id: CaHe doi: 10.1002/prot.24436 intvolume: ' 82' issue: '5' language: - iso: eng month: '05' oa_version: None page: 717 - 726 publication: 'Proteins: Structure, Function and Bioinformatics' publication_status: published publisher: Wiley-Blackwell publist_id: '5204' scopus_import: 1 status: public title: Theoretical tests of the mechanical protection strategy in protein nanomechanics type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2014' ... --- _id: '1884' abstract: - lang: eng text: Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts. author: - first_name: Dan full_name: Landau, Dan last_name: Landau - first_name: Chip full_name: Stewart, Chip last_name: Stewart - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Michael full_name: Lawrence, Michael last_name: Lawrence - first_name: Carrie full_name: Sougnez, Carrie last_name: Sougnez - first_name: Jennifer full_name: Brown, Jennifer last_name: Brown - first_name: Armando full_name: Lopez Guillermo, Armando last_name: Lopez Guillermo - first_name: Stacey full_name: Gabriel, Stacey last_name: Gabriel - first_name: Eric full_name: Lander, Eric last_name: Lander - first_name: Donna full_name: Neuberg, Donna last_name: Neuberg - first_name: Carlos full_name: López Otín, Carlos last_name: López Otín - first_name: Elias full_name: Campo, Elias last_name: Campo - first_name: Gad full_name: Getz, Gad last_name: Getz - first_name: Catherine full_name: Wu, Catherine last_name: Wu citation: ama: 'Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 2014;124(21):1952-1952.' apa: 'Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J., … Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. American Society of Hematology.' chicago: 'Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez, Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood. American Society of Hematology, 2014.' ieee: 'D. Landau et al., “Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples,” Blood, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014.' ista: 'Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 124(21), 1952–1952.' mla: 'Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.' short: D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz, C. Wu, Blood 124 (2014) 1952–1952. date_created: 2018-12-11T11:54:32Z date_published: 2014-12-04T00:00:00Z date_updated: 2021-01-12T06:53:50Z day: '04' department: - _id: KrCh intvolume: ' 124' issue: '21' language: - iso: eng main_file_link: - url: http://www.bloodjournal.org/content/124/21/1952?sso-checked=true month: '12' oa_version: None page: 1952 - 1952 publication: Blood publication_status: published publisher: American Society of Hematology publist_id: '5211' status: public title: 'Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2014' ... --- _id: '1889' abstract: - lang: eng text: We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity. acknowledgement: We would like to thank Max Lein and Andreas Deuchert for valuable suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully acknowledged. article_number: '1450012' article_processing_charge: No article_type: original author: - first_name: Gerhard full_name: Bräunlich, Gerhard last_name: Bräunlich - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 2014;26(7). doi:10.1142/S0129055X14500123 apa: Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123 chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123. ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free states for fermionic systems and the BCS approximation,” Reviews in Mathematical Physics, vol. 26, no. 7. World Scientific Publishing, 2014. ista: Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 26(7), 1450012. mla: Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123. short: G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26 (2014). date_created: 2018-12-11T11:54:33Z date_published: 2014-08-01T00:00:00Z date_updated: 2022-06-07T09:03:09Z day: '01' department: - _id: RoSe doi: 10.1142/S0129055X14500123 external_id: arxiv: - '1305.5135' intvolume: ' 26' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1305.5135 month: '08' oa: 1 oa_version: Submitted Version publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '5206' quality_controlled: '1' scopus_import: '1' status: public title: Translation-invariant quasi-free states for fermionic systems and the BCS approximation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1894' abstract: - lang: eng text: 'Background: Bacterial Dsb enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between their cysteine residues. The Dsb protein network has been well characterized in cells of the model microorganism Escherichia coli. To gain insight into the functioning of the Dsb system in epsilon-Proteobacteria, where it plays an important role in the colonization process, we studied two homologs of the main Escherichia coli Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter jejuni, the most frequently reported bacterial cause of human enteritis in the world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria, which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest that the two C. jejuni DsbAs play different roles in bacterial cells and have divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical role in the oxidative folding that ensures the activity of alkaline phosphatase CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA, encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated with bacterial spread and host colonization, as well as ensuring the oxidative folding of particular protein substrates. In contrast, CjDsbA2 activity does not affect the same processes and so far its oxidative folding activity has been demonstrated for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not exclusive and there is probably another protein to be identified in C. jejuni cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute the considerable insight to the Epsilonproteobacterial Dsb systems, which have been poorly understood so far.' article_number: e106247 author: - first_name: Anna full_name: Grabowska, Anna last_name: Grabowska - first_name: Ewa full_name: Wywiał, Ewa last_name: Wywiał - first_name: Stanislaw full_name: Dunin Horkawicz, Stanislaw last_name: Dunin Horkawicz - first_name: Anna full_name: Łasica, Anna last_name: Łasica - first_name: Marc full_name: Wösten, Marc last_name: Wösten - first_name: Anna A full_name: Nagy-Staron, Anna A id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87 last_name: Nagy-Staron - first_name: Renata full_name: Godlewska, Renata last_name: Godlewska - first_name: Katarzyna full_name: Bocian Ostrzycka, Katarzyna last_name: Bocian Ostrzycka - first_name: Katarzyna full_name: Pieńkowska, Katarzyna last_name: Pieńkowska - first_name: Paweł full_name: Łaniewski, Paweł last_name: Łaniewski - first_name: Janusz full_name: Bujnicki, Janusz last_name: Bujnicki - first_name: Jos full_name: Van Putten, Jos last_name: Van Putten - first_name: Elzbieta full_name: Jagusztyn Krynicka, Elzbieta last_name: Jagusztyn Krynicka citation: ama: Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247 apa: Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247 chicago: Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247. ieee: A. Grabowska et al., “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014. ista: Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247. mla: Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247. short: A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-09-02T00:00:00Z date_updated: 2021-01-12T06:53:54Z day: '02' ddc: - '570' department: - _id: CaGu doi: 10.1371/journal.pone.0106247 file: - access_level: open_access checksum: 7d02c3da7f72b82bb5d7932d80c3251f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:19Z date_updated: 2020-07-14T12:45:20Z file_id: '5205' file_name: IST-2016-438-v1+1_journal.pone.0106247.pdf file_size: 4248801 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 9' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5201' pubrep_id: '438' quality_controlled: '1' scopus_import: 1 status: public title: Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '1895' abstract: - lang: eng text: Major histocompatibility complex class I (MHCI) molecules were recently identified as novel regulators of synaptic plasticity. These molecules are expressed in various brain areas, especially in regions undergoing activity-dependent synaptic plasticity, but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin, which causes lack of cell surface expression of MHCI. First, we confirmed that MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin knock-out mice lacking cell surface expression of MHCI. We found that low frequency stimulation induced long-term depression in wild-type but not knock-out mice, whereas high frequency stimulation induced long-term potentiation in both genotypes, with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related behavior. Using this model, we analyzed the density of total AMPA receptors and their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture replica labeling. After repeated cocaine exposure, the density of GluR1 was increased, but there was no change in total AMPA receptors and GluR2 levels in wildtype mice. In contrast, following repeated cocaine exposure, increased densities of total AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results indicate that functional deficiency of MHCI enhances synaptic potentiation, induced by electrical and pharmacological stimulation. acknowledgement: This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153, from the Ministry of Education, Culture, Sports, Science and Technology of Japan. article_number: e107099 author: - first_name: Mitsuhiro full_name: Edamura, Mitsuhiro last_name: Edamura - first_name: Gen full_name: Murakami, Gen last_name: Murakami - first_name: Hongrui full_name: Meng, Hongrui last_name: Meng - first_name: Makoto full_name: Itakura, Makoto last_name: Itakura - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Atsuo full_name: Fukuda, Atsuo last_name: Fukuda - first_name: Daiichiro full_name: Nakahara, Daiichiro last_name: Nakahara citation: ama: Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107099 apa: Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A., & Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107099 chicago: Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099. ieee: M. Edamura et al., “Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014. ista: Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 9(9), e107099. mla: Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9, no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099. short: M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D. Nakahara, PLoS One 9 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-09-30T00:00:00Z date_updated: 2021-01-12T06:53:54Z day: '30' ddc: - '570' department: - _id: RySh doi: 10.1371/journal.pone.0107099 file: - access_level: open_access checksum: 1f3be936be93114596d61ba44cacee69 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:01Z date_updated: 2020-07-14T12:45:20Z file_id: '4724' file_name: IST-2016-439-v1+1_journal.pone.0107099.pdf file_size: 6262085 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 9' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5200' pubrep_id: '439' scopus_import: 1 status: public title: Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice 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: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '1893' abstract: - lang: eng text: Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants. acknowledgement: This work was supported by grants from the Research Foundation-Flanders (Odysseus). author: - first_name: Petra full_name: Nováková, Petra id: 44E59624-F248-11E8-B48F-1D18A9856A87 last_name: Nováková - first_name: Sibylle full_name: Hirsch, Sibylle last_name: Hirsch - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Ringo full_name: Van Wijk, Ringo last_name: Van Wijk - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Mareike full_name: Heilmann, Mareike last_name: Heilmann - first_name: Jennifer full_name: Lerche, Jennifer last_name: Lerche - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Mugurel full_name: Feraru, Mugurel last_name: Feraru - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Marc full_name: Van Montagu, Marc last_name: Van Montagu - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Teun full_name: Munnik, Teun last_name: Munnik - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823. doi:10.1073/pnas.1324264111 apa: Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., … Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111 chicago: Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111. ieee: P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014. ista: Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M, Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T, Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 111(7), 2818–2823. mla: Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111. short: P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann, J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T. Munnik, J. Friml, PNAS 111 (2014) 2818–2823. date_created: 2018-12-11T11:54:34Z date_published: 2014-02-18T00:00:00Z date_updated: 2021-01-12T06:53:53Z day: '18' department: - _id: JiFr doi: 10.1073/pnas.1324264111 ec_funded: 1 intvolume: ' 111' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/ month: '02' oa: 1 oa_version: Submitted Version page: 2818 - 2823 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: '5202' scopus_import: 1 status: public title: SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '1896' abstract: - lang: eng text: 'Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.' acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.). article_number: '032701' article_processing_charge: No author: - first_name: Richard full_name: Kollár, Richard last_name: Kollár - first_name: Katarína full_name: Bod'ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'ová orcid: 0000-0002-7214-0171 - first_name: Jozef full_name: Nosek, Jozef last_name: Nosek - first_name: Ľubomír full_name: Tomáška, Ľubomír last_name: Tomáška citation: ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701 apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701 chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701. ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014. ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701. mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701. short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-03-04T00:00:00Z date_updated: 2022-08-01T10:50:10Z day: '04' department: - _id: NiBa - _id: GaTk doi: 10.1103/PhysRevE.89.032701 intvolume: ' 89' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.0430 month: '03' oa: 1 oa_version: Submitted Version publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '5198' scopus_import: '1' status: public title: Mathematical model of alternative mechanism of telomere length maintenance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2014' ... --- _id: '1897' abstract: - lang: eng text: GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants. acknowledgement: This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.). author: - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Marisa full_name: Otegui, Marisa last_name: Otegui - first_name: Natsumaro full_name: Kutsuna, Natsumaro last_name: Kutsuna - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Tomoko full_name: Dainobu, Tomoko last_name: Dainobu - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Masaru full_name: Fujimoto, Masaru last_name: Fujimoto - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Daisuke full_name: Miki, Daisuke last_name: Miki - first_name: Hiroo full_name: Fukuda, Hiroo last_name: Fukuda - first_name: Akihiko full_name: Nakano, Akihiko last_name: Nakano - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880 apa: Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880 chicago: Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.125880. ieee: S. Naramoto et al., “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014. ista: Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076. mla: Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:10.1105/tpc.114.125880. short: S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076. date_created: 2018-12-11T11:54:36Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:53:55Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.114.125880 intvolume: ' 26' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/ month: '07' oa: 1 oa_version: Submitted Version page: 3062 - 3076 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '5199' scopus_import: 1 status: public title: Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1899' abstract: - lang: eng text: Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation. article_processing_charge: No article_type: original author: - first_name: Scott full_name: Williams, Scott last_name: Williams - first_name: Lyndsay full_name: Ratliff, Lyndsay last_name: Ratliff - first_name: Maria P full_name: Postiglione, Maria P id: 2C67902A-F248-11E8-B48F-1D18A9856A87 last_name: Postiglione - first_name: Juergen full_name: Knoblich, Juergen last_name: Knoblich - first_name: Elaine full_name: Fuchs, Elaine last_name: Fuchs citation: ama: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001 apa: Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001 chicago: Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich, and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb3001. ieee: S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,” Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014. ista: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 16(8), 758–769. mla: Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001. short: S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769. date_created: 2018-12-11T11:54:36Z date_published: 2014-07-13T00:00:00Z date_updated: 2021-01-12T06:53:55Z day: '13' department: - _id: SiHi doi: 10.1038/ncb3001 external_id: pmid: - '25016959' intvolume: ' 16' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/ month: '07' oa: 1 oa_version: Submitted Version page: 758 - 769 pmid: 1 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '5196' quality_controlled: '1' scopus_import: 1 status: public title: Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ...